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Mansoor AER, Edathadathil F, Suresh D, Krishna Y, George A, van Rheenen J, George IA, Kwon JH, Petersen EE, Westercamp M, Kumar A, Vayoth SO, Olsen MA, Leekha S, Singh SK, Warren DK, Gandra S. Carbapenem-resistant Enterobacterales peri-rectal colonization prevalence on admission to two intensive care units in an academic hospital in India. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2025; 5:e120. [PMID: 40528929 PMCID: PMC12171904 DOI: 10.1017/ash.2025.10036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Accepted: 04/16/2025] [Indexed: 06/20/2025]
Abstract
This study from a South Indian tertiary care hospital found a 41% peri-rectal Carbapenem-resistant Enterobacterales colonization prevalence at intensive care unit admission, with New Delhi metallo-β-lactamase as the predominant carbapenemase. It underscores the need for contextually appropriate, cost-effective infection prevention strategies to mitigate the spread of resistant organisms in Indian healthcare settings.
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Affiliation(s)
- Armaghan-e-Rehman Mansoor
- Division of Infectious Diseases, Department of Internal Medicine, University of Kentucky, Kentucky, USA
| | | | | | - Yathu Krishna
- Amrita Institute of Medical Sciences, Kochi, KL, India
| | - Anu George
- Amrita Institute of Medical Sciences, Kochi, KL, India
| | - Jacaranda van Rheenen
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, USA
| | - Ige A George
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, USA
| | - Jennie H Kwon
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, USA
| | - Emily E Petersen
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Matthew Westercamp
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anil Kumar
- Amrita Institute of Medical Sciences, Kochi, KL, India
| | | | - Margaret A Olsen
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, USA
| | - Surbhi Leekha
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, USA
| | | | - David K Warren
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, USA
| | - Sumanth Gandra
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, USA
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2
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Iseri E, Jakobsson G, Bertling S, Özenci V, Ekelund O, van der Wijngaart W, van Belkum A. Rapid diagnosis of urinary tract infection with miniaturised point-of-care cultivation on a dipstick. Eur J Clin Microbiol Infect Dis 2025; 44:1031-1040. [PMID: 40063324 DOI: 10.1007/s10096-025-05088-7] [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: 01/14/2025] [Accepted: 02/25/2025] [Indexed: 05/09/2025]
Abstract
PURPOSE Urinary Tract InfectionAQ1 (UTI) affects over 400 million people annually and globally and is a major reason for empiric antibiotic prescription by general practitioners (GPs). BACKGROUND A problem related to microbiological UTI diagnosis is the current lack of point of care (POC) diagnostics. In addition, remote settings, including low and middle income countries (LMIC), are hard to service. Compliance with requirements posed by the In Vitro Diagnostic Regulation (IVDR) and adherence to guidelines as defined by professional user groups are mandatory to pursue. In addition, the World Health Organisation (WHO) promotes optimization of antimicrobial use and more adequate microbiological diagnostics to cure UTI and combat antimicrobial resistance (AMR). METHODS Miniaturised chromogenic bacterial cultivation including rapid antimicrobial susceptibility testing (RAST) at the POC can be successfully used for the diagnosis of UTI. Using small and cost-effective dipsticks containing chromogenic cultivation media, UTI-causing bacteria can be detected, quantified and identified with good sensitivity and specificity. CONCLUSION Access to such trustworthy, easy-to-use and cost-efficient diagnostic tools at the POC would offer more timely results for optimised antibiotic treatment. This will improve UTI therapy and prevent AMR.
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Affiliation(s)
- Emre Iseri
- UtilizerTM AB, Kaptensvägen 5C, 132 46 Saltsjö Boo, Stockholm, Sweden
| | - Gino Jakobsson
- UtilizerTM AB, Kaptensvägen 5C, 132 46 Saltsjö Boo, Stockholm, Sweden
| | - Sofia Bertling
- UtilizerTM AB, Kaptensvägen 5C, 132 46 Saltsjö Boo, Stockholm, Sweden
| | - Volkan Özenci
- Department of Clinical Microbiology, Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, KarolinskaInstitutet, Stockholm, Sweden
| | - Oskar Ekelund
- Clinical Microbiology, Region Kronoberg. National Reference Laboratory for AST. WHO Collaborating Centre, Vaxjo, Sweden
| | - Wouter van der Wijngaart
- Division of Micro and Nanosystems, KTH Royal Institute for Technology, Malvinas Väg 10, Stockholm, Sweden
| | - Alex van Belkum
- Independant Microbiology Advisor, Jan Van Goyenplein 31, 2231 MM, Rijnsburg, The Netherlands.
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Burton M, Garcha A, Marrs ECL, Perry JD, Stanforth SP, Turnbull G, Turner HJ. Chromogenic hydroxyanthraquinone-based enzyme substrates for the detection of microbial β-d-galactosidase, β-d-glucuronidase and β-d-ribosidase. RSC Adv 2025; 15:4229-4235. [PMID: 39926229 PMCID: PMC11804412 DOI: 10.1039/d4ra06418f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 01/29/2025] [Indexed: 02/11/2025] Open
Abstract
Di-β-d-galactopyranoside derivatives of quinizarin (1,4-dihydroxyanthraquinone) and anthrarufin (1,5-dihydroxyanthraquinone) were evaluated as microbial enzyme substrates in Columbia agar medium for the detection of clinically important microorganisms. Furthermore, these substrates were evaluated both in the presence and absence of iron salts which could chelate to the aglycone after microbial hydrolysis of the substrate. The quinizarin-based substrate resulted in the formation of black microbial colonies in the presence of iron salts and orange colonies in their absence. In contrast, yellow-coloured microbial colonies were observed with the anthrarufin-based substrate regardless of whether iron salts were present or not. 1-Hydroxyanthraquinone-β-d-galactopyranoside also resulted in yellow-coloured microbial colonies in the absence of iron salts and an extended study of this substrate using 38 clinical strains of E. coli indicated its potential for identifying this microorganism when compared to a commercially available indoxyl based substrate. 1-Hydroxyanthraquinone-β-d-glucopyranuronide was also evaluated for E. coli detection, but this substrate was deemed less effective than its indoxyl-based counterpart. 1-Hydroxyanthraquinone-β-d-ribofuranoside was evaluated for its potential to detect Pseudomonas aeruginosa and this substrate shows promise for this application.
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Affiliation(s)
- Michael Burton
- Glycosynth Ltd 14 Craven Court, Winwick Quay, Cheshire Warrington WA2 8QU UK
| | - Amy Garcha
- Glycosynth Ltd 14 Craven Court, Winwick Quay, Cheshire Warrington WA2 8QU UK
| | - Emma C L Marrs
- Department of Microbiology, Freeman Hospital Newcastle upon Tyne NE7 7DN UK
| | - John D Perry
- Department of Microbiology, Freeman Hospital Newcastle upon Tyne NE7 7DN UK
- Department of Applied Sciences, Northumbria University Newcastle upon Tyne NE1 8ST UK
| | - Stephen P Stanforth
- Department of Applied Sciences, Northumbria University Newcastle upon Tyne NE1 8ST UK
| | - Graeme Turnbull
- Department of Applied Sciences, Northumbria University Newcastle upon Tyne NE1 8ST UK
| | - Hayley J Turner
- Glycosynth Ltd 14 Craven Court, Winwick Quay, Cheshire Warrington WA2 8QU UK
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Simner PJ, Pitout JDD, Dingle TC. Laboratory detection of carbapenemases among Gram-negative organisms. Clin Microbiol Rev 2024; 37:e0005422. [PMID: 39545731 PMCID: PMC11629623 DOI: 10.1128/cmr.00054-22] [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: 11/17/2024] Open
Abstract
SUMMARYThe carbapenems remain some of the most effective options available for treating patients with serious infections due to Gram-negative bacteria. Carbapenemases are enzymes that hydrolyze carbapenems and are the primary method driving carbapenem resistance globally. Detection of carbapenemases is required for patient management, the rapid implementation of infection prevention and control (IP&C) protocols, and for epidemiologic purposes. Therefore, clinical and public health microbiology laboratories must be able to detect and report carbapenemases among predominant Gram-negative organisms from both cultured isolates and direct from clinical specimens for treatment and surveillance purposes. There is not a "one size fits all" laboratory approach for the detection of bacteria with carbapenemases, and institutions need to determine what fits best with the goals of their antimicrobial stewardship and IP&C programs. Luckily, there are several options and approaches available for clinical laboratories to choose methods that best suits their individual needs. A laboratory approach to detect carbapenemases among bacterial isolates consists of two steps, namely a screening process (e.g., not susceptible to ertapenem, meropenem, and/or imipenem), followed by a confirmation test (i.e., phenotypic, genotypic or proteomic methods) for the presence of a carbapenemase. Direct from specimen testing for the most common carbapenemases generally involves detection via rapid, molecular approaches. The aim of this article is to provide brief overviews on Gram-negative bacteria carbapenem-resistant definitions, types of carbapenemases, global epidemiology, and then describe in detail the laboratory methods for the detection of carbapenemases among Gram-negative bacteria. We will specifically focus on the Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii complex.
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Affiliation(s)
- Patricia J. Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Johann D. D. Pitout
- Cummings School of Medicine, University of Calgary, Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Diagnostic Laboratory, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
| | - Tanis C. Dingle
- Cummings School of Medicine, University of Calgary, Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Public Health Laboratory, Calgary, Alberta, Canada
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Neyaz LA, Arafa SH, Alsulami FS, Ashi H, Elbanna K, Abulreesh HH. Culture-Based Standard Methods for the Isolation of Campylobacter spp. in Food and Water. Pol J Microbiol 2024; 73:433-454. [PMID: 39670639 PMCID: PMC11639288 DOI: 10.33073/pjm-2024-046] [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: 09/13/2024] [Accepted: 11/11/2024] [Indexed: 12/14/2024] Open
Abstract
Campylobacter spp. is a major source of global gastrointestinal infections. Their enteric infections are linked to the consumption of undercooked poultry products, contaminated milk and water, and the handling of wild animals and birds. The detection of Campylobacter spp. in water and food samples mainly depends on culture-based techniques. Public Health England (PHE), the U.S. Food and Drug Administration (FDA), and the International Standard Organization (ISO) have standardized Campylobacter spp. isolation and enumeration procedures for food and water samples, which involve the usage of selective agar media and enrichment broth. Different types of selective plating and enrichment media have been prepared for Campylobacter spp. detection and assessment during regular food surveillance and food poisoning. To date, culture media remains the standard option for microbiological food analysis and has been approved by the U.S. Environmental Protection Agency (US EPA), Food and Agriculture Organization (FAO), and World Health Organization (WHO). This review discusses the standard microbiological protocols for Campylobacter spp. isolation and enumeration in food and water and evaluates detection media (pre-enrichment, selective enrichment, and selective plating) for their rational applications. Moreover, it also elaborates on the advantages and disadvantages of recent chromogenic culture media in Campylobacter spp.-oriented food surveillance. This review also highlights the challenges of culture-based techniques, future developments, and alternative methods for Campylobacter spp. detection in food and water samples.
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Affiliation(s)
- Leena A. Neyaz
- Department of Biology, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
- Research Laboratories Unit, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sara H. Arafa
- Department of Biology, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
- Research Laboratories Unit, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Fatimah S. Alsulami
- Department of Biology, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
- Research Laboratories Unit, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Hayat Ashi
- Department of Biology, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
- Research Laboratories Unit, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Khaled Elbanna
- Department of Biology, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
- Research Laboratories Unit, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
- Department of Agricultural Microbiology, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | - Hussein H. Abulreesh
- Department of Biology, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
- Research Laboratories Unit, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
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Lévesque S, Rouleau S, Bergeron D, Brown N, Bekal S, Lalancette C, Alarie I. Xenophilus aerolatus isolate misidentified as Brucella spp. by MALDI-TOF MS (VITEK-MS) system. Diagn Microbiol Infect Dis 2024; 110:116543. [PMID: 39316926 DOI: 10.1016/j.diagmicrobio.2024.116543] [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: 08/14/2024] [Revised: 09/17/2024] [Accepted: 09/19/2024] [Indexed: 09/26/2024]
Abstract
We report the characterization of Xenophilus aerolatus strain identified from a screening rectal swab specimen in human, initially misidentified as Brucella spp. by MALDI-TOF MS (VITEK-MS system). The strain is able to growth on ColorexTM mSuperCARBA plate, suggesting carbapenem resistance. Whole genome sequencing identified several potential antimicrobial resistance mechanisms.
