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Nannapaneni VP, Rameshbabu M, Sundaramoorthy S, Sethuraman G. Source identification and clinical outcomes of Ralstonia outbreaks in a neonatal intensive care unit: A case series from a tertiary care centre. Trop Doct 2025; 55:113-120. [PMID: 40070147 DOI: 10.1177/00494755251323683] [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] [Indexed: 04/29/2025]
Abstract
BackgroundRalstonia species are emerging nosocomial pathogens linked to significant clinical disease in high-risk populations, particularly preterm neonates.ObjectiveTo study the clinical and epidemiological characteristics including source identification of Ralstonia outbreak in NICU.MethodsThis study was conducted in a tertiary care NICU in South India, identifying 14 cases of Ralstonia infection over two epochs: May to August 2021 and December 2022 to February 2023. We reviewed patient characteristics, clinical manifestations, antimicrobial profiles, and outcomes, alongside an epidemiological investigation for source identification.ResultsAmong the 14 cases, 13 were R. mannitolilytica and 1 was R. pickettii. No source was identified in the first epoch; however, contaminated sterile water ampoules used for IV preparations were implicated in the second. The mean gestation was 28 weeks (± 3), and the mean birth weight was 1192 g (± 539). Most neonates exhibited nonspecific symptoms. All isolates were sensitive to ciprofloxacin and trimethoprim-sulfamethoxazole, with all cases recovering fully.Teaching implicationsRalstonia species are capable of causing outbreaks and should prompt epidemiological surveillance for source identification. Clinical infection is usually mild with full recovery. Key interventions to prevent outbreaks include rigorous surveillance, infection control, and prompt antibiotic treatment.
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Affiliation(s)
- Vineetha Prasad Nannapaneni
- DM Postgraduate, Department of Neonatology, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Chennai, India
| | - Monisha Rameshbabu
- Assistant Professor, Department of Neonatology, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Chennai, India
| | | | - Giridhar Sethuraman
- Professor and HOD, Department of Neonatology, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Chennai, India
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Fink P, Menzel C, Kwon JH, Forchhammer K. A novel recombinant PHB production platform in filamentous cyanobacteria avoiding nitrogen starvation while preserving cell viability. Microb Cell Fact 2025; 24:43. [PMID: 39979956 PMCID: PMC11844001 DOI: 10.1186/s12934-025-02650-y] [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: 10/11/2024] [Accepted: 01/09/2025] [Indexed: 02/22/2025] Open
Abstract
During the past decades, the importance of developing sustainable, carbon dioxide (CO2)-neutral and biodegradable alternatives to conventional plastic has become evident in the context of global pollution issues. Therefore, heterotrophic bacteria such as Cupriavidus sp. have been intensively explored for the synthesis of the biodegradable polymer polyhydroxybutyrate (PHB). PHB is also naturally produced by a variety of phototrophic cyanobacteria, which only need sunlight and CO2, thereby allowing a CO2 negative, eco-friendly synthesis of this polymer. However, a major drawback of the use of cyanobacteria is the need of a two-stage production process, since relevant amount of PHB synthesis only occurs after transferring the cultures to conditions of nitrogen starvation, which hinders continuous, large-scale production.This study aimed at generating, by means of genetic engineering, a cyanobacterium that continuously produces PHB in large amounts. We choose a genetically amenable filamentous cyanobacterium of the genus Nostoc sp., which is a diazotrophic cyanobacterium, capable of atmospheric nitrogen (N2) fixation but naturally does not produce PHB. We transformed this Nostoc strain with various constructs containing the constitutive promotor PpsbA and the PHB synthesis operon phaC1AB from Cupriavidus necator H16. In fact, while the transformants initially produced PHB, the PHB-producing strains rapidly lost cell viability. Therefore, we next attempted further optimization of the biosynthetic gene cluster. The PHB operon was expanded with phasin gene phaP1 from Cupriavidus necator H16 in combination with the native intergenic region of apcBA from Nostoc sp. 7120. Finally, we succeeded in stabilized PHB production, whilst simultaneously avoiding decreasing cell viability. In conclusion, the recombinant Nostoc strain constructed in the present work constitutes the first example of a continuous and stable PHB production platform in cyanobacteria, which has been decoupled from nitrogen starvation and, hence, harbours great potential for sustainable, industrial PHB production.
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Affiliation(s)
- Phillipp Fink
- Organismic Interactions Department, Tübingen University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Claudia Menzel
- Organismic Interactions Department, Tübingen University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Jong-Hee Kwon
- Division of Applied Life Sciences (BK21), Gyeongsang National University, Jinju, 52828, Republic of Korea
- Department of Food Science & Technology, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Karl Forchhammer
- Organismic Interactions Department, Tübingen University, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
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Cai Y, Tao H, Gaballa A, Pi H, Helmann JD. The extracytoplasmic sigma factor σ X supports biofilm formation and increases biocontrol efficacy in Bacillus velezensis 118. Sci Rep 2025; 15:5315. [PMID: 39939707 PMCID: PMC11822112 DOI: 10.1038/s41598-025-89284-7] [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: 08/30/2024] [Accepted: 02/04/2025] [Indexed: 02/14/2025] Open
Abstract
Plant growth promoting rhizobacteria (PGPR) offer an environmentally friendly and sustainable approach to combat pathogens and enhance crop production. The biocontrol activity of PGPR depends on their ability to colonize plant roots and synthesize antimicrobial compounds that inhibit pathogens. However, the regulatory mechanisms underlying these processes remain unclear. In this study, we isolated and characterized Bacillus velezensis 118, a soil isolate that exhibits potent biocontrol activity against Fusarium wilt of banana. Deletion of sigX, encoding an extracytoplasmic function (ECF) sigma factor previously implicated in controlling biofilm architecture in B. subtilis, reduced biocontrol efficacy. The B. velezensis 118 sigX mutant displayed reduced biofilm formation but had only a minor defect in swarming motility and a negligible impact on lipopeptide production. These findings highlight the importance of regulatory processes important for root colonization in the effectiveness of Bacillus spp. as biocontrol agents against phytopathogens.
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Affiliation(s)
- Yanfei Cai
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, People's Republic of China
| | - Huan Tao
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, People's Republic of China
| | - Ahmed Gaballa
- Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101, USA
| | - Hualiang Pi
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA.
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101, USA.
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Dewberry RJ, Sharma P, Prom JL, Kinscherf NA, Lowe-Power T, Mazloom R, Zhang X, Liu H, Arif M, Stulberg M, Heath LS, Eversole K, Beattie GA, Vinatzer BA, Allen C. Genotypic and Phenotypic Analyses Show Ralstonia solanacearum Cool Virulence Is a Quantitative Trait Not Restricted to "Race 3 Biovar 2". PHYTOPATHOLOGY 2024; 114:2468-2480. [PMID: 39186006 DOI: 10.1094/phyto-06-24-0187-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Most Ralstonia solanacearum species complex strains cause bacterial wilts in tropical or subtropical zones, but the group known as race 3 biovar 2 (R3bv2) is cool virulent and causes potato brown rot at lower temperatures. R3bv2 has invaded potato-growing regions around the world but is not established in the United States. Phylogenetically, R3bv2 corresponds to a subset of the R. solanacearum phylotype IIB clade, but little is known about the distribution of the cool virulence phenotype within phylotype IIB. Therefore, genomes of 76 potentially cool virulent phylotype IIB strains and 30 public genomes were phylogenetically analyzed. A single clonal lineage within the sequevar 1 subclade of phylotype IIB that originated in South America has caused nearly all brown rot outbreaks worldwide. To correlate genotypes with relevant phenotypes, we quantified virulence of 10 Ralstonia strains on tomato and potato at both 22 and 28°C. Cool virulence on tomato did not predict cool virulence on potato. We found that cool virulence is a quantitative trait. Strains in the sequevar 1 pandemic clonal lineage caused the most disease, whereas other R3bv2 strains were only moderately cool virulent. However, some non-R3bv2 strains were highly cool virulent and aggressively colonized potato tubers. Thus, cool virulence is not consistently correlated with strains historically classified as the R3bv2 group. To aid in the detection of sequevar 1 strains, this group was genomically delimited in the LINbase web server, and a sequevar 1 diagnostic primer pair was developed and validated. We discuss implications of these results for the R3bv2 definition.
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Affiliation(s)
- Ronnie J Dewberry
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, U.S.A
| | - Parul Sharma
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
- Graduate Program in Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Jessica L Prom
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, U.S.A
| | - Noah A Kinscherf
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, U.S.A
| | - Tiffany Lowe-Power
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Reza Mazloom
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Xuemei Zhang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Haijie Liu
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | | | - Michael Stulberg
- U.S. Department of Agriculture-APHIS PPQ Science and Technology, Beltsville, MD 20705, U.S.A
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Kellye Eversole
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A., and Eversole Associates, Arlington, MA 02474, U.S.A
| | - Gwyn A Beattie
- Department of Plant Pathology, Entomology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, U.S.A
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Shahrvini T, McCullough M. A rare culprit: Ralstonia pickettii in a deep neck space infection. IDCases 2024; 38:e02071. [PMID: 39309035 PMCID: PMC11414541 DOI: 10.1016/j.idcr.2024.e02071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024] Open
Abstract
Ralstonia pickettii is a rare, emerging opportunistic pathogen that has been previously limited to nosocomial infections, often associated with contaminated sterile solutions. Here, we present the case of a neck abscess caused by R. pickettii, the first documented case of a deep neck space infection caused by this bacterium. The patient in this case had no risk factors for R. pickettii infection. By highlighting the atypical presentation and microbiology in this case, we aim to highlight the emergence of a wide spectrum of disease caused by R. pickettii.
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Affiliation(s)
- Tara Shahrvini
- David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles, CA 90095, United States
| | - Matthew McCullough
- David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles, CA 90095, United States
- Olive View-UCLA Medical Center, Department of Internal Medicine, 14445 Olive View Dr, Sylmar, CA 91342, United States
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Ilsan NA, Nurfajriah S, Inggraini M, Krishanti NPRA, Yunita M, Anindita R, Huang TW. Application of miniaturized most probable number method for bacterial detection in water samples: detection of multi-drug-resistant Ralstonia insidiosa in drinking water. JOURNAL OF WATER AND HEALTH 2024; 22:1618-1627. [PMID: 39340375 DOI: 10.2166/wh.2024.086] [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: 02/18/2024] [Accepted: 08/05/2024] [Indexed: 09/30/2024]
Abstract
The detection of bacterial contamination in drinking water is essential for monitoring the spread of foodborne diseases. We developed a simple, portable, and low-cost method of mini most probable number (mini MPN) to semi-enumerate bacterial suspension in water as a drinking water analogue. In this study, there is no significant difference between mini MPN and the standard method, technique plate count (TPC), at 10 and 100 CFU/ml Klebsiella pneumoniae suspension with a P-value of 0.28. For the ease-of-use aspect of this method, we tested several variables to prove it can be mass-applied in society. The usage of a sterile-plastic pipette, sample inoculation conducted in a biosafety cabinet (BSC), the usage of a 3-month storage medium, and incubation temperature conducted at room temperature compared to aseptic standard laboratory technique showed P-value > 0.05. In a trial for this method, we used commercialized drinking water for bacterial enumeration and characterization. We found multi-drug resistant (MDR) Ralstonia insidiosa which was resistant to at least four antimicrobial classes, including aminoglycosides, penicillins, cephalosporin, and carbapenem. Vitek 2 Compact was used for bacterial identification and antimicrobial susceptibility testing. A virulence test in Omphisa fuscidentalis larvae showed R. insidiosa strain D had a low virulence.
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Affiliation(s)
- Noor Andryan Ilsan
- Department of Medical Laboratory Technology, STIKes Mitra Keluarga, Bekasi City, West Java Province, Indonesia E-mail:
| | - Siti Nurfajriah
- Department of Medical Laboratory Technology, STIKes Mitra Keluarga, Bekasi City, West Java Province, Indonesia
| | - Maulin Inggraini
- Department of Medical Laboratory Technology, STIKes Mitra Keluarga, Bekasi City, West Java Province, Indonesia
| | - Ni Putu Ratna Ayu Krishanti
- Research Center for Applied Zoology, National Research and Innovation Agency, Soekarno Science and Techno Park, Jl. Raya Bogor KM 46, Cibinong, Bogor, West Java Province 16911, Indonesia
| | - Melda Yunita
- Department of Medical Education, Faculty of Medicine, Pattimura University, Ambon, Maluku, Indonesia
| | - Reza Anindita
- Department of Pharmacy, STIKes Mitra Keluarga, Bekasi City, West Java Province, Indonesia
| | - Tzu-Wen Huang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
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Li T, Luo W, Du C, Lin X, Lin G, Chen R, He H, Wang R, Lu L, Xie X. Functional and evolutionary comparative analysis of the DIR gene family in Nicotiana tabacum L. and Solanum tuberosum L. BMC Genomics 2024; 25:671. [PMID: 38970011 PMCID: PMC11229024 DOI: 10.1186/s12864-024-10577-8] [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: 04/11/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND The dirigent (DIR) genes encode proteins that act as crucial regulators of plant lignin biosynthesis. In Solanaceae species, members of the DIR gene family are intricately related to plant growth and development, playing a key role in responding to various biotic and abiotic stresses. It will be of great application significance to analyze the DIR gene family and expression profile under various pathogen stresses in Solanaceae species. RESULTS A total of 57 tobacco NtDIRs and 33 potato StDIRs were identified based on their respective genome sequences. Phylogenetic analysis of DIR genes in tobacco, potato, eggplant and Arabidopsis thaliana revealed three distinct subgroups (DIR-a, DIR-b/d and DIR-e). Gene structure and conserved motif analysis showed that a high degree of conservation in both exon/intron organization and protein motifs among tobacco and potato DIR genes, especially within members of the same subfamily. Total 8 pairs of tandem duplication genes (3 pairs in tobacco, 5 pairs in potato) and 13 pairs of segmental duplication genes (6 pairs in tobacco, 7 pairs in potato) were identified based on the analysis of gene duplication events. Cis-regulatory elements of the DIR promoters participated in hormone response, stress responses, circadian control, endosperm expression, and meristem expression. Transcriptomic data analysis under biotic stress revealed diverse response patterns among DIR gene family members to pathogens, indicating their functional divergence. After 96 h post-inoculation with Ralstonia solanacearum L. (Ras), tobacco seedlings exhibited typical symptoms of tobacco bacterial wilt. The qRT-PCR analysis of 11 selected NtDIR genes displayed differential expression pattern in response to the bacterial pathogen Ras infection. Using line 392278 of potato as material, typical symptoms of potato late blight manifested on the seedling leaves under Phytophthora infestans infection. The qRT-PCR analysis of 5 selected StDIR genes showed up-regulation in response to pathogen infection. Notably, three clustered genes (NtDIR2, NtDIR4, StDIR3) exhibited a robust response to pathogen infection, highlighting their essential roles in disease resistance. CONCLUSION The genome-wide identification, evolutionary analysis, and expression profiling of DIR genes in response to various pathogen infection in tobacco and potato have provided valuable insights into the roles of these genes under various stress conditions. Our results could provide a basis for further functional analysis of the DIR gene family under pathogen infection conditions.
