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Pérez-Gómez O, Domínguez-Maqueda M, García-Márquez J, Moriñigo MÁ, Tapia-Paniagua ST. Metabolite-Driven Modulation of Biofilm Formation in Shewanella: Insights from Shewanella sp. Pdp11 Extracellular Products. MICROBIAL ECOLOGY 2025; 88:55. [PMID: 40423845 DOI: 10.1007/s00248-025-02552-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2025] [Accepted: 05/09/2025] [Indexed: 05/28/2025]
Abstract
Biofilm formation is a survival strategy for bacteria, contributing to their persistence in natural and industrial environments. In this study, we investigated the ability of extracellular products (ECPs) produced by the probiotic strain Shewanella sp. Pdp11 under different culture conditions to inhibit biofilm formation in pathogenic and environmental Shewanella strains. ECPs from specific culture conditions altered biofilm formation in several Shewanella strains, with Shewanella hafniensis P14 displaying the highest sensitivity. Metabolomic analysis of the ECPs identified glycogen as a key metabolite associated with biofilm inhibition. Further genomic analysis of S. hafniensis P14 revealed an interruption in its glycogen synthesis pathway, suggesting a dependency on external glycogen-related metabolites for biofilm development. These findings demonstrate that Shewanella sp. Pdp11 ECPs can modify biofilm formation across multiple Shewanella strains, particularly in S. hafniensis P14 through glycogen-associated mechanisms.
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Affiliation(s)
- Olivia Pérez-Gómez
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, Málaga, Spain
| | - Marta Domínguez-Maqueda
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, Málaga, Spain
| | - Jorge García-Márquez
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, Málaga, Spain
| | - Miguel Ángel Moriñigo
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, Málaga, Spain
| | - Silvana T Tapia-Paniagua
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, Málaga, Spain.
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2
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Sher S, Richards GP, Parveen S, Williams HN. Characterization of Antibiotic Resistance in Shewanella Species: An Emerging Pathogen in Clinical and Environmental Settings. Microorganisms 2025; 13:1115. [PMID: 40431288 DOI: 10.3390/microorganisms13051115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2025] [Revised: 05/01/2025] [Accepted: 05/07/2025] [Indexed: 05/29/2025] Open
Abstract
Antibiotic resistance is increasing at an alarming rate worldwide, in large part due to their misuse and improper disposal. Antibiotics administered to treat human and animal diseases, including feed supplements for the treatment or prevention of disease in farm animals, have contributed greatly to the emergence of a multitude of antibiotic-resistant pathogens. Shewanella is one of many bacteria that have developed antibiotic resistance, and in some species, multiple-antibiotic resistance (MAR). Shewanella is a rod-shaped, Gram-negative, oxidase-positive, and H2S-producing bacterium that is naturally found in the marine environment. In humans, Shewanella spp. can cause skin and soft tissue infections, septicemia, cellulitis, osteomyelitis, and ear and wound infections. Some Shewanella have been shown to be resistant to a variety of antibiotics, including beta-lactams, aminoglycoside, quinolones, third- or fourth-generation cephalosporins, and carbapenems, due to the presence of genes such as the blaOXA-class D beta-lactamase-encoding gene, blaAmpC-class-C beta-lactamase-encoding gene, and the qnr gene. Bacteria can acquire and transmit these genes through different horizontal gene-transmission mechanisms such as transformation, transduction, and conjugation. The genes for antibiotic resistance are present on Shewanella chromosomes and plasmids. Apart from this, heavy metals such as arsenic, mercury, cadmium, and chromium can also increase antibiotic resistance in Shewanella due to co-selection processes such as co-resistance, cross resistance, and co-regulation mechanisms. Antibiotics and drugs enter Shewanella spp. through pores or gates in their cell wall and may be ejected from the bacteria by efflux pumps, which are the first line of bacterial defense against antibiotics. Multiple-drug resistant Shewanella can be particularly difficult to control. This review focuses on the phenotypic and genomic characteristics of Shewanella that are involved in the increase in antimicrobial resistance in this bacterium.
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Affiliation(s)
- Shahid Sher
- School of the Environment, Florida A&M University, Tallahassee, FL 32307, USA
| | - Gary P Richards
- U.S. Department of Agriculture, Agricultural Research Service, Delaware State University, Dover, DE 19901, USA
| | - Salina Parveen
- Department of Agriculture, Food and Resource Science, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Henry N Williams
- School of the Environment, Florida A&M University, Tallahassee, FL 32307, USA
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3
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Montúfar-Romero M, Valenzuela-Miranda D, Valenzuela-Muñoz V, Morales-Rivera MF, Gallardo-Escárate C. Microbiota Dysbiosis in Mytilus chilensis Is Induced by Hypoxia, Leading to Molecular and Functional Consequences. Microorganisms 2025; 13:825. [PMID: 40284661 PMCID: PMC12029581 DOI: 10.3390/microorganisms13040825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 03/22/2025] [Accepted: 03/29/2025] [Indexed: 04/29/2025] Open
Abstract
Bivalve microbiota play a vital role in host health, supporting nutrient processing, immunity, and disease resistance. However, the increasing hypoxia in Chilean coastal waters, caused by climate change and eutrophication, threatens to disrupt this microbial balance, potentially promoting pathogens and impairing essential functions. Mytilus chilensis is vulnerable to hypoxia-reoxygenation cycles, yet the effects on its microbiota remain poorly understood. This study investigates the impact of hypoxia on the structure and functional potential of the microbial communities residing in the gills and digestive glands of M. chilensis. Employing full-length 16S rRNA gene sequencing, we explored hypoxia's effects on microbial diversity and functional capacity. Our results revealed significant alterations in the microbial composition, with a shift towards facultative anaerobes thriving in low oxygen environments. Notably, there was a decrease in dominant bacterial taxa such as Rhodobacterales, while opportunistic pathogens such as Vibrio and Aeromonas exhibited increased abundance. Functional analysis indicated a decline in critical microbial functions associated with nutrient metabolism and immune support, potentially jeopardizing the health and survival of the host. This study sheds light on the intricate interactions between host-associated microbiota and environmental stressors, underlining the importance of managing the microbiota in the face of climate change and aquaculture practices.
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Affiliation(s)
- Milton Montúfar-Romero
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción 4030000, Chile; (M.M.-R.); (V.V.-M.); (M.F.M.-R.)
- Instituto Público de Investigación de Acuicultura y Pesca (IPIAP), Guayaquil 090314, Ecuador
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción 4030000, Chile; (M.M.-R.); (V.V.-M.); (M.F.M.-R.)
- Centro de Biotecnología, Universidad de Concepción, P.O. Box 160-C, Concepción 4030000, Chile
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción 4030000, Chile; (M.M.-R.); (V.V.-M.); (M.F.M.-R.)
- Center for Oceanographic Research COPAS COASTAL, Universidad de Concepción, Concepción 4070409, Chile
| | - María F. Morales-Rivera
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción 4030000, Chile; (M.M.-R.); (V.V.-M.); (M.F.M.-R.)
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción 4030000, Chile; (M.M.-R.); (V.V.-M.); (M.F.M.-R.)
- Center for Oceanographic Research COPAS COASTAL, Universidad de Concepción, Concepción 4070409, Chile
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4
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Seymour JR, McLellan SL. Climate change will amplify the impacts of harmful microorganisms in aquatic ecosystems. Nat Microbiol 2025; 10:615-626. [PMID: 40021939 DOI: 10.1038/s41564-025-01948-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/18/2024] [Indexed: 03/03/2025]
Abstract
More than 70% of the human population lives within five kilometres of a natural water feature. These aquatic ecosystems are heavily used for resource provision and recreation, and represent the interface between human populations and aquatic microbiomes, which can sometimes negatively impact human health. Diverse species of endemic aquatic microorganisms, including toxic microalgae and pathogenic bacteria, can be harmful to humans. Aquatic ecosystems are also subject to intrusions of allochthonous pathogenic microorganisms through pollution and runoff. Notably, environmental processes that amplify the abundance and impact of harmful aquatic microorganisms are occurring with increasing frequency owing to climate change. For instance, increases in water temperature stimulate outbreaks of pathogenic and toxic species, whereas more intense precipitation events escalate microbial contamination from stormwater discharge. In this Perspective we discuss the influence of aquatic microbiomes on the health and economies of human populations and examine how climate change is increasing these impacts.
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Affiliation(s)
- Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Broadway, New South Wales, Australia.
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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Palamae S, Suyapoh W, Boonrat O, Zhang B, Amin M, Buatong J, Benjakul S. Activity of Bambara Groundnut Seed Coat Extract Against Shewanella Species: Efficacy and Mechanisms of Action. Foods 2024; 13:3516. [PMID: 39517300 PMCID: PMC11545440 DOI: 10.3390/foods13213516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 10/23/2024] [Accepted: 10/31/2024] [Indexed: 11/16/2024] Open
Abstract
The Bambara groundnut is the indigenous legume in the southern part of Thailand. It contains a seed coat rich in polyphenols, which can serve as natural antimicrobial agents. The extracts from red and white seed coats of Bambara groundnuts, namely RSC and WSC, respectively, were prepared using an ultrasound-assisted extraction process. The extraction yield, total phenolic content (TPC), and antimicrobial activity of both extracts were examined. The RSC extract demonstrated a significantly higher extraction yield (8.35%) than WSC extract (2.34%) (p < 0.05). Furthermore, the TPC of RSC extract (420.98 ± 0.27 mg of gallic acid/g dry extract) was higher than that of WSC extract (28.29 ± 0.91 mg of gallic acid/g dry extract). The RSC extract exhibited stronger inhibition against Shewanella putrefaciens and S. algae than its WSC counterpart. Liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-TOF/MS) analysis indicated that the RSC extract was rich in flavonoids and polyphenols, while the WSC extract contained more triterpenoid saponins. Time-kill kinetics showed that the RSC extract reduced bacterial loads in a dose-dependent manner. Scanning electron microscopic images revealed that drastic bacterial cell membrane damage with a rough surface and the deformation of cells was caused by the extract. Furthermore, confocal laser scanning microscopic (CLSM) images confirmed the inhibition of S. algae biofilm formation by RSC extract. RSC extract also suppressed bacterial motility, induced protein leakage, and reduced extracellular protease activity, thus highlighting its potent bactericidal effects. These findings suggested that the RSC extract rich in phenolic compounds could serve as an antimicrobial agent and hold promise as a natural preservative for perishable foods, especially seafoods.
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Affiliation(s)
- Suriya Palamae
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand; (S.P.); (S.B.)
| | - Watcharapol Suyapoh
- Veterinary Pathology Unit, Department of Veterinary Science, Faculty of Veterinary Science, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand;
| | - Onpreeya Boonrat
- Medical Science Research and Innovation Institute, Research and Development Office, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand;
| | - Bin Zhang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Muhamad Amin
- Department of Aquaculture, Faculty of Fisheries and Marine, Universitas Airlangga, Campus C Jl, Mulyorejo, Surabaya 60115, East Java, Indonesia;
| | - Jirayu Buatong
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand; (S.P.); (S.B.)
| | - Soottawat Benjakul
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand; (S.P.); (S.B.)