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Affiliation(s)
- Simon Lévesque
- Service de microbiologie, CIUSSS de l'Estrie - Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada; Département de microbiologie et infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada.
| | - Samuel Rouleau
- Plateforme de RNomique, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Danny Bergeron
- Plateforme de RNomique, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Nathalie Brown
- Service de microbiologie, CIUSSS de l'Estrie - Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Cindy Lalancette
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Isabelle Alarie
- Service de microbiologie, CIUSSS de l'Estrie - Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada; Département de microbiologie et infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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Govindarajan DK, Eskeziyaw BM, Kandaswamy K, Mengistu DY. Diagnosis of extraintestinal pathogenic Escherichia coli pathogenesis in urinary tract infection. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 7:100296. [PMID: 39553200 PMCID: PMC11565050 DOI: 10.1016/j.crmicr.2024.100296] [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] [Indexed: 11/19/2024] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) is a virulent pathogen found in humans that causes the majority of urinary tract infections, and other infections such as meningitis and sepsis. ExPEC can enter the urinary tract through two modes: ascending from the bladder or descending from the kidneys. Human anatomical structures generally prevent the transmission of pathogens between the extra-intestinal area, kidneys, bladder, and urinary tract. However, adhesins, a virulence protein of ExPEC, promote the initial bacterial attachment and invasion of host cells. In addition to adhesion proteins, ExPEC contains iron acquisition systems and toxins to evade the host immune system, acquire essential nutrients, and gain antibiotic resistance. The presence of antibiotic-resistant genes makes treating ExPEC in urinary tract infections (UTIs) more complicated. Therefore, screening for the presence of ExPEC among other uropathogens in UTI patients is essential, as it can potentially aid in the effective treatment and mitigation of ExPEC pathogens. Several diagnostic techniques are available for detecting ExPEC, including urine culture, polymerase chain reaction, serological testing, loop-mediated isothermal amplification, and biochemical tests. This review addresses strain-specific diagnostic techniques for screening ExPEC in UTI patients.
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Affiliation(s)
| | | | - Kumaravel Kandaswamy
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, India
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Jiang YL, Lyu YY, Liu LL, Li ZP, Liu D, Tai JH, Hu XQ, Zhang WH, Chu WW, Zhao X, Huang W, Wu YL. Carbapenem-resistant Klebsiella oxytoca transmission linked to preoperative shaving in emergency neurosurgery, tracked by rapid detection via chromogenic medium and whole genome sequencing. Front Cell Infect Microbiol 2024; 14:1464411. [PMID: 39483120 PMCID: PMC11525008 DOI: 10.3389/fcimb.2024.1464411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 09/25/2024] [Indexed: 11/03/2024] Open
Abstract
Objectives This study describes the detection and tracking of emergency neurosurgical cross-transmission infections with carbapenem-resistant Klebsiella oxytoca (CRKO). Methods We conducted an epidemiological investigation and a rapid screening of 66 surveillance samples using the chromogenic selective medium. Two CRKO isolates from infected patients and three from the preoperative shaving razors had similar resistance profiles identified by the clinical laboratory. Results The whole genome sequencing (WGS) results identified all isolates as Klebsiella michiganensis (a species in the K. oxytoca complex) with sequence type 29 (ST29) and carrying resistance genes bla KPC-2 and bla OXY-5, as well as IncF plasmids. The pairwise average nucleotide identity values of 5 isolates ranged from 99.993% to 99.999%. Moreover, these isolates displayed a maximum genetic difference of 3 among 5,229 targets in the core genome multilocus sequence typing scheme, and the razors were confirmed as the contamination source. After the implementation of controls and standardized shaving procedures, no new CRKO infections occurred. Conclusion Contaminated razors can be sources of neurosurgical site infections with CRKO, and standard shaving procedures need to be established. Chromogenic selective medium can help rapidly identify targeted pathogens, and WGS technologies are effective mean in tracking the transmission source in an epidemic or outbreak investigation. Our findings increase the understanding of microbial transmission in surgery to improve patient care quality.
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Affiliation(s)
- Yun-Lan Jiang
- Department of Hospital Infection Prevention and Control, Anqing First People’s Hospital of Anhui Medical University, Anqing, Anhui, China
| | - Yi-Yu Lyu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Li-Li Liu
- Department of Hospital Infection Prevention and Control, Anqing First People’s Hospital of Anhui Medical University, Anqing, Anhui, China
| | - Zhi-Ping Li
- Department of Hospital Infection Prevention and Control, Anqing First People’s Hospital of Anhui Medical University, Anqing, Anhui, China
| | - Dan Liu
- Department of Hospital Infection Prevention and Control, Anqing First People’s Hospital of Anhui Medical University, Anqing, Anhui, China
| | - Jie-Hao Tai
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xiao-Qian Hu
- Department of Hospital Infection Prevention and Control, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Wen-Hui Zhang
- The Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Wen-Wen Chu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xue Zhao
- The Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Wei Huang
- Department of Laboratory Medicine, Shenzhen People’s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, Guangdong, China
- The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yi-Le Wu
- Department of Hospital Infection Prevention and Control, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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Sachu A, Sudersanan H, Sunny S, Mathew P, Kumar A, David A. Is routine screening for Candida auris necessary in ICU? IRANIAN JOURNAL OF MICROBIOLOGY 2024; 16:708-715. [PMID: 39534293 PMCID: PMC11551662 DOI: 10.18502/ijm.v16i5.16807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
Background and Objectives The capability to cause invasive infection, multi-drug resistance, and health care-associated outbreaks of Candida auris have made it a pathogen of great concern. Estimating how many patients in our intensive care unit had C. auris colonization and what characteristics put patients at risk for having Candida spp. colonization were the primary goals of the study. Materials and Methods Swabs from axilla and groin were collected from 229 patients getting admitted to the ICU. Samples were inoculated into CHROMagarTM Candida Plus medium. Colonies presumptively identified as C. auris by the presence of light blue with blue halo and were confirmed by VITEK-2. Results Our study showed that only one patient was colonized with C. auris. A total of 47 (20.5%) patients were colonized with Candida spp., of which Candida parapislosis was the predominant organism. History of antibiotic use and cerebrovascular accident were independent risk factors in Candida colonization. Conclusion Active screening for Candida auris in all patients is not required in our hospital as the prevalence was very low and not cost-effective. Therefore we plan to modify our screening strategy and use risk factors based surveillance strategy as it may serve as an ideal strategy.
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Affiliation(s)
- Arun Sachu
- Department of Micobiology, Believers Church Medical College, Thiruvalla, Kerala, India
| | - Harisree Sudersanan
- Department of Microbiology, Government TD Medical College, Alappuzha, Kerala, India
| | - Sanjo Sunny
- Department of Critical Care, Believers Church Medical College, Thiruvalla, Kerala, India
| | - Philip Mathew
- Department of Critical Care, Believers Church Medical College, Thiruvalla, Kerala, India
| | - Ajeesh Kumar
- Department of Critical Care, Believers Church Medical College, Thiruvalla, Kerala, India
| | - Alice David
- Head of Medical Research, Believers Church Medical College, Thiruvalla, Kerala, India
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Salamandane A, Leech J, Almeida R, Silva C, Crispie F, Cotter PD, Malfeito-Ferreira M, Brito L. Metagenomic analysis of the bacterial microbiome, resistome and virulome distinguishes Portuguese Serra da Estrela PDO cheeses from similar non-PDO cheeses: An exploratory approach. Food Res Int 2024; 189:114556. [PMID: 38876593 DOI: 10.1016/j.foodres.2024.114556] [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: 03/14/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 06/16/2024]
Abstract
This study aimed to evaluate the microbiome, resistome and virulome of two types of Portuguese cheese using high throughput sequencing (HTS). Culture-dependent chromogenic methods were also used for certain groups/microorganisms. Eight samples of raw ewe's milk cheese were obtained from four producers: two producers with cheeses with a PDO (Protected Designation of Origin) label and the other two producers with cheeses without a PDO label. Agar-based culture methods were used to quantify total mesophiles, Enterobacteriaceae, Escherichia coli, Staphylococcus, Enterococcus and lactic acid bacteria. The presence of Listeria monocytogenes and Salmonella was also investigated. The selected isolates were identified by 16S rRNA gene sequencing and evaluated to determine antibiotic resistance and the presence of virulence genes. The eight cheese samples analyzed broadly complied with EC regulations in terms of the microbiological safety criteria. The HTS results demonstrated that Leuconostoc mesenteroides, Lactococcus lactis, Lactobacillus plantarum, Lacticaseibacillus rhamnosus, Enterococcus durans and Lactobacillus coryniformis were the most prevalent bacterial species in cheeses. The composition of the bacterial community varied, not only between PDO and non-PDO cheeses, but also between producers, particularly between the two non-PDO cheeses. Alpha-diversity analyses showed that PDO cheeses had greater bacterial diversity than non-PDO cheeses, demonstrating that the diversity of spontaneously fermented foods is significantly higher in cheeses produced without the addition of food preservatives and dairy ferments. Despite complying with microbiological regulations, both PDO and non-PDO cheeses harbored potential virulence genes as well as antibiotic resistance genes. However, PDO cheeses exhibited fewer of these virulence and antibiotic resistance genes compared to non-PDO cheeses. Therefore, the combination of conventional microbiological methods and the metagenomic approach could contribute to improving the attribution of the PDO label to this type of cheese.
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Affiliation(s)
- Acácio Salamandane
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal; Faculdade de Ciências de Saúde, Universidade Lúrio, Campus Universitário de Marrere, Nampula 4250, Mozambique
| | - John Leech
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
| | - Rita Almeida
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Carolina Silva
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland; VistaMilk, Ireland
| | - Manuel Malfeito-Ferreira
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Luísa Brito
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal.
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Novazzi F, Arcari G, Drago Ferrante F, Boutahar S, Genoni AP, Carcione D, Cassani G, Gigante P, Carbotti M, Capuano R, Pasciuta R, Mancini N. Combined Use of Phenotypic Screening and of a Novel Commercial Assay (REALQUALITY Carba-Screen) for the Rapid Molecular Detection of Carbapenemases: A Single-Center Experience. Diagnostics (Basel) 2024; 14:1599. [PMID: 39125475 PMCID: PMC11311838 DOI: 10.3390/diagnostics14151599] [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: 06/18/2024] [Revised: 07/15/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Carbapenem resistance is a serious public health threat, causing numerous deaths annually primarily due to healthcare-associated infections. To face this menace, surveillance programs in high-risk patients are becoming a widespread practice. Here we report the performance of the combined use of a recently approved commercial multiplex real-time PCR assay (REALQUALITY Carba-Screen kit) with conventional phenotypic screening. In this three-month study, 479 rectal swabs from 309 patients across high-risk units were evaluated by combining the two approaches. Although the molecular assay showed a higher positivity rate than phenotypic screening (7.1% vs. 5%), it should be noted that the molecular method alone would have missed eight carbapenem-resistant isolates, while using only phenotypic screening would not have detected sixteen isolates. This demonstrates the complementary strengths of each method. Our study confirms the need for a combined approach to maximize the possible clinical impact of this kind of screening, ensuring a more comprehensive detection of resistant strains.
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Affiliation(s)
- Federica Novazzi
- Laboratory of Medical Microbiology and Virology, University Hospital of Varese, 21100 Varese, Italy; (F.N.); (G.A.)
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Gabriele Arcari
- Laboratory of Medical Microbiology and Virology, University Hospital of Varese, 21100 Varese, Italy; (F.N.); (G.A.)
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Francesca Drago Ferrante
- Laboratory of Medical Microbiology and Virology, University Hospital of Varese, 21100 Varese, Italy; (F.N.); (G.A.)
| | - Sara Boutahar
- Laboratory of Medical Microbiology and Virology, University Hospital of Varese, 21100 Varese, Italy; (F.N.); (G.A.)
| | - Angelo Paolo Genoni
- Laboratory of Medical Microbiology and Virology, University Hospital of Varese, 21100 Varese, Italy; (F.N.); (G.A.)
