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Hennessey M, Alarcon P, Samanta I, Fournié G, Paleja H, Papaiyan K, Gautham M. Formulating antibiotic policy: Analysis of India's ban on colistin use in food producing animals. Prev Vet Med 2025; 240:106534. [PMID: 40273740 DOI: 10.1016/j.prevetmed.2025.106534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Revised: 04/07/2025] [Accepted: 04/12/2025] [Indexed: 04/26/2025]
Abstract
Antibiotics remain key tools for maintaining human health, and in many settings, food production. However, emergence of antibiotic resistance has become a global challenge, one that has resulted in multi-national calls for policy to improve antibiotic use. One such call has been to restrict the use of antibiotics deemed critically important for human health, such as colistin, during the production of food producing animals. Between 2016 and 2019 numerous countries, including India, implemented policies to heavily restricted the use of colistin in livestock. While this represents a key shift in the antibiotic policy landscape, other classes of critically important antibiotics continue to be used during food production. This paper provides a policy analysis of India's 2019 colistin ban to provide insight into how this came to be and to identify factors which could shape the development of future legislation. The analysis revealed that while antibiotic reform in food production had been in the background of India's policy agenda for some time, it took key-focusing events to shift the policy climate into a period of action. These focusing events included reporting of mobile colistin resistance genes in bacteria isolated from pigs in China and colistin resistant bacteria isolated from food samples in India. Consistent narratives had been built around colistin's role as a last resort antibiotic which, together with relatively low proportion of colistin resistance in bacteria isolated from human patients, framed legislation as a worthwhile endeavour for policy makers. In addition, India acted as a global player in antibiotic stewardship and followed the precedent set by several other countries in restricting colistin use during food production. As most colistin for animal use was imported into India from China, and viable alternative animal treatments existed, there was limited industry opposition that could block legislation. We suggest evaluation of these five critical factors (focusing events, consistent narratives, worthwhile endeavour, precedent for change, and industry opposition) should be part of the policy formulation process for legislation regarding the use of other critically important antibiotics in food production.
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Affiliation(s)
- Mathew Hennessey
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, WOAH Collaborating Centre in Risk Analysis and Modelling, Royal Veterinary College, London, UK.
| | - Pablo Alarcon
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, WOAH Collaborating Centre in Risk Analysis and Modelling, Royal Veterinary College, London, UK
| | - Indranil Samanta
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Guillaume Fournié
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, WOAH Collaborating Centre in Risk Analysis and Modelling, Royal Veterinary College, London, UK; Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France; Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - Haidaruliman Paleja
- Department of Veterinary Biotechnology, College of Veterinary Science and Animal Husbandry, Kamdhenu University, Anand, India
| | - Kumaravel Papaiyan
- Dean, Veterinary College and Research Institute, Udumalpet, TANUVAS, India
| | - Meenakshi Gautham
- Department of Global Health and Development, Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK
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Aluzaite K, Soares MO, Hewitt C, Robotham J, Painter C, Woods B. Economic Evaluation of Interventions to Reduce Antimicrobial Resistance: A Systematic Literature Review of Methods. PHARMACOECONOMICS 2025; 43:631-646. [PMID: 40048093 DOI: 10.1007/s40273-024-01468-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/17/2024] [Indexed: 05/16/2025]
Abstract
BACKGROUND AND OBJECTIVE Economic evaluation of antimicrobial resistance (AMR) interventions is complicated by the multisectoral, inter-temporal and international aspects of the problem, further hindered by a lack of available data and theoretical understanding of the emergence and transmission of AMR. Despite the substantial global focus on the problem, there is a lack of comprehensive economic evaluation literature on AMR policies. The goal of this work is to review the available literature on the economic evaluation of AMR interventions focusing on methods used to quantify the effects on AMR and the associated health consequences and costs. METHODS The studies included in the review were identified by a previous study by Painter et al. that included all full economic evaluations of AMR policies in the peer-reviewed and grey literature published between 2000 and 2020. The current review extracted additional information to (1) summarise the types and the key features of the AMR intervention economic evaluation literature available; (2) systemise the types of intervention effects on AMR quantified and describe these across the dimensions of AMR burden: time, space, wider pathogen pool and different sectors (One Health framework); and (3) categorise the methods used to derive these outcomes and how were these linked to health consequences and costs. RESULTS Thirty-one studies were included within this review, of which 18 evaluated interventions that aimed to reduce infection rates and 11 evaluated interventions that aimed to optimise antimicrobial use. Almost all were conducted with a high-income and/or upper-middle income country perspective and focused on human health. Thirteen of 31 studies were cost-utility analyses. Fifteen of 31 and 7/31 studies estimated the AMR effects through decision tree and/or Markov models and transmission models, respectively. Transmission models and linkage of AMR outcomes to quality-adjusted life-years and costs were more common in evaluations of interventions aimed at reducing infection rates. Most of the included studies restricted the scope of evaluation to a short time horizon and a narrow geographical scope and did not consider the wider impact on other pathogens and other settings, potentially resulting in an incomplete capture of the effects of interventions. CONCLUSIONS This review found limited available literature that mainly focused on high-income countries and infection prevention/reduction strategies. Most evaluations used a narrow study scope, which might have prevented the full capture of the costs and outcomes associated with interventions. Finally, despite the known complexities associated with quantifying AMR effects, and the corresponding methodological challenges, the implications of these choices were rarely discussed explicitly.