- Department of Food and Nutrition, Kyung Hee University, Seoul 02447, Republic of Korea
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Wang L, Chen S, Xing M, Dong L, Zhu H, Lin Y, Li J, Sun T, Zhu X, Wang X. Genome characterization of Shewanella algae in Hainan Province, China. Front Microbiol 2024; 15:1474871. [PMID: 39417074 PMCID: PMC11480045 DOI: 10.3389/fmicb.2024.1474871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 09/23/2024] [Indexed: 10/19/2024] Open
Abstract
Shewanella algae is an emerging marine zoonotic pathogen. In this study, we first reported the Shewanella algae infections in patients and animals in Hainan Province, China. Currently, there is still relatively little known about the whole-genome characteristics of Shewanella algae in most tropical regions, including in southern China. Here, we sequenced the 62 Shewanella algae strains isolated from Hainan Province and combined with the whole genomes sequences of 144 Shewanella algae genomes from public databases to analyze genomic features. Phylogenetic analysis revealed that Shewanella algae is widely distributed in the marine environments of both temperate and tropical countries, exhibiting close phylogenetic relationships with genomes isolated from patients, animals, and plants. Thereby confirming that exposure to marine environments is a risk factor for Shewanella algae infections. Average nucleotide identity analysis indicated that the clonally identical genomes could be isolated from patients with different sample types at different times. Pan-genome analysis identified a total of 21,909 genes, including 1,563 core genes, 8,292 strain-specific genes, and 12,054 accessory genes. Multiple putative virulence-associated genes were identified, encompassing 14 categories and 16 subcategories, with 171 distinct virulence factors. Three different plasmid replicon types were detected in 33 genomes. Eleven classes of antibiotic resistance genes and 352 integrons were identified. Antimicrobial susceptibility testing revealed a high resistance rate to imipenem and colistin among the strains studied, with 5 strains exhibiting multidrug resistance. However, they were all sensitive to amikacin, minocycline, and tigecycline. Our findings clarify the genomic characteristics and population structure of Shewanella algae in Hainan Province. The results offer insights into the genetic basis of pathogenicity in Shewanella algae and enhance our understanding of its global phylogeography.
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Affiliation(s)
- Licheng Wang
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Shaojin Chen
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Mei Xing
- Wenchang People’s Hospital, Wenchang, China
| | - Lingzhi Dong
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Huaxiong Zhu
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Yujin Lin
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Jinyi Li
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Tuo Sun
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Xiong Zhu
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Xiaoxia Wang
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
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7
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Da YM, Li SS, Li YQ, Deng LY, Li MJ, Huang T, Sun QY, Shirin J, Zhou GW. Effects of cadmium on the intestinal health of the snail Bradybaena ravida Benson. ECOTOXICOLOGY (LONDON, ENGLAND) 2024; 33:849-858. [PMID: 39001972 DOI: 10.1007/s10646-024-02783-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/05/2024] [Indexed: 07/15/2024]
Abstract
The heavy metal cadmium (Cd) is a toxic and bioaccumulative metal that can be enriched in the tissues and organs of living organisms through the digestive tract. However, more research is needed to determine whether food-sourced Cd affects the homeostasis of host gut microflora. In this study, the snail Bradybaena ravida (Benson) was used as a model organism fed with mulberry leaves spiked with different concentrations of Cd (0, 0.052, 0.71, and 1.94 mg kg-1). By combining 16S rRNA high-throughput sequencing with biochemical characterization, it was found that there were increases in the overall microbial diversity and abundances of pathogenic bacteria such as Corynebacterium, Enterococcus, Aeromonas, and Rickettsia in the gut of B. ravida after exposure to Cd. However, the abundances of potential Cd-resistant microbes in the host's gut, including Sphingobacterium, Lactococcus, and Chryseobacterium, decreased with increasing Cd concentrations in the mulberry leaves. In addition, there was a significant reduction in activities of energy, nutrient metabolism, and antioxidant enzymes for gut microbiota of snails treated with high concentrations of Cd compared to those with low ones. These findings highlight the interaction of snail gut microbiota with Cd exposure, indicating the potential role of terrestrial animal gut microbiota in environmental monitoring through rapid recognition and response to environmental pollution.
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Affiliation(s)
- Yan-Mei Da
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Shun-Shun Li
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Yan-Qi Li
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Le-Yu Deng
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Ming-Jun Li
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Tao Huang
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Qing-Ye Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Jazbia Shirin
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Guo-Wei Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China.
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8
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Tsoukalas D, Hamed I, Hoel S, Lerfall J, Jakobsen AN. Effect of harvesting season and location on the microbial quality and community composition of the edible sea urchin (Echinus esculentus) gonads. Food Microbiol 2024; 123:104594. [PMID: 39038897 DOI: 10.1016/j.fm.2024.104594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 06/07/2024] [Accepted: 07/01/2024] [Indexed: 07/24/2024]
Abstract
Despite the crucial role of microbial community composition in the quality and stability of seafood, little emphasis has been given to the microbiota profile of sea urchin gonads. This study investigates the microbial quality and community composition of sea urchin gonads (Echinus esculentus) as a function of harvesting season (autumn, winter, spring, and summer) and location (one site proximal to urban activity areas while the other is located in open water close to the coastline). Significant season-dependent variations were found in psychrotrophic and aerobic plate counts, with higher counts in summer, followed by autumn, spring, and winter. H2S-producing bacteria and Pseudomonas spp. counts were unaffected by harvesting season or location. Sea urchin gonad microbial composition proved resilient and dynamic, primarily shaped by seasonal variations, and minimally influenced by location. Winter and spring samples exhibited higher diversity than autumn and summer. Key genera like Pseudomonas, Psychromonas, Vibrio, Chryseobacterium, Shewanella, and Photobacterium varied seasonally. Pseudomonas, Vibrio, and Photobacterium are crucial in assessing microbial quality and safety due to their roles as specific spoilage organisms (SSOs) and, in some cases, human pathogens. Though relative abundances differed slightly between locations, harvesting location did not notably impact microbial community shaping in gonads. However, the results suggest that harvesting locations near areas with urban activity may lead to contamination with specific bacterial species, possibly due to water quality variations. These findings emphasize the importance of considering seasonality when evaluating sea urchin gonad microbial quality. Identifying key genera enhances insights into potential SSOs and human pathogens, enhancing food safety considerations in the consumption of raw or lightly processed sea urchin gonads and guiding the development of preservation methods to extend shelf life.
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Affiliation(s)
- Dionysios Tsoukalas
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway.
| | - Imen Hamed
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway
| | - Sunniva Hoel
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway
| | - Jørgen Lerfall
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway
| | - Anita Nordeng Jakobsen
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway
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Han K, Yue J, Li J, Zhang J, Lin J, Zhuang Q, Li N, Li S, Rong C, Hua M, Liu Y, Yang D, Gu C, Chen L, Zeng H, Chen C. Emergence of mcr-4.3 genes in a novel Shewanella specie isolated from the Arctic environment. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105636. [PMID: 38972619 DOI: 10.1016/j.meegid.2024.105636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/28/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
Mobile colistin resistance (mcr) genes are pivotal contributors to last-line of antimicrobial resistance in human infections. Shewanella, historically recognized as a natural environmental bacterium with metal reduction capabilities, recently has been observed in clinical settings. However, limited knowledge has been explored on genetic differences between strains from non-clinical and clinical strains. In this study, we conducted the whole genome sequencing on six Arctic strains, illustrated the phylogenetic relationships on published 393 Shewanella strains that categorized the genus into four lineages (L1 to L4). Over 86.4% of clinical strain group (CG) strains belonged to L1 and L4, carrying mcr-4 genes and a complete metal-reduction pathways gene cluster. Remarkably, a novel Arctic Shewanella strain in L3, exhibits similar genetic characteristics with CG strains that carried both mcr-4 genes and a complete metal reduction pathway gene cluster. It raised concerns about the transmission ability from environment to clinic setting causing in the potential infections, and emphasized the need for monitoring the emerging strains with human infections.
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Affiliation(s)
- Kai Han
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jinglin Yue
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jiarui Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jiuming Zhang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Jing Lin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Qinghui Zhuang
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Na Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Sha Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chengbo Rong
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Mingxi Hua
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yuwei Liu
- Emergency Department, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Duo Yang
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chaoyang Gu
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Liang Chen
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hui Zeng
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chen Chen
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
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10
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Cerda Á, Rodríguez C, González M, González H, Serrano J, Leiva E. Feammox bacterial biofilm formation in HFMB. CHEMOSPHERE 2024; 358:142072. [PMID: 38657691 DOI: 10.1016/j.chemosphere.2024.142072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Nitrogen pollution has been increasing with the development of industrialization. Consequently, the excessive deposition of reactive nitrogen in the environment has generated the loss of biodiversity and eutrophication of different ecosystems. In 2005, a Feammox process was discovered that anaerobically metabolizes ammonium. Feammox with the use of hollow fiber membrane bioreactors (HFMB), based on the formation of biofilms of bacterial communities, has emerged as a possible efficient and sustainable method for ammonium removal in environments with high iron concentrations. This work sought to study the possibility of implementing, at laboratory scale, an efficient method by evaluating the use of HFMB. Samples from an internal circulation reactor (IC) incubated in culture media for Feammox bacteria. The cultures were enriched in a batch reactor to evaluate growth conditions. Next, HFMB assembly was performed, and Feammox parameters were monitored. Also, conventional PCR and scanning electron microscopy (SEM) analysis were performed to characterize the bacterial communities associated with biofilm formation. The use of sodium acetate presented the best performance for Feammox activity. The HFMB operation showed an ammonium (NH4+) removal of 50%. SEM analysis of the fibers illustrated the formation of biofilm networks formed by bacteria, which were identified as Albidiferax ferrireducens, Geobacter spp, Ferrovum myxofaciens, Shewanella spp., and Anammox. Functional genes Archaea/Bacteria ammonia monooxygenase, nrxA, hzsB, nirS and nosZ were also identified. The implementation of HFMB Feammox could be used as a sustainable tool for the removal of ammonium from wastewater produced because of anthropogenic activities.
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Affiliation(s)
- Ámbar Cerda
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| | - Carolina Rodríguez
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| | - Macarena González
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| | - Heylin González
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| | - Jennyfer Serrano
- Escuela de Biotecnología, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Santiago 8580745, Chile.
| | - Eduardo Leiva
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile; Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
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11
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Ghotekar BK, Kulkarni SS. Total Synthesis of the Conjugation-Ready Tetrasaccharide Repeating Unit of Shewanella japonica Type Strain KMM 3299 T. Org Lett 2024; 26:4346-4350. [PMID: 38722236 DOI: 10.1021/acs.orglett.4c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Here we report the first total synthesis of the conjugation-ready tetrasaccharide repeating unit of Shewanella japonica type strain KMM 3299T. The presence of rare deoxyamino sugars and installation of three consecutive 1,2-cis glycosidic linkages makes the synthesis formidable. The challenging late-stage oxidation was overcome by using a galacturonate donor. The total synthesis was completed via a longest linear sequence of 22 steps in an overall yield of 3.5% starting from d-mannose.
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Affiliation(s)
- Balasaheb K Ghotekar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Suvarn S Kulkarni
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Li Y, Qi R, Yang H, Zhang XL, Wu Y, Huang BH, Zhao Q, Gu YF. Analysis of clinical characteristics of infections caused by Shewanella species. Indian J Med Microbiol 2024; 49:100574. [PMID: 38561026 DOI: 10.1016/j.ijmmb.2024.100574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/14/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
PURPOSE The Shewanella genus is a rare pathogen of marine origin. In recent years, there has been a continuous increase in infection cases caused by this bacterium, and we have observed the uniqueness of infections caused by this microorganism. MATERIALS AND METHODS This study conducted a retrospective analysis of the medical history and laboratory examination data of patients infected with the Shewanella genus over the past decade. Additionally, it employed bioinformatics methods to analyze the relevant virulence factors and antibiotic resistance genes associated with the Shewanella genus. RESULTS Over the past 10 years, we have isolated 51 cases of Shewanella, with 68.82% being Shewanella putrefaciens (35/51 cases) and 31.37% being Shewanella algae (16/51 cases). Infected individuals often had underlying diseases, with 39.22% (20/51) having malignant tumors and 25.49% (13/51) having liver and biliary system diseases primarily characterized by stones. The majority of patients, 62.74% (32/51), exhibited mixed infections, including one case with a combination of infections from three other types of bacteria and five cases with a combination of infections from two other types of bacteria. The identified microorganisms were commonly resistant to ticarcillin-clavulanic acid (23.5%), followed by cefoperazone-sulbactam (19.6%), ciprofloxacin (17.6%), and cefotaxime (17.6%). Bioinformatics analysis indicates that Shewanella can express bile hydrolysis regulators and fatty acid metabolism regulators that aid in adapting to the unique environment of the biliary tract. Additionally, it expresses abundant catalase, superoxide dismutase, and two-component signal transduction system proteins, which may be related to environmental adaptation. Shewanella also expresses various antibiotic resistance genes, including beta-lactamases and aminoglycoside modification enzymes. Iron carriers may be one of its important virulence factors. CONCLUSIONS We speculate that the Shewanella genus may exist as a specific colonizer in the human body, and under certain conditions, it may act as a pathogen, leading to biliary infections in the host.