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Affiliation(s)
- Tong Li
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Wenbin Luo
- Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Chaofan Du
- Longyan Tobacco Company, Longyan, 364000, China
| | - Xiaolu Lin
- Longyan Tobacco Company, Longyan, 364000, China
| | - Guojian Lin
- Longyan Tobacco Company, Longyan, 364000, China
| | - Rui Chen
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Huaqin He
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Ruiqi Wang
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Libin Lu
- Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China.
| | - Xiaofang Xie
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China.
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture & Forestry University, Fuzhou, 350002, China.
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Bing H, Qi C, Gu J, Zhao T, Yu X, Cai Y, Zhang Y, Li A, Wang X, Zhao J, Xiang W. Isolation and identification of NEAU-CP5: A seed-endophytic strain of B. velezensis that controls tomato bacterial wilt. Microb Pathog 2024; 192:106707. [PMID: 38777241 DOI: 10.1016/j.micpath.2024.106707] [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: 12/30/2023] [Revised: 04/29/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
Bacterial wilt of tomato caused by Ralstonia solanacearum is a critical soilborne disease that drastically reduces yield. In the current study, an endophytic strain NEAU-CP5 with strong antagonistic activity against R. solanacearum was isolated from tomato seeds and characterized. The strain was identified as Bacillus velezensis based on 16S rRNA gene and whole genome sequence analysis. NEAU-CP5 can secrete amylase, protease, and cellulase, and also produce known antibacterial metabolites, including cyclo (leucylprolyl), cyclo (phenylalanyl-prolyl), cyclo (Pro-Gly), 3-benzyl-2,5-piperazinedione, pentadecanoic acid, eicosane, 2-methyoic acid, isovaleric acid, dibuty phthalate, and esters of fatty acids (HFDU), which may be responsible for its strong antibacterial activity. Fourteen gene clusters associated with antibacterial properties were also identified in the whole genome sequence of NEAU-CP5. Pot experiment demonstrated that the application of 108 CFU/mL NEAU-CP5 on tomato plants significantly reduced the incidence of tomato bacterial wilt by 68.36 ± 1.67 %. NEAU-CP5 also increased the activity of defense-related enzymes (CAT, POD, PPO, SOD, and PAL) in tomato plants. This is the first report of an effective control of bacterial wilt on tomato plants by B. velezensis and highlights the potential of NEAU-CP5 as a potential biocontrol agent for the management of tomato bacterial wilt.
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Affiliation(s)
- Hui Bing
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Cuiping Qi
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Jinzhao Gu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Tianxin Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Xiaoyan Yu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Yang Cai
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Yance Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Ailin Li
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China.
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China.
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Xue M, Huang R, Liu W, Cheng J, Liu Y, Zhang J, Wang L, Liu D, Jiang H. Identification and characterization of a potential strain for the production of polyhydroxyalkanoate from glycerol. Front Microbiol 2024; 15:1413120. [PMID: 38966388 PMCID: PMC11223650 DOI: 10.3389/fmicb.2024.1413120] [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: 04/06/2024] [Accepted: 05/20/2024] [Indexed: 07/06/2024] Open
Abstract
While poly (3-hydroxybutyrate) (PHB) holds promise as a bioplastic, its commercial utilization has been hampered by the high cost of raw materials. However, glycerol emerges as a viable feedstock for PHB production, offering a sustainable production approach and substantial cost reduction potential. Glycerol stands out as a promising feedstock for PHB production, offering a pathway toward sustainable manufacturing and considerable cost savings. The identification and characterization of strains capable of converting glycerol into PHB represent a pivotal strategy in advancing PHB production research. In this study, we isolated a strain, Ralstonia sp. RRA (RRA). The strain exhibits remarkable proficiency in synthesizing PHB from glycerol. With glycerol as the carbon source, RRA achieved a specific growth rate of 0.19 h-1, attaining a PHB content of approximately 50% within 30 h. Through third-generation genome and transcriptome sequencing, we elucidated the genome composition and identified a total of eight genes (glpR, glpD, glpS, glpT, glpP, glpQ, glpV, and glpK) involved in the glycerol metabolism pathway. Leveraging these findings, the strain RRA demonstrates significant promise in producing PHB from low-cost renewable carbon sources.
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Affiliation(s)
- Mengheng Xue
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Rong Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wei Liu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jian Cheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Yuwan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jie Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Limei Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Dingyu Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Huifeng Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
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Ismail S, Giacinti G, Raynaud CD, Cameleyre X, Alfenore S, Guillouet S, Gorret N. Impact of the environmental parameters on single cell protein production and composition by Cupriavidus necator. J Biotechnol 2024; 388:83-95. [PMID: 38621427 DOI: 10.1016/j.jbiotec.2024.04.009] [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: 11/17/2023] [Revised: 01/26/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
Due to the rapid increase in the world's population, many developing countries are facing malnutrition problems, including famine and food insecurity. Particularly, the deficiency of protein sources becomes a serious problem for human and animal nutrition. In this context, Single Cell Proteins, could be exploited as an alternative source of unconventional proteins. The aim of the study was to investigate SCP production and composition by Cupriavidus necator under various environmental conditions, temperature and pH values. A mono-factorial approach was implemented using batch bioreactor cultures under well-controlled conditions. Results were compared in terms of bacterial growth and SCP composition (proteins, nucleic acids, amino acids and elemental formula). Complementary analyses were performed by flow cytometry to study cell morphology, membrane permeability and the presence of Poly(3-hydroxybutyrate) (PHB) production. Our data confirmed the ability of C. necator to produce high amount of proteins (69 %DW at 30 °C and pH7). The results showed that temperature and pH independently impact SCP production and composition. This impact was particularly observed at the highest temperature (40 °C) and also the lowest pH value (pH5) providing lower growth rates, cell elongation, changes in granularity and lower amounts of proteins (down to 44 %DW at pH5) and nucleic acids. These low percentages were related to the production of PHB production (up to 44 %DW at 40 °C) which is the first report of a PHB accumulation in C. necator under nutrient unlimited conditions.
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Affiliation(s)
- Siwar Ismail
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Géraldine Giacinti
- Laboratoire de Chimie Agro-Industrielle, LCA, Université de Toulouse, INRAe, Toulouse, France; Centre d'Application et de Traitement des Agro-Ressources (CATAR), Toulouse-INP, Toulouse, France
| | - Christine Delagado Raynaud
- Laboratoire de Chimie Agro-Industrielle, LCA, Université de Toulouse, INRAe, Toulouse, France; Centre d'Application et de Traitement des Agro-Ressources (CATAR), Toulouse-INP, Toulouse, France
| | - Xavier Cameleyre
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | | | - Nathalie Gorret
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
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11
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Steyaert S, Peeters C, Wieme AD, Muyldermans A, Vandoorslaer K, Spilker T, Wybo I, Piérard D, LiPuma JJ, Vandamme P. Novel Ralstonia species from human infections: improved matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based identification and analysis of antimicrobial resistance patterns. Microbiol Spectr 2024; 12:e0402123. [PMID: 38661349 PMCID: PMC11237764 DOI: 10.1128/spectrum.04021-23] [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: 11/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
A collection of 161 Ralstonia isolates, including 90 isolates from persons with cystic fibrosis, 27 isolates from other human clinical samples, 8 isolates from the hospital environment, 7 isolates from industrial samples, and 19 environmental isolates, was subjected to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification and yielded confident species level identification scores for only 62 (39%) of the isolates, including four that proved misidentified subsequently. Whole-genome sequence analysis of 32 representative isolates for which no confident MALDI-TOF MS species level identification was obtained revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively, and provided the basis for updating an in-house MALDI-TOF MS database. A reanalysis of all mass spectra with the updated MALDI-TOF MS database increased the percentage of isolates with confident species level identification up to 77%. The antimicrobial susceptibility of 30 isolates mainly representing novel human clinical and environmental Ralstonia species was tested toward 17 antimicrobial agents and demonstrated that the novel Ralstonia species were generally multi-resistant, yet susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline. An analysis of genomic antimicrobial resistance genes in 32 novel and publicly available genome sequences revealed broadly distributed beta-lactam resistance determinants.IMPORTANCEThe present study demonstrated that a commercial matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification database can be tailored to improve the identification of Ralstonia species. It also revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively. An analysis of minimum inhibitory concentration values demonstrated that the novel Ralstonia species were generally multi-resistant but susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline.
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Affiliation(s)
- Stephanie Steyaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
| | - Anneleen D. Wieme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Astrid Muyldermans
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Theodore Spilker
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ingrid Wybo
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Denis Piérard
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - John J. LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
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12
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Sheng Z, Li J, Han G, Fan R, Zhu P, Fang X. Molecular epidemiological and clinical infection characteristics analysis of Ralstonia. Eur J Clin Microbiol Infect Dis 2024; 43:1161-1170. [PMID: 38639850 PMCID: PMC11178629 DOI: 10.1007/s10096-024-04823-w] [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: 01/26/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024]
Abstract
PURPOSE This study was to clarify the molecular epidemiology and clinical infection characteristics of Ralstonia pickettii and establish sequence typing system. METHODS 48 nonrepetitive Ralstonia pickettii strains were collected from January 2008 to December 2013 at the Chinese People's Liberation Army General Hospital (PLAGH) and were identified through a specific PCR experiment, 16 S rDNA experiment and VITEK 2 system to compare the identification accuracy. The sequence types of the strains were analyzed by multilocus sequence typing (MLST) method. The antibiotic sensitivity of these strains was determined with disc diffusion tests and broth microdilution method. The clinical data of Ralstonia pickettii infected patients were collected. RESULTS All of the 48 strains were identified as Ralstonia pickettii by VITEK 2 system. 30 and 34 strains were identified as Ralstonia pickettii by PCR and 16 S rDNA experiment respectively. ST9 was the most sequence types (STs) in these 18 STs of 42 strains. 42 strains were divided into 2 groups (A and B) and 18 genotypes. Ralstonia pickettii was sensitive to some cephalosporins, β-lactam/β-lactamase inhibitor, levofloxacin and trimethoprim/sulfamethoxazole. Cough, sputum, shortness of breath and pulmonary rales were the common clinical symptoms of most Ralstonia pickettii infected patients. CONCLUSION We established a sequence typing system with a relatively fine resolution and the PCR assay is a faster and more sensitive method for clinical identification of Ralstonia pickettii. ST9 is the most common sequence types of Ralstonia pickettii. The most common clinical characteristics of Ralstonia pickettii infected patients were cough, sputum, shortness of breath and pulmonary rales.
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Affiliation(s)
- Zhaojun Sheng
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Jiaxin Li
- Department of Respiratory and Critical Care Medicine, Aerospace Center Hospital, Beijing, China
| | - Guojing Han
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Ru Fan
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Pingjun Zhu
- Department of Respiratory and Critical Care Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.
| | - Xiangqun Fang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.
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13
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Yadav M, Sathe J, Teronpi V, Kumar A. Navigating the signaling landscape of Ralstonia solanacearum: a study of bacterial two-component systems. World J Microbiol Biotechnol 2024; 40:153. [PMID: 38564115 DOI: 10.1007/s11274-024-03950-y] [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: 01/16/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024]
Abstract
Ralstonia solanacearum, the bacterium that causes bacterial wilt, is a destructive phytopathogen that can infect over 450 different plant species. Several agriculturally significant crop plants, including eggplant, tomato, pepper, potato, and ginger, are highly susceptible to this plant disease, which has a global impact on crop quality and yield. There is currently no known preventive method that works well for bacterial wilt. Bacteria use two-component systems (TCSs) to sense their environment constantly and react appropriately. This is achieved by an extracellular sensor kinase (SK) capable of sensing a suitable signal and a cytoplasmic response regulator (RR) which gives a downstream response. Moreover, our investigation revealed that R. solanacearum GMI1000 possesses a substantial count of TCSs, specifically comprising 36 RRs and 27 SKs. While TCSs are known targets for various human pathogenic bacteria, such as Salmonella, the role of TCSs in R. solanacearum remains largely unexplored in this context. Notably, numerous inhibitors targeting TCSs have been identified, including GHL (Gyrase, Hsp, and MutL) compounds, Walk inhibitors, and anti-TCS medications like Radicicol. Consequently, the investigation into the involvement of TCSs in virulence and pathogenesis has gained traction; however, further research is imperative to ascertain whether TCSs could potentially supplant conventional anti-wilt therapies. This review delves into the prospective utilization of TCSs as an alternative anti-wilt therapy, focusing on the lethal phytopathogen R. solanacearum.
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Affiliation(s)
- Mohit Yadav
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Janhavi Sathe
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, 560065, India
| | - Valentina Teronpi
- Department of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya, Behali, Biswanath, Assam, 784184, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India.