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Affiliation(s)
- Kristina Aluzaite
- Centre for Health Economics, Alcuin a Block, University of York, York, YO10 5DD, UK.
- UK Health Security Agency, London, UK.
| | - Marta O Soares
- Centre for Health Economics, Alcuin a Block, University of York, York, YO10 5DD, UK
| | - Catherine Hewitt
- York Trials Unit, Department of Health Sciences, University of York, York, UK
| | | | - Chris Painter
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Lao-Oxford-Mahosot Hospital-Welcome Trust Research Unit (LOMWRU), Mahosot Hospital, Vientiane, Lao PDR
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Beth Woods
- Centre for Health Economics, Alcuin a Block, University of York, York, YO10 5DD, UK
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3
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Liu Z, Ma S, Zhao C, Yan S, Zhu L. Tenfold multiplex PCR method for simultaneous detection of mcr-1 to mcr-10 genes and application for retrospective investigations of Salmonella and Escherichia coli isolates in China. Microb Pathog 2025; 203:107478. [PMID: 40086740 DOI: 10.1016/j.micpath.2025.107478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 02/26/2025] [Accepted: 03/11/2025] [Indexed: 03/16/2025]
Abstract
The increasing prevalence of antimicrobial resistance has raised significant concern globally. Colistin is currently considered a last resort for treating Gram-negative bacterial infections. However, the emergence of colistin resistance has led to a difficult situation against bacterial infections. Therefore, the monitoring of colistin resistance is of great importance for the control of bacterial infections. The mobile colistin resistance (mcr) gene has been identified as a colistin resistance gene, and ten mcr genes (mcr-1 to mcr-10) have been identified to date. Hence, the detection of mcr genes can help predict bacterial colistin resistance at the molecular level. However, there have not been reported multiplex PCR methods for simultaneously detecting mcr-1 to mcr-10 until now. In this study, we established a one-step multiplex PCR method for simultaneous detection of mcr-1 to mcr-10 for the first time. Furthermore, we retrospectively investigated the prevalence of the ten mcr genes in Escherichia coli (E. coli) and Salmonella isolates in China. The results showed that the mcr detection rate of Salmonella isolated during 2004-2019 was 4.73 % (16/338), and only mcr-9 was harbored. As well, the mcr detection rate of E. coli isolated during 2012-2015 was 20.42 % (49/240) and only mcr-1 was identified. Moreover, we also investigated the relationship between mcr harboring and colistin phenotype-resistance. The broth micro-dilution assay results showed that all mcr-1-positive E. coli isolates were colistin-resistant. However, all mcr-9-positive Salmonella isolates did not represent colistin-resistance. Our findings are beneficial for the monitoring and control of colistin resistance.
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Affiliation(s)
- Zhenhai Liu
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Shunan Ma
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Chen Zhao
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Shigan Yan
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
| | - Liping Zhu
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
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4
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Mistry K, Thumbi D, Li XR, Charlebois A, Avery BP, Deckert AE, Cormier AC, Murphy C, Kearney A, Campbell J, Christianson S, Alexander DC, El Bailey S, Bekal S, Chui L, Ding X, Dingle T, Haldane D, Hoang L, Minion J, Patel S, Zahariadis G, Nadon C, Mulvey MR, Carson CA, Reid-Smith RJ, Bharat A. One Health study of mobile colistin resistance ( mcr) in Salmonella enterica in Canada, 2017-2022. Microbiol Spectr 2025:e0215624. [PMID: 40387317 DOI: 10.1128/spectrum.02156-24] [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: 08/27/2024] [Accepted: 04/07/2025] [Indexed: 05/20/2025] Open
Abstract
Colistin is a last-resort treatment for highly drug-resistant bacterial infections. Of 47,184 Salmonella isolates collected from 2017 to 2022 in Canada from human and animal/food sources, mobile colistin resistance (mcr) variants conferring colistin resistance were detected exclusively in humans (n = 15). These variants were mcr-1.1 (n = 7), mcr-3.1 (n = 5), mcr-3.2 (n = 2), and mcr-1.2 (n = 1). The most common mcr-containing serotypes were I 4,[5],12:i:- (n = 8) and Typhimurium (n = 3). The proportion of Salmonella carrying mcr genes remains low in Canada (0.03%). IMPORTANCE Colistin can be used in combination with other drugs as salvage therapy for extensively drug-resistant infections. If mobile colistin resistance (mcr) becomes widely disseminated in Enterobacterales, colistin will no longer be an option for salvage therapy in otherwise untreatable infections. While colistin is not commonly used to treat human Salmonella infections, Salmonella represents an important reservoir of mcr genes that may be transmitted to other gram-negative bacteria. Our aim was to determine the occurrence of mcr genes in Salmonella isolates collected from humans, food animals, and retail meats in Canada.