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Affiliation(s)
- Yu Li
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, 264000, PR China.
| | - Rong Qi
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, 264000, PR China.
| | - Hui Yang
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, 264000, PR China.
| | - Xiao-Lu Zhang
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, 264000, PR China.
| | - Yan Wu
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, 264000, PR China.
| | - Bao-Hua Huang
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, 264000, PR China.
| | - Qi Zhao
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, 264000, PR China.
| | - Yu-Feng Gu
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, 264000, PR China.
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Wang H, Xia F, Xia Y, Li J, Hu Y, Deng Y, Zou M. Pangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance. BMC Genomics 2024; 25:216. [PMID: 38413855 PMCID: PMC10898099 DOI: 10.1186/s12864-024-10146-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/19/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Shewanella xiamenensis, widely distributed in natural environments, has long been considered as opportunistic pathogen. Recently, significant changes in the resistance spectrum have been observed in S. xiamenensis, due to acquired antibiotic resistance genes. Therefore, a pan-genome analysis was conducted to illuminate the genomic changes in S. xiamenensis. RESULTS Phylogenetic analysis revealed three major clusters and three singletons, among which close relationship between several strains was discovered, regardless of their host and niches. The "open" genomes with diversity of accessory and strain-specific genomes took advantage towards diversity environments. The purifying selection pressure was the main force on genome evolution, especially in conservative genes. Only 53 gene families were under positive selection pressure. Phenotypic resistance analysis revealed 21 strains were classified as multi-drug resistance (MDR). Ten types of antibiotic resistance genes and two heavy metal resistance operons were discovered in S. xiamenensis. Mobile genetic elements and horizontal gene transfer increased genome diversity and were closely related to MDR strains. S. xiamenensis carried a variety of virulence genes and macromolecular secretion systems, indicating their important roles in pathogenicity and adaptability. Type IV secretion system was discovered in 15 genomes with various sequence structures, indicating it was originated from different donors through horizontal gene transfer. CONCLUSIONS This study provided with a detailed insight into the changes in the pan-genome of S. xiamenensis, highlighting its capability to acquire new mobile genetic elements and resistance genes for its adaptation to environment and pathogenicity to human and animals.
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Affiliation(s)
- Haichen Wang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Fengjun Xia
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Yubing Xia
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Jun Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Yongmei Hu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Yating Deng
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Mingxiang Zou
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China.
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China.
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Kang Y, Yu K, Huang Z, Pang B, Liu S, Peng T, Li Y, Wang D. Prevalence and molecular characteristics of Shewanella infection in diarrhea patients in Beijing, China 2017-2019. Front Microbiol 2024; 15:1293577. [PMID: 38357347 PMCID: PMC10866003 DOI: 10.3389/fmicb.2024.1293577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/03/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Shewanella is an important opportunistic pathogen distributed in marine environments that has caused an increasing number of clinical infections. However, there are few reports on the distribution and characteristics of Shewanella in the diarrheal pathogen spectrum. In this study, we have systematically described the prevalence of Shewanella infections in diarrhea patients in Beijing, China 2017-2019, and genome characteristics and antimicrobial susceptibility of Shewanella isolates. Methods Stool samples were collected from diarrhea patients in a surveillance project from 2017 to 2019. Shewanella strains were isolated, and identified using VITEKR 2 COMPACT and MALDI-TOF MS. Average nucleotide identity (ANI) analysis, multi-locus sequence typing (MLST), phylogenetic analysis, virulence-associated genes and antimicrobial resistance genes analysis were used for genome characteristics description. The antibiotic susceptibility test was performed with microbroth dilution method. Results 1104 fecal samples were collected, and the Shewanella detection rate was 2.36% (26/1104). The main manifestations of infection caused by Shewanella spp. were diarrhea (100%, 26/26), abdominal pain (65.38%, 17/26), and vomiting (38.46%, 10/26). The 26 isolates were classified into 3 species (S. algae (n = 18), S. indica (n = 5), and S. chilikensis (n = 3)) and 22 sequence types. Core genome single nucleotide polymorphism-based evolutionary tree identified three clone groups corresponding to three infection events in the same months in 2017 and 2019. The putative virulence-associated gene pool consisted of 56 potential virulence genes, including 19 virulence gene factors. The resistance rates of the 26 isolates to 17 antibiotics from high to low were as follows: polymyxin E (76.92%), cefotaxime (57.69%), ampicillin (50%), ampicillin-sulbactam (34.62%), nalidixic acid (15.38%), ciprofloxacin (11.54%), selectrin (3.846%,1/26), and tetracycline (3.846%, 1/26). The rate of multidrug resistance was 38.46% (10/26). Discussion Monitoring for Shewanella spp. should be added to the routine surveillance of infectious diarrhea during the epidemic season.
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Affiliation(s)
- Ying Kang
- Shunyi District Center for Disease Control and Prevention, Beijing, China
- Workstation for Microbial Infectious Disease, Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Keyi Yu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Zhenzhou Huang
- Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Bo Pang
- Workstation for Microbial Infectious Disease, Shunyi District Center for Disease Control and Prevention, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Shengtian Liu
- Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Tao Peng
- Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Ying Li
- Shunyi District Center for Disease Control and Prevention, Beijing, China
- Workstation for Microbial Infectious Disease, Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Duochun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
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Zhang Y, Pan M, Wang Q, Wang L, Liao L. Complete Genome Sequence and Pan-Genome Analysis of Shewanella oncorhynchi Z-P2, a Siderophore Putrebactin-Producing Bacterium. Microorganisms 2023; 11:2961. [PMID: 38138105 PMCID: PMC10745600 DOI: 10.3390/microorganisms11122961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
In this study, we reported the complete genome sequence of Shewanella oncorhynchi for the first time. S. oncorhynchi Z-P2 is a bacterium that produces the siderophore putrebactin. Its genome consists of a circular chromosome of 5,034,612 bp with a G + C content of 45.4%. A total of 4544 protein-coding genes, 109 tRNAs and 31 rRNAs were annotated by the RAST. Five non-ribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) gene clusters were identified by the antiSMASH analysis. The pan-genome analysis of Z-P2 and 10 Shewanella putrefaciens revealed 9228 pan-gene clusters and 2681 core gene clusters, with Z-P2 having 618 unique gene clusters. Additionally, the gene cluster involved in putrebactin biosynthesis in Z-P2 was annotated, and the mechanism of putrebactin biosynthesis was analyzed. The putrebactin produced by Z-P2 was detected using UPLC-MS analysis, with an [M + H]+ molecular ion at m/z 373.21. These findings provide valuable support for further research on the genetic engineering of putrebactin biosynthetic genes of Z-P2 and their potential applications.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (Y.Z.); (L.W.)
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China; (M.P.); (Q.W.)
| | - Mengjie Pan
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China; (M.P.); (Q.W.)
| | - Qiaoyun Wang
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China; (M.P.); (Q.W.)
| | - Lan Wang
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (Y.Z.); (L.W.)
| | - Li Liao
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (Y.Z.); (L.W.)
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Paździor E, Bomba A, Tłuścik K, Nadolna-Ałtyn K, Podolska M, Reichert M, Wasyl D, Pękala-Safińska A. Phylogenetic analysis of Shewanella spp. isolated from fish. JOURNAL OF FISH DISEASES 2023; 46:1163-1171. [PMID: 37453080 DOI: 10.1111/jfd.13834] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Different species of Shewanella spp. widely inhabit freshwater and marine environments. Some of them are opportunistic fish pathogens. The application of high-throughput sequencing enabled the characterization and taxonomic reclassification of many Shewanella spp. species. Still, some strains collected from fish need to be better recognized. The aim of the present study was to classify and determine the phylogenetic relationships of Shewanella spp. collected from fish. The complete genomes of 94 strains of Shewanella spp. from different fish species were sequenced using Illumina platform (MiSeq). The 16S rRNA gene, genomic features and whole-genome relationships of those bacteria were comprehensively analysed in comparison to reference strains. Whole-genome analysis showed that the tested Shewanella spp. strains were clustered into six groups similar to reference strains of S. xiamenensis, S. oneidensis, S. glacialipiscicola, S. hafniensis, S. baltica and S. oncorhynchi. Our study indicates that the whole-genome sequence analysis enabled taxonomic classification and assessment of the diversity of the Shewanella spp. strains, as opposed to recently the gold standard method of 16S rRNA amplicon sequencing. The high genetic diversity and low similarity to the reference genome of S. oneidensis indicate that the group of strains may be a subspecies or even new species. Furthermore, we showed that the most frequent Shewanella spp. species occurring in freshwater fish in our study is the recently described species S. oncorhynchi.
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Affiliation(s)
- Ewa Paździor
- Department of Fish Diseases, National Veterinary Research Institute, Puławy, Poland
| | - Arkadiusz Bomba
- Depratment of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
| | - Katarzyna Tłuścik
- Depratment of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
| | - Katarzyna Nadolna-Ałtyn
- Department of Fisheries Resources, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Magdalena Podolska
- Department of Fisheries Resources, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Michał Reichert
- Department of Fish Diseases, National Veterinary Research Institute, Puławy, Poland
| | - Dariusz Wasyl
- Depratment of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Agnieszka Pękala-Safińska
- Department of Preclinical Sciences and Infectious Diseases, Faculty of Veterinary Medicine and Animal Science, Poznań University of Life Sciences, Poznań, Poland
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Pan Y, Qian J, Ma X, Huang W, Fang JKH, Arif I, Wang Y, Shang Y, Hu M. Response of moulting genes and gut microbiome to nano-plastics and copper in juvenile horseshoe crab Tachypleus tridentatus. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106128. [PMID: 37587001 DOI: 10.1016/j.marenvres.2023.106128] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023]
Abstract
Nanoplastics (NPs) and heavy metals are typical marine pollutants, affecting the gut microbiota composition and molting rate of marine organisms. Currently, there is a lack of research on the toxicological effects of combined exposure to horseshoe crabs. In this study, we investigated the effects of NPs and copper on the expression of molt-related genes and gut microbiome in juvenile tri-spine horseshoe crabs Tachypleus tridentatus by exposing them to NPs (100 nm, 104 particles L-1) and/or Cu2+ (10 μgL-1) in seawater for 21 days. Compared with the control group, the relative mRNA expression of ecdysone receptor (EcR), retinoid x receptor (RXR), calmodulin-A-like isoform X1 (CaM X1), and heat shock 70 kDa protein (Hsp70) were significantly increased under the combined stress of NPs and Cu2+. There were no significant differences in the diversity and abundance indices of the gut microbial population of horseshoe crabs between the NPs and/or Cu2+ groups and the control group. According to linear discriminant analysis, Oleobacillus was the most abundant microorganism in the NPs and Cu2+ stress groups. These results indicate that exposure to either NPs stress alone or combined NPs and Cu2+ stress can promote the expression levels of juvenile molting genes. NPs exposure has a greater impact on the gut microbial community structure of juvenile horseshoe crabs compared to Cu2+ exposure. This study is helpful for predicting the growth and development of horseshoe crabs under complex environmental pollution.
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Affiliation(s)
- Yiting Pan
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, PR China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Jin Qian
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, PR China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Xiaowan Ma
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, 536000, PR China
| | - Wei Huang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, PR China
| | - James Kar-Hei Fang
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong Special Administrative Region, PR China
| | - Iqra Arif
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, PR China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Youji Wang
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, PR China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Yueyong Shang
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, PR China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, PR China.
| | - Menghong Hu
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, PR China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, PR China.