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Davide Carcione
- Laboratory of Clinical Microbiology and Virology, ASST Valle Olona, 21013 Gallarate, Italy
| | - Gianluca Cassani
- Laboratory of Medical Microbiology and Virology, University Hospital of Varese, 21100 Varese, Italy; (F.N.); (G.A.)
| | - Paolo Gigante
- Laboratory of Medical Microbiology and Virology, University Hospital of Varese, 21100 Varese, Italy; (F.N.); (G.A.)
| | - Mattia Carbotti
- Laboratory of Medical Microbiology and Virology, University Hospital of Varese, 21100 Varese, Italy; (F.N.); (G.A.)
| | - Riccardo Capuano
- Laboratory of Medical Microbiology and Virology, University Hospital of Varese, 21100 Varese, Italy; (F.N.); (G.A.)
| | - Renée Pasciuta
- Laboratory of Medical Microbiology and Virology, University Hospital of Varese, 21100 Varese, Italy; (F.N.); (G.A.)
| | - Nicasio Mancini
- Laboratory of Medical Microbiology and Virology, University Hospital of Varese, 21100 Varese, Italy; (F.N.); (G.A.)
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
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12
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Balaji L, Subramaniam J. Bridging Diagnostic Gaps: Utilising HiCrome Agar and Tetrazolium Reduction Medium for the Rapid and Presumptive Identification and Speciation of Candida Species in Vulvovaginal Candidiasis in Low-Resource Environments. Cureus 2024; 16:e65601. [PMID: 39205720 PMCID: PMC11357716 DOI: 10.7759/cureus.65601] [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: 07/06/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
Background Vulvovaginal candidiasis (VVC) is a common fungal infection caused by an overgrowth of Candida species, primarily Candida albicans (C. albicans). Using HiCrome agar and tetrazolium reduction medium offers cost-effectiveness in Candida detection by eliminating the need for additional tests, reducing equipment costs compared to automated systems, and simplifying workflow with direct species identification while maintaining high specificity. They expedite detection by directly identifying Candida species based on colony colour, bypassing the multiple steps of phenotypic methods. This efficiency saves time in the laboratory, providing rapid results without the extended processing times associated with automated systems and facilitating prompt diagnosis and treatment decisions. These diagnostic tools are especially valuable in low-resource environments where a quick and accurate diagnosis of VVC is crucial for effective treatment and management of antifungal resistance. Aims and objectives This study aims to evaluate the efficacy of HiCrome agar and tetrazolium reduction medium's efficacy in speciating Candida species in VVC cases. Materials and methods A cross-sectional observational study was conducted at Saveetha Medical College and Hospitals, Chennai, India, over six months. High vaginal swabs from 126 patients suspected of VVC were collected and plated on Sabouraud dextrose agar (SDA), HiCrome Candida differential agar (Himedia, Mumbai, India), and tetrazolium reduction medium. The results were compared with those obtained from the VITEK2 compact system (bioMérieux, Marcy-l'Étoile, France). Results Of the 126 samples, 74.6% showed single yeast infections, 7.9% displayed mixed yeast infections, and 17.5% showed no growth. A total of 114 Candida isolates were identified. Both HiCrome agar and tetrazolium reduction medium accurately identified all isolates, with complete concordance with the VITEK2 compact system. The most commonly isolated species were C. albicans (55.2%), Candida tropicalis (32.4%), Candida glabrata (8.8%), and Candida parapsilosis (3.6%). Both media provided rapid and accurate presumptive identification in low-resource settings. Conclusions HiCrome agar and tetrazolium reduction medium demonstrated high sensitivity and specificity in identifying Candida species. These methods are reliable for rapid and accurate diagnosis, particularly in resource-limited settings. However, they may require supplementary tests for definitive species identification. The adoption of these diagnostic tools represents a significant advancement in clinical microbiology, improving VVC management and addressing antifungal resistance.
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Affiliation(s)
- Lavanya Balaji
- Department of Microbiology, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Jayakumar Subramaniam
- Department of Microbiology, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
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13
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Vatopoulos A. Clinical Microbiology: where do we stand? FRONTIERS IN ANTIBIOTICS 2024; 3:1250632. [PMID: 39816265 PMCID: PMC11731818 DOI: 10.3389/frabi.2024.1250632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/29/2024] [Indexed: 01/18/2025]
Abstract
Clinical Microbiology has developed during the last 100 years, simultaneous with the discovery of microorganisms as causes of infections. Globalization and One Health determine present needs whereas molecular biology, automation, artificial intelligence, and bioinformatics are new tools that characterize the new developments in the field.
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Affiliation(s)
- Alkiviadis Vatopoulos
- Department of Public Health Policy, School of Public Health, University of West Attica, Athens, Greece
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14
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Aruhomukama D, Magiidu WT, Katende G, Ebwongu RI, Bulafu D, Kasolo R, Nakabuye H, Musoke D, Asiimwe B. Evaluation of three protocols for direct susceptibility testing for gram negative-Enterobacteriaceae from patient samples in Uganda with SMS reporting. Sci Rep 2024; 14:2730. [PMID: 38302620 PMCID: PMC10834995 DOI: 10.1038/s41598-024-53230-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: 10/03/2023] [Accepted: 01/30/2024] [Indexed: 02/03/2024] Open
Abstract
In Uganda, the challenge of generating and timely reporting essential antimicrobial resistance (AMR) data has led to overreliance on empirical antibiotic therapy, exacerbating the AMR crisis. To address this issue, this study aimed to adapt a one-step AMR testing protocol alongside an SMS (Short Message Service) result relay system (SRRS), with the potential to reduce the turnaround time for AMR testing and result communication from 4 days or more to 1 day in Ugandan clinical microbiology laboratories. Out of the 377 samples examined, 54 isolates were obtained. Notably, E. coli (61%) and K. pneumoniae (33%) were the most frequently identified, majority testing positive for ESBL. Evaluation of three AMR testing protocols revealed varying sensitivity and specificity, with Protocol A (ChromID ESBL-based) demonstrating high sensitivity (100%) but no calculable specificity, Protocol B (ceftazidime-based) showing high sensitivity (100%) and relatively low specificity (7.1%), and Protocol C (cefotaxime-based) exhibiting high sensitivity (97.8%) but no calculable specificity. ESBL positivity strongly correlated with resistance to specific antibiotics, including cefotaxime, ampicillin, and aztreonam (100%), cefuroxime (96%), ceftriaxone (93%), and trimethoprim sulfamethoxazole (87%). The potential of integrating an SRRS underscored the crucial role this could have in enabling efficient healthcare communication in AMR management. This study underscores the substantial potential of the tested protocols for accurately detecting ESBL production in clinical samples, potentially, providing a critical foundation for predicting and reporting AMR patterns. Although considerations related to specificity warrant careful assessment before widespread clinical adoption.
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Affiliation(s)
- Dickson Aruhomukama
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Walusimbi Talemwa Magiidu
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - George Katende
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Robert Innocent Ebwongu
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Douglas Bulafu
- Department of Disease Control and Environmental Health, School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Rajab Kasolo
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Hellen Nakabuye
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - David Musoke
- Department of Disease Control and Environmental Health, School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Benon Asiimwe
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
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15
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Correia JL, Fiuza JG, Ferreira G, Almeida MD, Moreira D, Neto VD. Embolic stroke and misidentification candida species endocarditis: Case presentation and literature review. Diagn Microbiol Infect Dis 2024; 108:116133. [PMID: 37984110 DOI: 10.1016/j.diagmicrobio.2023.116133] [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: 08/04/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/22/2023]
Abstract
Fungal endocarditis is a rare but serious form of infective endocarditis associated with high morbidity and mortality. Among fungal pathogens, Candida species are the most frequently isolated and commonly found in individuals with predisposing factors, such as prosthetic heart valves. The clinical presentation of endocarditis is highly variable and nonspecific, often including symptoms and signs of embolization. In this paper, we present a case of fungal prosthetic valve endocarditis in which the initial presentation was an acute ischemic stroke. The initial misidentification of Candida famata was attributed to limitations in the presumptive methodology used through selective chromogenic culture identification. However, the surgical specimen underwent mass spectrometry, leading to the correct identification of Candida guilliermondii instead of Candida famata. Furthermore, we conducted a non-systematic narrative review of the literature on Candida endocarditis. Our findings underscore the importance of considering fungal endocarditis in the differential diagnosis of patients with possible extracardiac complications, particularly those with a history of heart valve replacement. Early diagnosis and a comprehensive treatment strategy tailored by species identification and antifungal susceptibility testing are crucial in improving patient outcomes.
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Affiliation(s)
| | | | | | | | | | - Vanda Devesa Neto
- Tondela-Viseu Hospital Center, Viseu, Portugal; Faculty of Health Sciences - University of Beira Interior, Covilhã, Portugal
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16
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Wang Z, Pang Y, Chung CR, Wang HY, Cui H, Chiang YC, Horng JT, Lu JJ, Lee TY. A risk assessment framework for multidrug-resistant Staphylococcus aureus using machine learning and mass spectrometry technology. Brief Bioinform 2023; 24:bbad330. [PMID: 37742050 DOI: 10.1093/bib/bbad330] [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: 04/12/2023] [Revised: 07/19/2023] [Accepted: 08/31/2023] [Indexed: 09/25/2023] Open
Abstract
The emergence of multidrug-resistant bacteria is a critical global crisis that poses a serious threat to public health, particularly with the rise of multidrug-resistant Staphylococcus aureus. Accurate assessment of drug resistance is essential for appropriate treatment and prevention of transmission of these deadly pathogens. Early detection of drug resistance in patients is critical for providing timely treatment and reducing the spread of multidrug-resistant bacteria. This study aims to develop a novel risk assessment framework for S. aureus that can accurately determine the resistance to multiple antibiotics. The comprehensive 7-year study involved ˃20 000 isolates with susceptibility testing profiles of six antibiotics. By incorporating mass spectrometry and machine learning, the study was able to predict the susceptibility to four different antibiotics with high accuracy. To validate the accuracy of our models, we externally tested on an independent cohort and achieved impressive results with an area under the receiver operating characteristic curve of 0. 94, 0.90, 0.86 and 0.91, and an area under the precision-recall curve of 0.93, 0.87, 0.87 and 0.81, respectively, for oxacillin, clindamycin, erythromycin and trimethoprim-sulfamethoxazole. In addition, the framework evaluated the level of multidrug resistance of the isolates by using the predicted drug resistance probabilities, interpreting them in the context of a multidrug resistance risk score and analyzing the performance contribution of different sample groups. The results of this study provide an efficient method for early antibiotic decision-making and a better understanding of the multidrug resistance risk of S. aureus.
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Affiliation(s)
- Zhuo Wang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong 518172, China
| | - Yuxuan Pang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong 518172, China
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong 518172, China
| | - Chia-Ru Chung
- Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan 333423, Taiwan
| | - Haiyan Cui
- Department of Clinical Laboratory, Longgang District People's Hospital of Shenzhen & The Second Affiliated Hospital of the Chinese University of Hong Kong, Shenzhen, China
| | - Ying-Chih Chiang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong, 518172, China
| | - Jorng-Tzong Horng
- Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan 333423, Taiwan
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan 33303, Taiwan
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 33303, Taiwan
| | - Tzong-Yi Lee
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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Abstract
Clostridioides difficile (C. difficile) infection is still a threat to many healthcare settings worldwide. Clostridioides difficile epidemiology has changed over the last 20 years, largely due to the emergence of hypervirulent and antimicrobial-resistant C. difficile strains. The excessive use of antimicrobials, the absence of optimal antibiotic policies, and suboptimal infection control practices have fueled the development of this pressing health issue. The prudent use of antimicrobials, particularly broad-spectrum agents, and simple infection control measures, such as hand hygiene, can significantly reduce C. difficile infection rates. Moreover, the early detection of these infections and understanding their epidemiological behavior using accurate laboratory methods are the cornerstone to decreasing the incidence of C. difficile infection and preventing further spread. Although there is no consensus on the single best laboratory method for the diagnosis of C. difficile infection, the use of 2 or more techniques can improve diagnostic accuracy, and it is recommended.
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Affiliation(s)
- Ibrahim A. Al-Zahrani
- From the Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, and from the Special Infectious Agents Unit-Biosafety Level-3, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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18
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Tommasoni C, Fiore E, Lisuzzo A, Gianesella M. Mastitis in Dairy Cattle: On-Farm Diagnostics and Future Perspectives. Animals (Basel) 2023; 13:2538. [PMID: 37570346 PMCID: PMC10417731 DOI: 10.3390/ani13152538] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Mastitis is one of the most important diseases in dairy cattle farms, and it can affect the health status of the udder and the quantity and quality of milk yielded. The correct management of mastitis is based both on preventive and treatment action. With the increasing concern for antimicrobial resistance, it is strongly recommended to treat only the mammary quarters presenting intramammary infection. For this reason, a timely and accurate diagnosis is fundamental. The possibility to detect and characterize mastitis directly on farm would be very useful to choose the correct management protocol. Some on-field diagnostic tools are already routinely applied to detect mastitis, such as the California Mastitis Test and on-farm culture. Other instruments are emerging to perform a timely diagnosis and to characterize mastitis, such as Infra-Red Thermography, mammary ultrasound evaluation and blood gas analysis, even if their application still needs to be improved. The main purpose of this article is to present an overview of the methods currently used to control, detect, and characterize mastitis in dairy cows, in order to perform a timely diagnosis and to choose the most appropriate management protocol, with a specific focus on on-farm diagnostic tools.