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Affiliation(s)
- Ketna Mistry
- National Microbiology Laboratory Branch, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - David Thumbi
- National Microbiology Laboratory Branch, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Xiao Rui Li
- National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Audrey Charlebois
- National Microbiology Laboratory Branch, Public Health Agency of Canada, Saint-Hyacinthe, Québec, Canada
| | - Brent P Avery
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Anne E Deckert
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Ashley C Cormier
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Colleen Murphy
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Ashley Kearney
- National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jennifer Campbell
- National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Sara Christianson
- National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - David C Alexander
- Cadham Provinical Laboratory, Diagnostic Services, Shared Health, Winnipeg, Manitoba, Canada
- Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sameh El Bailey
- Department of Laboratory Medicine, Horizon Health Network, Saint John, New Brunswick, Canada
| | - Sadjia Bekal
- Département de Bactériologie, Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Linda Chui
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaofeng Ding
- Provincial Laboratory Services, Queen Elizabeth Hospital, Charlottetown, Prince Edward Island, Canada
| | - Tanis Dingle
- Alberta Precision Laboratories, Public Health Laboratory, Calgary, Alberta, Canada
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - David Haldane
- Department of Pathology and Laboratory Medicine, Queen Elizabeth II Health Sciences Centre, Halifax, Nova Scotia, Canada
| | - Linda Hoang
- Public Health Laboratory, British Columbia Center for Disease Control, Vancouver, British Columbia, Canada
| | - Jessica Minion
- Saskatchewan Health Authority, Department of Laboratory Medicine, Roy Romanow Provincial Laboratory, Regina, Saskatchewan, Canada
| | - Samir Patel
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - George Zahariadis
- Department of Pathology and Laboratory Medicine, Newfoundland and Labrador Public Health and Microbiology Laboratory, St. John's, Newfoundland and Labrador, Canada
| | - Celine Nadon
- National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Carolee A Carson
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Richard J Reid-Smith
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Amrita Bharat
- National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
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5
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Wachino JI. Horizontal Gene Transfer Systems for Spread of Antibiotic Resistance in Gram-Negative Bacteria. Microbiol Immunol 2025. [PMID: 40370256 DOI: 10.1111/1348-0421.13222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2025] [Accepted: 04/04/2025] [Indexed: 05/16/2025]
Abstract
Antibiotic-resistant bacteria have become a significant global threat to public health due to the increasing difficulty in treatment. These bacteria acquire resistance by incorporating various antibiotic resistance genes (ARGs) through specialized gene transfer mechanisms, allowing them to evade antibiotic attacks. Conjugation, transformation, and transduction are well-established mechanisms that drive the acquisition and dissemination of ARGs in Gram-negative bacteria. In particular, the horizontal transfer of plasmids carrying multiple ARGs is highly problematic, as it can instantly convert susceptible bacteria into multidrug-resistant ones. Transduction, mediated by bacteriophages that package ARG-containing chromosomal DNA from host cells, also plays a crucial role in ARG spread without requiring direct cell-to-cell contact. Recently, a novel horizontal gene transfer (HGT) mechanism involving outer membrane vesicles (OMVs) has been identified as a key player in ARG dissemination. OMVs-nanoscale, spherical structures produced by bacteria during growth-have been found to carry small plasmids and chromosomal DNA fragments containing ARGs from their host bacteria. This newly discovered transfer process, termed "vesiduction," enables intercellular DNA exchange and further contributes to the spread of antibiotic resistance. Additionally, mobile genetic elements such as transposons, insertion sequences, and site-specific recombination systems like integrons facilitate rearrangement of ARGs, including their translocation between chromosomes and plasmids. This review explores the molecular mechanisms underlying the HGT of ARGs, with a particular focus on clinically isolated antibiotic-resistant Gram-negative bacteria.