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Oduro D, Darko S, Blankson ER, Mensah GI. Assessment of Bacteria Contaminants in Different Zones and Point Sources of Sandy Beaches in Accra, Ghana. Microbiol Insights 2023; 16:11786361231195152. [PMID: 37693208 PMCID: PMC10492474 DOI: 10.1177/11786361231195152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023] Open
Abstract
Background Bacteria are ubiquitous in the marine environment. Increasing concern for human health has led to growing interest in contamination on public beaches. The presence of pathogenic microorganisms originating from anthropogenic activities such as defecation and disposal of sewage on beaches are of special concern. In this study, presence of pathogenic bacteria and bacterial load in beach zones and point sources were investigated. Methods Sand core samples from the subtidal zone, intertidal zone, supratidal zone and point sources from 5 beaches in Accra, Ghana, were collected and analysed. Total aerobic, coliform and Escherichia (E. coli) counts were determined for each zone in the respective beaches. Bacteria isolates were presumptively identified using biochemical tests and confirmed with MALDI-TOF MS. Results Mean total aerobic count and total coliform counts ranged from 2.10 to 3.01 log CFU/g and 0.29 to 2.18 log CFU/g respectively while E. coli counts ranged from 0.12 to 1.71 log CFU/g for the beaches. Total aerobic count from point sources was 2.4-folds higher than the subtidal zone while total coliform counts were 5-folds higher in the point sources compared to the supratidal zone. Point sources had 10 times (P = .0016) more E. coli counts as compared to the subtidal zone. Isolates recovered (n = 35) belonged to 10 bacteria genera. These were Bacillus spp. (25.7%), Acinetobacter spp. (14.3%), Aeromonas spp. (14.3%), Klebsiella pneumoniae (14.3%), Aerococcus viridans (8.6%), Staphylococcus spp. (8.6%), Shewanella profunda (5.7%), Rheinheimera soli (2.9%), Pseudomonas aeruginosa (2.9%), and Exiguobacterium aurantiacum (2.9%). Conclusion Point sources are major contributors to contamination on beaches. The presence of potentially pathogenic bacteria in beach sand could be a public health risk. Sensitization on cleanliness in the marine environment including beaches in Ghana is needed to enhance public health and safety.
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Affiliation(s)
- Daniel Oduro
- Department of Animal Biology and Conservation Science, University of Ghana, Legon, Accra, Ghana
| | - Stephanie Darko
- Department of Animal Biology and Conservation Science, University of Ghana, Legon, Accra, Ghana
| | | | - Gloria Ivy Mensah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
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Hughey MC, Warne R, Dulmage A, Reeve RE, Curtis GH, Whitfield K, Schock DM, Crespi E. Diet- and salinity-induced modifications of the gut microbiota are associated with differential physiological responses to ranavirus infection in Rana sylvatica. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220121. [PMID: 37305908 PMCID: PMC10258663 DOI: 10.1098/rstb.2022.0121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/26/2023] [Indexed: 06/13/2023] Open
Abstract
Greater knowledge of how host-microbiome interactions vary with anthropogenic environmental change and influence pathogenic infections is needed to better understand stress-mediated disease outcomes. We investigated how increasing salinization in freshwaters (e.g. due to road de-icing salt runoff) and associated increases in growth of nutritional algae influenced gut bacterial assembly, host physiology and responses to ranavirus exposure in larval wood frogs (Rana sylvatica). Elevating salinity and supplementing a basic larval diet with algae increased larval growth and also increased ranavirus loads. However, larvae given algae did not exhibit elevated kidney corticosterone levels, accelerated development or weight loss post-infection, whereas larvae fed a basic diet did. Thus, algal supplementation reversed a potentially maladaptive stress response to infection observed in prior studies in this system. Algae supplementation also reduced gut bacterial diversity. Notably, we observed higher relative abundances of Firmicutes in treatments with algae-a pattern consistent with increased growth and fat deposition in mammals-that may contribute to the diminished stress responses to infection via regulation of host metabolism and endocrine function. Our study informs mechanistic hypotheses about the role of microbiome mediation of host responses to infection that can be tested in future experiments in this host-pathogen system. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
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Affiliation(s)
- Myra C. Hughey
- Department of Biology, Vassar College, Poughkeepsie, NY 12604, USA
| | - Robin Warne
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
| | - Alexa Dulmage
- School of Biological Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | - Robyn E. Reeve
- School of Biological Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | - Grace H. Curtis
- School of Biological Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | - Kourtnie Whitfield
- School of Biological Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | | | - Erica Crespi
- School of Biological Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
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20
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Hou D, Lian T, Guo G, Gong H, Wu C, Han P, Weng S, He J. Integration of microbiome and Koch's postulates to reveal multiple bacterial pathogens of whitish muscle syndrome in mud crab, Scylla paramamosain. MICROBIOME 2023; 11:155. [PMID: 37475003 PMCID: PMC10357871 DOI: 10.1186/s40168-023-01570-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/12/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND For more than a century, the Koch's postulates have been the golden rule for determining the causative agents in diseases. However, in cases of multiple pathogens-one disease, in which different pathogens can cause the same disease, the selection of microorganisms that regress infection is hard when Koch's postulates are applied. Microbiome approaches can obtain relatively complete information about disease-related microorganisms and can guide the selection of target microorganisms for regression infection. In the present study, whitish muscle syndrome (WMS) of Scylla paramamosain, which has typical symptoms with whitish muscle and blackened hemolymph was used as an example to establish a new research strategy that integrates microbiome approaches and Koch's postulates to determinate causative agents of multiple pathogens-one disease. RESULTS Microbiome results revealed that Aeromonas, Acinetobacter, Shewanella, Chryseomicrobium, Exiguobacterium, Vibrio and Flavobacterium, and Kurtzmaniella in hemolymph were bacterial and fungal indicators for WMS. A total of 23 bacteria and 14 fungi were isolated from hemolymph and muscle tissues, and among the bacteria, Shewanella chilikensis, S. xiamenensis, Vibrio alginolyticus, S. putrefaciens, V. fluvialis, and V. parahaemolyticus were present in hemolymph and/or muscle tissues in each WMS crab, and the last three species were also present in three Healthy crabs. The target bacteria and fungi were further screened to regression infections based on two criteria: whether they belonged to the indicator genera for WMS, whether they were isolated from both hemolymph and muscle tissues in most WMS crabs. Only S. chilikensis, S. putrefaciens, S. xiamenensis, V. alginolyticus, V. fluvialis, and V. parahaemolyticus met both two criteria. The six bacteria that met both two criteria and six fungi and another bacterium that unmatched any of two criteria were used to perform regression infection experiments based on Koch's postulates. S. chilikensis, S. putrefaciens, S. xiamenensis, V. alginolyticus, V. fluvialis, and V. parahaemolyticus met both two criteria, and the results indicate that they cause WMS in crabs independently. CONCLUSIONS This study fully demonstrated that our research strategy that integrates the microbiome and Koch's postulates can maximize the ability to catch pathogens in one net for the situation of multiple pathogens-one disease. Video Abstract.
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Affiliation(s)
- Dongwei Hou
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Taixin Lian
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Guangyu Guo
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Han Gong
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Chengcheng Wu
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Peiyun Han
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, People's Republic of China
| | - Jianguo He
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China.
- Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, People's Republic of China.
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21
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Jiang X, Miao B, Zhao X, Bai X, Yuan M, Chen X, Gong X, Liu Z, Li J, Meng S, Han X, Li J. Unveiling the Emergence and Genetic Diversity of OXA-48-like Carbapenemase Variants in Shewanella xiamenensis. Microorganisms 2023; 11:1325. [PMID: 37317299 DOI: 10.3390/microorganisms11051325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
An increase in the carbapenem-hydrolyzing capacity of class D β-lactamase has been observed in strains of multiple species, posing a significant challenge to the control of antibiotic resistance. In this study, we aimed to investigate the genetic diversity and phylogenetic characteristics of new blaOXA-48-like variants derived from Shewanella xiamenensis. Three ertapenem-non-susceptible S. xiamenensis strains were identified, one isolated from the blood sample of an inpatient, the other two isolated from the aquatic environment. Phenotypic characterization confirmed that the strains were carbapenemase producers and exhibited antimicrobial resistance patterns to ertapenem, with some showing lower susceptibility to imipenem, chloramphenicol, ciprofloxacin, and tetracycline. No significant resistance to cephalosporins was observed. Sequence analysis revealed that one strain harbored blaOXA-181 and the other two strains harbored blaOXA-48-like genes, with open reading frame (ORF) similarities with blaOXA-48 ranging from 98.49% to 99.62%. The two novel blaOXA-48-like genes, named blaOXA-1038 and blaOXA-1039, respectively, were cloned and expressed in E. coli. The three OXA-48-like enzymes demonstrated significant hydrolysis activity against meropenem, and the classical β-lactamase inhibitor had no significant inhibitory effect. In conclusion, this study demonstrated the diversity of the blaOXA gene and highlighted the emergence of novel OXA carbapenemases in S. xiamenensis. Further attention to S. xiamenensis and OXA carbapenemases is recommended for the effective prevention and control of antibiotic-resistant bacteria.
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Affiliation(s)
- Xueqi Jiang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Beibei Miao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiaofei Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xuemei Bai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Min Yuan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xia Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xinyi Gong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Zeliang Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jie Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shuang Meng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiao Han
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Juan Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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22
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Zu B, Li W, Yang Q, Guo J, An J, Li J, Mei X. Ingestion of microplastics by silver carp (Hypophthalmichthys molitrix) larvae: Quantification of ingestion and assessment of microbiota dysbiosis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 257:106475. [PMID: 36881946 DOI: 10.1016/j.aquatox.2023.106475] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
The adverse effects of microplastics ingested by aquatic organisms have been reported previously. However, most studies are primarily qualitative; therefore, it is challenging to determine the direct interactions between microplastics and organisms. In this study, for the first time, the microplastic intake behavior of silver carp (Hypophthalmichthys molitrix) larvae, a popular fish in China, as well as intestine accumulation and excretion of the microplastics were quantitatively investigated. The results showed that the intake of microplastics by silver carp larvae was negatively correlated with the particle size of microplastics but positively correlated with the exposure concentration. After intaking microplastics of different sizes, small-sized microplastics (≤ 150 μm) were rapidly excreted from the intestine of silver carp, whereas some large-sized microplastics (≥ 300 μm) remained in the intestine for a long time. The presence of food significantly increased the intake of large-sized microplastics, while small-sized microplastics intake was unaffected by the food. More importantly, the ingested microplastics caused specific changes in the diversity of intestinal microflora, potentially leading to abnormal immune and metabolic functions. The results of this study provide a new understanding on the potential impacts of microplastics on aquatic organisms.
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Affiliation(s)
- Bo Zu
- College of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - Wang Li
- College of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China.
| | - Qingwei Yang
- College of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China.
| | - Juncheng Guo
- College of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - Junwen An
- College of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - Jiawen Li
- Chongqing Research Academy of Ecology and Environmental Sciences, Chongqing 401147, China
| | - Xueyu Mei
- Chongqing Yi Da Environmental Protection Engineering Co., Ltd., Chongqing 400060, China
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23
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Martín-Rodríguez AJ, Thorell K, Joffré E, Jensie-Markopoulos S, Moore ERB, Sjöling Å. Shewanella septentrionalis sp. nov. and Shewanella holmiensis sp. nov., isolated from Baltic Sea water and sediments. Int J Syst Evol Microbiol 2023; 73. [PMID: 37083582 DOI: 10.1099/ijsem.0.005767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Two bacterial strains, SP1W3T and SP1S2-7T, were isolated from samples of water and sediments collected in Vaxholm, a town located on the Stockholm archipelago in the Baltic Sea, in November 2021. The strains were identified as novel genomic species within the genus Shewanella, based upon comparative analysis of whole genome sequence data. Strain SP1W3T (genome size, 5.20 Mbp; G+C content, 46.0 mol%), isolated from water, was determined to be most closely related to S. hafniensis ATCC-BAA 1207T and S. baltica NCTC 10735T, with digital DNA-DNA hybridization (dDDH) values of 61.7% and 60.4 %, respectively. Strain SP1S2-7T (genome size, 4.26 Mbp; G+C content, 41.5 mol%), isolated from sediments, was observed to be most closely related to S. aestuarii JCM17801T, with a pairwise dDDH value of 33.8 %. Polyphasic analyses of physiological and phenotypic characteristics, in addition to genomic analyses, confirmed that each of these two strains represent distinct, novel species within the genus Shewanella, for which the names Shewanella septentrionalis sp. nov. (type strain SP1W3T=CCUG 76164T=CECT 30651T) and Shewanella holmiensis sp. nov. (type strain SP1S2-7T=CCUG 76165T=CECT 30652T) are proposed.