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14
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Ding S, Ma Z, Yu L, Lan G, Tang Y, Li Z, He Z, She X. Comparative genomics and host range analysis of four Ralstonia pseudosolanacearum strains isolated from sunflower reveals genomic and phenotypic differences. BMC Genomics 2024; 25:191. [PMID: 38373891 PMCID: PMC10875864 DOI: 10.1186/s12864-024-10087-7] [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: 07/13/2023] [Accepted: 02/02/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Bacterial wilt caused by Ralstonia solanacearum species complex (RSSC) is one of the devastating diseases in crop production, seriously reducing the yield of crops. R. pseudosolanacearum, is known for its broad infrasubspecific diversity and comprises 36 sequevars that are currently known. Previous studies found that R. pseudosolanacearum contained four sequevars (13, 14, 17 and 54) isolated from sunflowers sown in the same field. RESULTS Here, we provided the complete genomes and the results of genome comparison of the four sequevars strains (RS639, RS642, RS647, and RS650). Four strains showed different pathogenicities to the same cultivars and different host ranges. Their genome sizes were about 5.84 ~ 5.94 Mb, encoding 5002 ~ 5079 genes and the average G + C content of 66.85% ~ 67%. Among the coding genes, 146 ~ 159 specific gene families (contained 150 ~ 160 genes) were found in the chromosomes and 34 ~ 77 specific gene families (contained 34 ~ 78 genes) in the megaplasmids from four strains. The average nucleotide identify (ANI) values between any two strains ranged from 99.05% ~ 99.71%, and the proportion of the total base length of collinear blocks accounts for the total gene length of corresponding genome was all more than 93.82%. Then, we performed a search for genomic islands, prophage sequences, the gene clusters macromolecular secretion systems, type III secreted effectors and other virulence factors in these strains, which provided detailed comparison results of their presence and distinctive features compared to the reference strain GMI1000. Among them, the number and types of T2SS gene clusters were different in the four strains, among which RS650 included all five types. T4SS gene cluster of RS639 and RS647 were missed. In the T6SS gene cluster, several genes were inserted in the RS639, RS647, and RS650, and gene deletion was also detected in the RS642. A total of 78 kinds of type III secreted effectors were found, which included 52 core and 9 specific effectors in four strains. CONCLUSION This study not only provided the complete genomes of multiple R. pseudosolanacearum strains isolated from a new host, but also revealed the differences in their genomic levels through comparative genomics. Furthermore, these findings expand human knowledge about the range of hosts that Ralstonia can infect, and potentially contribute to exploring rules and factors of the genetic evolution and analyzing its pathogenic mechanism.
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Affiliation(s)
- Shanwen Ding
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Zijun Ma
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Lin Yu
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Guobing Lan
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Yafei Tang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Zhenggang Li
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Zifu He
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China.
| | - Xiaoman She
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China.
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15
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Yuan C, An T, Li X, Zou J, Lin Z, Gu J, Hu R, Fang Z. Genomic analysis of Ralstonia pickettii reveals the genetic features for potential pathogenicity and adaptive evolution in drinking water. Front Microbiol 2024; 14:1272636. [PMID: 38370577 PMCID: PMC10869594 DOI: 10.3389/fmicb.2023.1272636] [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: 08/04/2023] [Accepted: 12/13/2023] [Indexed: 02/20/2024] Open
Abstract
Ralstonia pickettii, the most critical clinical pathogen of the genus Ralstonia, has been identified as a causative agent of numerous harmful infections. Additionally, Ralstonia pickettii demonstrates adaptability to extreme environmental conditions, such as those found in drinking water. In this study, we conducted a comprehensive genomic analysis to investigate the genomic characteristics related to potential pathogenicity and adaptive evolution in drinking water environments of Ralstonia pickettii. Through phylogenetic analysis and population genetic analysis, we divided Ralstonia pickettii into five Groups, two of which were associated with drinking water environments. The open pan-genome with a large and flexible gene repertoire indicated a high genetic plasticity. Significant differences in functional enrichment were observed between the core- and pan-genome of different groups. Diverse mobile genetic elements (MGEs), extensive genomic rearrangements, and horizontal gene transfer (HGT) events played a crucial role in generating genetic diversity. In drinking water environments, Ralstonia pickettii exhibited strong adaptability, and the acquisition of specific adaptive genes was potentially facilitated by genomic islands (GIs) and HGT. Furthermore, environmental pressures drove the adaptive evolution of Ralstonia pickettii, leading to the accumulation of unique mutations in key genes. These mutations may have a significant impact on various physiological functions, particularly carbon metabolism and energy metabolism. The presence of virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance indicated the potential pathogenicity of Ralstonia pickettii, making it capable of causing multiple nosocomial infections. This study provides comprehensive insights into the potential pathogenicity and adaptive evolution of Ralstonia pickettii in drinking water environments from a genomic perspective.
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Affiliation(s)
- Chao Yuan
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin, China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, China
- School of Public Health, Tianjin Medical University, Tianjin, China
| | - Tianfeng An
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin, China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, China
- School of Public Health, Tianjin Medical University, Tianjin, China
| | - Xinlong Li
- School of Public Health, Tianjin Medical University, Tianjin, China
| | - Jiao Zou
- School of Public Health, Tianjin Medical University, Tianjin, China
| | - Zhan Lin
- School of Public Health, Tianjin Medical University, Tianjin, China
| | - Jiale Gu
- School of Public Health, Tianjin Medical University, Tianjin, China
| | - Ruixia Hu
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin, China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, China
- School of Public Health, Tianjin Medical University, Tianjin, China
| | - Zhongze Fang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin, China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, China
- School of Public Health, Tianjin Medical University, Tianjin, China
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16
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Kiyan V, Smagulova A, Kukhar Y, Savin T, Bekenova A, Uakhit R. Morphological and Molecular Characterization of Bacterial Pathogens Associated with Leaf Mottle of Sunflower in Northern Kazakhstan. PLANT DISEASE 2024; 108:264-269. [PMID: 37642546 DOI: 10.1094/pdis-07-23-1352-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Leaf mottle is a serious disease in the common sunflower (Helianthus annuus L.), which affects plant growth and development and seed quality and yield. Over the past few years, the North Kazakhstan region, a sunflower-producing area in Kazakhstan, has been seriously affected by leaf mottle. Since 2021, symptomatic leaves have been collected from production areas of this base to determine the pathogens causing sunflower foliar diseases. One hundred bacterial strains were isolated, and two genera and five species were identified based on morphological characteristics, molecular genetics, and phylogenetic analysis (16S gene region). The genus Bacillus was represented by four species: Bacillus subtilis, B. megaterium, B. amyloliquefaciens, and B. flexus. The genus Paenibacillus was represented by one species, P. peoriae. Pathogenicity experiments showed that B. subtilis, B. megaterium, B. flexus, and P. peoriae could cause leaf mottle disease symptoms. However, disease symptoms caused by B. flexus were highly similar to those observed on infected leaves under natural conditions in the field. Therefore, these bacterial isolates were found to be the primary pathogens causing sunflower leaf mottle, and B. flexus was the most common and virulent pathogen in this study. In addition, this is the first report of B. megaterium, B. flexus, and P. peoriae as pathogens associated with sunflower leaf mottle in Kazakhstan.
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Affiliation(s)
- Vladimir Kiyan
- National Center of Biotechnology, Astana 010000, Kazakhstan
- Research Platform of Agricultural Biotechnology, S. Seifullin Kazakh Agrotechnical University, Astana 010011, Kazakhstan
| | - Ainura Smagulova
- National Center of Biotechnology, Astana 010000, Kazakhstan
- Research Platform of Agricultural Biotechnology, S. Seifullin Kazakh Agrotechnical University, Astana 010011, Kazakhstan
| | - Yelena Kukhar
- Research Platform of Agricultural Biotechnology, S. Seifullin Kazakh Agrotechnical University, Astana 010011, Kazakhstan
| | - Timur Savin
- Research Platform of Agricultural Biotechnology, S. Seifullin Kazakh Agrotechnical University, Astana 010011, Kazakhstan
| | - Aiganym Bekenova
- Research Platform of Agricultural Biotechnology, S. Seifullin Kazakh Agrotechnical University, Astana 010011, Kazakhstan
| | - Rabiga Uakhit
- National Center of Biotechnology, Astana 010000, Kazakhstan
- Research Platform of Agricultural Biotechnology, S. Seifullin Kazakh Agrotechnical University, Astana 010011, Kazakhstan
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17
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Bhatt S, Faridi N, Raj SMP, Agarwal A, Punetha M. Recent advances in immuno-based methods for the detection of Ralstonia solanacearum. J Microbiol Methods 2024; 217-218:106889. [PMID: 38211840 DOI: 10.1016/j.mimet.2024.106889] [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: 10/10/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
Ralstonia solanacearum (RS) is a widely recognized phytopathogenic bacterium which is responsible for causing devastating losses in a wide range of economically significant crops. Timely and accurate detection of this pathogen is pivotal to implementing effective disease management strategies and preventing crop losses. This review provides a comprehensive overview of recent advances in immuno-based detection methods for RS. The review begins by introducing RS, highlighting its destructive potential and the need for point-of-care detection techniques. Subsequently, it explores traditional detection methods and their limitations, emphasizing the need for innovative approaches. The main focus of this review is on immuno-based detection methods and it discusses recent advancements in serological detection techniques. Furthermore, the review sheds light on the challenges and prospects of immuno-based detection of RS. It emphasizes the importance of developing rapid, field-deployable assays that can be used by farmers and researchers alike. In conclusion, this review provides valuable insights into the recent advances in immuno-based detection methods for RS.
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Affiliation(s)
- Shalini Bhatt
- P P Savani University, Surat 394125, Gujarat, India; Defence Institute of Bio-Energy Research (DIBER), DRDO, Nainital, Haldwani 263139, Uttarakhand, India.
| | - Neha Faridi
- Defence Institute of Bio-Energy Research (DIBER), DRDO, Nainital, Haldwani 263139, Uttarakhand, India
| | - S Merwyn P Raj
- Defence Institute of Bio-Energy Research (DIBER), DRDO, Nainital, Haldwani 263139, Uttarakhand, India
| | - Ankur Agarwal
- Defence Institute of Bio-Energy Research (DIBER), DRDO, Nainital, Haldwani 263139, Uttarakhand, India
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18
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Chen W, Zhang JW, Qin BX, Xie HT, Zhang Z, Qiao XZ, Li SK, Asif M, Guo S, Cui LX, Wang PP, Dong LH, Guo QG, Jiang WJ, Ma P, Xia ZY, Lu CH, Zhang LQ. Quantitative detection of the Ralstonia solanacearum species complex in soil by qPCR combined with a recombinant internal control strain. Microbiol Spectr 2023; 11:e0021023. [PMID: 37966217 PMCID: PMC10715031 DOI: 10.1128/spectrum.00210-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE DNA-based detection and quantification of soil-borne pathogens, such as the Ralstonia solanacearum species complex (RSSC), plays a vital role in risk assessment, but meanwhile, precise quantification is difficult due to the poor purity and yield of the soil DNA retrieved. The internal sample process control (ISPC) strain RsPC we developed solved this problem and significantly improved the accuracy of quantification of RSSC in different soils. ISPC-based quantitative PCR detection is a method especially suitable for the quantitative detection of microbes in complex matrices (such as soil and sludge) containing various PCR inhibitors and for those not easy to lyse (like Gram-positive bacteria, fungi, and thick-wall cells like resting spores). In addition, the use of ISPC strains removes additional workload on the preparation of high-quality template DNA and facilitates the development of high-throughput quantitative detection techniques for soil microbes.
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Affiliation(s)
- Wei Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Jun-Wei Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Bi-Xia Qin
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Xixiangtang District, Nanning, China
| | - Hui-Ting Xie
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Xixiangtang District, Nanning, China
| | - Zhi Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Xiu-Ze Qiao
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Shan-Kui Li
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Muhammad Asif
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Song Guo
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Li-Xian Cui
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Xixiangtang District, Nanning, China
| | - Pei-Pei Wang
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Centre of Hebei Province, Lianchi District, Baoding, China
| | - Li-Hong Dong
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Centre of Hebei Province, Lianchi District, Baoding, China
| | - Qing-Gang Guo
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Centre of Hebei Province, Lianchi District, Baoding, China
| | - Wen-Jun Jiang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Ping Ma
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Centre of Hebei Province, Lianchi District, Baoding, China
| | - Zhen-Yuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Wuhua District, Kunming, China
| | - Can-Hua Lu
- Yunnan Academy of Tobacco Agricultural Sciences, Wuhua District, Kunming, China
| | - Li-Qun Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
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Morlino MS, Serna García R, Savio F, Zampieri G, Morosinotto T, Treu L, Campanaro S. Cupriavidus necator as a platform for polyhydroxyalkanoate production: An overview of strains, metabolism, and modeling approaches. Biotechnol Adv 2023; 69:108264. [PMID: 37775073 DOI: 10.1016/j.biotechadv.2023.108264] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Cupriavidus necator is a bacterium with a high phenotypic diversity and versatile metabolic capabilities. It has been extensively studied as a model hydrogen oxidizer, as well as a producer of polyhydroxyalkanoates (PHA), plastic-like biopolymers with a high potential to substitute petroleum-based materials. Thanks to its adaptability to diverse metabolic lifestyles and to the ability to accumulate large amounts of PHA, C. necator is employed in many biotechnological processes, with particular focus on PHA production from waste carbon sources. The large availability of genomic information has enabled a characterization of C. necator's metabolism, leading to the establishment of metabolic models which are used to devise and optimize culture conditions and genetic engineering approaches. In this work, the characteristics of available C. necator strains and genomes are reviewed, underlining how a thorough comprehension of the genetic variability of C. necator is lacking and it could be instrumental for wider application of this microorganism. The metabolic paradigms of C. necator and how they are connected to PHA production and accumulation are described, also recapitulating the variety of carbon substrates used for PHA accumulation, highlighting the most promising strategies to increase the yield. Finally, the review describes and critically analyzes currently available genome-scale metabolic models and reduced metabolic network applications commonly employed in the optimization of PHA production. Overall, it appears that the capacity of C. necator of performing CO2 bioconversion to PHA is still underexplored, both in biotechnological applications and in metabolic modeling. However, the accurate characterization of this organism and the efforts in using it for gas fermentation can help tackle this challenging perspective in the future.