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Affiliation(s)
- Jun-Ichi Wachino
- Department of Clinical Microbiology, Faculty of Medical Sciences, Fujita Health University, Toyoake, Aichi, Japan
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6
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Li J, Chang J, Ma J, Zhou W, Yang Y, Wu J, Guan C, Yuan X, Xu L, Yu B, Su F, Ye S, Chen Y, Zhao G, Tang B. Genome-based assessment of antimicrobial resistance of Escherichia coli recovered from diseased swine in eastern China for a 12-year period. mBio 2025; 16:e0065125. [PMID: 40243369 PMCID: PMC12077178 DOI: 10.1128/mbio.00651-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2025] [Accepted: 03/24/2025] [Indexed: 04/18/2025] Open
Abstract
The global rise of antimicrobial resistance (AMR), driven by antibiotic use in healthcare and agriculture, poses a major public health threat. While AMR in clinical settings is well studied, there is a gap in understanding the resistance profiles of Escherichia coli from diseased livestock, particularly regarding zoonotic transmission. This study analyzes 114 E. coli isolates from diseased swine over 12 years, revealing that 99.12% were multidrug-resistant. Resistance was highest for ampicillin and amoxicillin/clavulanic acid (100%), followed by ciprofloxacin (96.49%) and tetracycline (94.74%). Furthermore, 21.05% of isolates were resistant to colistin, and 1.75% to tigecycline. A total of 76 antimicrobial resistance genes (ARGs) were identified, with mcr-1 found in 18.42%, mcr-3 in 4.39%, and tet(X4) in 1.75%. Significant co-occurrence of ARGs and plasmids suggests potential for co-selective dissemination. This study is the first to report enterotoxigenic E. coli (ETEC) strains carrying both mcr-1 and mcr-3 genes. After the 2017 colistin ban in China, mcr-1 detection rates significantly decreased, while florfenicol resistance rates increased in 2018-2021 (94.29%) compared to 2010-2017 (79.55%). This work provides valuable insights into the AMR profiles of E. coli from diseased swine and highlights trends that can inform strategies for monitoring and controlling public health risks associated with zoonotic E. coli transmission.IMPORTANCEThis study highlights the critical role of diseased and deceased swine in the spread of antimicrobial resistance (AMR), providing new insights into the transmission of resistance genes in zoonotic contexts. By analyzing E. coli from diseased swine, we identify key resistance genes such as mcr-1, mcr-3, and tet(X4), which pose significant public health risks, especially regarding last-resort antibiotics like colistin. Moreover, the study identifies novel transmission patterns of mcr genes, including ETEC strains carrying the mcr-3 gene and strains harboring both mcr-1 and mcr-3 genes. The role of plasmids in horizontal gene transfer is also revealed, facilitating rapid AMR spread across species. The long-term persistence of resistant strains highlights the challenges in controlling AMR in livestock. These findings underscore the need for enhanced surveillance and a One Health approach to mitigate AMR risks across animal, human, and environmental health.
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Affiliation(s)
- Junxing Li
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jiang Chang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jiangang Ma
- Xianghu Laboratory, Hangzhou, Zhejiang, China
| | - Wei Zhou
- Zhejiang Provincial Center for Animal Disease Prevention and Control, Hangzhou, China
| | - Yue Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jing Wu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Chunjiu Guan
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Xiufang Yuan
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Lihua Xu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Bin Yu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Fei Su
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Shiyi Ye
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Yijie Chen
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Guoping Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Biao Tang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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7
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Zhang XW, Huang XY, Zhou ZY, Li BL, Lu JH, Song JJ, Li XY. Genetic framework and evolutionary dynamics of mcr-positive Klebsiella pneumoniae from 2000 to 2023. Int J Antimicrob Agents 2025:107533. [PMID: 40345343 DOI: 10.1016/j.ijantimicag.2025.107533] [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: 11/20/2024] [Revised: 02/04/2025] [Accepted: 05/01/2025] [Indexed: 05/11/2025]
Abstract
The international transmission of the colistin resistance gene mcr in Enterobacteriaceae poses significant public health burdens, while the understanding of the population structure and evolutionary history of mcr-positive Klebsiella pneumoniae worldwide remains unclear. Here, we conducted a genomic analysis on 463 sequences of K. pneumoniae harboring mcr genes from public database between 2000 and 2023. A total of 6 mcr variants (mcr-1, -2, -3, -8 to -10) were detected, with mcr-9 (36.1%), mcr-1 (33.7%) and mcr-8 (29.2%) genes being the most common. 43.4% of total isolates (201/463) carried carbapenemase genes (blaNDM, blaKPC, blaIMP, blaOXA-48/181/232, blaVIM and blaGES) and 15.3% of isolates (71/463) contained hypervirulent genes (iucA or iroB). Correlation analysis indicated mcr-1/8/9 genes were positively correlated with specific genomic elements that were rarely described, including mcr-1 with iucABC and iutA; mcr-8 with oqxB; mcr-9 with dfrA19, ISEsa and repA (R absolute value > 0.3, p<0.01). The population of K. pneumoniae can be classified into 6 clusters, some isolates co-harboring mcr and carbapenemase genes exhibited high level of genetic similarity and dispersed in several countries, indicating the possibility of clonal transmission. mcr-9 gene was introduced into K. pneumoniae in 1978 before the time of mcr-1 gene in 1988 and mcr-8 gene in 1993. We found mcr-1/8/9 genes in K. pneumoniae evolved high-risk lineages in specific geographical location (China, Thailand and the United Kingdom) that most isolates typically contained iucA, blaNDM or blaKPC. This study highlighted that continuous surveillance for the evolution of mcr-positive K. pneumoniae harboring iucA or carbapenemase genes is essential.