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Affiliation(s)
- Chiara Tommasoni
- Department of Animal Medicine, Production and Health, University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (E.F.); (A.L.); (M.G.)
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19
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Avberšek M, Ihssen J, Faccio G, Spitz U, Cugmas B. Chromogenic culture media complements diagnostic cytology in the visual identification of pathogenic skin bacteria in dogs and cats. Front Vet Sci 2023; 10:1152229. [PMID: 37496749 PMCID: PMC10367103 DOI: 10.3389/fvets.2023.1152229] [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: 01/27/2023] [Accepted: 06/16/2023] [Indexed: 07/28/2023] Open
Abstract
In dogs and cats, bacterial skin infections (pyoderma and otitis externa) are a common cause for visiting the veterinary clinic. The most frequent skin pathogens are Staphylococcus pseudintermedius, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa, often requiring different therapeutic antibiotic protocols. Unfavorably, existing diagnostics based on cytology cannot reveal bacterial species but only bacterial shapes such as cocci or rods. This microscopic limitation could be overcome by clinical translation of affordable chromogenic media, which enable species identification based on bacterial colonies growing in different colors and sizes. In this study, we determined how well inexperienced general veterinary clinicians identified bacterial pathogens from the skin and ears on two commercial (Chromatic™ MH and Flexicult® Vet) and one custom-made Mueller Hinton agar-based chromogenic medium. For this purpose, four veterinarians evaluated 100 unique samples representing 10 bacterial species. On average, clinicians correctly identified between 72.1 and 86.3% of bacterial species. Colony colors developed quickly on the Chromatic™ MH medium, leading to the highest 81.6% identification accuracy after 24 h incubation. However, Flexicult® Vet exhibited the highest accuracy of 86.3% after prolonged 48 h incubation. Evaluators easily recognized bacteria displaying uniquely colored colonies like green-brown Pseudomonas aeruginosa, blue Enterococcus faecalis, orange-brown Proteus spp., and red Escherichia coli. Oppositely, staphylococci shared uncharacteristically pale pink colonies causing misidentifications among the genus, deteriorating overall accuracy by around 10 percentage points (from 90.9%). Another reason for identification errors was the evaluators' inexperience, reflected in not recognizing colony size differences. For example, although Streptococcus canis exhibited the tiniest colonies, the species was frequently mistaken for other cocci. Finally, around 10% of errors were negligence-related slips due to unconsidered sample history. To conclude, the introduction of chromogenic media into veterinary clinics can significantly complement diagnostics in skin inflammations by identifying pathogen species in around 80% of cases. The extra information may help in therapeutic dilemmas on antibiotics and standard antimicrobial susceptibility testing. Additional personnel training and evaluation help by visuals, flowcharts, checklists, and, if necessary, microbiologists could further improve identification accuracy.
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Affiliation(s)
- Miha Avberšek
- Veterinary Clinic Zamba, Vets4science d.o.o., Celje, Slovenia
| | | | | | | | - Blaž Cugmas
- Veterinary Clinic Zamba, Vets4science d.o.o., Celje, Slovenia
- Institute of Atomic Physics and Spectroscopy, University of Latvia, Riga, Latvia
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20
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Bocchetti M, Ferraro MG, Melisi F, Grisolia P, Scrima M, Cossu AM, Yau TO. Overview of current detection methods and microRNA potential in Clostridioides difficile infection screening. World J Gastroenterol 2023; 29:3385-3399. [PMID: 37389232 PMCID: PMC10303512 DOI: 10.3748/wjg.v29.i22.3385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/23/2023] [Accepted: 05/04/2023] [Indexed: 06/06/2023] Open
Abstract
Clostridioides difficile (formerly called Clostridium difficile, C. difficile) infection (CDI) is listed as an urgent threat on the 2019 antibiotic resistance threats report in the United States by the Centers for Disease Control and Prevention. Early detection and appropriate disease management appear to be essential. Meanwhile, although the majority of cases are hospital-acquired CDI, community-acquired CDI cases are also on the rise, and this vulnerability is not limited to immunocompromised patients. Gastrointestinal treatments and/or gastrointestinal tract surgeries may be required for patients diagnosed with digestive diseases. Such treatments could suppress or interfere with the patient's immune system and disrupt gut flora homeostasis, creating a suitable microecosystem for C. difficile overgrowth. Currently, stool-based non-invasive screening is the first-line approach to CDI diagnosis, but the accuracy is varied due to different clinical microbiology detection methods; therefore, improving reliability is clearly required. In this review, we briefly summarised the life cycle and toxicity of C. difficile, and we examined existing diagnostic approaches with an emphasis on novel biomarkers such as microRNAs. These biomarkers can be easily detected through non-invasive liquid biopsy and can yield crucial information about ongoing pathological phenomena, particularly in CDI.
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Affiliation(s)
- Marco Bocchetti
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Maria Grazia Ferraro
- School of Infection and Immunity, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
- Department of Pharmacy, School of Medicine and Surgery, University of Naples “Federico II,” Naples 80131, Italy
| | - Federica Melisi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Piera Grisolia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Marianna Scrima
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Alessia Maria Cossu
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Tung On Yau
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom
- Department of Rural Land Use, Scotland’s Rural College, Aberdeen AB21 9YA, Scotland, United Kingdom
- Department of Health Science, University of the People, Pasadena, CA 9110112, United States
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21
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Elbehiry A, Abalkhail A, Marzouk E, Elmanssury AE, Almuzaini AM, Alfheeaid H, Alshahrani MT, Huraysh N, Ibrahem M, Alzaben F, Alanazi F, Alzaben M, Anagreyyah SA, Bayameen AM, Draz A, Abu-Okail A. An Overview of the Public Health Challenges in Diagnosing and Controlling Human Foodborne Pathogens. Vaccines (Basel) 2023; 11:vaccines11040725. [PMID: 37112637 PMCID: PMC10143666 DOI: 10.3390/vaccines11040725] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Pathogens found in food are believed to be the leading cause of foodborne illnesses; and they are considered a serious problem with global ramifications. During the last few decades, a lot of attention has been paid to determining the microorganisms that cause foodborne illnesses and developing new methods to identify them. Foodborne pathogen identification technologies have evolved rapidly over the last few decades, with the newer technologies focusing on immunoassays, genome-wide approaches, biosensors, and mass spectrometry as the primary methods of identification. Bacteriophages (phages), probiotics and prebiotics were known to have the ability to combat bacterial diseases since the turn of the 20th century. A primary focus of phage use was the development of medical therapies; however, its use quickly expanded to other applications in biotechnology and industry. A similar argument can be made with regards to the food safety industry, as diseases directly endanger the health of customers. Recently, a lot of attention has been paid to bacteriophages, probiotics and prebiotics most likely due to the exhaustion of traditional antibiotics. Reviewing a variety of current quick identification techniques is the purpose of this study. Using these techniques, we are able to quickly identify foodborne pathogenic bacteria, which forms the basis for future research advances. A review of recent studies on the use of phages, probiotics and prebiotics as a means of combating significant foodborne diseases is also presented. Furthermore, we discussed the advantages of using phages as well as the challenges they face, especially given their prevalent application in food safety.
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Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia (E.M.)
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32511, Egypt
- Correspondence:
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia (E.M.)
| | - Eman Marzouk
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia (E.M.)
| | - Ahmed Elnadif Elmanssury
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia (E.M.)
| | - Abdulaziz M. Almuzaini
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Hani Alfheeaid
- Department of Food Science and Human Nutrition, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 51452, Saudi Arabia
- Human Nutrition, School of Medicine, Nursing and Dentistry, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G31 2ER, UK
| | - Mohammed T. Alshahrani
- Department of Neurology, Prince Sultan Military Medical City, Riyadh 12233, Saudi Arabia
| | - Nasser Huraysh
- Department of Family Medicine, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Mai Ibrahem
- Department of Public Health, College of Applied Medical Science, King Khalid University, Abha 61421, Saudi Arabia;
- Department of Aquatic Animal Medicine and Management, Faculty of Veterinary Medicine, Cairo University, Cairo 12211, Egypt
| | - Feras Alzaben
- Department of Food Service, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Farhan Alanazi
- Supply Administration, Armed Forces Hospital, King Abdul Aziz Naval Base in Jubail, Jubail 35517, Saudi Arabia
| | - Mohammed Alzaben
- Department of Food Factories Inspection, Operation Sector, Saudi Food and Drug Authority, Riyadh 13513, Saudi Arabia
| | | | | | - Abdelmaged Draz
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Akram Abu-Okail
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
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Yin M, Wang Z, Xie P, Han L, Li L, Wang H, Qiao X, Deng Q. Fluorescence sensing platform for Cronobacter sakazakii based on the cationic metal-organic frameworks modified upconversion nanoparticles. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Jian X, Guo X, Cai Z, Wei L, Wang L, Xing XH, Zhang C. Single-cell microliter-droplet screening system (MISS Cell): An integrated platform for automated high-throughput microbial monoclonal cultivation and picking. Biotechnol Bioeng 2023; 120:778-792. [PMID: 36477904 DOI: 10.1002/bit.28300] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/18/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022]
Abstract
Solid plates have been used for microbial monoclonal isolation, cultivation, and colony picking since 1881. However, the process is labor- and resource-intensive for high-throughput requirements. Currently, several instruments have been integrated for automated and high-throughput picking, but complicated and expensive. To address these issues, we report a novel integrated platform, the single-cell microliter-droplet screening system (MISS Cell), for automated, high-throughput microbial monoclonal colony cultivation and picking. We verified the monoclonality of droplet cultures in the MISS Cell and characterized culture performance. Compared with solid plates, the MISS Cell generated a larger number of monoclonal colonies with higher initial growth rates using fewer resources. Finally, we established a workflow for automated high-throughput screening of Corynebacterium glutamicum using the MISS Cell and identified high glutamate-producing strains. The MISS Cell can serve as a universal platform to efficiently produce monoclonal colonies in high-throughput applications, overcoming the limitations of solid plates to promote rapid development in biotechnology.
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Affiliation(s)
- Xingjin Jian
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
| | - Xiaojie Guo
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
| | - Zhengshuo Cai
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
| | - Longfeng Wei
- College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Liyan Wang
- Luoyang TMAXTREE Biotechnology Co., Ltd., Luoyang, China
| | - Xin-Hui Xing
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
| | - Chong Zhang
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
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Soto-Beltrá N M, Lee BG, Amézquita-López BA, Quiñones B. Overview of methodologies for the culturing, recovery and detection of Campylobacter. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2023; 33:307-323. [PMID: 35168460 DOI: 10.1080/09603123.2022.2029366] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Campylobacter species are responsible for human gastroenteritis with diverse clinical spectra, ranging from acute watery or bloody diarrhea to life-threatening autoimmune disorders. Given the importance of Campylobacter in causing human illness, this article has reviewed the transmission and attribution sources as well as methodologies for the detection and virulence characterization of campylobacteria. The recovery and detection of Campylobacter from clinical, food and environmental samples has been achieved by the combinatorial use of selective enrichment and culturing methods. Biochemical, immunological, and nucleic acid-based methodologies have enabled the detection and differentiation of closely related Campylobacter isolates in foodborne outbreak investigations and have assessed the diversity and phylogenetic relationships of these bacterial pathogens. Analyses of motility, adherence, and invasiveness in host cells have assessed the pathogenic potential of campylobacteria. Further examination of determinants conferring antimicrobial resistance in Campylobacter have supported the growing need to closely monitor antimicrobials use in clinical and agricultural sectors.