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Affiliation(s)
- Maria Silvia Morlino
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Rebecca Serna García
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain
| | - Filippo Savio
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Guido Zampieri
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Tomas Morosinotto
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
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Fan Y, Wang S, Song M, Zhou L, Liu C, Yang Y, Yu S, Yang M. Specific biomarker mining and rapid detection of Burkholderia cepacia complex by recombinase polymerase amplification. Front Microbiol 2023; 14:1270760. [PMID: 37779692 PMCID: PMC10539473 DOI: 10.3389/fmicb.2023.1270760] [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: 08/01/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
Objective To mine specific proteins and their protein-coding genes as suitable molecular biomarkers for the Burkholderia cepacia Complex (BCC) bacteria detection based on mega analysis of microbial proteomic and genomic data comparisons and to develop a real-time recombinase polymerase amplification (rt-RPA) assay for rapid isothermal screening for pharmaceutical and personal care products. Methods We constructed an automatic screening framework based on Python to compare the microbial proteomes of 78 BCC strains and 263 non-BCC strains to identify BCC-specific protein sequences. In addition, the specific protein-coding gene and its core DNA sequence were validated in silico with a self-built genome database containing 158 thousand bacteria. The appropriate methodology for BCC detection using rt-RPA was evaluated by 58 strains in pure culture and 33 batches of artificially contaminated pharmaceutical and personal care products. Results We identified the protein SecY and its protein-coding gene secY through the automatic comparison framework. The virtual evaluation of the conserved region of the secY gene showed more than 99.8% specificity from the genome database, and it can distinguish all known BCC species from other bacteria by phylogenetic analysis. Furthermore, the detection limit of the rt-RPA assay targeting the secY gene was 5.6 × 102 CFU of BCC bacteria in pure culture or 1.2 pg of BCC bacteria genomic DNA within 30 min. It was validated to detect <1 CFU/portion of BCC bacteria from artificially contaminated samples after a pre-enrichment process. The relative trueness and sensitivity of the rt-RPA assay were 100% in practice compared to the reference methods. Conclusion The automatic comparison framework for molecular biomarker mining is straightforward, universal, applicable, and efficient. Based on recognizing the BCC-specific protein SecY and its gene, we successfully established the rt-RPA assay for rapid detection in pharmaceutical and personal care products.
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Affiliation(s)
- Yiling Fan
- China State Institute of Pharmaceutical Industry, Shanghai, China
- National Medical Products Administration Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Shujuan Wang
- National Medical Products Administration Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Minghui Song
- National Medical Products Administration Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Liangliang Zhou
- College of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, Jiangxi, China
| | - Chengzhi Liu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou, China
| | - Yan Yang
- National Medical Products Administration Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Shuijing Yu
- College of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, Jiangxi, China
| | - Meicheng Yang
- China State Institute of Pharmaceutical Industry, Shanghai, China
- Shanghai Food and Drug Packaging Material Control Center, Shanghai, China
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21
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Rabea A, Naeem E, Balabel NM, Daigham GE. Management of potato brown rot disease using chemically synthesized CuO-NPs and MgO-NPs. BOTANICAL STUDIES 2023; 64:20. [PMID: 37458850 DOI: 10.1186/s40529-023-00393-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/01/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Potatoes are a crucial vegetable crop in Egypt in terms of production and consumption. However, the potato industry suffers significant annual losses due to brown rot disease. This study aimed to suppress Ralstonia solanacearum (R. solanacearum), the causative agent of brown rot disease in potatoes, using efficient and economical medications such as CuO and MgO metal oxide nanoparticles, both in vitro and in vivo, to reduce the risk of pesticide residues. RESULTS CuO and MgO metal oxide nanoparticles were synthesized via a simple chemical process. The average particle size, morphology, and structure of the nanoparticles were characterized using UV-visible spectroscopy, transmission electron microscopy (TEM), zeta potential analysis, X-ray diffraction (XRD), and Fourier transform infrared (FTIR) spectroscopy. The growth of R. solanacearum was strongly inhibited by CuO and MgO NPs at a concentration of 3 mg/mL, resulting in zones of inhibition (ZOI) of 19.3 mm and 17 mm, respectively. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of CuO-NPs and MgO-NPs were 0.5, 0.6, and 0.6, 0.75 mg/mL, respectively. When applied in vivo through seed dressing and tuber soaking at their respective MIC concentrations, CuO-NPs and MgO-NPs significantly reduced the incidence of brown rot disease to 71.2% and 69.4%, respectively, compared to 43.0% and 39.5% in bulk CuSO4 and bulk MgSO4 treatments, respectively. Furthermore, CuO-NPs and MgO-NPs significantly increased the yield, total chlorophyll content, and enzyme efficiency of potato plants compared with the infected control plants. TEM revealed that the bacterial cytomembrane was severely damaged by nanomechanical forces after interaction with CuO-NPs and MgO-NPs, as evidenced by lipid peroxidation and ultrastructural investigations. CONCLUSION The results of this study suggest that CuO-NPs and MgO-NPs can be used as intelligent agents to manage plant pathogens in agriculture. The use of metal oxide nanoparticles could provide a risk-free alternative for treating plant diseases, which are currently one of the biggest challenges faced by the potato industry in Egypt. The significant increase in yield, photosynthetic pigments, enzymatic activity, and total phenol-promoted resistance to R. solanacearum in potato plants treated with CuO-NPs and MgO-NPs compared to infected control plants highlights the potential benefits for the potato industry in Egypt. Further investigations are needed to explore using metal oxide nanoparticles for treating other plant diseases.
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Affiliation(s)
- Amira Rabea
- Bacterial Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - E Naeem
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University (Girls Branch), Cairo, Egypt
| | - Naglaa M Balabel
- Bacterial Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza, Egypt
- Potato Brown Rot Project, Ministry of Agriculture, Dokki, Giza, Egypt
| | - Ghadir E Daigham
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University (Girls Branch), Cairo, Egypt.
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Yadav DK, Devappa V, Kashyap AS, Kumar N, Rana VS, Sunita K, Singh D. Boosting the Biocontrol Efficacy of Bacillus amyloliquefaciens DSBA-11 through Physical and Chemical Mutagens to Control Bacterial Wilt Disease of Tomato Caused by Ralstonia solanacearum. Microorganisms 2023; 11:1790. [PMID: 37512962 PMCID: PMC10383371 DOI: 10.3390/microorganisms11071790] [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: 05/09/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Bacterial wilt disease of tomato (Solanum lycopersicum L.), incited by Ralstonia solanacearum (Smith), is a serious agricultural problem in India. In this investigation, chemical mutagenic agents (NTG and HNO2 treatment) and ultraviolet (UV) irradiation have been used to enhance the antagonistic property of Bacillus amyloliquefaciens DSBA-11 against R. solanacearum UTT-25 towards an effective management of tomato wilt disease. The investigation established the fact that maximum inhibition to R. solanacearum UTT-25 was exerted by the derivative strain MHNO2-20 treated with nitrous acid (HNO2) and then by the derivative strain MNTG-21 treated with NTG. The exertion was significantly higher than that of the parent B. amyloliquefaciens DSBA-11. These two potential derivatives viz. MNTG-21, MHNO2-20 along with MUV-19, and a wild derivative strain of B. amyloliquefaciens i.e.,DSBA-11 were selected for GC/MS analysis. Through this analysis 18 major compounds were detected. Among the compounds thus detected, the compound 3-isobutyl hexahydropyrrolo (1,2), pyrazine-1,4-dione (4.67%) was at maximum proportion in the variant MHNO2-20 at higher retention time (RT) of 43.19 s. Bio-efficacy assessment observed a record of minimum intensity (9.28%) in wilt disease and the highest bio-control (88.75%) in derivative strain MHNO2-20-treated plants after 30 days of inoculation. The derivative strain MHNO2-20, developed by treating B. amyloliquefaciens with nitrous acid (HNO2), was therefore found to have a higher bio-efficacy to control bacterial wilt disease of tomato under glasshouse conditions than a wild-type strain.
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Affiliation(s)
- Dhananjay Kumar Yadav
- Division of Plant Pathology, ICAR, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Venkatappa Devappa
- Department of Plant Pathology, College of Horticulture, University of Horticultural Sciences, UHS Campus, Bagalkot, GKVK Post, Bengaluru 560065, India
| | | | - Narendra Kumar
- Amity Institute of Biotechnology, Amity University Haryana, Manesar, Gurgaon 122413, India
| | - V S Rana
- Division of Agriculture Chemical, Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Kumari Sunita
- Department of Botany, Deen Dayal Upadhayay Gorakhpur University, Gorakhpur 273009, India
| | - Dinesh Singh
- Division of Plant Pathology, ICAR, Indian Agricultural Research Institute, New Delhi 110012, India
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Fan Z, Mei Y, Xing J, Chen T, Hu D, Liu H, Li Y, Liu D, Liu Z, Liang Y. Loop-mediated isothermal amplification (LAMP)/Cas12a assay for detection of Ralstonia solanacearum in tomato. Front Bioeng Biotechnol 2023; 11:1188176. [PMID: 37284238 PMCID: PMC10239818 DOI: 10.3389/fbioe.2023.1188176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/11/2023] [Indexed: 06/08/2023] Open
Abstract
Introduction: Bacterial wilt (BW) caused by the aerobic, Gram-negative pathogenic species Ralstonia solanacearum (RS) is a major disease impacting commercial agriculture worldwide. Asian phylotype I of RS is the cause of tomato bacterial wilt, which has caused severe economic losses in southern China for many years. An urgent priority in control of bacterial wilt is development of rapid, sensitive, effective methods for detection of RS. Methods: We describe here a novel RS detection assay based on combination of loop-mediated isothermal amplification (LAMP) and CRISPR/Cas12a. crRNA1, with high trans-cleavage activity targeting hrpB gene, was selected out of four candidate crRNAs. Two visual detection techniques, involving naked-eye observation of fluorescence and lateral flow strips, were tested and displayed high sensitivity and strong specificity. Results and Discussion: The LAMP/Cas12a assay accurately detected RS phylotype Ⅰ in 14 test strains, and showed low detection limit (2.0 × 100 copies). RS in tomato stem tissue and soil samples from two field sites with suspected BW infection was identified accurately, suggesting potential application of LAMP/Cas12a assay as point-of-care test (POCT). The overall detection process took less than 2 h and did not require professional lab equipment. Our findings, taken together, indicate that LAMP/Cas12a assay can be developed as an effective, inexpensive technique for field detection and monitoring of RS.
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Affiliation(s)
- Zhiyu Fan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuxia Mei
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiawei Xing
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tian Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Di Hu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hui Liu
- GNSS Research Center, Wuhan University, Wuhan, China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Derui Liu
- Hubei Jiamachi Ecological Agriculture Co, Ltd, Yichang, China
- Hubei Yishizhuang Agricultural Technology Co, Ltd, Yichang, China
| | - Zufeng Liu
- Hubei Jiamachi Ecological Agriculture Co, Ltd, Yichang, China
- Hubei Yishizhuang Agricultural Technology Co, Ltd, Yichang, China
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Lin SZ, Qian MJ, Wang YW, Chen QD, Wang WQ, Li JY, Yang RT, Wang XY, Mu CY, Jiang K. Children with infectious pneumonia caused by Ralstonia insidiosa: A case report. World J Clin Cases 2023; 11:2002-2008. [PMID: 36998962 PMCID: PMC10044956 DOI: 10.12998/wjcc.v11.i9.2002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/02/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Ralstonia is a Gram-negative non-fermentative bacterium widespread in nature, and includes four species, Ralstonia pickettii, Ralstonia solanacearum, Ralstonia mannitolilytica, and Ralstonia insidiosa, which were proposed in 2003. Ralstonia is mainly found in the external water environment, including municipal and medical water purification systems. This bacterium has low toxicity and is a conditional pathogen. It has been reported in recent years that infections due to Ralstonia are increasing. Previous studies have shown that most cases of infection are caused by Ralstonia pickettii, a few by Ralstonia mannitolilytica, and infections caused by Ralstonia insidiosa are rare.
CASE SUMMARY A 2-year-old Chinese child suffered from intermittent fever and cough for 20 d and was admitted to hospital with bronchial pneumonia. Bronchoscopy and alveolar lavage fluid culture confirmed Ralstonia insidiosa pneumonia. The infection was well controlled after treatment with meropenem and azithromycin.
CONCLUSION Ralstonia infections are increasing, and we report a rare case of Ralstonia insidiosa infection in a child. Clinicians should be vigilant about Ralstonia infections.
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Affiliation(s)
- Shuang-Zhu Lin
- Diagnosis and Treatment Center for Children, Affiliated Hospital of Changchun University of Chinese Medicine, Changchun 130021, Jilin Province, China
| | - Mei-Jia Qian
- Diagnosis and Treatment Center for Children, Affiliated Hospital of Changchun University of Chinese Medicine, Changchun 130021, Jilin Province, China
| | - Yan-Wei Wang
- Department of Imaging, Affiliated Hospital of Changchun University of Chinese Medicine, Changchun 130021, Jilin Province, China
| | - Qian-Dui Chen
- College of Integrated Chinese and Western Medicine, Changchun University of Chinese Medicine, Changchun 130117, Jilin Province, China
| | - Wan-Qi Wang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, Jilin Province, China
| | - Jia-Yi Li
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, Jilin Province, China
| | - Rui-Tong Yang
- College of Integrated Chinese and Western Medicine, Changchun University of Chinese Medicine, Changchun 130117, Jilin Province, China
| | - Xin-Yao Wang
- College of Integrated Chinese and Western Medicine, Changchun University of Chinese Medicine, Changchun 130117, Jilin Province, China
| | - Chun-Yu Mu
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, Jilin Province, China
| | - Kai Jiang
- Diagnosis and Treatment Center for Children, Affiliated Hospital of Changchun University of Chinese Medicine, Changchun 130021, Jilin Province, China
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Liu JY, Zhang JF, Wu HL, Chen Z, Li SY, Li HM, Zhang CP, Zhou YQ, Lu CH. Proposal to classify Ralstonia solanacearum phylotype I strains as Ralstonia nicotianae sp. nov., and a genomic comparison between members of the genus Ralstonia. Front Microbiol 2023; 14:1135872. [PMID: 37032877 PMCID: PMC10073495 DOI: 10.3389/fmicb.2023.1135872] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/07/2023] [Indexed: 04/11/2023] Open
Abstract
A Gram-negative, aerobic, rod-shaped, motile bacterium with multi-flagella, strain RST, was isolated from bacterial wilt of tobacco in Yuxi city of Yunnan province, China. The strain contains the major fatty acids of C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The polar lipid profile of strain RST consists of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminophospholipid. Strain RST contains ubiquinones Q-7 and Q-8. 16S rRNA gene sequence (1,407 bp) analysis showed that strain RST is closely related to members of the genus Ralstonia and shares the highest sequence identities with R. pseudosolanacearum LMG 9673T (99.50%), R. syzygii subsp. indonesiensis LMG 27703T (99.50%), R. solanacearum LMG 2299T (99.28%), and R. syzygii subsp. celebesensis LMG 27706T (99.21%). The 16S rRNA gene sequence identities between strain RST and other members of the genus Ralstonia were below 98.00%. Genome sequencing yielded a genome size of 5.61 Mbp and a G + C content of 67.1 mol%. The genomic comparison showed average nucleotide identity (ANIb) values between strain RST and R. pseudosolanacearum LMG 9673T, R. solanacearum LMG 2299T, and R. syzygii subsp. indonesiensis UQRS 627T of 95.23, 89.43, and 91.41%, respectively, and the corresponding digital DNA-DNA hybridization (dDDH) values (yielded by formula 2) were 66.20, 44.80, and 47.50%, respectively. In addition, strains belonging to R. solanacearum phylotype I shared both ANIb and dDDH with strain RST above the species cut-off values of 96 and 70%, respectively. The ANIb and dDDH values between the genome sequences from 12 strains of R. solanacearum phylotype III (Current R. pseudosolanacearum) and those of strain RST were below the species cut-off values. Based on these data, we concluded that strains of phylotype I, including RST, represent a novel species of the genus Ralstonia, for which the name Ralstonia nicotianae sp. nov. is proposed. The type strain of Ralstonia nicotianae sp. nov. is RST (=GDMCC 1.3533T = JCM 35814T).