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Affiliation(s)
| | - Kaisa Thorell
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Enrique Joffré
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Susanne Jensie-Markopoulos
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital and Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Edward R B Moore
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital and Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Chemistry and Molecular Biology (CMB) , University of Gothenburg, Gothenburg, Sweden
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24
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Yang J, Xu J, Ling Z, Zhou X, Si Y, Liu X, Ji F. Prognostic effects of the gastric mucosal microbiota in gastric cancer. Cancer Sci 2023; 114:1075-1085. [PMID: 36403134 PMCID: PMC9986079 DOI: 10.1111/cas.15661] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/22/2022] [Accepted: 11/13/2022] [Indexed: 11/21/2022] Open
Abstract
Gastric cancer (GC) is one of the most common malignant tumors with a high incidence and mortality. Microbiota play a significant role in human health and disease. We aimed to investigate the prognostic value of the gastric microbiota in different stomach microhabitats. We used our previously published 16S rRNA gene sequence data. We retrospectively enrolled a cohort of 132 patients with GC with complete prognostic information and selected 78 normal tissues, 49 peritumoral tissues, and 112 tumoral tissues for microbiota analysis. Patients with different prognoses showed different gastric microbiota compositions and diversity. The association network of the abundant gastric microbiota was more complicated in patients with poor prognoses. In the peritumoral microhabitat of patients with good prognoses, Helicobacter was significantly increased, whereas Halomonas and Shewanella were significantly decreased relative to that in the peritumoral microhabitat of patients with poor prognoses. PiCRUSt analysis revealed that the peritumoral microbiota had more different Kyoto Encyclopedia of Genes and Genomes pathways than did the tumoral and normal microbiota. This study evaluated the long-term prognostic value of the gastric mucosal microbiota in patients with GC. These findings suggested that the characteristic alterations of the gastric mucosal microbiota may be markers for clinical outcomes in these patients.
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Affiliation(s)
- Jinpu Yang
- Department of Gastroenterology, The First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang ProvinceChina
| | - Jiaren Xu
- Department of Gastrointestinal Surgery, The First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang ProvinceChina
| | - Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of MedicineZhejiang UniversityZhejiangHangzhouChina
| | - Xinxin Zhou
- Department of Gastroenterology, The First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang ProvinceChina
| | - Yongqiang Si
- Department of Gastrointestinal Surgery, The First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang ProvinceChina
| | - Xiaosun Liu
- Department of Gastrointestinal Surgery, The First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang ProvinceChina
| | - Feng Ji
- Department of Gastroenterology, The First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang ProvinceChina
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25
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Kijewska A, Koroza A, Grudlewska-Buda K, Kijewski T, Wiktorczyk-Kapischke N, Zorena K, Skowron K. Molluscs-A ticking microbial bomb. Front Microbiol 2023; 13:1061223. [PMID: 36699600 PMCID: PMC9868776 DOI: 10.3389/fmicb.2022.1061223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Bivalve shellfish consumption (ark shells, clams, cockles, and oysters) has increased over the last decades. Following this trend, infectious disease outbreaks associated with their consumption have been reported more frequently. Molluscs are a diverse group of organisms found wild and farmed. They are common on our tables, but unfortunately, despite their great taste, they can also pose a threat as a potential vector for numerous species of pathogenic microorganisms. Clams, in particular, might be filled with pathogens because of their filter-feeding diet. This specific way of feeding favors the accumulation of excessive amounts of pathogenic microorganisms like Vibrio spp., including Vibrio cholerae and V. parahaemolyticus, Pseudomonas aeruginosa, Escherichia coli, Arcobacter spp., and fecal coliforms, and intestinal enterococci. The problems of pathogen dissemination and disease outbreaks caused by exogenous bacteria in many geographical regions quickly became an unwanted effect of globalized food supply chains, global climate change, and natural pathogen transmission dynamics. Moreover, some pathogens like Shewanella spp., with high zoonotic potential, are spreading worldwide along with food transport. These bacteria, contained in food, are also responsible for the potential transmission of antibiotic-resistance genes to species belonging to the human microbiota. Finally, they end up in wastewater, thus colonizing new areas, which enables them to introduce new antibiotic-resistance genes (ARG) into the environment and extend the existing spectrum of ARGs already present in local biomes. Foodborne pathogens require modern methods of detection. Similarly, detecting ARGs is necessary to prevent resistance dissemination in new environments, thus preventing future outbreaks, which could threaten associated consumers and workers in the food processing industry.
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Affiliation(s)
- Agnieszka Kijewska
- Department of Immunobiology and Environmental Microbiology, Institute of Maritime and Tropical Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Aleksandra Koroza
- Department of Climate and Ocean Research and Education Laboratory, Institute of Oceanology Polish Academy of Science, Sopot, Poland
| | - Katarzyna Grudlewska-Buda
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum, Bydgoszcz, Poland
| | - Tomasz Kijewski
- Department of Climate and Ocean Research and Education Laboratory, Institute of Oceanology Polish Academy of Science, Sopot, Poland
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum, Bydgoszcz, Poland
| | - Katarzyna Zorena
- Department of Immunobiology and Environmental Microbiology, Institute of Maritime and Tropical Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum, Bydgoszcz, Poland,*Correspondence: Krzysztof Skowron,
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26
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Muacevic A, Adler JR, Silva AR, Tavares R, Rodrigues P. Shewanella algae, an Emerging Human Pathogen: A Series of Four Cases From a Portuguese Hospital. Cureus 2023; 15:e33686. [PMID: 36788829 PMCID: PMC9920493 DOI: 10.7759/cureus.33686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2023] [Indexed: 01/13/2023] Open
Abstract
Shewanella algae is a rod-shaped, Gram-negative bacterium that is considered an emerging human pathogen. Traditionally associated with warmer climates, S. algae has now been isolated from patients worldwide, and reports of infection are increasing. In a regional hospital on the outskirts of Lisbon, Portugal, four cases have been detected in the past 10 years. Two of the patients were migrants from African countries with daily contact with water; the other two patients were Portuguese, and no epidemiological risk factors were found among them. These are the first cases reported in Portugal. Risk factors associated with S. algae infection in patients discussed in this paper include the following: human immunodeficiency virus (HIV) infection, chronic venous insufficiency, lower limb ulcers, chronic kidney disease, diabetes, arterial hypertension, dilated cardiomyopathy, atrial fibrillation, chronic hepatic disease, and chronic pancreatitis. One patient died in the intensive care unit with septic shock and disseminated intravascular coagulation from a fulminant infection secondary to S. algae bacteraemia. The four clinical cases presented in this case series highlight the clinical features of this infection so that other physicians can successfully identify and treat S. algae infections.
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27
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Cerbino GN, Traglia GM, Ayala Nuñez T, Parmeciano Di Noto G, Ramírez MS, Centrón D, Iriarte A, Quiroga C. Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages. Front Microbiol 2023; 14:1124225. [PMID: 36925471 PMCID: PMC10011109 DOI: 10.3389/fmicb.2023.1124225] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.
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Affiliation(s)
- Gabriela N Cerbino
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - German M Traglia
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Teolincacihuatl Ayala Nuñez
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Gisela Parmeciano Di Noto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - María Soledad Ramírez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University, Fullerton, Fullerton, CA, United States
| | - Daniela Centrón
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Quiroga
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
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28
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Yu K, Huang Z, Xiao Y, Wang D. Shewanella infection in humans: Epidemiology, clinical features and pathogenicity. Virulence 2022; 13:1515-1532. [PMID: 36065099 PMCID: PMC9481105 DOI: 10.1080/21505594.2022.2117831] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The genus Shewanella consists of Gram-negative proteobacteria that are ubiquitously distributed in environment. As the members of this genus have rapidly increased within the past decade, several species have become emerging pathogens worldwide, attracting the attention of the medical community. These species are also associated with severe community- and hospital-acquired infections. Patients infected with Shewanella spp. had experiences of occupational or recreational exposure; meanwhile, the process of infection is complex and the pathogenicity is influenced by a variety of factors. Here, an exhaustive internet-based literature search was carried out in PUBMED using terms “Achromobacter putrefaciens,” “Pseudomonas putrefaciens,” “Alteromonas putrefaciens” and “Shewanella” to search literatures published between 1978 and June 2022. We provided a comprehensive review on the epidemiology, clinical features and pathogenicity of Shewanella, which will contribute a better understanding of its clinical aetiology, and facilitate the timely diagnosis and effective treatment of Shewanella infection for clinicians and public health professionals.
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Affiliation(s)
- Keyi Yu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Zhenzhou Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Yue Xiao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Duochun Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
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Wen Y, Xie X, Xu P, Yang C, Zhu Z, Zhu J, Lv J, Zhang H, Chen L, Du H. NDM-1 and OXA-48-Like Carbapenemases (OXA-48, OXA-181 and OXA-252) Co-Producing Shewanella xiamenensis from Hospital Wastewater, China. Infect Drug Resist 2022; 15:6927-6938. [PMID: 36471715 PMCID: PMC9719275 DOI: 10.2147/idr.s386345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/09/2022] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Shewanella genus, as an important carrier of resistance genes, has the potential to transmit resistance to many antimicrobials in many circumstances, especially in aquatic environment. The aim of the study was to describe the risk of Shewanella xiamenensis in hospital environment through analysis of genomic comparison and resistance status. METHODS Seven S. xiamenensis strains were isolated from hospital wastewater. PCR and Sanger sequencing were carried out for detection of common carbapenemase genes. Antimicrobial susceptibility testing was performed to determine the antimicrobial profile. Whole genome sequencing was applied, and sequences were further used for genomic analysis. RESULTS Seven Shewanella xiamenensis were all positive for bla NDM and bla OXA-48. Antimicrobial susceptibility testing showed all Shewanella xiamenensis were resistant to cefotaxime, ceftazidime, imipenem, meropenem, gentamycin and trimethoprim-sulfamethoxazole. Whole genome sequencing and phylogenetic analysis demonstrated the diversity of Shewanella xiamenensis despite isolating from one wastewater pool. CONCLUSION To the best of our knowledge, this is the first report of detection of three types bla OXA-48-like genes in one hospital in China. And we have detected multi-drug resistant S. xiamenensis from hospital wastewater. This emphasizes that the presence of naturally existing carbapenemases in the environment may be significantly overlooked and that the bla OXA-48-like genes in China may originate through the horizontal gene transfer from S. xiamenensis to Enterobacterales rather than import from other countries.
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Affiliation(s)
- Yicheng Wen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Xiaofang Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Ping Xu
- Department of Clinical Laboratory, The Fifth People’s Hospital of Suzhou, Suzhou, Jiangsu, People’s Republic of China
| | - Chengcheng Yang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Zhichen Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Jie Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Jingnan Lv
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
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Li R, Zhang L, Lu X, Peng K, Liu Y, Xiao X, Song H, Wang Z. Occurrence and Characterization of NDM-1-Producing Shewanella spp. and Acinetobacter portensis Co-Harboring tet(X3) in a Chinese Dairy Farm. Antibiotics (Basel) 2022; 11:1422. [PMID: 36290080 PMCID: PMC9598548 DOI: 10.3390/antibiotics11101422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 08/15/2023] Open
Abstract
Bacteria with carbapenem or tigecycline resistance have been spreading widely among humans, animals and the environment globally, being great threats to public health. However, bacteria co-carrying drug resistance genes of carbapenem and tigecycline in Shewanella and Acinetobacter species remain to be investigated. Here, we detected nine blaNDM-1-carrying Shewanella spp. isolates as well as three A. portensis isolates co-harboring tet(X3) and blaNDM-1 from seventy-two samples collected from a dairy farm in China. To explore their genomic characteristic and transmission mechanism, we utilized various methods, including PCR, antimicrobial susceptibility testing, conjugation experiment, whole-genome sequencing, circular intermediate identification and bioinformatics analysis. Clonal dissemination was found among three A. portensis, of which tet(X3) and blaNDM-1 were located on a novel non-conjugative plasmid pJNE5-X3_NDM-1 (333,311 bp), and the circular intermediate ΔISCR2-tet(X3)-blaNDM-1 was identified. Moreover, there was another copy of tet(X3) on the chromosome of A. portensis. It was verified that blaNDM-1 could be transferred to Escherichia coli C600 from Shewanella spp. by conjugation, and self-transmissible IncA/C2 plasmids mediated the transmission of blaNDM-1 in Shewanella spp. strains. Stringent surveillance was warranted to curb the transmission of such vital resistance genes.