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Affiliation(s)
- Marcela Soto-Beltrá N
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, México
| | - Bertram G Lee
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture/Agricultural Research Service,Western Regional Research Center, Albany, CA, USA
| | | | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture/Agricultural Research Service,Western Regional Research Center, Albany, CA, USA
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Nualmalang R, Thanomsridetchai N, Teethaisong Y, Sukphopetch P, Tangwattanachuleeporn M. Identification of Pathogenic and Opportunistic Yeasts in Pigeon Excreta by MALDI-TOF Mass Spectrometry and Their Prevalence in Chon Buri Province, Thailand. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3191. [PMID: 36833884 PMCID: PMC9967633 DOI: 10.3390/ijerph20043191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Pigeon excreta can cause environmental and public health issues, particularly in urban and public areas. They are reservoirs of several human pathogens including fungi, bacteria, and viruses. Epidemiological data of pathogenic and opportunistic yeasts in pigeon droppings in Chon Buri, one of the most reputable tourist cities of Thailand, are scarce. The present study aimed to identify yeasts in pigeon droppings by MALDI-TOF mass spectrometry, and to study their prevalence in Chon Buri, Thailand. A total of 200 pigeon fecal samples were collected randomly from all 11 districts of Chon Buri. A sum of 393 yeast-like colonies were isolated on Sabourand's dextrose agar and CHROMagar media. These isolates were further confirmed for their species by MALDI-TOF MS. Twenty-four yeast species belonging to 11 different genera were identified in pigeon fecal samples. Candida spp., predominantly C. krusei (14.32%), were the most prevalent yeast species. Other yeast species, including C. glabrata (12.73%), C. metapsilosis (11.93%), Lodderomyces elongisporus (10.87%), C. tropicalis (7.16%), C. albicans (5.83%), and Cryptococcus neoformans (4.77%) were identified. This study provides valuable epidemiological data and diversity of yeasts in pigeon droppings in Chon Buri, Thailand, and also supports the use of MALDI-TOF MS for yeast identification and epidemiological surveillance.
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Affiliation(s)
- Rungnapa Nualmalang
- Department of Medical Sciences, Faculty of Allied Health Sciences, Burapha University, Mueang, Chonburi 20131, Thailand
| | - Natthapaninee Thanomsridetchai
- Department of Medical Technology, Faculty of Allied Health Sciences, Burapha University, Mueang, Chonburi 20131, Thailand
| | - Yothin Teethaisong
- Department of Medical Sciences, Faculty of Allied Health Sciences, Burapha University, Mueang, Chonburi 20131, Thailand
- Research Unit for Sensor Innovation (RUSI), Burapha University, Mueang, Chonburi 20131, Thailand
| | - Passanesh Sukphopetch
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Marut Tangwattanachuleeporn
- Department of Medical Sciences, Faculty of Allied Health Sciences, Burapha University, Mueang, Chonburi 20131, Thailand
- Research Unit for Sensor Innovation (RUSI), Burapha University, Mueang, Chonburi 20131, Thailand
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Li H, Hsieh K, Wong PK, Mach KE, Liao JC, Wang TH. Single-cell pathogen diagnostics for combating antibiotic resistance. NATURE REVIEWS. METHODS PRIMERS 2023; 3:6. [PMID: 39917628 PMCID: PMC11800871 DOI: 10.1038/s43586-022-00190-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/06/2022] [Indexed: 02/09/2025]
Abstract
Bacterial infections and antimicrobial resistance are a major cause for morbidity and mortality worldwide. Antimicrobial resistance often arises from antimicrobial misuse, where physicians empirically treat suspected bacterial infections with broad-spectrum antibiotics until standard culture-based diagnostic tests can be completed. There has been a tremendous effort to develop rapid diagnostics in support of the transition from empirical treatment of bacterial infections towards a more precise and personalized approach. Single-cell pathogen diagnostics hold particular promise, enabling unprecedented quantitative precision and rapid turnaround times. This Primer provides a guide for assessing, designing, implementing and applying single-cell pathogen diagnostics. First, single-cell pathogen diagnostic platforms are introduced based on three essential capabilities: cell isolation, detection assay and output measurement. Representative results, common analysis methods and key applications are highlighted, with an emphasis on initial screening of bacterial infection, bacterial species identification and antimicrobial susceptibility testing. Finally, the limitations of existing platforms are discussed, with perspectives offered and an outlook towards clinical deployment. This Primer hopes to inspire and propel new platforms that can realize the vision of precise and personalized bacterial infection treatments in the near future.
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Affiliation(s)
- Hui Li
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Present address: School of Electrical, Computer and Biomedical Engineering, Southern Illinois University, Carbondale, IL, USA
- These authors contributed equally: Hui Li, Kuangwen Hsieh
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
- These authors contributed equally: Hui Li, Kuangwen Hsieh
| | - Pak Kin Wong
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Kathleen E. Mach
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph C. Liao
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
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Usefulness of Chromogenic Media with Fluconazole Supplementation for Presumptive Identification of Candida auris. Diagnostics (Basel) 2023; 13:diagnostics13020231. [PMID: 36673041 PMCID: PMC9857578 DOI: 10.3390/diagnostics13020231] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/23/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Introduction:Candida auris is a major threat to public health. Rapid detection is essential for early treatment and transmission control. The use of chromogenic media allows the presumptive identification of this new species. The aim of this study is to describe the morphological characteristics of C. auris colonies on three commercial chromogenic media. Methods: Nineteen C. auris isolates from different countries/clades and 18 isolates of other species were cultivated in CHROMagarTM Candida Plus, HiCromeTM Candida, CHROMagar-Candida, and fluconazole-supplemented (32 mg/L) CHROMagar-Candida media. Results: On CHROMagarTM Candida Plus and HiCromeTM Candida, C. auris isolates from Colombia, Venezuela, India, Korea, and Japan displayed blue-shaded colonies, while isolates from Spain and Germany exhibited light pink shades with a bluish halo. All isolates showed white to pink colonies on CHROMagar-Candida. On CHROMagar Candida supplemented with fluconazole, whilst C. auris, C. glabrata, or C. krusei showed a similar pink color at 48 h incubation, phenotypic differentiation was possible by the rough, paraffin-like texture or the intense purple color acquired by C. krusei and C. glabrata, respectively. Moreover, in this medium, the presence of C. auris in combination with other species of similar color was not limiting for its early identification, due to this medium selecting only strains resistant to this antifungal. Conclusions: The use of chromogenic media such as CHROMagarTM Candida Plus facilitates a presumptive identification of C. auris. However, this identification can be difficult in the presence of mixed cultures. In these cases, the use of CHROMagarTM Candida medium with 32 mg/L fluconazole offers better performance for the identification of C. auris by inhibiting fluconazole-susceptible strains and selecting rare or high fluconazole MIC (>32 mg/L) isolates.
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Kovács R, Majoros L, Stemler J, Cornely OA, Salmanton-García J. Unveiling the Hungarian landscape of laboratory and clinical management capacities for invasive fungal infections: navigating the frontlines against fungal menaces. Ther Adv Infect Dis 2023; 10:20499361231219315. [PMID: 38116297 PMCID: PMC10729621 DOI: 10.1177/20499361231219315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023] Open
Abstract
Background Antifungal diagnostic capacity has been documented in various countries, there is a lack of comprehensive research on clinical mycology diagnostics and treatment in Hungary. Methods We conducted an online survey encompassing questions that explored various aspects of the mycology diagnostic and antifungal therapy-related information. The survey aimed to gather details about institutional profiles, perceptions of invasive fungal infections (IFIs), and access to microscopy, culture, serology, antigen detection, molecular testing, and therapeutic drug monitoring. Results As of May 2023, a total of 17 institutions responded to the questionnaire. Seven participants categorized the institutional incidence of IFI as 'very low', four as 'low', and six as 'mild'. The majority of centers identified Candida spp. (94%) and Aspergillus spp. (82%) as the most prevalent fungal pathogens. Nearly half of the laboratories (47%) reported using matrix-assisted laser desorption/ionization-time of flight mass spectrometry for identification. All institutions had access to microscopy and culture-based diagnostic approaches. A significant number of centers had access to antigen detection (71%) and various molecular assays (59%). Regarding antifungal agents, all reporting sites used at least one triazole, with voriconazole (77%) being the most common mold-active azole. Furthermore, 71% of the centers applied at least one formulation of amphotericin B, and 65% to one echinocandin. However, only 18% of the centers used 5-flucytosine. Conclusion Resource availability for diagnosing and treating IFI in Hungary varies across hospitals based on location. Surveys help identify gaps and limitations in this area. To address these challenges, interregional cooperation within Hungary could be a facilitating strategy.
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Affiliation(s)
- Renátó Kovács
- Department of Medical Microbiology, Faculty of Medicine, Clinical Center, University of Debrecen, Nagyerdei krt. 98., Debrecen HU-4032, Hungary
| | - László Majoros
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Medical Microbiology, Clinical Center, University of Debrecen, Debrecen, Hungary
| | - Jannik Stemler
- Faculty of Medicine and University Hospital Cologne, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn-Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Oliver Andreas Cornely
- Faculty of Medicine and University Hospital Cologne, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn-Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Clinical Trials Centre Cologne (ZKS Köln), University of Cologne, Cologne, Germany
| | - Jon Salmanton-García
- Faculty of Medicine and University Hospital Cologne, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn-Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
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Wei X, Gu Q, Feng Y, Zhang Y, Li Y, Zhang S, Zhang J, Wu S, Yang X, Ye Q, Ding Y, Wang J, Chen M, Wu Q. Sensitive and Selective Detection of Enterococcus faecalis Using a New Turn-on Fluorogenic β-glucosidase Substrate Combined with a Modified Selective Broth. Photochem Photobiol 2023; 99:68-77. [PMID: 35699359 DOI: 10.1111/php.13662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/02/2022] [Indexed: 01/25/2023]
Abstract
A new, simple-to-synthesize and sensitive turn-on fluorogenic substrate (CFMU-Glu) for β-glucosidase activity was developed. This probe was based on a 7-hydroxycoumarin derivative (CFMU) that could emit green fluorescence and had the low pKa value of 5.61 ± 0.01. CFMU-Glu could be used for sensitive monitoring of the almond βGLU and Enterococcus faecalis (E. faecalis) at the optimal pHs of 6.50 and 7.00, respectively. Moreover, a new sensitive and selective fluorogenic broth (PBF-B) for E. faecalis, utilizing CFMU-Glu and polymyxin B, was also developed. Polymyxin B was discovered to can significantly improve the detection selectivity and signal intensity. The proposed 4-four method using PBF-B and a microcentrifuge tube could provide fluorogenic detection limits of 5.01 × 104 and 1.0 × 105 CFU mL-1 by fluorescence microplate reader and naked eye, respectively; it could also provide a turn-on chromogenic detection limit of 1.0 × 106 CFU mL-1 by naked eye. The proposed method could detect 8 CFU mL-1 of E. faecalis in drinking water, Liangcha (herbal tea) and milk samples within 10 h, without pre-enrichment.
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Affiliation(s)
- Xianhu Wei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ying Feng
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Youxiong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shuhong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaojuan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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Kumari M, Swarupa P, Kesari KK, Kumar A. Microbial Inoculants as Plant Biostimulants: A Review on Risk Status. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010012. [PMID: 36675961 PMCID: PMC9860928 DOI: 10.3390/life13010012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Modern agriculture systems are copiously dependent on agrochemicals such as chemical fertilizers and pesticides intended to increase crop production and yield. The indiscriminate use of these chemicals not only affects the growth of plants due to the accumulation of toxic compounds, but also degrades the quality and life-supporting properties of soil. There is a dire need to develop some green approach that can resolve these issues and restore soil fertility and sustainability. The use of plant biostimulants has emerged as an environmentally friendly and acceptable method to increase crop productivity. Biostimulants contain biological substances which may be capable of increasing or stimulating plant growth in an eco-friendly manner. They are mostly biofertilizers that provide nutrients and protect plants from environmental stresses such as drought and salinity. In contrast to the protection of crop products, biostimulants not only act on the plant's vigor but also do not respond to direct actions against pests or diseases. Plant biostimulants improve nutrient mobilization and uptake, tolerance to stress, and thus crop quality when applied to plants directly or in the rhizospheric region. They foster plant growth and development by positively affecting the crop life-cycle starting from seed germination to plant maturity. Legalized application of biostimulants causes no hazardous effects on the environment and primarily provides nutrition to plants. It nurtures the growth of soil microorganisms, which leads to enhanced soil fertility and also improves plant metabolism. Additionally, it may positively influence the exogenous microbes and alter the equilibrium of the microfloral composition of the soil milieu. This review frequently cites the characterization of microbial plant biostimulants that belong to either a high-risk group or are closely related to human pathogens such as Pueudomonas, Klebsiella, Enterobacter, Acinetobacter, etc. These related pathogens cause ailments including septicemia, gastroenteritis, wound infections, inflammation in the respiratory system, meningitis, etc., of varied severity under different conditions of health status such as immunocompromized and comorbidity. Thus it may attract the related concern to review the risk status of biostimulants for their legalized applications in agriculture. This study mainly emphasizes microbial plant biostimulants and their safe application concerns.