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Affiliation(s)
- Xi-Wei Zhang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China
| | - Xi-Yi Huang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China; Department of Clinical Laboratory, Lecong Hospital of Shunde, Foshan, Guangdong, P.R. China
| | - Zhuo-Yang Zhou
- Department of Clinical Laboratory, Lecong Hospital of Shunde, Foshan, Guangdong, P.R. China
| | - Bo-Lin Li
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China
| | - Jie-Hong Lu
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China
| | - Jing-Jie Song
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China.
| | - Xiao-Yan Li
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China.
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8
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Wu H, Ren Y, Zhang J, Xue J, Chen L, Chen H, Yang X, Wang H. Research progress of LpxC inhibitor on Gram-negative bacteria. Eur J Med Chem 2025; 289:117440. [PMID: 40020426 DOI: 10.1016/j.ejmech.2025.117440] [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: 01/13/2025] [Revised: 02/20/2025] [Accepted: 02/21/2025] [Indexed: 03/03/2025]
Abstract
UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) is a metalloprotein that utilizes zinc as a cofactor. LpxC plays a crucial role in catalyzing the synthesis of Lipid A, a major component of the outer membrane lipopolysaccharide in Gram-negative (G-) bacteria, and LpxC shares no common amino acid sequence with various mammalian enzyme proteins. LpxC is essential for the survival of Gram-negative bacteria, making it a promising target for the antibacterial drug development. In recent years, numerous LpxC inhibitors have been reported, which can be broadly categorized into hydroxamic acid and non-hydroxamic acid based on their structural characteristics. Although no LpxC inhibitors are currently available on the market, several candidate small molecules are anticipated to enter clinical trials. The current manuscript offers a comprehensive review of the structures, enzyme catalytic mechanisms, and research progress of novel LpxC inhibitors, with the objective of providing insights and directions for future research in the development of LpxC inhibitors as new antibacterial agents.
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Affiliation(s)
- Han Wu
- School of Pharmacy, Minzu University of China, Beijing, 100081, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, China; Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, 100081, China
| | - Yixin Ren
- School of Pharmacy, Minzu University of China, Beijing, 100081, China; Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, 100081, China; Institute of National Security, Minzu University of China, Beijing, 100081, China
| | - Jungan Zhang
- School of Pharmacy, Minzu University of China, Beijing, 100081, China; Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, 100081, China
| | - Jingsu Xue
- School of Pharmacy, Minzu University of China, Beijing, 100081, China; Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, 100081, China; Institute of National Security, Minzu University of China, Beijing, 100081, China
| | - Lulu Chen
- School of Pharmacy, Minzu University of China, Beijing, 100081, China; Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, 100081, China; Institute of National Security, Minzu University of China, Beijing, 100081, China
| | - Hongtong Chen
- Beijing Key Laboratory of Antimicrobial Agents/Laboratory of Pharmacology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Xinyi Yang
- Beijing Key Laboratory of Antimicrobial Agents/Laboratory of Pharmacology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Hao Wang
- School of Pharmacy, Minzu University of China, Beijing, 100081, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, China; Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, 100081, China; Institute of National Security, Minzu University of China, Beijing, 100081, China.