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Affiliation(s)
- Jun-Ying Liu
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
- Institute of Biology and Environmental Engineering, Yuxi Normal University, Yuxi, China
| | - Jian-Feng Zhang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Han-Lian Wu
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Zhen Chen
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Shu-Ying Li
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Hong-Mei Li
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Cui-Ping Zhang
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Yuan-Qing Zhou
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Can-Hua Lu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
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Zhao Q, Geng MY, Xia CJ, Lei T, Wang J, Cao CD, Wang J. Identification, genetic diversity, and pathogenicity of Ralstonia pseudosolanacearum causing cigar tobacco bacterial wilt in China. FEMS Microbiol Ecol 2023; 99:fiad018. [PMID: 36822630 DOI: 10.1093/femsec/fiad018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/17/2022] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Ralstonia pseudosolanacearum, previously known as R. solanacearum species complex (RSSC) phylotypes I and III, is a plant pathogenic bacterium causing significant yield losses in economical crops. In the May of 2020 and 2021, cigar tobacco bacterial wilt was first observed in fields in Danzhou, Hainan Province, China. A total of eight bacterial isolates were isolated and identified as R. pseudosolanacearum with race 1, biovar III by 16S rRNA gene sequencing, Biolog, and host identification. The amino acid sequence showed that Hainan strains and 15 R. pseudosolanacearum reference strains from flue-cured tobacco in Shandong and Guizhou Provinces, all belonged to RS1000 type containing the avrA gene, only Guizhou strains also had the popP1 gene. On the basis of phylotype-specific multiplex PCR amplification, mismatch repair gene and endoglucanase gene-base tree, Hainan strains were identified as phylotype I sequevar 70, and showed stronger pathogenic capabilities on three different varieties than those reference strains. This is the first report of cigar tobacco bacterial wilt caused by R. pseudosolanacearum sequevar 70. The results revealed the diversity of RSSC in Nicotiana tabacum in China and provided useful information regarding the epidemiology of cigar tobacco wilt disease, as well as the breeding for disease resistance in local cigar tobacco.
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Affiliation(s)
- Qian Zhao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No.4 Keyuanjing, Laoshan District, Qingdao, Shandong 266101, China
- Nanjing Agricultural University, No.1 Weigang, Xuanwu District, Nanjing, Jiangsu 210095, China
| | - Ming-Yan Geng
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No.4 Keyuanjing, Laoshan District, Qingdao, Shandong 266101, China
| | - Chang-Jian Xia
- Haikou Cigar Research Institute, Hainan Provincial Branch of China National Tobacco Corporation, No.120 Hongchenghu Road, Qiongshan District, Haikou, Hainan 571103, China
| | - Ting Lei
- Qiannan Branch of Guizhou Tobacco Corporation, No.8 Hebin, Duyun, Guizhou 558000, China
| | - Jie Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No.4 Keyuanjing, Laoshan District, Qingdao, Shandong 266101, China
| | - Chang-Dai Cao
- Rizhao Branch of Shandong Tobacco Corporation, No.269 Juzhou, Donggang District, Rizhao, Shandong 276800, China
| | - Jing Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No.4 Keyuanjing, Laoshan District, Qingdao, Shandong 266101, China
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Tessema GL, Seid HE. Potato bacterial wilt in Ethiopia: history, current status, and future perspectives. PeerJ 2023; 11:e14661. [PMID: 36691487 PMCID: PMC9864131 DOI: 10.7717/peerj.14661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/08/2022] [Indexed: 01/19/2023] Open
Abstract
Background Potato is an essential food staple and a critical tuber crop for rural livelihoods in Ethiopia, where many pathogenic pests are threatening production. Bacterial wilt, also known as brown rot of potato, ranks among the diseases that most affect many potato farmers in Ethiopia and the disease losses dramatically threatening the vibrant potato sector even in the highlands of the country where it has been uncommon so far. Methodology To devise a strategy towards boosting potato productivity in Ethiopia where food insecurity is most prevalent, production constraints should be investigated and properly addressed. Hence, we have used existing reviews and reports on the subjects, such as textbooks, and proceeding and conference abstracts in Plant Protection Society of Ethiopia; Web of Science; Google Scholar; Research Gate and CIP's database to document most relevant information on the occurrence, distribution, and disease management of bacterial wilt in Ethiopia. Results Provision of comprehensive information on potato bacterial wilt occurrence, distribution, and management techniques are crucial for potato growers, researchers and stakeholders engaged on potato industry. In this review, we provided insights on the history, status, and future perspectives of potato bacterial wilt in Ethiopia. Conclusions Awareness of potato bacterial wilt and integrated disease management approaches could bring a fundamental impact to the farming community mostly to smallholder farmers in developing countries. This document compiled such imperative information targeting bacterial wilt management techniques to ensure food security.
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Lu CH, Zhang YY, Jiang N, Chen W, Shao X, Zhao ZM, Lu WL, Hu X, Xi YX, Zou SY, Wei QJ, Lin ZL, Gong L, Gai XT, Zhang LQ, Li JY, Jin Y, Xia ZY. Ralstonia chuxiongensis sp. nov., Ralstonia mojiangensis sp. nov., and Ralstonia soli sp. nov., isolated from tobacco fields, are three novel species in the family Burkholderiaceae. Front Microbiol 2023; 14:1179087. [PMID: 37213510 PMCID: PMC10196183 DOI: 10.3389/fmicb.2023.1179087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/14/2023] [Indexed: 05/23/2023] Open
Abstract
Eight Gram-negative, aerobic, motile with paired polar flagella and rod-shaped bacteria were isolated from six tobacco fields in Yunnan, PR China. 16S rRNA gene sequence analysis revealed that all the strains belonged to the genus Ralstonia. Among them, strain 22TCCZM03-6 had an identical 16S rRNA sequence to that of R. wenshanensis 56D2T, and the other strains were closely related to R. pickettii DSM 6297T (98.34–99.86%), R. wenshanensis 56D2T (98.70–99.64%), and R. insidiosa CCUG 46789T (97.34–98.56%). Genome sequencing yielded sizes ranging from 5.17 to 5.72 Mb, with overall G + C contents of 63.3–64.1%. Pairwise genome comparisons showed that strain 22TCCZM03-6 shared average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values above the species cut-off with R. wenshanensis 56D2T, suggesting that strain 22TCCZM03-6 is a special strain of the R. wenshanensis. Five strains, including 21MJYT02-10T, 21LDWP02-16, 22TCJT01-1, 22TCCZM01-4, and 22TCJT01-2, had ANI values >95% and dDDH values >70% when compared with each other. These five strains had ANI values of 73.32–94.17% and dDDH of 22.0–55.20% with the type strains of the genus Ralstonia individually, supporting these five strains as a novel species in the genus Ralstonia. In addition, strains 21YRMH01-3T and 21MJYT02-11T represent two independent species. They both had ANI and dDDH values below the thresholds for species delineation when compared with the type species of the genus Ralstonia. In strains 21YRMH01-3T and 21MJYT02-10T, the main fatty acids were summed features 3, 8, and C16:0; however, strain 21MJYT02-11T contained C16:0, cyclo-C17:0, and summed features 3 as major fatty acids. The main polar lipids, including diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine, were identified from strains 21YRMH01-3T, 21MJYT02-10T, and 21MJYT02-11T. The ubiquinones Q-7 and Q-8 were also detected in these strains, with Q-8 being the predominant quinone. Based on the above data, we propose that the eight strains represent one known species and three novel species in the genus Ralstonia, for which the names Ralstonia chuxiongensis sp. nov., Ralstonia mojiangensis sp. nov., and Ralstonia soli sp. nov. are proposed. The type strains are 21YRMH01-3T (=GDMCC 1.3534T = JCM 35818T), 21MJYT02-10T (=GDMCC 1.3531T = JCM 35816T), and 21MJYT02-11T (=GDMCC 1.3532T = JCM 35817T), respectively.
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Affiliation(s)
- Can-Hua Lu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
- *Correspondence: Zhen-Yuan Xia, ; Can-Hua Lu,
| | - Ying-Ying Zhang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Ning Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Wei Chen
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiaoli Shao
- Puer Branch of Yunnan Tobacco Company, Puer, China
| | - Zhi-Ming Zhao
- Baoshan Branch of Yunnan Tobacco Company, Baoshan, China
| | - Wen-Lin Lu
- Zhaotong Branch of Yunnan Tobacco Company, Zhaoyang, China
| | - Xiaodong Hu
- Chuxiong Branch of Yunnan Tobacco Company, Chuxiong, China
| | - Yi-Xuan Xi
- Baoshan Branch of Yunnan Tobacco Company, Baoshan, China
| | - Si-Yuan Zou
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Qiu-Ju Wei
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Zhong-Long Lin
- China National Tobacco Corporation Yunnan Company, Kunming, China
| | - Li Gong
- Puer Branch of Yunnan Tobacco Company, Puer, China
| | - Xiao-Tong Gai
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Li-Qun Zhang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Jun-Ying Li
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Yan Jin
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Zhen-Yuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
- *Correspondence: Zhen-Yuan Xia, ; Can-Hua Lu,
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Chen N, Shao Q, Lu Q, Li X, Gao Y. Transcriptome analysis reveals differential transcription in tomato (Solanum lycopersicum) following inoculation with Ralstonia solanacearum. Sci Rep 2022; 12:22137. [PMID: 36550145 PMCID: PMC9780229 DOI: 10.1038/s41598-022-26693-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Tomato (Solanum lycopersicum L.) is a major Solanaceae crop worldwide and is vulnerable to bacterial wilt (BW) caused by Ralstonia solanacearum during the production process. BW has become a growing concern that could enormously deplete the tomato yield from 50 to 100% and decrease the quality. Research on the molecular mechanism of tomato regulating BW resistance is still limited. In this study, two tomato inbred lines (Hm 2-2, resistant to BW; and BY 1-2, susceptible to BW) were used to explore the molecular mechanism of tomato in response to R. solanacearum infection by RNA-sequencing (RNA-seq) technology. We identified 1923 differentially expressed genes (DEGs) between Hm 2-2 and BY 1-2 after R. solanacearum inoculation. Among these DEGs, 828 were up-regulated while 1095 were down-regulated in R-3dpi (Hm 2-2 at 3 days post-inoculation with R. solanacearum) vs. R-mock (mock-inoculated Hm 2-2); 1087 and 2187 were up- and down-regulated, respectively, in S-3dpi (BY 1-2 at 3 days post-inoculation with R. solanacearum) vs. S-mock (mock-inoculated BY 1-2). Moreover, Gene Ontology (GO) enrichment analysis revealed that the largest amount of DEGs were annotated with the Biological Process terms, followed by Cellular Component and Molecular Function terms. A total of 114, 124, 85, and 89 regulated (or altered) pathways were identified in R-3dpi vs. R-mock, S-3dpi vs. S-mock, R-mock vs. S-mock, and R-3dpi vs. S-3dpi comparisons, respectively, by Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. These clarified the molecular function and resistance pathways of DEGs. Furthermore, quantitative RT-PCR (qRT-PCR) analysis confirmed the expression patterns of eight randomly selected DEGs, which suggested that the RNA-seq results were reliable. Subsequently, in order to further verify the reliability of the transcriptome data and the accuracy of qRT-PCR results, WRKY75, one of the eight DEGs was silenced by virus-induced gene silencing (VIGS) and the defense response of plants to R. solanacearum infection was analyzed. In conclusion, the findings of this study provide profound insight into the potential mechanism of tomato in response to R. solanacearum infection, which lays an important foundation for future studies on BW.
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Affiliation(s)
- Na Chen
- grid.449868.f0000 0000 9798 3808College of Life Science and Resources and Environment, Yichun University, Yichun, 336000 China
| | - Qin Shao
- grid.449868.f0000 0000 9798 3808College of Life Science and Resources and Environment, Yichun University, Yichun, 336000 China
| | - Qineng Lu
- grid.449868.f0000 0000 9798 3808College of Life Science and Resources and Environment, Yichun University, Yichun, 336000 China
| | - Xiaopeng Li
- grid.449868.f0000 0000 9798 3808College of Life Science and Resources and Environment, Yichun University, Yichun, 336000 China
| | - Yang Gao
- grid.449868.f0000 0000 9798 3808College of Life Science and Resources and Environment, Yichun University, Yichun, 336000 China
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Lu CH, Chen W, Yin HH, Lin ZL, Li JY, Ma JH, Gai XT, Jiang N, Cao ZH, Qian L, Zhang LQ, Jin Y, Xia ZY. Ralstonia wenshanensis sp. nov., a novel bacterium isolated from a tobacco field in Yunnan, China. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748420 DOI: 10.1099/ijsem.0.005622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A Gram-negative, aerobic, motile with paired polar flagella and rod-shaped bacterium strain (56D2T) was isolated from tobacco planting soil in Yunnan, PR China. Major fatty acids were C16 : 1 ω7c (summed feature 3), C16 : 0 and C18 : 1 ω7c (summed feature 8). The polar lipid profile of strain 56D2T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid and one unidentified glycolipid. Moreover, strain 56D2T contained ubiquinone Q-8 as the sole respiratory quinone. 16S rRNA gene sequence analysis showed that strain 56D2T was closely related to members of the genus Ralstonia and the two type strains with the highest sequence identities were R. mannitolilytica LMG 6866T (98.36 %) and R. pickettii K-288T (98.22 %). The 16S rRNA gene sequence identities between strain 56D2T and other members of the genus Ralstonia were below 98.00 %. Genome sequencing revealed a genome size of 5.87 Mb and a G+C content of 63.7 mol%. The average nucleotide identity values between strain 56D2T and R. pickettii K-288T, R. mannitolilytica LMG 6866 T and R. insidiosa CCUG 46789T were less than 95 %, and the in silico DNA-DNA hybridization values (yielded by formula 2) were less than 70 %. Based on these data, we conclude that strain 56D2T represents a novel species of the genus Ralstonia, for which the name Ralstonia wenshanensis sp. nov. is proposed. The type strain of Ralstonia wenshanensis sp. nov. is 56D2T (=CCTCC AB 2021466T=GDMCC 1.2886T=JCM 35178T).