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Affiliation(s)
- Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Lifei Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyu Lu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Yuan Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Xia Xiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Hongqin Song
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Palevich N, Palevich FP, Gardner A, Brightwell G, Mills J. Genome collection of Shewanella spp. isolated from spoiled lamb. Front Microbiol 2022; 13:976152. [PMID: 36238595 PMCID: PMC9552011 DOI: 10.3389/fmicb.2022.976152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
The diversity of the genus Shewanella and their roles across a variety of ecological niches is largely unknown highlighting the phylogenetic diversity of these bacteria. From a food safety perspective, Shewanella species have been recognized as causative spoilage agents of vacuum-packed meat products. However, the genetic basis and metabolic pathways for the spoilage mechanism are yet to be explored due to the unavailability of relevant Shewanella strains and genomic resources. In this study, whole-genome sequencing of 32 Shewanella strains isolated from vacuum-packaged refrigerated spoiled lamb was performed to examine their roles in meat spoilage. Phylogenomic reconstruction revealed their genomic diversity with 28 Shewanella spp. strains belonging to the same putative novel species, two Shewanella glacialipiscicola strains (SM77 and SM91), Shewanella xiamenensis NZRM825, and Shewanella putrefaciens DSM 50426 (ATCC 8072) isolated from butter. Genome-wide clustering of orthologous gene families revealed functional groupings within the major Shewanella cluster but also considerable plasticity across the different species. Pan-genome analysis revealed conserved occurrence of spoilage genes associated with sulfur and putrescine metabolism, while the complete set of trimethylamine metabolism genes was observed in only Shewanella sp. SM74, S. glacialipiscicola SM77 and SM91 strains. Through comparative genomics, some variations were also identified pertaining to genes associated with adaptation to environmental cues such as temperature, osmotic, salt, oxidative, antimicrobial peptide, and drug resistance stresses. Here we provide a reference collection of draft Shewanella genomes for subsequent species descriptions and future investigations into the molecular spoilage mechanisms for further applications in the meat industry.
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Huang G, Wang S, Wang J, Tian L, Yu Y, Zuo X, Li Y. Bile reflux alters the profile of the gastric mucosa microbiota. Front Cell Infect Microbiol 2022; 12:940687. [PMID: 36159635 PMCID: PMC9500345 DOI: 10.3389/fcimb.2022.940687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/22/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Bile reflux can cause inflammation, gastric mucosa atrophy, and diseases such as stomach cancer. Alkaline bile flowing back into the stomach affects the intragastric environment and can alter the gastric bacterial community. We sought to identify the characteristics of the stomach mucosal microbiota in patients with bile reflux. METHODS Gastric mucosal samples were collected from 52 and 40 chronic gastritis patients with and without bile reflux, respectively. The bacterial profile was determined using 16S rRNA gene analysis. RESULTS In the absence of H. pylori infection, the richness (based on the Sobs and Chao1 indices; P <0.05) and diversity (based on Shannon indices; P <0.05) of gastric mucosa microbiota were higher in patients with bile reflux patients than in those without. There was a marked difference in the microbiota structure between patients with and without bile reflux (ANOSIM, R=0.058, P=0.011). While the genera, Comamonas, Halomonas, Bradymonas, Pseudomonas, Marinobacter, Arthrobacter, and Shewanella were enriched in patients with bile reflux, the genera, Haemophilus, Porphyromonas, and Subdoligranulum, were enriched in those without bile reflux. CONCLUSION Our results demonstrate that bile reflux significantly alters the composition of the gastric microbiota.
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Affiliation(s)
| | | | | | | | - Yanbo Yu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
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Yang Y, Li H, Wei Y, Chen Z, Chen T, Liang Y, Yin J, Yang D, Yang Z, Shi D, Zhou S, Wang H, Li J, Jin M. Comprehensive insights into profiles and bacterial sources of intracellular and extracellular antibiotic resistance genes in groundwater. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119541. [PMID: 35623567 DOI: 10.1016/j.envpol.2022.119541] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/17/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance genes (ARGs), especially last-resort ARGs (LARGs), are receiving extensive attention as emerging environmental contaminants in groundwater. However, their prevalent intracellular and extracellular patterns and bacterial sources in groundwater remain unclear. Herein, groundwater samples were collected in Tianjin, and characterized based on the profiles of intracellular ARGs (iARGs) and extracellular ARGs (eARGs), as well as the resident bacterial communities and extracellular DNA (eDNA)-releasing bacterial communities. The quantitative real-time PCR assays showed that eARGs presented fewer subtypes than iARGs and generally displayed lower detection frequencies than the corresponding iARGs. Similarly, LARGs exhibited lower detection frequencies than common ARGs, but the total abundance showed no significant differences between them. Genes vanA and blaVIM were the observed dominant LARGs, and aadA was the observed common ARG independent of location inside or outside the bacteria. Furthermore, the top 10 phyla showed much difference between the main eDNA-releasing bacteria and the dominant resident bacteria. Proteobacteria was the predominant resident bacterial phyla while dominating the source of eDNA in groundwater. Despite representing a minor portion of the abundance in the resident bacteria, Actinobacteriota, Acidobacteriota, and Chloroflex surprisingly accounted for a large majority of eDNA release. Co-occurrence patterns among persistent ARGs, the resident bacteria, and eDNA-releasing bacteria revealed that the dominant common iARG aadA and intracellular LARGs blaVIM and vanA had significant positive correlations with Methylobacterium_Methylorubrum and Shewanella. Meanwhile, the dominant extracellular LARG blaVIM may be released by bacteria belonging to at least five genera, including Ellin6067, Bifidobacterium, Blautia, Veillonella, and Dechloromonas. Collectively, the findings of this study extend our understanding regarding the distribution of ARGs and their bacterial sources in groundwater, and indicate the serious pollution of LARGs in groundwater, which poses potential risks to public health.
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Affiliation(s)
- Yidi Yang
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Haibei Li
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Yijun Wei
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Zhengshan Chen
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Tianjiao Chen
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Yongbing Liang
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Jing Yin
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Dong Yang
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Zhongwei Yang
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Danyang Shi
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Shuqing Zhou
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Huaran Wang
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Junwen Li
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Min Jin
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China.
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Riboflavin-rich Agar Enhances the Rate of Extracellular Electron Transfer from Electrogenic Bacteria Inside a Thin-layer System. Bioelectrochemistry 2022; 148:108252. [DOI: 10.1016/j.bioelechem.2022.108252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/22/2022]
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Ayala Nuñez T, Cerbino GN, Rapisardi MF, Quiroga C, Centrón D. Novel Mobile Integrons and Strain-Specific Integrase Genes within Shewanella spp. Unveil Multiple Lateral Genetic Transfer Events within The Genus. Microorganisms 2022; 10:microorganisms10061102. [PMID: 35744620 PMCID: PMC9229058 DOI: 10.3390/microorganisms10061102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Shewanella spp. are Gram-negative bacteria that thrive in aquatic niches and also can cause infectious diseases as opportunistic pathogens. Chromosomal (CI) and mobile integrons (MI) were previously described in some Shewanella isolates. Here, we evaluated the occurrence of integrase genes, the integron systems and their genetic surroundings in the genus. We identified 22 integrase gene types, 17 of which were newly described, showing traits of multiple events of lateral genetic transfer (LGT). Phylogenetic analysis showed that most of them were strain-specific, except for Shewanella algae, where SonIntIA-like may have co-evolved within the host as typical CIs. It is noteworthy that co-existence of up to five different integrase genes within a strain, as well as their wide dissemination to Alteromonadales, Vibrionales, Chromatiales, Oceanospirillales and Enterobacterales was observed. In addition, identification of two novel MIs suggests that continuous LGT events may have occurred resembling the behavior of class 1 integrons. The constant emergence of determinants associated to antimicrobial resistance worldwide, concomitantly with novel MIs in strains capable to harbor several types of integrons, may be an alarming threat for the recruitment of novel antimicrobial resistance gene cassettes in the genus Shewanella, with its consequent contribution towards multidrug resistance in clinical isolates.
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Affiliation(s)
- Teolincacihuatl Ayala Nuñez
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
| | - Gabriela N. Cerbino
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
| | - María Florencia Rapisardi
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
| | - Cecilia Quiroga
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
- Laboratorio de Investigación en Biología del ARN Bacteriano IMPaM (UBA/CONICET), Faculty of Medicine, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina
- Correspondence: or (C.Q.); (D.C.); Tel.: +54-11-5285-3500 (C.Q.); +54-911-50987496 (D.C.)
| | - Daniela Centrón
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos IMPaM (UBA/CONICET), Faculty of Medicine, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina
- Correspondence: or (C.Q.); (D.C.); Tel.: +54-11-5285-3500 (C.Q.); +54-911-50987496 (D.C.)
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Ng WWS, Shum HP, To KKW, Sridhar S. Emerging Infections Due to Shewanella spp.: A Case Series of 128 Cases Over 10 Years. Front Med (Lausanne) 2022; 9:850938. [PMID: 35573023 PMCID: PMC9100594 DOI: 10.3389/fmed.2022.850938] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundShewanella species are emerging pathogens that can cause severe hepatobiliary, skin and soft tissue, gastrointestinal, respiratory infections, and bacteremia. Here we reported the largest case series of infections caused by Shewanella species.AimTo identify the clinical features and risk factors predisposing to Shewanella infections. To evaluate resistance pattern of Shewanella species and appropriateness of antibiotic use in the study cohort.MethodsPatients admitted to a regional hospital in Hong Kong with Shewanella species infection from April 1, 2010 to December 31, 2020 were included. Demographics, antibiotics, microbiology, and outcomes were retrospectively analyzed.FindingsOver the 10 years, we identified 128 patients with Shewanella species infection. 61.7% were male with a median age of 78 (IQR 65–87). Important underlying diseases included hepatobiliary diseases (63.3%), malignancy (26.6%), chronic kidney disease or end-stage renal failure (25.8%), and diabetes mellitus (22.7%). Hepatobiliary infections (60.4%) were the most common clinical manifestation. Majority (92.2%) were infected with Shewanella algae, while 7.8% were infected with Shewanella putrefaciens. The identified organisms were usually susceptible to ceftazidime (98.7%), gentamicin (97.4%), cefoperazone-sulbactam (93.5%) and ciprofloxacin (90.3%). Imipenem-susceptible strains were only present in 76.6% of isolates.ConclusionThis largest case series suggested that Shewanella infections are commonly associated with underlying comorbidities, especially with hepatobiliary diseases and malignancy. Although Shewanella species remained largely susceptible to third and fourth generation cephalosporins and aminoglycosides, carbapenem resistance has been on a significant rise.
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Affiliation(s)
- Wincy Wing-Sze Ng
- Department of Intensive Care, Pamela Youde Nethersole Eastern Hospital, Hong Kong, Hong Kong SAR, China
- *Correspondence: Wincy Wing-Sze Ng
| | - Hoi-Ping Shum
- Department of Intensive Care, Pamela Youde Nethersole Eastern Hospital, Hong Kong, Hong Kong SAR, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Siddharth Sridhar
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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Yan Y, Chai X, Chen Y, Zhang X. The Fulminating Course of Infection Caused by Shewanella algae: A Case Report. Infect Drug Resist 2022; 15:1645-1650. [PMID: 35422640 PMCID: PMC9005229 DOI: 10.2147/idr.s357181] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/26/2022] [Indexed: 11/23/2022] Open
Abstract
Shewanella algae, a Gram-negative bacillus found in warm saltwater environments, has been increasingly recognized as a human pathogen that can cause infection of the skin and soft tissue, ear, blood, and intra-abdominal. In this case, we report a Shewanella algae infection that caused sepsis, renal insufficiency, cardiac dysfunction, fistula and massive pleural effusion after surgery in a 73-year-old man with cancer of the esophagus and cardia.