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Affiliation(s)
- Menka Kumari
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand Cheri-Manatu, Kamre, Kanke, Rachi 835222, India
| | - Preeti Swarupa
- Department of Microbiology, Patna Women’s College, Patna 800001, India
| | - Kavindra Kumar Kesari
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150 Espoo, Finland
- Department of Applied Physics, School of Science, Aalto University, 02150 Espoo, Finland
- Correspondence: or (K.K.K.); (A.K.)
| | - Anil Kumar
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand Cheri-Manatu, Kamre, Kanke, Rachi 835222, India
- Correspondence: or (K.K.K.); (A.K.)
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Sachu A, Samuel AK. Evaluation of chromogenic agar medium, can it be a suitable alternative to conventional culture system for identification of uropathogens? IRANIAN JOURNAL OF MICROBIOLOGY 2022; 14:825-831. [PMID: 36721445 PMCID: PMC9867613 DOI: 10.18502/ijm.v14i6.11257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background and Objectives Urinary tract infections (UTI) account for major proportion of outpatient load and hospital admission globally. In most of the clinical microbiology laboratories MacConkey agar (MAC) and Cystine lactose electrolyte-deficient (CLED) agar are being used for identification of uropathogens. The main objective of the present study was to evaluate the usefulness of HiCromeTM UTI by comparing isolation rate and presumptive identification of uropathogens against CLED and MAC agar. Materials and Methods This study was conducted over a period of three months on 672 non-duplicate midstream and/or catheter-catch urine samples. All samples were inoculated on to HiCromeTM UTI, CLED agar and MacConkey agar. Results Among the 672 samples received for culture, 113 (16.8%) showed significant growth. Among the 672 samples, 95 (14.1%) showed growth of a single organism while 18 (2.7%) showed polymicrobial growth. The rate of isolation and presumptive identification of the isolates and polymicrobial growth was found significantly higher on HiCromeTM UTI Agar. Conclusion HiCromeTM UTI Agar has the potential to streamline processing of samples for urine culture in a way that will reduce the workload for technicians, reduce turnaround time which in turn will benefit the laboratory ultimately leading to better patient care.
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Affiliation(s)
- Arun Sachu
- Department of Microbiology, Believers Church Medical College, Thiruvalla, Kerala, India,Corresponding author: Arun Sachu, MD, Department of Microbiology, Believers Church Medical College, Thiruvalla, Kerala, India. Tel: +91-9745051455 Fax: +91-4692742820
| | - Abel K Samuel
- Department of Community Medicine, Believers Church Medical College, Thiruvalla, Kerala, India
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Development of a Real-Time Recombinase-Aided Amplification Method to Rapidly Detect Methicillin-Resistant Staphylococcus aureus. Microorganisms 2022; 10:microorganisms10122351. [PMID: 36557604 PMCID: PMC9784193 DOI: 10.3390/microorganisms10122351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/03/2022] [Accepted: 10/31/2022] [Indexed: 11/29/2022] Open
Abstract
Methicillin-resistant staphylococcus aureus (MRSA) is a major pathogen responsible for human hospital and community-onset diseases and severe invasive livestock infections. Rapid detection of MRSA is essential to control the spread of MRSA. Conventional identification methods and antibacterial susceptibility tests of MRSA are time-consuming. The commonly used qPCR assay also has the disadvantages of being complicated and expensive, restricting its application in resource-limited clinical laboratories. Here, a real-time fluorescent recombinase-assisted amplification (RAA) assay targeting the most conserved regions within the mecA gene of MRSA was developed and evaluated to detect MRSA. The detection limit of this assay was determined to be 10 copies/reaction of positive plasmids. The established RAA assay showed high specificity for MRSA detection without cross-reactivities with other clinically relevant bacteria. The diagnostic performance of real-time RAA was evaluated using 67 clinical S. aureus isolates from dairy farms, which were detected in parallel using the TaqMan probe qPCR assay. The results showed that 56 and 54 samples tested positive for MRSA by RAA and qPCR, respectively. The overall agreement between both assays was 97.01% (65/67), with a kappa value of 0.9517 (p < 0.001). Further linear regression analysis demonstrated that the detection results between the two assays were significantly correlated (R2 = 0.9012, p < 0.0001), indicating that this RAA assay possesses similar detection performance to the qPCR assay. In conclusion, our newly established RAA assay is a time-saving and convenient diagnostic tool suitable for MRSA detection and screening.
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Marathe A, Zhu Y, Chaturvedi V, Chaturvedi S. Utility of CHROMagar™ Candida Plus for presumptive identification of Candida auris from surveillance samples. Mycopathologia 2022; 187:527-534. [PMCID: PMC9647746 DOI: 10.1007/s11046-022-00656-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/01/2022] [Indexed: 11/11/2022]
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Li D, Yi J, Han G, Qiao L. MALDI-TOF Mass Spectrometry in Clinical Analysis and Research. ACS MEASUREMENT SCIENCE AU 2022; 2:385-404. [PMID: 36785658 PMCID: PMC9885950 DOI: 10.1021/acsmeasuresciau.2c00019] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 05/04/2023]
Abstract
In the decade after being awarded the Nobel Prize in Chemistry in 2002, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used as an analytical chemistry tool for the detection of large and small molecules (e.g., polymers, proteins, peptides, nucleic acids, amino acids, lipids, etc.) and for clinical analysis and research (e.g., pathogen identification, genetic disorders screening, cancer diagnosis, etc.). In view of the fast development of MALDI-TOF MS in clinical usage, this review systematically summarizes the most important applications of MALDI-TOF MS in clinical analysis and research by analyzing MALDI TOF MS-related reviews collected in the Web of Science database. On the basis of the analysis of keyword co-occurrence of over 2000 review articles, four themes consisting of "pathogen identification", "disease diagnosis", "nucleic acids analysis", and "small molecules analysis" were found. For each theme, the review further outlined their application implications, analytical methods, and systems as well as limitations that need to be addressed. Overall, the review summarizes and elaborates on the clinical applications of MALDI-TOF MS, providing a comprehensive picture for researchers embarking on MALDI TOF MS-related clinical analysis and research.
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Boutal H, Moguet C, Pommiès L, Simon S, Naas T, Volland H. The Revolution of Lateral Flow Assay in the Field of AMR Detection. Diagnostics (Basel) 2022; 12:1744. [PMID: 35885647 PMCID: PMC9317642 DOI: 10.3390/diagnostics12071744] [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: 06/20/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
The global spread of antimicrobial resistant (AMR) bacteria represents a considerable public health concern, yet their detection and identification of their resistance mechanisms remain challenging. Optimal diagnostic tests should provide rapid results at low cost to enable implementation in any microbiology laboratory. Lateral flow assays (LFA) meet these requirements and have become essential tools to combat AMR. This review presents the versatility of LFA developed for the AMR detection field, with particular attention to those directly triggering β-lactamases, their performances, and specific limitations. It considers how LFA can be modified by detecting not only the enzyme, but also its β-lactamase activity for a broader clinical sensitivity. Moreover, although LFA allow a short time-to-result, they are generally only implemented after fastidious and time-consuming techniques. We present a sample processing device that shortens and simplifies the handling of clinical samples before the use of LFA. Finally, the capacity of LFA to detect amplified genetic determinants of AMR by isothermal PCR will be discussed. LFA are inexpensive, rapid, and efficient tools that are easy to implement in the routine workflow of laboratories as new first-line tests against AMR with bacterial colonies, and in the near future directly with biological media.
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Affiliation(s)
- Hervé Boutal
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
| | - Christian Moguet
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
| | - Lilas Pommiès
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
| | - Stéphanie Simon
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
| | - Thierry Naas
- Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, 94270 Le Kremlin-Bicêtre, France;
- Team Resist, UMR1184, Université Paris-Saclay—INSERM—CEA, LabEx Lermit, 91190 Gif-sur-Yvette, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
| | - Hervé Volland
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
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Nehra M, Kumar V, Kumar R, Dilbaghi N, Kumar S. Current Scenario of Pathogen Detection Techniques in Agro-Food Sector. BIOSENSORS 2022; 12:489. [PMID: 35884292 PMCID: PMC9313409 DOI: 10.3390/bios12070489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 05/05/2023]
Abstract
Over the past-decade, agricultural products (such as vegetables and fruits) have been reported as the major vehicles for foodborne diseases, which are limiting food resources. The spread of infectious diseases due to foodborne pathogens poses a global threat to human health and the economy. The accurate and timely detection of infectious disease and of causative pathogens is crucial in the prevention and treatment of disease. Negligence in the detection of pathogenic substances can be catastrophic and lead to a pandemic. Despite the revolution in health diagnostics, much attention has been paid to the agro-food sector regarding the detection of food contaminants (such as pathogens). The conventional analytical techniques for pathogen detection are reliable and still in operation. However, laborious procedures and time-consuming detection via these approaches emphasize the need for simple, easy-to-use, and affordable detection techniques. The rapid detection of pathogens from food is essential to avoid the morbidity and mortality originating from the suboptimal nature of empiric pathogen treatment. This review critically discusses both the conventional and emerging bio-molecular approaches for pathogen detection in agro-food.
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Affiliation(s)
- Monika Nehra
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Virendra Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Rajesh Kumar
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
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Evaluation of a Novel Chromogenic Medium for the Detection of Pseudomonas aeruginosa in Respiratory Samples from Patients with Cystic Fibrosis. Microorganisms 2022; 10:microorganisms10051004. [PMID: 35630446 PMCID: PMC9144526 DOI: 10.3390/microorganisms10051004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 02/01/2023] Open
Abstract
Pseudomonas aeruginosa is a dominant cause of respiratory infection in individuals with cystic fibrosis (CF), leading to significant morbidity and mortality. Detection of P. aeruginosa is conducted by culture of respiratory samples but this process may occasionally be compromised due to overgrowth by other bacteria and fungi. We aimed to evaluate a novel chromogenic medium, Pseudomonas aeruginosa chromogenic agar (PACA), for culture of P. aeruginosa from respiratory samples, from patients with CF. A total of 198 respiratory samples were cultured onto PACA and three other media: CHROMID®P. aeruginosa, CHROMagar™ Pseudomonas and MacConkey agar. P. aeruginosa was recovered from 66 samples (33%), using a combination of all media. After 72 h incubation, the sensitivity of the four chromogenic media was as follows: 91% for PACA and CHROMagar™ Pseudomonas, 85% for CHROMID®P. aeruginosa and 83% for MacConkey agar. For the three chromogenic media, the positive predictive value after 72 h was as follows: 95% for PACA, 56% for CHROMagar™ Pseudomonas and 86% for CHROMID®P. aeruginosa. PACA proved to be a highly effective culture medium for the isolation and specific detection of P. aeruginosa from respiratory samples.
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Morsby JJ, Smith BD. Advances in Optical Sensors of N-Acetyl-β-d-hexosaminidase ( N-Acetyl-β-d-glucosaminidase). Bioconjug Chem 2022; 33:544-554. [PMID: 35302753 PMCID: PMC9870670 DOI: 10.1021/acs.bioconjchem.2c00057] [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: 01/26/2023]
Abstract
N-Acetyl-β-d-hexosaminidases (EC 3.2.1.52) are exo-acting glycosyl hydrolases that remove N-acetyl-β-d-glucosamine (Glc-NAc) or N-acetyl-β-d-galactosamine (Gal-NAc) from the nonreducing ends of various biomolecules including oligosaccharides, glycoproteins, and glycolipids. The same enzymes are sometimes called N-acetyl-β-d-glucosaminidases, and this review article employs the shorthand descriptor HEX(NAG) to indicate that the terms HEX or NAG are used interchangeably in the literature. The wide distribution of HEX(NAG) throughout the biosphere and its intracellular location in lysosomes combine to make it an important enzyme in food science, agriculture, cell biology, medical diagnostics, and chemotherapy. For more than 50 years, researchers have employed chromogenic derivatives of N-acetyl-β-d-glucosaminide in basic assays for biomedical research and clinical chemistry. Recent conceptual and synthetic innovations in molecular fluorescence sensors, along with concurrent technical improvements in instrumentation, have produced a growing number of new fluorescent imaging and diagnostics methods. A systematic summary of the recent advances in optical sensors for HEX(NAG) is provided under the following headings: assessing kidney health, detection and treatment of infectious disease, fluorescence imaging of cancer, treatment of lysosomal disorders, and reactive probes for chemical biology. The article concludes with some comments on likely future directions.