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Souza HCAD, Panzenhagen P, Dos Santos AMP, Portes AB, Fidelis J, Conte-Junior CA. Unravelling the advances of CRISPR-Cas9 as a precise antimicrobial therapy: A systematic review. J Glob Antimicrob Resist 2025; 42:51-60. [PMID: 39954947 DOI: 10.1016/j.jgar.2025.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 01/21/2025] [Accepted: 02/06/2025] [Indexed: 02/17/2025] Open
Abstract
Antimicrobial resistance is a critical public health threat, compromising treatment effectiveness. The spread of resistant pathogens, facilitated by genetic variability and horizontal gene transfer, primarily through plasmids, poses significant challenges to health systems. OBJECTIVE This review explores the potential of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology and Cas9 nucleases in combating antimicrobial resistance. METHODS The literature review followed the PRISMA guidelines using PubMed, Embase, and Scopus databases until July 2023. RESULTS The Enterobacterales family, particularly Escherichia coli, was the main focus. The resistance genes targeted were mainly associated with β-lactam antibiotics, specifically bla genes, and colistin resistance linked to the mcr-1 gene. Plasmid vectors have been the primary delivery method for the CRISPR-Cas9 system, with conjugative plasmids resensitizing bacterial strains to various antimicrobials. Other delivery methods included electroporation, phage-mediated delivery, and nanoparticles. The efficacy of the CRISPR-Cas9 system in resensitizing bacterial strains ranged from 4.7% to 100%. CONCLUSIONS Despite challenges in delivery strategies and clinical application, studies integrating nanotechnology present promising approaches to overcome these limitations. This review highlights new perspectives for the clinical use of CRISPR-Cas9 as a specific and efficient antimicrobial agent, potentially replacing traditional broad-spectrum antimicrobials in the future.
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Affiliation(s)
- Hannay Crystynah Almeida de Souza
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Department of Biochemistry, Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Graduate Program in Biochemistry (PPGBq), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Department of Biochemistry, Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Graduate Program in Biochemistry (PPGBq), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil; Analytical and Molecular Laboratory Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil.
| | - Anamaria Mota Pereira Dos Santos
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Department of Biochemistry, Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Graduate Program in Veterinary Hygiene (PGHIGVET), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Niterói, RJ, Brazil
| | - Ana Beatriz Portes
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Department of Biochemistry, Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Department of General Microbiology, Laboratory of Microorganism Structure, Institute of Microbiology Paulo de Góes (IMPG), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana Fidelis
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Department of Biochemistry, Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Graduate Program in Food Science, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carlos Adam Conte-Junior
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Department of Biochemistry, Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Graduate Program in Biochemistry (PPGBq), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil; Analytical and Molecular Laboratory Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Graduate Program in Veterinary Hygiene (PGHIGVET), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Niterói, RJ, Brazil
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10
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Luk-In S, Phopin K, Bangmuangngam S, Chatsuwan T, Wannigama DL, Shein AMS, Plongla R, Lawung R, Yainoy S, Eiamphungporn W, Chatupheeraphat C, Tantimongcolwat T. Inhibitory effects of benzyl isothiocyanate on widespread mcr-1-harbouring IncX4 plasmid transfer. Sci Rep 2025; 15:12892. [PMID: 40234663 PMCID: PMC12000558 DOI: 10.1038/s41598-025-97424-2] [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: 07/24/2024] [Accepted: 04/04/2025] [Indexed: 04/17/2025] Open
Abstract
The global dissemination of mobile colistin resistance (mcr) genes represents a significant public health threat due to colistin's critical role in treating multidrug-resistant (MDR) bacterial infections. We identified high rates of carbapenem resistance in Escherichia coli (27.82%) and Klebsiella pneumoniae (57.98%) and colistin resistance in E. coli (7.52%) and K. pneumoniae (19.68%) among MDR clinical isolates in Thailand. We reported sequences of self-transferable IncX4 plasmids (~ 34 kb) that facilitated the spread of the mcr-1.1 gene among six diverse MDR strains, often co-transferring blaCTX-M-55. Additionally, E. coli ST101 was found to co-transfer mcr-1.1, mcr-3.5, blaCTX-M-55, and tet(X4) via three plasmids (~ 34-kb IncX4, ~ 84-kb IncFII, ~ 278-kb IncHI2), resulting in increases in MICs for colistin, ceftriaxone, and tigecycline. Core SNP analysis revealed that closely related IncX4 plasmids harbouring mcr-1 (< 35 SNP differences) were reported from at least 12 countries. We first demonstrated the inhibitory effects of benzyl isothiocyanate (BITC) on the conjugation of mcr-1-bearing IncX4 plasmids to 1.57 ± 1.00% to 48.86 ± 12.31% relative to control (100%), targeting VirB4 and VirB11 proteins, reducing ATPase activity by over 30%. This study highlights the widespread mcr-1-harbouring IncX4 plasmids and proposes BITC as a potential inhibitor to control the dissemination of colistin resistance.
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Affiliation(s)
- Sirirat Luk-In
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Kamonrat Phopin
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Sasina Bangmuangngam
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Department of Infectious Diseases, Faculty of Medicine Yamagata University and Yamagata University Hospital, Yamagata, Japan
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries, The University of Sheffield, Sheffield, United Kingdom
- Pathogen Hunter's Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata, 990-2212, Japan
| | - Aye Mya Sithu Shein
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rongpong Plongla
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Ratana Lawung
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Sakda Yainoy
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Warawan Eiamphungporn
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Chawalit Chatupheeraphat
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Tanawut Tantimongcolwat
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand.