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Affiliation(s)
- Can-Hua Lu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Wei Chen
- Colledge of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Hong-Hui Yin
- Wenshan Branch of Yunnan Provincial Tobacco Company, Wenshan 663000, PR China
| | - Zhong-Long Lin
- China National Tobacco Corporation Yunnan Company, Kunming 650011, PR China
| | - Jun-Ying Li
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Jun-Hong Ma
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Xiao-Tong Gai
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Ning Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Zheng-Hua Cao
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Lei Qian
- Hongta Branch of Yuxi Tobacco Company, Yuxi 653100, PR China
| | - Li-Qun Zhang
- Colledge of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Yan Jin
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Zhen-Yuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
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A consolidative synopsis of the MALDI-TOF MS accomplishments for the rapid diagnosis of microbial plant disease pathogens. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ghorai AK, Dutta S, Roy Barman A. Genetic diversity of Ralstonia solanacearum causing vascular bacterial wilt under different agro-climatic regions of West Bengal, India. PLoS One 2022; 17:e0274780. [PMID: 36137083 PMCID: PMC9498970 DOI: 10.1371/journal.pone.0274780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
The bacterial wilt disease of solanaceous crops incited by Ralstonia solanacearum is a menace to the production of solanaceous vegetables all over the world. Among the agro climatic zones of West Bengal, India growing solanaceous vegetables, the maximum and minimum incidence of bacterial wilt was observed in Red and Lateritic zone (42.4%) and Coastal and Saline zone (26.9%), respectively. The present investigation reports the occurrence of bacterial wilt of Bottle gourd by R. solanacearum Sequevar 1–48 for the first time in India. Two new biovars (6 and 3b) along with biovar 3 have been found to be prevalent in West Bengal. Under West Bengal condition, the most predominant Sequevar was I-48 (75%) followed by I-47 (25%). Low genetic variation (18.9%) among agro climatic zones (ACZs) compared to high genetic variation (81.1%) within revealed occurrence of gene flow among these ACZs. Standard genetic diversity indices based on the concatenated sequences of the seven genes revealed ACZ-6 as highly diverse among five agro climatic zones. The multi locus sequence analysis illustrated occurrence of synonymous or purifying selection in the selected genes in West Bengal and across world. Under West Bengal conditions maximum nucleotide diversity was observed for the gene gyrB. Occurrence of significant recombination was confirmed by pairwise homoplasy test (θ = 0.47*) among the RSSC isolates of West Bengal, belonging to Phylotype I. Phylotype I isolates of West Bengal are involved in exchange of genetic material with Phylotype II isolates. In case of worldwide RSSC collection, eleven significant recombination events were observed among the five phylotypes. Phylotype IV was genetically most diverse among all the Phylotypes. The most recombinogenic phylotype was Phylotype III. Further, the most diverse gene contributing to the evolution of RSSC worldwide was observed to be endoglucanase (egl).
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Affiliation(s)
- Ankit Kumar Ghorai
- Department of Plant Pathology, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, India
| | - Subrata Dutta
- Department of Plant Pathology, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, India
| | - Ashis Roy Barman
- Department of Plant Pathology, RRS (CSZ), Bidhan Chandra Krishi Viswavidyalaya, Akshaynagar, Kakdwip, South 24-Parganas, India
- * E-mail:
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Son HF, Ahn JW, Hong J, Seok J, Jin KS, Kim KJ. Crystal structure of multi-functional enzyme FadB from Cupriavidus necator: Non-formation of FadAB complex. Arch Biochem Biophys 2022; 730:109391. [PMID: 36087768 DOI: 10.1016/j.abb.2022.109391] [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: 05/19/2022] [Revised: 08/14/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022]
Abstract
Cupriavidus necator H16 is a gram-negative chemolithoautotrophic bacterium that has been extensively studied for biosynthesis and biodegradation of polyhydroxyalkanoate (PHA) plastics. To improve our understanding of fatty acid metabolism for PHA production, we determined the crystal structure of multi-functional enoyl-CoA hydratase from Cupriavidus necator H16 (CnFadB). The predicted model of CnFadB created by AlphaFold was used to solve the phase problem during determination of the crystal structure of the protein. The CnFadB structure consists of two distinctive domains, an N-terminal enol-CoA hydratase (ECH) domain and a C-terminal 3-hydroxyacyl-CoA dehydrogenase (HAD) domain, and the substrate- and cofactor-binding modes of these two functional domains were identified. Unlike other known FadB enzymes that exist as dimers complexed with FadA, CnFadB functions as a monomer without forming a complex with CnFadA. Small angle X-ray scattering (SAXS) measurement further proved that CnFadB exists as a monomer in solution. The non-sequential action of FadA and FadB in C. necator appears to affect β-oxidation and PHA synthesis/degradation.
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Affiliation(s)
- Hyeoncheol Francis Son
- Clean Energy Research Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Jae-Woo Ahn
- Postech Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea; Center for Biomolecular Capture Technology, Bio Open Innovation Center, Pohang University of Science and Technology, 47 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jiyeon Hong
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea
| | - Jihye Seok
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, 80 Jigokro-127-beongil, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea.
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Tian X, Jing N, Duan W, Wu X, Zhang C, Wang S, Yan T. Septic Shock After Kidney Transplant: A Rare Bloodstream Ralstonia mannitolilytica Infection. Infect Drug Resist 2022; 15:3841-3845. [PMID: 35899082 PMCID: PMC9309314 DOI: 10.2147/idr.s370170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/29/2022] [Indexed: 11/25/2022] Open
Abstract
Background Ralstonia mannitolilytica, an emerging opportunistic pathogen, can infect immunocompromised patients but is a rare cause of severe sepsis and septic shock in kidney transplant recipients (KTRs). Case Presentation We present a case of septic shock after renal transplant in a 41-year-old male, which was finally proven to be caused by Ralstonia mannitolilytica through blood cultures and mass spectrometric analysis following the negative result of metagenomic next-generation sequencing (mNGS). He was finally cured after the application of sensitive antibiotics (sulfamethoxazole-trimethoprim, amikacin and piperacillin-tazobactam) based on the drug sensitivity test results. The patient had a satisfactory recovery with no complications during a 6-month follow-up period. Conclusion This study highlights that Ralstonia mannitolilytica is an easily overlooked cause of septic shock in KTRs requiring a detailed inquiry of medical history with inflammatory markers monitored closely. Traditional blood cultures still should be taken seriously. It also provides a cautionary tale that negative results of mNGS have to be interpreted with caution.
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Affiliation(s)
- Xiangyong Tian
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, People's Republic of China
| | - Nan Jing
- Department of Clinical Microbiology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, People's Republic of China
| | - Wenjing Duan
- Department of the Clinical Research Center, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, People's Republic of China
| | - Xiaoqiang Wu
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, People's Republic of China
| | - Chan Zhang
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, People's Republic of China
| | - Shanmei Wang
- Department of Clinical Microbiology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, People's Republic of China
| | - Tianzhong Yan
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, People's Republic of China
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Tüzemen NÜ, Önal U, Kazak E, Tezgeç N, Eren H, Şimşek H, Bakkaloğlu Z, Ünaldı Ö, Çelebi S, Yılmaz E, Hacımustafaoğlu M, Akalın EH, Özakın C. An outbreak of Ralstonia insidiosa bloodstream infections caused by contaminated heparinized syringes. J Infect Chemother 2022; 28:1387-1392. [PMID: 35760221 DOI: 10.1016/j.jiac.2022.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 10/17/2022]
Abstract
INTRODUCTION Ralstonia insidiosa, a gram-negative waterborne bacteria able to survive and grow in any type of water source, can cause nosocomial infections, and are considered emerging pathogens of infectious diseases in hospital settings. In this study, we report an outbreak of R. insidiosa at our center related to contaminated heparinized syringes. MATERIAL AND METHODS The present study was conducted in a tertiary care university hospital in Turkey. An outbreak analysis was performed between September 2021 and December 2021. Microbiological samples were obtained from environmental sources and from patient blood cultures. Species identification was performed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). To investigate the clonality of strains, all confirmed isolates were sent to the National Reference Laboratory and pulsed-field gel electrophoresis (PFGE) was used to perform molecular typing. RESULTS Seventeen R. insidiosa isolates were identified from the blood cultures of 13 patients from various wards and intensive care units. Isolates from seven patient blood cultures and two heparinized blood gas syringes were characterized by PFGE. All isolates were found to belong to the same clone of R. insidiosa. CONCLUSION R. insidiosa was identified as the cause of a nosocomial infection outbreak in our hospital, which was then rapidly controlled by the infection-control team. When rare waterborne microorganisms grow in blood or other body fluid cultures, clinicians and the infection-control team should be made aware of a possible outbreak.
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Affiliation(s)
- Nazmiye Ülkü Tüzemen
- Department of Medical Microbiology, Bursa Uludag University, Faculty of Medicine, Bursa, Turkey.
| | - Uğur Önal
- Department of Infectious Diseases and Clinical Microbiology, Bursa Uludag University, Faculty of Medicine, Bursa, Turkey.
| | - Esra Kazak
- Department of Infectious Diseases and Clinical Microbiology, Bursa Uludag University, Faculty of Medicine, Bursa, Turkey.
| | - Nergiz Tezgeç
- Infection Control Team, Bursa Uludag University, Faculty of Medicine, Bursa, Turkey.
| | - Hale Eren
- Infection Control Team, Bursa Uludag University, Faculty of Medicine, Bursa, Turkey.
| | - Hüsniye Şimşek
- Ministry of Health General Directorate of Public Health, Department of Microbiology Reference Laboratory and Biological Products, Ankara, Turkey.
| | - Zekiye Bakkaloğlu
- Ministry of Health General Directorate of Public Health, Department of Microbiology Reference Laboratory and Biological Products, Ankara, Turkey.
| | - Özlem Ünaldı
- Ministry of Health General Directorate of Public Health, Department of Microbiology Reference Laboratory and Biological Products, Ankara, Turkey.
| | - Solmaz Çelebi
- Department of Pediatric Infectious Disease, Bursa Uludag University, Faculty of Medicine, Bursa, Turkey.
| | - Emel Yılmaz
- Department of Infectious Diseases and Clinical Microbiology, Bursa Uludag University, Faculty of Medicine, Bursa, Turkey.
| | - Mustafa Hacımustafaoğlu
- Department of Pediatric Infectious Disease, Bursa Uludag University, Faculty of Medicine, Bursa, Turkey.
| | - Emin Halis Akalın
- Department of Infectious Diseases and Clinical Microbiology, Bursa Uludag University, Faculty of Medicine, Bursa, Turkey.
| | - Cüneyt Özakın
- Department of Medical Microbiology, Bursa Uludag University, Faculty of Medicine, Bursa, Turkey.
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Lee S, Chakma N, Joung S, Lee JM, Lee J. QTL Mapping for Resistance to Bacterial Wilt Caused by Two Isolates of Ralstonia solanacearum in Chili Pepper (Capsicum annuum L.). PLANTS 2022; 11:plants11121551. [PMID: 35736702 PMCID: PMC9229654 DOI: 10.3390/plants11121551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022]
Abstract
Bacterial wilt caused by the β-proteobacterium Ralstonia solanacearum is one of the most destructive soil-borne pathogens in peppers (Capsicum annuum L.) worldwide. Cultivated pepper fields in Korea face a continuous spread of this pathogen due to global warming. The most efficient and sustainable strategy for controlling bacterial wilt is to develop resistant pepper varieties. Resistance, which is quantitatively inherited, occurs differentially depending on R. solanacearum isolates. Therefore, in this study, we aimed to identify resistance quantitative trait loci (QTLs) in two F2 populations derived from self-pollination of a highly resistant pepper cultivar ‘Konesian hot’ using a moderately pathogenic ‘HS’ isolate and a highly pathogenic ‘HWA’ isolate of R. solanacearum for inoculation, via genotyping-by-sequencing analysis. QTL analysis revealed five QTLs, Bwr6w-7.2, Bwr6w-8.1, Bwr6w-9.1, Bwr6w-9.2, and Bwr6w-10.1, conferring resistance to the ‘HS’ isolate with R2 values of 13.05, 12.67, 15.07, 10.46, and 9.69%, respectively, and three QTLs, Bwr6w-5.1, Bwr6w-6.1, and Bwr6w-7.1, resistant to the ‘HWA’ isolate with phenotypic variances of 19.67, 16.50, and 12.56%, respectively. Additionally, six high-resolution melting (HRM) markers closely linked to the QTLs were developed. In all the markers, the mean disease index of the paternal genotype was significantly lower than that of the maternal genotype. The QTLs and HRM markers are expected to be useful for the development of pepper varieties with high resistance to bacterial wilt.
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Affiliation(s)
- Saeyoung Lee
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea; (S.L.); (N.C.); (S.J.)
| | - Nidhi Chakma
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea; (S.L.); (N.C.); (S.J.)
| | - Sunjeong Joung
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea; (S.L.); (N.C.); (S.J.)
| | - Je Min Lee
- Department of Horticultural Science, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Korea;
| | - Jundae Lee
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea; (S.L.); (N.C.); (S.J.)