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Affiliation(s)
- Yun Yan
- Department of Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Xin Chai
- Department of Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Yu Chen
- Department of Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi’an, People’s Republic of China
- Correspondence: Yu Chen; Xijing Zhang, Department of Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi’an, People’s Republic of China, Tel +862984775344, Fax +862983244986, Email ;
| | - Xijing Zhang
- Department of Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi’an, People’s Republic of China
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Liu L, Wang W, Wu S, Gao H. Recent Advances in the Siderophore Biology of Shewanella. Front Microbiol 2022; 13:823758. [PMID: 35250939 PMCID: PMC8891985 DOI: 10.3389/fmicb.2022.823758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the abundance of iron in nature, iron acquisition is a challenge for life in general because the element mostly exists in the extremely insoluble ferric (Fe3+) form in oxic environments. To overcome this, microbes have evolved multiple iron uptake strategies, a common one of which is through the secretion of siderophores, which are iron-chelating metabolites generated endogenously. Siderophore-mediated iron transport, a standby when default iron transport routes are abolished under iron rich conditions, is essential under iron starvation conditions. While there has been a wealth of knowledge about the molecular basis of siderophore synthesis, uptake and regulation in model bacteria, we still know surprisingly little about siderophore biology in diverse environmental microbes. Shewanella represent a group of γ-proteobacteria capable of respiring a variety of organic and inorganic substrates, including iron ores. This respiratory process relies on a large number of iron proteins, c-type cytochromes in particular. Thus, iron plays an essential and special role in physiology of Shewanella. In addition, these bacteria use a single siderophore biosynthetic system to produce an array of macrocyclic dihydroxamate siderophores, some of which show particular biological activities. In this review, we first outline current understanding of siderophore synthesis, uptake and regulation in model bacteria, and subsequently discuss the siderophore biology in Shewanella.
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Affiliation(s)
- Lulu Liu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wei Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shihua Wu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
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Lizárraga WC, Mormontoy CG, Calla H, Castañeda M, Taira M, Garcia R, Marín C, Abanto M, Ramirez P. Complete genome sequence of Shewanella algae strain 2NE11, a decolorizing bacterium isolated from industrial effluent in Peru. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2022; 33:e00704. [PMID: 35145887 PMCID: PMC8816663 DOI: 10.1016/j.btre.2022.e00704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/28/2021] [Accepted: 01/19/2022] [Indexed: 12/14/2022]
Abstract
Shewanella is a microbial group with high potential to be applied in textile effluents bioremediation due to its ability to use a wide variety of substrates as a final electron acceptor in respiration. The present research aimed to describe a new strain, Shewanella algae 2NE11, a decolorizing bacterium isolated from industrial effluent in Peru. S. algae 2NE11 showed an optimal growth under pH 6-9, temperature between 30-40 °C, and 0-4 % NaCl. It can tolerate high concentrations of NaCl until 10% and low temperatures as 4 °C. It decolorizes azo and anthraquinone dyes with a decolorization rate of 89-97%. We performed next-generation sequencing (Pacific Bioscience®) and achieved its complete genome sequence with a length of 5,030,813bp and a GC content of 52.98%. Genomic characterization revealed the presence of protein-coding genes related to decolorization like azoreductase, dyp-peroxidase, oxidoreductases, and the complete Mtr respiratory pathway. Likewise, we identified other properties such as the presence of metal resistant genes, and genes related to lactate and N-acetylglucosamine metabolism. These results highlight its potential to be applied in the bioremediation of textile effluents and guide future research on decolorization metabolic pathways.
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Affiliation(s)
- Wendy C Lizárraga
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Carlo G Mormontoy
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Hedersson Calla
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Maria Castañeda
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Mario Taira
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Ruth Garcia
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Claudia Marín
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Michel Abanto
- Núcleo Científico y Tecnológico en Biorecursos - BIOREN, Universidad de La Frontera, Temuco, Chile
| | - Pablo Ramirez
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
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Huang Z, Yu K, Fu S, Xiao Y, Wei Q, Wang D. Genomic analysis reveals high intra-species diversity of Shewanella algae. Microb Genom 2022; 8. [PMID: 35143386 PMCID: PMC8942018 DOI: 10.1099/mgen.0.000786] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Shewanella algae is widely distributed in marine and freshwater habitats, and has been proved to be an emerging marine zoonotic and human pathogen. However, the genomic characteristics and pathogenicity of Shewanella algae are unclear. Here, the whole-genome features of 55 S. algae strains isolated from different sources were described. Pan-genome analysis yielded 2863 (19.4 %) genes shared among all strains. Functional annotation of the core genome showed that the main functions are focused on basic lifestyle such as metabolism and energy production. Meanwhile, the phylogenetic tree of the single nucleotide polymorphisms (SNPs) of core genome divided the 55 strains into three clades, with the majority of strains from China falling into the first two clades. As for the accessory genome, 167 genomic islands (GIs) and 65 phage-related elements were detected. The CRISPR-Cas system with a high degree of confidence was predicted in 23 strains. The GIs carried a suite of virulence genes and mobile genetic elements, while prophages contained several transposases and integrases. Horizontal genes transfer based on homology analysis indicated that these GIs and prophages were parts of major drivers for the evolution and the environmental adaptation of S. algae. In addition, a rich putative virulence-associated gene pool was found. Eight classes of antibiotic-associated resistance genes were detected, and the carriage rate of β-lactam resistance genes was 100 %. In conclusion, S. algae exhibits a high intra-species diversity in the aspects of population structure, virulence-associated genes and potential drug resistance, which is helpful for its evolution in pathogenesis and environmental adaptability.
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Affiliation(s)
- Zhenzhou Huang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, PR China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, PR China
| | - Keyi Yu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, PR China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, PR China
| | - Songzhe Fu
- Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of Education, Dalian, PR China.,College of Marine Science and Environment, Dalian Ocean University, Dalian, PR China
| | - Yue Xiao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, PR China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, PR China
| | - Qiang Wei
- Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, PR China
| | - Duochun Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, PR China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, PR China
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41
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Benaissa E, Maleb A, Elouennass M. Shewanella putrefaciens: a rare cause of purulent otorrhoea. Access Microbiol 2022; 4:000469.v3. [PMID: 36910504 PMCID: PMC9996131 DOI: 10.1099/acmi.0.000469.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/01/2022] [Indexed: 12/12/2022] Open
Abstract
Shewanella putrefaciens is a Gram-negative, non-fermenting, motile and oxidase-positive bacillus. Its incrimination in human pathology is very rare, although there has been a resurgence in Shewanella infections in recent years. We report the first case in Morocco of a purulent otorrhoea caused by S. putrefaciens , resistant to conventional treatment, occurring in a 25-year-old female, afebrile, without deterioration of the general state and possibly acquired during sea bathing. We also describe the bacteriological characteristics of and antibiotic susceptibility results for the isolate.
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Affiliation(s)
- Elmostafa Benaissa
- Epidemiology and Bacterial Resistance Research Team/BIO-INOVA Centre, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco.,Department of Bacteriology, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Adil Maleb
- Laboratory of Microbiology, Mohammed VI University Hospital, Faculty of Medicine and Pharmacy, University Mohammed I, Oujda, Morocco
| | - Mostafa Elouennass
- Epidemiology and Bacterial Resistance Research Team/BIO-INOVA Centre, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco.,Department of Bacteriology, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
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Chakraborty K, Kizhakkekalam VK, Joy M, Chakraborty RD. Bacillibactin class of siderophore antibiotics from a marine symbiotic Bacillus as promising antibacterial agents. Appl Microbiol Biotechnol 2021; 106:329-340. [PMID: 34913995 DOI: 10.1007/s00253-021-11632-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/13/2021] [Accepted: 10/05/2021] [Indexed: 10/19/2022]
Abstract
Preliminary antibacterial metabolite production screening unveiled that B. amyloliquefaciens MTCC 12,713 associated with the intertidal red alga Kappaphycus alverezii exhibited potential inhibitory effects against drug-resistant pathogens methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecalis, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Four homologous siderophore types of bacillibactins were isolated from a heterotrophic marine bacterium through bioactivity-guided purification. All detectable natural product gene clusters in B. amyloliquefaciens MTCC 12,713 were analyzed by sequencing the complete genome of the bacterium. The studied compounds displayed broad spectrum bactericidal activity against multidrug-resistant strains with a range of minimum inhibitory concentration values from 1.56 to 6.25 µg/mL, whereas standard antibiotic chloramphenicol was active at 6.25 to 12.5 µg/mL. Structure-bioactivity relationship assessment showed that higher electronic values were responsible for antibacterial properties against the nosocomial pathogens. The 2, 3-dihydroxybenzoate (dhb)-assisted biosynthetic pathway of catecholate-enclosed bacillibactins was proposed through the bacillibactin synthase multienzyme complex catalysis followed by dimerization of dhbACEBF operons with 16 genes (~ 12 kb bacterial genome). The present findings recognized an undescribed 4-methoxy-11'-pentanoyloxy-bacillibactin C as a source of potential antibacterial agent for use against drug-resistant pathogens for pharmaceutical applications. KEY POINTS: • Bacillus amyloliquefaciens in association with Kappaphycus alverezii was isolated • Four antibacterial bacillibactin analogs were identified from symbiotic bacterium • 4-Methoxy-11'-pentanoyloxy-bacillibactin C showed potential antibacterial activity.
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Affiliation(s)
- Kajal Chakraborty
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India.
| | - Vinaya Kizhakkepatt Kizhakkekalam
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India.,Faculty of Marine Sciences, Lakeside Campus, Cochin University of Science and Technology, Cochin, Kerala State, India
| | - Minju Joy
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India
| | - Rekha Devi Chakraborty
- Crustacean Fisheries Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, Kerala State, India
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Sacristán C, Costa-Silva S, Reisfeld L, Navas-Suárez PE, Ewbank AC, Duarte-Benvenuto A, Coelho Couto de Azevedo Fernandes N, Albergaria Ressio R, Antonelli M, Rocha Lorenço J, Favero CM, Marigo J, Kolesnikovas CKM, Catão-Dias JL. Novel alphaherpesvirus in a wild South American sea lion (Otaria byronia) with pulmonary tuberculosis. Braz J Microbiol 2021; 52:2489-2498. [PMID: 34580836 PMCID: PMC8578510 DOI: 10.1007/s42770-021-00614-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/19/2021] [Indexed: 11/28/2022] Open
Abstract
In 2017, an adult male South American sea lion (Otaria byronia), presenting emaciation and a cervical abscess, stranded alive in Florianópolis, southern Brazil. The animal was directed to a rehabilitation center, dying a few days later. On necropsy, the main gross findings were necrotizing lymphadenitis of the right prescapular lymph node and nodular bronchopneumonia. A novel alphaherpesvirus, tentatively named Otariid alphaherpesvirus 1, was amplified in several tissue samples. No histopathologic findings associated with viral infection were observed. Additionally, pulmonary tuberculosis by Mycobacterium pinnipedii was diagnosed by histopathological, immunohistochemical, and molecular techniques. Several bacteria were cultured from antemortem and postmortem samples, including Proteus mirabilis from the cervical abscess and cardiac blood, and Escherichia coli from the cervical abscess and pericardial effusion. Flavivirus, morbillivirus, and Apicomplexa were not detected by molecular techniques. Herein, we report a novel alphaherpesvirus in a pinniped species of the family Otariidae. Although previously described in Southern Hemisphere pinniped species, including South American sea lions, there is limited information regarding M. pinnipedii impact over this group. Further research is required to determine the associated pathogenesis of this novel herpesvirus, and prevalence of Otariid alphaherpesvirus 1 and M. pinnipedii in the reproductive colonies.