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11
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Başaran SN, Öksüz L. Newly developed antibiotics against multidrug-resistant and carbapenem-resistant Gram-negative bacteria: action and resistance mechanisms. Arch Microbiol 2025; 207:110. [PMID: 40172627 DOI: 10.1007/s00203-025-04298-z] [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: 01/08/2025] [Revised: 02/20/2025] [Accepted: 03/06/2025] [Indexed: 04/04/2025]
Abstract
Antimicrobial resistance stands as one of the most urgent global health concerns in the twenty-first century, with projections suggesting that deaths related to drug-resistant infections could escalate to 10 million by 2050 if proactive measures are not implemented. In intensive care settings, managing infections caused by multidrug-resistant (MDR) Gram-negative bacteria is particularly challenging, posing a significant threat to public health and contributing substantially to both morbidity and mortality. There are numerous studies on the antibiotics responsible for resistance in Gram-negative bacteria, but comprehensive research on resistance mechanisms against new antibiotics is rare. Considering the possibility that antibiotics may no longer be effective in combating diseases, it is crucial to comprehend the problem of emerging resistance to newly developed antibiotics and to implement preventive measures to curb the spread of resistance. Mutations in porins and efflux pumps play a crucial role in antibiotic resistance by altering drug permeability and active efflux. Porin modifications reduce the influx of antibiotics, whereas overexpression of efflux pumps, particularly those in the resistance-nodulation-cell division (RND) family, actively expels antibiotics from bacterial cells, significantly lowering intracellular drug concentrations and leading to treatment failure.This review examines the mechanisms of action, resistance profiles, and pharmacokinetic/pharmacodynamic characteristics of newly developed antibiotics designed to combat infections caused by MDR and carbapenem-resistant Gram-negative pathogens. The antibiotics discussed include ceftazidime-avibactam, imipenem-relebactam, ceftolozane-tazobactam, meropenem-vaborbactam, aztreonam-avibactam, delafloxacin, temocillin, plazomicin, cefiderocol, and eravacycline.
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Affiliation(s)
- Sena Nur Başaran
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey.
- Istanbul University, Institute of Graduate Studies in Health Sciences, Istanbul, Turkey.
- Department of Medical Microbiology, Faculty of Medicine, Agri Ibrahim Cecen University, Agri, Turkey.
| | - Lütfiye Öksüz
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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12
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Zhao L, Xu J, Liu S, Du J, Jia X, Wang Z, Ge L, Cui K, Ga Y, Li X, Xia X. Inosine monophosphate overcomes the coexisting resistance of mcr-1 and bla NDM-1 in Escherichia coli. J Adv Res 2025:S2090-1232(25)00203-6. [PMID: 40139526 DOI: 10.1016/j.jare.2025.03.043] [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: 12/05/2024] [Revised: 03/09/2025] [Accepted: 03/22/2025] [Indexed: 03/29/2025] Open
Abstract
INTRODUCTION The rise of antibiotic-resistant bacteria, particularly those harboring mcr-1 and blaNDM-1, threatens public health by reducing the efficacy of colistin and carbapenems. Recently, the co-spread of mcr-1 and blaNDM-1 has been reported, and the emergence of dual-resistant Enterobacteriaceae severely exacerbates antimicrobial resistance. OBJECTIVES This study aims to investigate the impact of mcr-1 and blaNDM-1 expression on metabolism in Escherichia coli and to identify potential antimicrobial agents capable of overcoming the resistance conferred by these genes. METHODS We employed non-targeted metabolomics to profile the metabolic perturbations of E. coli strains harboring mcr-1 and blaNDM-1. The bactericidal effects of the differential metabolite, inosine monophosphate (IMP), were assessed both in vitro using time-killing assays and in vivo using a mouse infection model. The antimicrobial mechanism of IMP was elucidated through transcriptomic analysis and biochemical approaches. RESULTS Metabolic profiling revealed significant alterations in the purine pathway, with IMP demonstrating potent bactericidal activity against E. coli strains carrying both resistance genes. IMP increased membrane permeability, disrupted proton motive force, reduced ATP levels, induced oxidative damage by promoting reactive oxygen species and inhibiting bacterial antioxidant defenses, and improved the survival rate of infected mice. CONCLUSION Our findings suggest that IMP could be a promising candidate for combating mcr-1 and blaNDM-1-mediated resistance and provide a novel approach for discovering antimicrobial agents against colistin- and carbapenem-resistant bacteria.