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Affiliation(s)
| | - Bradley D. Smith
- Corresponding Author: Bradley D. Smith - Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, IN 46556, USA.
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Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods. Antibiotics (Basel) 2022; 11:antibiotics11040427. [PMID: 35453179 PMCID: PMC9024665 DOI: 10.3390/antibiotics11040427] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Antimicrobial resistance (AMR) has emerged as a major threat to public health globally. Accurate and rapid detection of resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment, combined with antimicrobial stewardship, are essential for controlling the emergence and spread of AMR. This article reviews common antimicrobial susceptibility testing (AST) methods and relevant issues concerning the advantages and disadvantages of each method. Although accurate, classic technologies used in clinical microbiology to profile antimicrobial susceptibility are time-consuming and relatively expensive. As a result, physicians often prescribe empirical antimicrobial therapies and broad-spectrum antibiotics. Although recently developed AST systems have shown advantages over traditional methods in terms of testing speed and the potential for providing a deeper insight into resistance mechanisms, extensive validation is required to translate these methodologies to clinical practice. With a continuous increase in antimicrobial resistance, additional efforts are needed to develop innovative, rapid, accurate, and portable diagnostic tools for AST. The wide implementation of novel devices would enable the identification of the optimal treatment approaches and the surveillance of antibiotic resistance in health, agriculture, and the environment, allowing monitoring and better tackling the emergence of AMR.
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Novel Chromogenic Medium CHROMagarTM Candida Plus for Detection of Candida auris and Other Candida Species from Surveillance and Environmental Samples: A Multicenter Study. J Fungi (Basel) 2022; 8:jof8030281. [PMID: 35330283 PMCID: PMC8950881 DOI: 10.3390/jof8030281] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 02/04/2023] Open
Abstract
Epidemiological trends show a dramatic increase in the prevalence of fungal infections, and in the isolation of multidrug-resistant species, such as Candida auris. CHROMagarTM Candida (CC; CHROMagar, Paris, France) and other chromogenic media, which are widely used in the clinical laboratory because they allow a rapid identification of most Candida species. Recently, CHROMagarTM Candida Plus (CC-Plus; CHROMagar, Paris, France) was developed to detect and differentiate C. auris in addition to other major clinical Candida species, such as C. albicans, C. tropicalis, C. glabrata, or C. krusei. C. auris colonies display a differential light blue color with a blue halo. A multicentric study was designed to evaluate the performance of the CC-Plus medium in the detection of Candida species in patients’ surveillance and environmental samples from three Spanish hospitals with active C. auris outbreaks. A total of 364 patients’ surveillance samples and 212 environmental samples were tested. Samples were inoculated in CC and CC-Plus in parallel, and the plates were read at 24 and 48 h. All recovered colonies were presumptively identified according to colony color described by manufacturer, and the definitive identification was performed by mass spectrometry at 48 h. A total of 134 C. auris isolates were obtained (101 from patients’ surveillance samples, and 33 from environmental samples). Sensitivity, specificity, and predictive positive and negative values were 99.5%, 100%, 100%, and 99.1%, respectively, for the main clinical Candida species, showing that CC-Plus is comparable to CC, with the advantage of being able to differentiate C. auris from C. parapsilosis. Furthermore, CC-Plus was able to detect one C. albicans, one C. glabrata, and eight C. auris that did not grow in CC. Additionally, the yeast colonies were generally larger, suggesting that this novel medium could be a richer medium, and suitable for surveillance and environmental cultures of C. auris and other clinically relevant Candida species.
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Căpățînă D, Feier B, Hosu O, Tertiș M, Cristea C. Analytical methods for the characterization and diagnosis of infection with Pseudomonas aeruginosa: A critical review. Anal Chim Acta 2022; 1204:339696. [DOI: 10.1016/j.aca.2022.339696] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/05/2022] [Accepted: 03/06/2022] [Indexed: 12/11/2022]
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Mendonça A, Santos H, Franco-Duarte R, Sampaio P. Fungal infections diagnosis - Past, present and future. Res Microbiol 2022; 173:103915. [PMID: 34863883 PMCID: PMC8634697 DOI: 10.1016/j.resmic.2021.103915] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 01/07/2023]
Abstract
Despite the scientific advances observed in the recent decades and the emergence of new methodologies, the diagnosis of systemic fungal infections persists as a problematic issue. Fungal cultivation, the standard method that allows a proven diagnosis, has numerous disadvantages, as low sensitivity (only 50% of the patients present positive fungal cultures), and long growth time. These are factors that delay the patient's treatment and, consequently, lead to higher hospital costs. To improve the accuracy and quickness of fungal infections diagnosis, several new methodologies attempt to be implemented in clinical microbiology laboratories. Most of these innovative methods are independent of pathogen isolation, which means that the diagnosis goes from being considered proven to probable. In spite of the advantage of being culture-independent, the majority of the methods lack standardization. PCR-based methods are becoming more and more commonly used, which has earned them an important place in hospital laboratories. This can be perceived now, as PCR-based methodologies have proved to be an essential tool fighting against the COVID-19 pandemic. This review aims to go through the main steps of the diagnosis for systemic fungal infection, from diagnostic classifications, through methodologies considered as "gold standard", to the molecular methods currently used, and finally mentioning some of the more futuristic approaches.
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Jia Z, Müller M, Le Gall T, Riool M, Müller M, Zaat SA, Montier T, Schönherr H. Multiplexed detection and differentiation of bacterial enzymes and bacteria by color-encoded sensor hydrogels. Bioact Mater 2021; 6:4286-4300. [PMID: 33997506 PMCID: PMC8105640 DOI: 10.1016/j.bioactmat.2021.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/12/2021] [Accepted: 04/09/2021] [Indexed: 12/19/2022] Open
Abstract
We report on the fabrication and characterization of color-encoded chitosan hydrogels for the rapid, sensitive and specific detection of bacterial enzymes as well as the selective detection of a set of tested bacteria through characteristic enzyme reactions. These patterned sensor hydrogels are functionalized with three different colorimetric enzyme substrates affording the multiplexed detection and differentiation of α-glucosidase, β-galactosidase and β-glucuronidase. The limits of detection of the hydrogels for an observation time of 60 min using a conventional microplate reader correspond to concentrations of 0.2, 3.4 and 4.5 nM of these enzymes, respectively. Based on their different enzyme expression patterns, Staphylococcus aureus strain RN4220, methicillin-resistant S. aureus (MRSA) strain N315, both producing α-glucosidase, but not β-glucuronidase and β-galactosidase, Escherichia coli strain DH5α, producing β-glucuronidase and α-glucosidase, but not β-galactosidase, and the enterohemorrhagic E. coli (EHEC) strain E32511, producing β-galactosidase, but none of the other two enzymes, can be reliably and rapidly distinguished from each other. These results confirm the applicability of enzyme sensing hydrogels for the detection and discrimination of specific enzymes to facilitate differentiation of bacterial strains. Patterned hydrogels thus possess the potential to be further refined as detection units of a multiplexed format to identify certain bacteria for future application in point-of-care microbiological diagnostics in food safety and medical settings.
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Affiliation(s)
- Zhiyuan Jia
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076, Siegen, Germany
| | - Mareike Müller
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076, Siegen, Germany
| | - Tony Le Gall
- Univ Brest, INSERM, EFS, UMR 1078 GGFB, F-29200, Brest, France
| | - Martijn Riool
- Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Max Müller
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076, Siegen, Germany
| | - Sebastian A.J. Zaat
- Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Tristan Montier
- Univ Brest, INSERM, EFS, UMR 1078 GGFB, F-29200, Brest, France
- CHRU de Brest, Service de génétique médicale et de biologie de la reproduction, Centre de Référence des Maladies Rares « Maladies neuromusculaires », F-29200, Brest, France
| | - Holger Schönherr
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076, Siegen, Germany
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Validation of Selective Agars for Detection and Quantification of Escherichia coli Strains Resistant to Critically Important Antimicrobials. Microbiol Spectr 2021; 9:e0066421. [PMID: 34756091 PMCID: PMC8579925 DOI: 10.1128/spectrum.00664-21] [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: 11/20/2022] Open
Abstract
Success in the global fight against antimicrobial resistance (AMR) is likely to improve if surveillance can be performed on an epidemiological scale. An approach based on agars with incorporated antimicrobials has enormous potential to achieve this. However, there is a need to identify the combinations of selective agars and key antimicrobials yielding the most accurate counts of susceptible and resistant organisms. A series of experiments involving 1,202 plates identified the best candidate combinations from six commercially available agars and five antimicrobials, using 18 Escherichia coli strains as either pure cultures or inocula-spiked feces. The effects of various design factors on colony counts were analyzed in generalized linear models. Without antimicrobials, Brilliance E. coli and CHROMagar ECC agars yielded 28.9% and 23.5% more colonies, respectively, than MacConkey agar. The order of superiority of agars remained unchanged when fecal samples with or without spiking of resistant E. coli strains were inoculated onto agars with or without specific antimicrobials. When antimicrobials were incorporated at various concentrations, it was revealed that ampicillin, tetracycline, and ciprofloxacin were suitable for incorporation into Brilliance and CHROMagar agars at all defined concentrations. Gentamicin was suitable for incorporation only at 8 and 16 μg/ml, while ceftiofur was suitable only at 1 μg/ml. CHROMagar extended-spectrum β-lactamase (ESBL) agar supported growth of a wider diversity of extended-spectrum-cephalosporin-resistant E. coli strains. The findings demonstrate the potential for agars with incorporated antimicrobials to be combined with laboratory-based robotics to deliver AMR surveillance on a vast scale with greater sensitivity of detection and strategic relevance. IMPORTANCE Established models of surveillance for AMR in livestock typically have a low sampling intensity, which creates a tremendous barrier to understanding the variation of resistance among animal and food enterprises. However, developments in laboratory robotics now make it possible to rapidly and affordably process large volumes of samples. Combined with modern selective agars incorporating antimicrobials, this forms the basis of a novel surveillance process for identifying resistant bacteria by chromogenic reactions, including accurately detecting and quantifying the presence of bacteria even when they are present at low concentrations. Because Escherichia coli is a widely preferred indicator bacterium for AMR surveillance, this study identifies the optimal selective agar for quantifying resistant E. coli strains by assessing the growth performance on agars with antimicrobials. The findings are the first step toward exploiting laboratory robotics in an up-scaled approach to AMR surveillance in livestock, with wider adaptations in food, clinical microbiology, and public health.
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A Galactosidase-Activatable Fluorescent Probe for Detection of Bacteria Based on BODIPY. Molecules 2021; 26:molecules26196072. [PMID: 34641615 PMCID: PMC8512000 DOI: 10.3390/molecules26196072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Pathogenic E. coli infection is one of the most widespread foodborne diseases, so the development of sensitive, reliable and easy operating detection tests is a key issue for food safety. Identifying bacteria with a fluorescent medium is more sensitive and faster than using chromogenic media. This study designed and synthesized a β-galactosidase-activatable fluorescent probe BOD-Gal for the sensitive detection of E. coli. It employed a biocompatible and photostable 4,4-difluoro-3a,4a-diaza-s-indancene (BODIPY) as the fluorophore to form a β-O-glycosidic bond with galactose, allowing the BOD-Gal to show significant on-off fluorescent signals for in vitro and in vivo bacterial detection. This work shows the potential for the use of a BODIPY based enzyme substrate for pathogen detection.