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Affiliation(s)
- Carlos Sacristán
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil.
| | - Samira Costa-Silva
- Associação R3 Animal, Florianópolis, SC, 88061-500, Brazil
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
| | | | - Pedro Enrique Navas-Suárez
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
| | - Ana Carolina Ewbank
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
| | - Aricia Duarte-Benvenuto
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
| | - Natália Coelho Couto de Azevedo Fernandes
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
- Centro de Patologia, Instituto Adolfo Lutz, São Paulo, SP, 01246000, Brazil
| | | | | | | | - Cíntia Maria Favero
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
| | - Juliana Marigo
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
| | | | - José Luiz Catão-Dias
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
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Wu J, Liu DF, Li HH, Min D, Liu JQ, Xu P, Li WW, Yu HQ, Zhu YG. Controlling pathogenic risks of water treatment biotechnologies at the source by genetic editing means. Environ Microbiol 2021; 23:7578-7590. [PMID: 34837302 DOI: 10.1111/1462-2920.15851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/27/2022]
Abstract
Antimicrobial-resistant pathogens in the environment and wastewater treatment systems, many of which are also important pollutant degraders and are difficult to control by traditional disinfection approaches, have become an unprecedented treat to ecological security and human health. Here, we propose the adoption of genetic editing techniques as a highly targeted, efficient and simple tool to control the risks of environmental pathogens at the source. An 'all-in-one' plasmid system was constructed in Aeromonas hydrophila to accurately identify and selectively inactivate multiple key virulence factor genes and antibiotic resistance genes via base editing, enabling significantly suppressed bacterial virulence and resistance without impairing their normal phenotype and pollutant-degradation functions. Its safe application for bioaugmented treatment of synthetic textile wastewater was also demonstrated. This genetic-editing technique may offer a promising solution to control the health risks of environmental microorganisms via targeted gene inactivation, thereby facilitating safer application of water treatment biotechnologies.
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Affiliation(s)
- Jie Wu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.,University of Science and Technology of China-City University of Hong Kong Joint Advanced Research Center, Suzhou Institute for Advance Research of USTC, Suzhou, 215123, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.,Anhui Key Laboratory of Sewage Purification and Ecological Rehabilitation Materials, Hefei, 230601, China
| | - Hui-Hui Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Jia-Qi Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Peng Xu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.,University of Science and Technology of China-City University of Hong Kong Joint Advanced Research Center, Suzhou Institute for Advance Research of USTC, Suzhou, 215123, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yong-Guan Zhu
- CAS Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
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45
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Jian H, Xu G, Yi Y, Hao Y, Wang Y, Xiong L, Wang S, Liu S, Meng C, Wang J, Zhang Y, Chen C, Feng X, Luo H, Zhang H, Zhang X, Wang L, Wang Z, Deng Z, Xiao X. The origin and impeded dissemination of the DNA phosphorothioation system in prokaryotes. Nat Commun 2021; 12:6382. [PMID: 34737280 PMCID: PMC8569181 DOI: 10.1038/s41467-021-26636-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Phosphorothioate (PT) modification by the dnd gene cluster is the first identified DNA backbone modification and constitute an epigenetic system with multiple functions, including antioxidant ability, restriction modification, and virus resistance. Despite these advantages for hosting dnd systems, they are surprisingly distributed sporadically among contemporary prokaryotic genomes. To address this ecological paradox, we systematically investigate the occurrence and phylogeny of dnd systems, and they are suggested to have originated in ancient Cyanobacteria after the Great Oxygenation Event. Interestingly, the occurrence of dnd systems and prophages is significantly negatively correlated. Further, we experimentally confirm that PT modification activates the filamentous phage SW1 by altering the binding affinity of repressor and the transcription level of its encoding gene. Competition assays, concurrent epigenomic and transcriptomic sequencing subsequently show that PT modification affects the expression of a variety of metabolic genes, which reduces the competitive fitness of the marine bacterium Shewanella piezotolerans WP3. Our findings strongly suggest that a series of negative effects on microorganisms caused by dnd systems limit horizontal gene transfer, thus leading to their sporadic distribution. Overall, our study reveals putative evolutionary scenario of the dnd system and provides novel insights into the physiological and ecological influences of PT modification.
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Affiliation(s)
- Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Guanpeng Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Xiong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Siyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Canxing Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiahua Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xiaoyuan Feng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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Ohama Y, Aoki K, Harada S, Nagasawa T, Sawabe T, Nonaka L, Moriya K, Ishii Y, Tateda K. Genetic Environment Surrounding blaOXA-55-like in Clinical Isolates of Shewanella algae Clade and Enhanced Expression of blaOXA-55-like in a Carbapenem-Resistant Isolate. mSphere 2021; 6:e0059321. [PMID: 34643423 PMCID: PMC8513682 DOI: 10.1128/msphere.00593-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/23/2021] [Indexed: 11/20/2022] Open
Abstract
Although Shewanella spp. are most frequently isolated from marine environments; more rarely, they have been implicated in human infections. Shewanella spp. are also recognized as the origin of genes for carbapenem-hydrolyzing class D β-lactamases. Due to the spread globally among Enterobacterales in recent years, risk assessments of both clinical and environmental Shewanella strains are urgently needed. In this study, we analyzed the whole-genome sequences of 10 clinical isolates and 13 environmental isolates of Shewanella spp. and compared them with those of Shewanella species strains registered in public databases. In addition, the levels of blaOXA-55-like transcription and β-lactamase activity of a carbapenem-resistant Shewanella algae isolate were compared with those of carbapenem-susceptible S. algae clade isolates. All clinical isolates were genetically identified as S. algae clade (S. algae, Shewanella chilikensis, and Shewanella carassii), whereas all but one of the environmental isolates were identified as various Shewanella spp. outside the S. algae clade. Although all isolates of the S. algae clade commonly possessed an approximately 12,500-bp genetic region harboring blaOXA-55-like, genetic structures outside this region were different among species. Among S. algae clade isolates, only one showed carbapenem resistance, and this isolate showed a high level of blaOXA-55-like transcription and β-lactamase activity. Although this study documented the importance of the S. algae clade in human infections and the relationship between enhanced production of OXA-55-like and resistance to carbapenems in S. algae, further studies are needed to elucidate the generalizability of these findings. IMPORTANCEShewanella spp., which are known to carry chromosomally located blaOXA genes, have mainly been isolated from marine environments; however, they can also cause infections in humans. In this study, we compared the molecular characteristics of clinical isolates of Shewanella spp. with those originating from environmental sources. All 10 clinical isolates were genetically identified as members of the Shewanella algae clade (S. algae, S. chilikensis, and S. carassii); however, all but one of the 13 environmental isolates were identified as Shewanella species members outside the S. algae clade. Although all the S. algae clade isolates possessed an approximately 12,500-bp genetic region harboring blaOXA-55-like, only one isolate showed carbapenem resistance. The carbapenem-resistant isolate showed a high level of blaOXA-55-like transcription and β-lactamase activity compared with the carbapenem-susceptible isolates. To confirm the clinical significance and antimicrobial resistance mechanisms of the S. algae clade members, analysis involving more clinical isolates should be performed in the future.
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Affiliation(s)
- Yuki Ohama
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Tokyo, Japan
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Sohei Harada
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Tokyo, Japan
| | - Tatsuya Nagasawa
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Lisa Nonaka
- Department of Nutritional Science, Faculty of Human Life Science, Shokei Gakuen, Kumamoto, Japan
| | - Kyoji Moriya
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
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47
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Complete Genome Sequence and Methylome of the Type Strain of Shewanella algae. Microbiol Resour Announc 2021; 10:e0055921. [PMID: 34351223 PMCID: PMC8340859 DOI: 10.1128/mra.00559-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the complete genome sequence and base modification analysis of the Shewanella algae type strain CECT 5071 (= OK-1 = ATCC 51192 = DSM 9167 = IAM 14159). The genome is composed of a single chromosome of 4,924,764 bp, with a GC content of 53.10%.
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Sanz-García F, Gil-Gil T, Laborda P, Ochoa-Sánchez LE, Martínez JL, Hernando-Amado S. Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat. Int J Mol Sci 2021; 22:8080. [PMID: 34360847 PMCID: PMC8347278 DOI: 10.3390/ijms22158080] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/24/2022] Open
Abstract
The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.
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Affiliation(s)
| | | | | | | | - José L. Martínez
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain; (F.S.-G.); (T.G.-G.); (P.L.); (L.E.O.-S.); (S.H.-A.)
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Shewanella oneidensis MR-1 as a bacterial platform for electro-biotechnology. Essays Biochem 2021; 65:355-364. [PMID: 33769488 PMCID: PMC8314016 DOI: 10.1042/ebc20200178] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022]
Abstract
The genus Shewanella comprises over 70 species of heterotrophic bacteria with versatile respiratory capacities. Some of these bacteria are known to be pathogens of fishes and animals, while many are non-pathogens considered to play important roles in the global carbon cycle. A representative strain is Shewanella oneidensis MR-1 that has been intensively studied for its ability to respire diverse electron acceptors, such as oxygen, nitrate, sulfur compounds, metals, and organics. In addition, studies have been focused on its ability as an electrochemically active bacterium that is capable of discharging electrons to and receiving electrons from electrodes in bioelectrochemical systems (BESs) for balancing intracellular redox states. This ability is expected to be applied to electro-fermentation (EF) for producing value-added chemicals that conventional fermentation technologies are difficult to produce efficiently. Researchers are also attempting to utilize its electrochemical ability for controlling gene expression, for which electro-genetics (EG) has been coined. Here we review fundamental knowledge on this bacterium and discuss future directions of studies on its applications to electro-biotechnology (EB).
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Klūga A, Terentjeva M, Vukovic NL, Kačániová M. Antimicrobial Activity and Chemical Composition of Essential Oils against Pathogenic Microorganisms of Freshwater Fish. PLANTS 2021; 10:plants10071265. [PMID: 34206270 PMCID: PMC8309039 DOI: 10.3390/plants10071265] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/26/2021] [Accepted: 06/15/2021] [Indexed: 11/21/2022]
Abstract
Antimicrobials are widely applied in aquaculture for treatment of infectious diseases in fish. The increased antimicrobial resistance of fish pathogens to conventional antimicrobial treatment highlights the need for research on the antibacterial properties of natural products—in this case, essential oils (EOs). The aim of the present study was to detect the antimicrobial activity of the essential oils on pathogenic microorganisms found in freshwater fish. Freshwater fish isolates of Aerococcus spp., Aeromonas spp., Enterococcus spp., Escherichia spp., Pseudomonas spp., Shewanella spp., Yersinia spp., and Vagococcus spp. were tested for antimicrobial resistance and antimicrobial activity against 14 commercially available essential oils. Antimicrobial resistance was identified in Pseudomonas spp. isolates against cefepime and ciprofloxacin; while all Aeromonas, Enterococcus, and Yersinia isolates were fully susceptible. All tested EOs revealed antimicrobial activity against the tested freshwater fish isolates at different extents. Cinnamomum camphora exhibited strong antimicrobial activity against Aeromonas spp. (3.12 μL/mL), Enterococcus spp. (0.78–1.56 μL/mL), and Pseudomonas spp. with the MIC method. EOs of Gaultheria procumbens and Litsea cubeba showed strong antibacterial activity against Yersinia spp. and Vacococcus spp. (6.25 μL/mL). The study shows the antimicrobial activity of EOs against the most relevant freshwater fish pathogens and indicates the application opportunities in aquaculture.
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Affiliation(s)
- Alīna Klūga
- Institute of Food and Environmental Hygiene, Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, K. Helmaņa iela 8, LV-3004 Jelgava, Latvia; (A.K.); (M.T.)
| | - Margarita Terentjeva
- Institute of Food and Environmental Hygiene, Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, K. Helmaņa iela 8, LV-3004 Jelgava, Latvia; (A.K.); (M.T.)
| | - Nenad L. Vukovic
- Department of Chemistry, Faculty of Science, University of Kragujevac, P.O. Box 12, 34 000 Kragujevac, Serbia;
| | - Miroslava Kačániová
- Department of Fruit Sciences, Viticulture and Enology, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
- Department of Bioenergy, Food Technology and Microbiology, Institute of Food Technology and Nutrition, University of Rzeszow, Zelwerowicza St. 4, 35601 Rzeszow, Poland
- Correspondence: ; Tel.: +421-376-414-715
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