- Correspondence: ; Tel.: +82-63-270-2560
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Cyle KT, Klein AR, Aristilde L, Martínez CE. Dynamic utilization of low-molecular-weight organic substrates across a microbial growth rate gradient. J Appl Microbiol 2022; 133:1479-1495. [PMID: 35665577 DOI: 10.1111/jam.15652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 11/28/2022]
Abstract
AIM Low-molecular-weight organic substances (LMWOSs) are at the nexus between microorganisms, plant roots, detritus, and the soil mineral matrix. Nominal oxidation state of carbon (NOSC) has been suggested a potential parameter for modeling microbial uptake rates of LMWOSs and the efficiency of carbon incorporation into new biomass. METHODS AND RESULTS In this study, we assessed the role of compound class and oxidation state on uptake kinetics and substrate-specific carbon use efficiency (SUE) during the growth of three model soil microorganisms, a fungal isolate (Penicillium spinulosum) and two bacterial isolates (Paraburkholderia solitsugae, and Ralstonia pickettii). Isolates were chosen that spanned a growth rate gradient (0.046-0.316 h-1 ) in media containing 34 common LMWOSs at realistically low initial concentrations (25 μM each). Clustered, co-utilization of LMWOSs occurred for all three organisms. Potential trends (p < 0.05) for early utilization of more oxidized substrates were present for the two bacterial isolates (P. solitsugae and R. pickettii), but high variability (R2 < 0.15) and a small effect of NOSC indicate these relationships are not useful for prediction. The SUEs of selected substrates ranged from 0.16-0.99 and there was no observed relationship between NOSC and SUE. CONCLUSION Our results do not provide compelling population-level support for NOSC as a predictive tool for either uptake kinetics or the efficiency of use of LMWOS in soil solution. SIGNIFICANCE AND IMPACT OF THE STUDY Metabolic strategies of organisms are likely more important than chemical identity in determining LMWOS cycling in soils. Previous community-level observations may be biased towards fast-responding bacterial community members.
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Affiliation(s)
- K Taylor Cyle
- Soil and Crop Sciences, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Annaleise R Klein
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853.,Australian Synchrotron, Australian Nuclear Science and Technology Organisation, Clayton, VIC 3168, Australia
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853.,Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - Carmen Enid Martínez
- Soil and Crop Sciences, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
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Ferraz Helene LC, Klepa MS, Hungria M. New Insights into the Taxonomy of Bacteria in the Genomic Era and a Case Study with Rhizobia. Int J Microbiol 2022; 2022:4623713. [PMID: 35637770 PMCID: PMC9148247 DOI: 10.1155/2022/4623713] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/09/2022] [Indexed: 12/15/2022] Open
Abstract
Since early studies, the history of prokaryotes taxonomy has dealt with many changes driven by the development of new and more robust technologies. As a result, the number of new taxa descriptions is exponentially increasing, while an increasing number of others has been subject of reclassification, demanding from the taxonomists more effort to maintain an organized hierarchical system. However, expectations are that the taxonomy of prokaryotes will acquire a more stable status with the genomic era. Other analyses may continue to be necessary to determine microbial features, but the use of genomic data might be sufficient to provide reliable taxa delineation, helping taxonomy to reach the goal of correct classification and identification. Here we describe the evolution of prokaryotes' taxonomy until the genomic era, emphasizing bacteria and taking as an example the history of rhizobia taxonomy. This example was chosen because of the importance of the symbiotic nitrogen fixation of legumes with rhizobia to the nitrogen input to both natural ecosystems and agricultural crops. This case study reports the technological advances and the methodologies used to classify and identify bacterial species and indicates the actual rules required for an accurate description of new taxa.
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Affiliation(s)
- Luisa Caroline Ferraz Helene
- Embrapa Soja, CP 4006, 86085-981 Londrina, PR, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, DF, Brazil
| | - Milena Serenato Klepa
- Embrapa Soja, CP 4006, 86085-981 Londrina, PR, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, CP 10011, 86057-970 Londrina, PR, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70040-020 Brasília, DF, Brazil
| | - Mariangela Hungria
- Embrapa Soja, CP 4006, 86085-981 Londrina, PR, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, DF, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, CP 10011, 86057-970 Londrina, PR, Brazil
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Khairy AM, Tohamy MRA, Zayed MA, Mahmoud SF, El-Tahan AM, El-Saadony MT, Mesiha PK. Eco-friendly application of nano-chitosan for controlling potato and tomato bacterial wilt. Saudi J Biol Sci 2022; 29:2199-2209. [PMID: 35531227 PMCID: PMC9073058 DOI: 10.1016/j.sjbs.2021.11.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/01/2021] [Accepted: 11/17/2021] [Indexed: 02/02/2023] Open
Abstract
Bacterial wilt is one of the main diseases of Solanum spp., which caused by Ralstonia solanacearum (RS), formerly known as Pseudomonas solanacearum. Different concentrations of chitosan nanoparticles have been evaluated as one of the alternative methods of disease management in vitro and in vivo to reduce the risks of pesticide residues. Results in vitro experiment indicated that RS5 isolate was the most virulence one compared to RS1 and RS3. Increasing concentration of nano-chitosan, lead to increase inhibition zone, and this was observed at higher concentrations (100 and 200 µg/ml). In vivo results showed the highest concentration of spraying chitosan nanoparticles increase percentage reduction of disease incidence and severity, in effected potato and tomato plants. Recorded data of disease incidence and severity in treated potato plants were 78.93% and 71.85%, while on tomato plants were 81.64% and 77.63%, respectively compared to untreated infected potato plants were recorded 15.38%, 20.87%, and tomato plants were 20.98% and 28.64%. Results also revealed that 100 µg/ml of chitosan nanoparticles the lowest treatments used as soil amended curative treatments led to incease percentage reduction of disease incidence and severity, respectively on potato and tomato plants, but less than preventive treatment. The results registered that on potato plant were 54.93% and 52.65%, whilst recorded on tomato plants were 59.93% and 56.74%. Transmission electron microscopy (TEM) micrpgraphs illustrated that morphological of healthy R. solanacearum cells were undesirably stained with uranyl. The electron-dense uranyl acetate dye was limited to the cell surface slightly than the cytoplasm, which designated the integrity of the cell film of healthy cells. While bacterial cells treated with nano-chitosan, showed modification in the external shape, such as lysis of the cell wall and loss of cell flagella. Also, the result of using Random amplified polymorphic DNA (RAPD)-PCR observed that differences in treated Ralstonia solanancearum genotype by nano-chitosan compared to the genotype of the same untreated isolate.
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Affiliation(s)
- Ahmed M Khairy
- Plant Pathology Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Mohamed R A Tohamy
- Plant Pathology Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Mohamed A Zayed
- Plant Pathology Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Samy F Mahmoud
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Amira M El-Tahan
- Plant Production Department, Arid Lands Cultivation Research Institute, The City of Scientific Research and Technological Applications, SRTA-City. Borg El Arab, Alexandria, Egypt
| | - Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Phelimon K Mesiha
- Plant Pathology Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
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Alderley CL, Greenrod STE, Friman V. Plant pathogenic bacterium can rapidly evolve tolerance to an antimicrobial plant allelochemical. Evol Appl 2022; 15:735-750. [PMID: 35603031 PMCID: PMC9108312 DOI: 10.1111/eva.13363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/13/2021] [Accepted: 02/10/2022] [Indexed: 11/30/2022] Open
Abstract
Crop losses to plant pathogens are a growing threat to global food security and more effective control strategies are urgently required. Biofumigation, an agricultural technique where Brassica plant tissues are mulched into soils to release antimicrobial plant allelochemicals called isothiocyanates (ITCs), has been proposed as an environmentally friendly alternative to agrochemicals. Whilst biofumigation has been shown to suppress a range of plant pathogens, its effects on plant pathogenic bacteria remain largely unexplored. Here, we used a laboratory model system to compare the efficacy of different types of ITCs against Ralstonia solanacearum plant bacterial pathogen. Additionally, we evaluated the potential for ITC-tolerance evolution under high, intermediate, and low transfer frequency ITC exposure treatments. We found that allyl-ITC was the most efficient compound at suppressing R. solanacearum growth, and its efficacy was not improved when combined with other types of ITCs. Despite consistent pathogen growth suppression, ITC tolerance evolution was observed in the low transfer frequency exposure treatment, leading to cross-tolerance to ampicillin beta-lactam antibiotic. Mechanistically, tolerance was linked to insertion sequence movement at four positions in genes that were potentially associated with stress responses (H-NS histone like protein), cell growth and competitiveness (acyltransferase), iron storage ([2-Fe-2S]-binding protein) and calcium ion sequestration (calcium-binding protein). Interestingly, pathogen adaptation to the growth media also indirectly selected for increased ITC tolerance through potential adaptations linked with metabolism and antibiotic resistance (dehydrogenase-like protein) and transmembrane protein movement (Tat pathway signal protein). Together, our results suggest that R. solanacearum can rapidly evolve tolerance to allyl-ITC plant allelochemical which could constrain the long-term efficiency of biofumigation biocontrol and potentially shape pathogen evolution with plants.
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Abd-Elrahim R, Tohamy MR, Atia MM, Elashtokhy MM, Ali MA. Bactericidal activity of some plant essential oils against Ralstonia solanacearum infection. Saudi J Biol Sci 2022; 29:2163-2172. [PMID: 35531193 PMCID: PMC9073021 DOI: 10.1016/j.sjbs.2021.11.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/21/2021] [Accepted: 11/17/2021] [Indexed: 11/21/2022] Open
Abstract
Potato plants and their tubers in Egypt are affected by one of the most renowned soil-borne pathogen, Ralstonia solanacearum, that caused brown rot in potato tubers and wilt in plants. There is no efficient therapeutic bactericide so; control of bacterial wilt is very rough. The study investigated three different concentrations of seven essential plant oils under in vitro and in vivo conditions as a result of their effects on Ralstonia solanacearum growth and their possibility use as potato seed pieces dressing for controlling bacterial wilt disease incidence. In vitro, anise oil at the three tested different concentrations (0.04, 0.07, and 0.14% vol/vol) was the most effective one inhibiting the growth of T4 and W9 isolates of Ralstonia solanacearum then pursued by thyme, lemongrass, and clove oils. On the other hand, rocket oil at the tested concentration was the least effective one followed by fennel oil. However, wheat germ oil was not completely effective. In vivo, experiment revealed that anise oil at the three concentrations significantly reduced disease incidence and severity in sponta and hermes potato cultivars and their effect was associated with increase of peroxidase, polyphenoloxidase, phenols and the foliar fresh weight of treated plants as well as the weight of tubers/plant followed by thyme and lemongrass oils compared to the infected untreated control. Morphological differences in bacterial cell structure have been observed using a transmission electron microscope (TEM). Anise oil at higher concentration caused of cell wall rupture and degraded cellular components.
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Affiliation(s)
- Rahma Abd-Elrahim
- Plant Pathology Dept., Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Mohamed R.A. Tohamy
- Plant Pathology Dept., Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Mahmoud M. Atia
- Plant Pathology Dept., Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | | | - Mohamed A.S. Ali
- Plant Pathology Dept., Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
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Jovicevic MI, Unic-Stojanovic DR, Djukic SV, Brkic SS, Djokovic IL, Rankovic-Nicic LD, Tanaskovic SZ, Cirkovic IB. Ralstonia pickettii bacteremia in a cardiac surgery patient in Belgrade, Serbia. Acta Microbiol Immunol Hung 2022. [PMID: 35298410 DOI: 10.1556/030.2022.01703] [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: 01/03/2022] [Accepted: 02/28/2022] [Indexed: 11/19/2022]
Abstract
Ralstonia pickettii is an opportunistic bacterium found in the water environment with an increasing incidence as a nosocomial pathogen. The objectives of this study were to describe R. pickettii bacteremia in a cardiac surgery patient and to evaluate its ability to grow in a saline solution and to form biofilm. The patient in this study underwent mitral and aortic valve replacement surgery with two aortocoronary bypasses. She developed signs of respiratory and renal failure, therefore hemodialysis was started. After 25 days in an intensive care unit, the patient had recurrent episodes of fever with signs of bacteremia. R. pickettii was identified from blood cultures by MALDI-TOF MS. Antimicrobial susceptibility testing was performed using disc diffusion and broth microdilution methods in accordance with EUCAST methodology and results were interpreted following clinical breakpoints for Pseudomonas spp. The isolate was susceptible to all tested antimicrobial agents except aminoglycosides and colistin. Survival of R. pickettii was analyzed in saline solution with four different starting concentrations at 25 °C and 37 °C for six days. Biofilm capacity was tested using the microtiter plate method. R. pickettii showed substantial growth in saline solution, with starting concentration of 2 CFU ml-1 reaching 107 CFU ml-1 after six days. There was no significant difference between growth at 25 °C and 37 °C. This indicates that storage of contaminated solutions at room temperature can enhance the count of R. pickettii. Our strain did not show the capacity to form biofilm. The patient responded well to adequate treatment with ceftazidime, and after 48 days in ICU she was discharged to convalesce.
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Affiliation(s)
- Milos I Jovicevic
- 1 University of Belgrade - Faculty of Medicine, Institute of Microbiology and Immunology, Belgrade, Serbia
| | - Dragana R Unic-Stojanovic
- 2 Cardiovascular Institute Dedinje, Belgrade, Serbia
- 3 University of Belgrade - Faculty of Medicine, Belgrade, Serbia
| | - Slobodanka V Djukic
- 1 University of Belgrade - Faculty of Medicine, Institute of Microbiology and Immunology, Belgrade, Serbia
| | - Snezana S Brkic
- 4 Institute for Laboratory Diagnostics "Konzilijum", Belgrade, Serbia
| | | | | | - Slobodan Z Tanaskovic
- 2 Cardiovascular Institute Dedinje, Belgrade, Serbia
- 3 University of Belgrade - Faculty of Medicine, Belgrade, Serbia
| | - Ivana B Cirkovic
- 1 University of Belgrade - Faculty of Medicine, Institute of Microbiology and Immunology, Belgrade, Serbia
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Chauhan P, Gupta A, Sahu C, Desai N, Nityanand S. Outbreak of Ralstonia mannitolilytica Infection in Hemato-Oncology Unit: Case Series and Review of Literature. Indian J Med Paediatr Oncol 2022. [DOI: 10.1055/s-0042-1742448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Abstract
Ralstonia mannitolilytica is a Gram-negative, nonfermentative, soil bacterium that is reported to cause opportunistic infections in immunocompromised patients in nosocomial settings. After extensive review of literature, it was found that this is second outbreak reported from India. This study is a retrospective analysis of the clinical features, outcome, and source identification of R. mannitolilytica infection outbreak in a hemato-oncology unit of a tertiary care center of North India between February 2020 and March 2020. We report an outbreak of R. mannitolilytica bacteremia (with or without septic shock) in five patients admitted in hemato-oncology unit at a tertiary care institute in North India for 1 month period. Four patients were cured after administration of appropriate antibiotics as per sensitivity reports, while one patient died of septicemia due to delayed diagnosis. Environmental cultures revealed multidose saline bottles used for administration of drugs as the source of outbreak. Following implementation of use of single dose diluents and flushing solutions in patients with central venous catheter, no new case was reported. Clinicians and microbiologists should keep high index of suspicion to identify these organisms as timely diagnosis is the only key to improve outcomes.