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Le Moigne V, Roux AL, Mahoudo H, Christien G, Ferroni A, Dumitrescu O, Lina G, Bouchara JP, Plésiat P, Gaillard JL, Canaan S, Héry-Arnaud G, Herrmann JL. Serological biomarkers for the diagnosis of Mycobacterium abscessus infections in cystic fibrosis patients. J Cyst Fibros 2021; 21:353-360. [PMID: 34511392 DOI: 10.1016/j.jcf.2021.08.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/19/2021] [Accepted: 08/23/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Culture conditions sometimes make it difficult to detect non-tuberculous mycobacteria (NTM), particularly Mycobacterium abscessus, an emerging cystic fibrosis (CF) pathogen. The diagnosis of NTM positive cases not detected by classical culture methods might benefit from the development of a serological assay. METHODS As part of a diagnostic accuracy study, a total of 173 sera CF-patients, including 33 patients with M. abscessus positive cultures, and 31 non-CF healthy controls (HC) were evaluated. Four M. abscessus antigens were used separately, comprising two surface extracts (Interphase (INP) and a TLR2 positive extract (TLR2eF)) and two recombinant proteins (rMAB_2545c and rMAB_0555 also known as the phospholipase C (rPLC)). RESULTS TLR2eF and rPLC were the most efficient antigens to discriminate NTM-culture positive CF-patients from NTM-culture negative CF-patients. The best clinical values were obtained for the detection of M. abscessus-culture positive CF-patients; with sensitivities for the TLR2eF and rPLC of 81.2% (95% CI:65.7-92.3%) and 87.9% (95% CI:71.9-95.6%) respectively, and specificities of 88.9% (95% CI:85.3-94.8%) and 84.8% (95% CI:80.6-91.5%) respectively. When considering as positive all sera, giving a positive response in at least one of the two tests, and, as negative, all sera negative for both tests, we obtained a sensitivity of 93.9% and a specificity of 80.7% for the detection of M. abscessus-culture positive CF-patients. CONCLUSION High antibody titers against TLR2eF and rPLC were obtained in M. abscessus-culture positive CF-patients, allowing us to consider these serological markers as potential tools in the detection of CF-patients infected with M. abscessus.
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Affiliation(s)
- Vincent Le Moigne
- Université Paris Saclay, UVSQ, Inserm, Infection et Inflammation, Montigny-le-Bretonneux, France.
| | - Anne-Laure Roux
- Université Paris Saclay, UVSQ, Inserm, Infection et Inflammation, Montigny-le-Bretonneux, France; AP-HP, GHU Paris Saclay, Hôpital Ambroise Paré, Service de Microbiologie, Boulogne-Billancourt, France
| | - Hélène Mahoudo
- Université Paris Saclay, UVSQ, Inserm, Infection et Inflammation, Montigny-le-Bretonneux, France
| | - Gaëtan Christien
- Université Paris Saclay, UVSQ, Inserm, Infection et Inflammation, Montigny-le-Bretonneux, France
| | - Agnès Ferroni
- AP-HP, GHU Paris, Hôpital Necker-Enfants Malades, Service de Microbiologie, Paris 15e, France
| | - Oana Dumitrescu
- Hospices Civils de Lyon, Hôpital de la Croix Rousse-Centre de Biologie Nord, Institut des Agents Infectieux, Laboratoire de Bactériologie, Grande Rue de la Croix Rousse, 69004, Lyon, France; Centre International de Recherche en Infectiologie, INSERM U1111, Université de Lyon, Lyon, France
| | - Gérard Lina
- Hospices Civils de Lyon, Hôpital de la Croix Rousse-Centre de Biologie Nord, Institut des Agents Infectieux, Laboratoire de Bactériologie, Grande Rue de la Croix Rousse, 69004, Lyon, France; Centre International de Recherche en Infectiologie, INSERM U1111, Université de Lyon, Lyon, France
| | - Jean-Philippe Bouchara
- CHU, Service de Parasitologie-Mycologie, Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), UNIV Angers, UNIV Brest, SFR 4208 ICAT, Angers, France
| | - Patrick Plésiat
- Laboratoire de Bactériologie, CHRU de Besançon, UMR CNRS 6249 Chrono-Environnement, Faculté de Médecine-Pharmacie, Université de Bourgogne Franche-Comté, Besançon, France
| | - Jean-Louis Gaillard
- Université Paris Saclay, UVSQ, Inserm, Infection et Inflammation, Montigny-le-Bretonneux, France; AP-HP, GHU Paris Saclay, Hôpital Ambroise Paré, Service de Microbiologie, Boulogne-Billancourt, France
| | - Stéphane Canaan
- Université Aix-Marseille, CNRS, LISM, IMM FR3479, Marseille, France
| | - Geneviève Héry-Arnaud
- Département de bactériologie-virologie, hygiène et parasitologie-mycologie, centre hospitalier régional universitaire (CHRU) de Brest, Brest, France; Inserm, EFS, UMR 1078 France « génétique, génomique fonctionnelle et biotechnologies », GGB, université Brest, 29200 Brest, France
| | - Jean-Louis Herrmann
- Université Paris Saclay, UVSQ, Inserm, Infection et Inflammation, Montigny-le-Bretonneux, France; AP-HP, GHU Paris Saclay, Hôpital Raymond Poincaré, Service de Microbiologie, Garches, France.
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Złoch M, Maślak E, Kupczyk W, Jackowski M, Pomastowski P, Buszewski B. Culturomics Approach to Identify Diabetic Foot Infection Bacteria. Int J Mol Sci 2021; 22:ijms22179574. [PMID: 34502482 PMCID: PMC8431627 DOI: 10.3390/ijms22179574] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/18/2022] Open
Abstract
The main goal of the study was to evaluate the usefulness of the culturomics approach in the reflection of diabetic foot infections (DFIs) microbial compositions in Poland. Superficial swab samples of 16 diabetic foot infection patients (Provincial Polyclinical Hospital in Toruń, Poland) were subjected to culturing using 10 different types of media followed by the identification via the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and Biotyper platform. Identified 204 bacterial isolates representing 18 different species—mostly Enterococcus faecalis (63%) and Staphylococcus aureus (44%). Most of the infections (81%) demonstrated a polymicrobial character. Great differences in the species coverage, the number of isolated Gram-positive and Gram-negative bacteria, and the efficiency of the microbial composition reflection between the investigated media were revealed. The use of commonly recommended blood agar allowed to reveal only 53% of the entire microbial composition of the diabetic foot infection samples, which considerably improved when the chromagar orientation and vancomycin-resistant enterococi agar were applied. In general, efficiency increased in the following order: selective < universal < enriched < differential media. Performed analysis also revealed the impact of the culture media composition on the molecular profiles of some bacterial species, such as Corynebacterium striatum, Proteus mirabilis or Morganella morganii that contributed to the differences in the identification quality. Our results indicated that the culturomics approach can significantly improve the accuracy of the reflection of the diabetic foot infections microbial compositions as long as an appropriate media set is selected. The chromagar orientation and vancomycin-resistant enterococi agar media which were used for the first time to study diabetic foot infection microbial profiles demonstrate the highest utility in the culturomics approach and should be included in further studies directed to find a faster and more reliable diabetic foot infection diagnostic tool.
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Affiliation(s)
- Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (P.P.); (B.B.)
- Correspondence: ; Tel.: +48-56-611-60-60
| | - Ewelina Maślak
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (P.P.); (B.B.)
| | - Wojciech Kupczyk
- Department of General, Gastroenterological and Oncological Surgery, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Torun, Poland; (W.K.); (M.J.)
| | - Marek Jackowski
- Department of General, Gastroenterological and Oncological Surgery, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Torun, Poland; (W.K.); (M.J.)
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (P.P.); (B.B.)
| | - Bogusław Buszewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (P.P.); (B.B.)
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7 Str., 87-100 Toruń, Poland
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Lephart P, LeBar W, Newton D. Behind Every Great Infection Prevention Program is a Great Microbiology Laboratory: Key Components and Strategies for an Effective Partnership. Infect Dis Clin North Am 2021; 35:789-802. [PMID: 34362544 DOI: 10.1016/j.idc.2021.04.012] [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: 11/18/2022]
Abstract
A great clinical microbiology laboratory supporting a great infection prevention program requires focusing on the following services: rapid and accurate identification of pathogens associated with health care-associated infections; asymptomatic surveillance for health care-acquired pathogens before infections arise; routine use of broad and flexible antimicrobial susceptibility testing to direct optimal therapy; implementation of epidemiologic tracking tools to identify outbreaks; development of clear result communication with interpretative comments for clinicians. These goals are best realized in a collaborative relationship with the infection prevention program so that both can benefit from the shared priorities of providing the best patient care.
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Affiliation(s)
- Paul Lephart
- Clinical Microbiology Laboratory, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA.
| | - William LeBar
- Clinical Microbiology Laboratory, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA
| | - Duane Newton
- NaviDx Consulting, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA
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Evaluation of CHROMagar™-Serratia agar, a new chromogenic medium for the detection and isolation of Serratia marcescens. Eur J Clin Microbiol Infect Dis 2021; 40:2593-2596. [PMID: 34363530 PMCID: PMC8590650 DOI: 10.1007/s10096-021-04328-w] [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] [Received: 03/05/2021] [Accepted: 07/29/2021] [Indexed: 11/27/2022]
Abstract
A comparative analysis of the performance of the new selective chromogenic CHROMagar™-Serratia culture medium for detection and isolation of Serratia marcescens was undertaken. A total of 134 clinical isolates (95 S. marcescens with and without carbapenemase production and 39 non-S. marcescens isolates) and 96 epidemiological samples (46 rectal swabs and 50 from environmental surfaces) were studied. Diagnostic values when compared with CHROMagar™-Orientation medium were 96.8% sensitivity, 100% specificity, 100% positive predictive value and 88.5% negative predictive value. In conclusion, CHROMagar™-Serratia shows an excellent ability for differentiation of S. marcescens among clinical isolates and in environmental samples.
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Salamandane A, Vila-Boa F, Malfeito-Ferreira M, Brito L. High Fecal Contamination and High Levels of Antibiotic-Resistant Enterobacteriaceae in Water Consumed in the City of Maputo, Mozambique. BIOLOGY 2021; 10:biology10060558. [PMID: 34203039 PMCID: PMC8235334 DOI: 10.3390/biology10060558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 12/14/2022]
Abstract
Simple Summary The high number of diarrheal disease cases in developing countries is related to sanitation conditions, consumption of untreated water, and poor individual and collective hygiene. In this study, the microbiological quality of water sold and consumed in the city of Maputo, Mozambique, and the antibiotic resistance profile of Enterobacteriaceae isolated from these samples were evaluated. The results showed the occurrence of microorganisms that indicate fecal contamination with enterococci, fecal coliforms, and Escherichia coli above the limit legally allowed for drinking water. The antibiotic resistance profile revealed the existence of antibiotic-resistant bacteria. These results show the need to improve the water supply system in the city of Maputo and to educate the population on hygiene to reduce health risks and promote well-being. Abstract In the city of Maputo, Mozambique, food and water are often sold on the streets. Street water is packaged, distributed, and sold not paying attention to good hygienic practices, and its consumption is often associated with the occurrence of diarrheal diseases. Coincidentally, the increase of diarrheal diseases promotes the inappropriate use of antibiotics that might cause the emergence of antibiotic-resistant bacterial strains. In this context, the present study aimed to assess the microbiological quality of water sold on the streets of Maputo, as well as the antibiotic resistance profile of selected Enterobacteriaceae isolates. The 118 water samples analyzed were from street home-bottled water (n = 81), municipal water distribution systems (tap water) (n = 25), and selected supply wells in several neighborhoods (n = 12). The samples were analyzed for total mesophilic microorganisms, fecal enterococci, fecal coliforms, Escherichia coli, and Vibrio spp. The results showed a high level of fecal contamination in all types of water samples. In home-bottled water, fecal coliforms were found in 88% of the samples, and E. coli in 66% of the samples. In tap water, fecal coliforms were found in 64%, and E. coli in 28% of the samples. In water from supply wells, fecal coliforms and E. coli were found in 83% of the samples. From 33 presumptive Vibrio spp. colonies, only three were identified as V. fluvialis. The remaining isolates belonged to Aeromonas spp. (n = 14) and Klebsiella spp. (n = 16). Of 44 selected Enterobacteriaceae isolates from water samples (28 isolates of E. coli and 16 isolates of Klebsiella spp.), 45.5% were not susceptible to the beta-lactams ampicillin and imipenem, 43.2% to amoxicillin, and 31.8% to amoxicillin/clavulanic acid. Regarding non-beta-lactam antibiotics, there was a high percentage of isolates with tolerance to tetracycline (52.3%) and azithromycin (31.8%). In conclusion, water in Maputo represents a risk for human health due to its high fecal contamination. This situation is made more serious by the fact that a relatively high percentage of isolates with multidrug resistance (40%) were found among Enterobacteriaceae. The dissemination of these results can raise awareness of the urgent need to reduce water contamination in Maputo and other cities in Mozambique.
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