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Affiliation(s)
- Priyanka Chauhan
- Department of Haematology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Anshul Gupta
- Department of Haematology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Chinmoy Sahu
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Nihar Desai
- Department of Haematology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Soniya Nityanand
- Department of Haematology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
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Chen K, He R, Wang L, Liu L, Huang X, Ping J, Huang C, Wang X, Liu Y. The dominant microbial metabolic pathway of the petroleum hydrocarbons in the soil of shale gas field: Carbon fixation instead of CO 2 emissions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151074. [PMID: 34678370 DOI: 10.1016/j.scitotenv.2021.151074] [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: 07/19/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 05/20/2023]
Abstract
In shale gas mining areas, indigenous microorganisms degrade organic pollutants such as petroleum hydrocarbons into carbon dioxide (CO2) and water (H2O) through aerobic metabolism. A large quantity of CO2 emissions will exacerbate the "Greenhouse effect". Based on the clean sieved soil and oil-based drilling fluid in the shale gas mining area, this experiment set three concentration gradients (3523 ± 159 mg/kg, 8715 ± 820 mg/kg and 22,031 ± 1533 mg/kg) to treat the soil, and each group was disposed for the same amount of time (63 days). By analyzing the dynamic changes of microbial diversity and the abundance of key functional genes for carbon fixation, the impact of petroleum hydrocarbons on carbon fixation potential was discovered, and the natural attenuation law of petroleum hydrocarbons in contaminated soil was explored. It provided the scientific research basis of ecology for the carbon cycle, carbon allocation, and carbon fixation in microbial remediation of petroleum hydrocarbon contaminated soil. The results obtained indicated the following: i) The removal rate of petroleum hydrocarbons under high-concentration pollution (45.33 ± 3.90%) was significantly lower than low and medium-concentration pollution. The TPH concentration removal rate of each group was the largest in the early stage of culture (1-5d), and there was no significant correlation between the TPH content and the community composition (R2 = 0.0736, P > 0.05). ii) Composition and function of Carbon Fixation associated microbiota were assessed by 16S rRNA sequencing and PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) analysis. The main carbon fixation pathway in this study is the reductive citric acid cycle, because there was no shortage of enzymes that can affect subsequent reactions.
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Affiliation(s)
- Kejin Chen
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Rong He
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Li'ao Wang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Lingyue Liu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Xin Huang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Juan Ping
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Chuan Huang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Xiang Wang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China.
| | - Yuanyuan Liu
- College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China.
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Viability, Stability and Biocontrol Activity in Planta of Specific Ralstonia solanacearum Bacteriophages after Their Conservation Prior to Commercialization and Use. Viruses 2022; 14:v14020183. [PMID: 35215777 PMCID: PMC8876693 DOI: 10.3390/v14020183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 02/04/2023] Open
Abstract
Ralstonia solanacearum is a pathogen that causes bacterial wilt producing severe damage in staple solanaceous crops. Traditional control has low efficacy and/or environmental impact. Recently, the bases of a new biotechnological method by lytic bacteriophages vRsoP-WF2, vRsoP-WM2 and vRsoP-WR2 with specific activity against R. solanacearum were established. However, some aspects remain unknown, such as the survival and maintenance of the lytic activity after submission to a preservation method as the lyophilization. To this end, viability and stability of lyophilized vRsoP-WF2, vRsoP-WM2 and vRsoP-WR2 and their capacity for bacterial wilt biocontrol have been determined against one pathogenic Spanish reference strain of R. solanacearum in susceptible tomato plants in different conditions and making use of various cryoprotectants. The assays carried out have shown satisfactory results with respect to the viability and stability of the bacteriophages after the lyophilization process, maintaining high titers throughout the experimental period, and with respect to the capacity of the bacteriophages for the biological control of bacterial wilt, controlling this disease in more than 50% of the plants. The results offer good prospects for the use of lyophilization as a conservation method for the lytic bacteriophages of R. solanacearum in view of their commercialization as biocontrol agents.
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Lu CH, Li JY, Mi MG, Lin ZL, Jiang N, Gai XT, Jun-Hong M, Lei LP, Xia ZY. Complete Genome Sequence of Ralstonia syzygii subsp. indonesiensis Strain LLRS-1, Isolated from Wilted Tobacco in China. PHYTOPATHOLOGY 2021; 111:2392-2395. [PMID: 34100304 DOI: 10.1094/phyto-04-21-0138-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Here, we present the complete genome sequence and annotation of Ralstonia syzygii subsp. indonesiensis strain LLRS-1, which caused bacterial wilt on flue-cured tobacco in Yunnan Province, southwest China. Strain LLRS-1 is the first R. syzygii strain identified to be pathogenic to tobacco in China. The completely assembled genome of strain LLRS-1 consists of a 3,648,314-bp circular chromosome and a 2,046,405-bp megaplasmid with 5,190 protein-coding genes, 55 transfer RNAs, 28 small RNAs, 3 structural RNAs (5S, 16S, and 23S), and a G+C content of 67.05%.
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Affiliation(s)
- Can-Hua Lu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021 China
| | - Jun-Ying Li
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021 China
| | - Meng-Ge Mi
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300384, China
| | - Zhong-Long Lin
- China National Tobacco Corporation Yunnan Company, Kunming, 650011 China
| | - Ning Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021 China
| | - Xiao-Tong Gai
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021 China
| | - Ma Jun-Hong
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021 China
| | - Li-Ping Lei
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021 China
| | - Zhen-Yuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021 China
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Michail G, Karapetsi L, Madesis P, Reizopoulou A, Vagelas I. Metataxonomic Analysis of Bacteria Entrapped in a Stalactite's Core and Their Possible Environmental Origins. Microorganisms 2021; 9:microorganisms9122411. [PMID: 34946013 PMCID: PMC8705861 DOI: 10.3390/microorganisms9122411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 02/02/2023] Open
Abstract
Much is known about microbes originally identified in caves, but little is known about the entrapment of microbes (bacteria) in stalactites and their possible environmental origins. This study presents data regarding the significant environmental distribution of prokaryotic bacterial taxa of a Greek stalactite core. We investigated the involvement of those bacteria communities in stalactites using a metataxonomic analysis approach of partial 16S rRNA genes. The metataxonomic analysis of stalactite core material revealed an exceptionally broad ecological spectrum of bacteria classified as members of Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and other unclassified bacteria. We concluded that (i) the bacterial transport process is possible through water movement from the upper ground cave environment, forming cave speleothems such as stalactites, (ii) bacterial genera such as Polaromonas, Thioprofundum, and phylum Verrucomicrobia trapped inside the stalactite support the paleoecology, paleomicrobiology, and paleoclimate variations, (iii) the entrapment of certain bacteria taxa associated with water, soil, animals, and plants such as Micrococcales, Propionibacteriales, Acidimicrobiales, Pseudonocardiales, and α-, β-, and γ-Proteobacteria.
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Affiliation(s)
- George Michail
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
- Correspondence:
| | - Lefkothea Karapetsi
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece; (L.K.); (P.M.)
- Centre for Research and Technology (CERTH), Institute of Applied Biosciences (INAB), 57001 Thessaloniki, Greece
| | - Panagiotis Madesis
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece; (L.K.); (P.M.)
- Centre for Research and Technology (CERTH), Institute of Applied Biosciences (INAB), 57001 Thessaloniki, Greece
| | | | - Ioannis Vagelas
- Department of Agriculture Crop Production and Rural Environment, University of Thessaly, 38446 Volos, Greece;
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Influence of Silicon on Biocontrol Strategies to Manage Biotic Stress for Crop Protection, Performance, and Improvement. PLANTS 2021; 10:plants10102163. [PMID: 34685972 PMCID: PMC8537781 DOI: 10.3390/plants10102163] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022]
Abstract
Silicon (Si) has never been acknowledged as a vital nutrient though it confers a crucial role in a variety of plants. Si may usually be expressed more clearly in Si-accumulating plants subjected to biotic stress. It safeguards several plant species from disease. It is considered as a common element in the lithosphere of up to 30% of soils, with most minerals and rocks containing silicon, and is classified as a "significant non-essential" element for plants. Plant roots absorb Si, which is subsequently transferred to the aboveground parts through transpiration stream. The soluble Si in cytosol activates metabolic processes that create jasmonic acid and herbivore-induced organic compounds in plants to extend their defense against biotic stressors. The soluble Si in the plant tissues also attracts natural predators and parasitoids during pest infestation to boost biological control, and it acts as a natural insect repellent. However, so far scientists, policymakers, and farmers have paid little attention to its usage as a pesticide. The recent developments in the era of genomics and metabolomics have opened a new window of knowledge in designing molecular strategies integrated with the role of Si in stress mitigation in plants. Accordingly, the present review summarizes the current status of Si-mediated plant defense against insect, fungal, and bacterial attacks. It was noted that the Si-application quenches biotic stress on a long-term basis, which could be beneficial for ecologically integrated strategy instead of using pesticides in the near future for crop improvement and to enhance productivity.
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Characterization of clinical Ralstonia strains and their taxonomic position. Antonie van Leeuwenhoek 2021; 114:1721-1733. [PMID: 34463860 PMCID: PMC8448721 DOI: 10.1007/s10482-021-01637-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 08/03/2021] [Indexed: 12/03/2022]
Abstract
To improve understanding of the role of Ralstonia in cystic fibrosis (CF), whole genomes of 18 strains from clinical samples were sequenced using Illumina technology. Sequences were analysed by core genome Multi-Locus Sequence Typing, Average Nucleotide Identity based on BLAST (ANIb), RAST annotation, and by ResFinder. Phylogenetic analysis was performed for the 16S rRNA gene, and the OXA-22 and OXA-60 ß-lactamase families. The minimal inhibitory concentrations (MICs) were determined using broth microdilution. ANIb data for the 18 isolates and 54 strains from GenBank, supported by phylogenetic analysis, showed that 8 groups of clusters (A-H), as well as subgroups that should be considered as species or subspecies. Groups A-C contain strains previously identified as Ralstonia solanacearum and Ralstonia pseudosolanacearum. We propose that group A is a novel species. Group B and C are Ralstonia syzygii, Ralstonia solanacearum, respectively. Group D is composed of Ralstonia mannitolilytica and Group E of Ralstonia pickettii. Group F and G should be considered novel species. Group H strains belong to R. insidiosa. OXA-22 and OXA-60 family ß-lactamases were encoded by all strains. Co-trimoxazole generally showed high activity with low MICs (≤1 mg/l) as did ciprofloxacin (≤0.12 mg/l). MICs against the other antibiotics were more variable, but generally high. RAST annotation revealed limited differences between the strains, and virulence factors were not identified. The taxonomy of the genus Ralstonia is in need of revision, but sequencing additional isolates is needed. Antibiotic resistance levels are high. Annotation did not identify potential virulence factors.
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Pandey A, Moon H, Choi S, Yoon H, Prokchorchik M, Jayaraman J, Sujeevan R, Kang YM, McCann HC, Segonzac C, Kim CM, Park SJ, Sohn KH. Ralstonia solanacearum Type III Effector RipJ Triggers Bacterial Wilt Resistance in Solanum pimpinellifolium. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:962-972. [PMID: 33881922 DOI: 10.1094/mpmi-09-20-0256-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Ralstonia solanacearum causes bacterial wilt disease in solanaceous crops. Identification of avirulence type III-secreted effectors recognized by specific disease resistance proteins in host plant species is an important step toward developing durable resistance in crops. In the present study, we show that R. solanacearum effector RipJ functions as an avirulence determinant in Solanum pimpinellifolium LA2093. In all, 10 candidate avirulence effectors were shortlisted based on the effector repertoire comparison between avirulent Pe_9 and virulent Pe_1 strains. Infection assays with transgenic strain Pe_1 individually carrying a candidate avirulence effector from Pe_9 revealed that only RipJ elicits strong bacterial wilt resistance in S. pimpinellifolium LA2093. Furthermore, we identified that several RipJ natural variants do not induce bacterial wilt resistance in S. pimpinellifolium LA2093. RipJ belongs to the YopJ family of acetyltransferases. Our sequence analysis indicated the presence of partially conserved putative catalytic residues. Interestingly, the conserved amino acid residues in the acetyltransferase catalytic triad are not required for effector-triggered immunity. In addition, we show that RipJ does not autoacetylate its lysine residues. Our study reports the identification of the first R. solanacearum avirulence protein that triggers bacterial wilt resistance in tomato. We expect that our discovery of RipJ as an avirulence protein will accelerate the development of bacterial wilt-resistant tomato varieties in the future.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Ankita Pandey
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Hayoung Moon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Sera Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Hayeon Yoon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Germany
| | - Jay Jayaraman
- New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Auckland 1025, New Zealand
| | - Rajendran Sujeevan
- Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan 54538, Republic of Korea
| | - Yu Mi Kang
- Division of Horticulture Industry, Wonkwang University, Iksan 554438, Republic of Korea
| | - Honour C McCann
- Institute of Advanced Studies, Massey University, Auckland 0745, New Zealand
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Cécile Segonzac
- Department of Plant Science, Plant Genome and Breeding Institute, Agricultural Life Science Research Institute, Seoul National University, 08826, Seoul, Republic of Korea
- Plant Immunity Research Center, Seoul National University, 08826, Seoul, Republic of Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, 08826, Seoul, Republic of Korea
| | - Chul Min Kim
- Division of Horticulture Industry, Wonkwang University, Iksan 554438, Republic of Korea
| | - Soon Ju Park
- Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan 54538, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- School of Interdisciplinary Biosciences and Bioengineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
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