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Affiliation(s)
- Liang Zhao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jian Xu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Saiwa Liu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jingjing Du
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xixi Jia
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhinan Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lirui Ge
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Kexin Cui
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yu Ga
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaowei Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xi Xia
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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13
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Xu T, Fang D, Li F, Wang Z, Liu Y. Vitamin B6 resensitizes mcr-carrying Gram-negative bacteria to colistin. Commun Biol 2025; 8:459. [PMID: 40108411 PMCID: PMC11923103 DOI: 10.1038/s42003-025-07911-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Accepted: 03/10/2025] [Indexed: 03/22/2025] Open
Abstract
Antimicrobial resistance poses a severe threat to human health, with colistin serving as a critical medication in clinical trials against multidrug-resistant Gram-negative bacteria. However, the efficacy of colistin is increasingly compromised due to the rise of MCR-positive bacteria worldwide. Here, we reveal a notable metabolic disparity between mcr-positive and -negative bacteria through transcriptome and metabolomics analysis. Specifically, pyridoxal 5'-phosphate (PLP), the active form of vitamin B6, was significantly diminished in mcr-positive bacteria. Conversely, supplementing with PLP could reverse the metabolic profile of drug-resistant bacteria and effectively restore colistin's bactericidal properties. Mechanistically, PLP was found to augment bacterial proton motive force by inhibiting the Kdp transport system, a bacterial K+ transport ATPase, thereby facilitating the binding of the positively charged colistin to the negatively charged bacterial membrane components. Furthermore, PLP supplementation triggers ferroptosis-like death by accumulating ferrous ions and inducing lipid peroxidation. These two modes of action collectively resensitize mcr-harboring Gram-negative bacteria to colistin therapy. Altogether, our study provides a novel metabolic-driven antibiotic sensitization strategy to tackle antibiotic resistance and identifies a potentially safe antibiotic synergist.
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Affiliation(s)
- Tianqi Xu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Dan Fang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Fulei Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China.
| | - Yuan Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China.
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China.
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14
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Coluzzi C, Rocha EPC. The Spread of Antibiotic Resistance Is Driven by Plasmids Among the Fastest Evolving and of Broadest Host Range. Mol Biol Evol 2025; 42:msaf060. [PMID: 40098486 PMCID: PMC11952959 DOI: 10.1093/molbev/msaf060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Accepted: 01/27/2025] [Indexed: 03/19/2025] Open
Abstract
Microorganisms endure novel challenges for which other microorganisms in other biomes may have already evolved solutions. This is the case of nosocomial bacteria under antibiotic therapy because antibiotics are of ancient natural origin and resistances to them have previously emerged in environmental bacteria. In such cases, the rate of adaptation crucially depends on the acquisition of genes by horizontal transfer of plasmids from distantly related bacteria in different biomes. We hypothesized that such processes should be driven by plasmids among the most mobile and evolvable. We confirmed these predictions by showing that plasmid species encoding antibiotic resistance are very mobile, have broad host ranges, while showing higher rates of homologous recombination and faster turnover of gene repertoires than the other plasmids. These characteristics remain outstanding when we remove resistance plasmids from our dataset, suggesting that antibiotic resistance genes are preferentially acquired and carried by plasmid species that are intrinsically very mobile and plastic. Evolvability and mobility facilitate the transfer of antibiotic resistance, and presumably of other phenotypes, across distant taxonomic groups and biomes. Hence, plasmid species, and possibly those of other mobile genetic elements, have differentiated and predictable roles in the spread of novel traits.
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Affiliation(s)
- Charles Coluzzi
- Institut Pasteur, Université Paris Cité, Microbial Evolutionary Genomics, CNRS UMR3525, 75724 Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, Microbial Evolutionary Genomics, CNRS UMR3525, 75724 Paris, France
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15
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Li Z, Li Z, Peng Y, Zhang M, Wen Y, Lu X, Kan B. Genomic diversity of mcr-carrying plasmids and the role of type IV secretion systems in IncI2 plasmids conjugation. Commun Biol 2025; 8:342. [PMID: 40025288 PMCID: PMC11873049 DOI: 10.1038/s42003-025-07748-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 02/14/2025] [Indexed: 03/04/2025] Open
Abstract
The rapid dissemination of colistin resistance via mcr-carrying plasmids (pMCRs) poses a significant public health challenge. This study examined the genomic diversity and conjugation mechanisms of pMCRs, with a particular focus on the role of type IV secretion systems (T4SS) in IncI2 plasmids. The 868 complete plasmid sequences revealed various replicon types of pMCRs, with IncI2 as the primary epidemic type, and the co-transfer risk of multidrug resistance genes associated with IncHI2. T4SS was identified in 89.9% of pMCRs, with the T4SS sequence exclusively carried by IncI2 being conserved and typical of the VirB/D4 type, consisting of 12 subunits. Conjugation assays confirmed the essential role of the pilus subunit VirB2 and the significant impact of VirB5P3 on conjugation. This was further validated in the in vivo intra-species competitive conjugation of Escherichia coli. Structural predictions show that a hypervariable region at the C-terminus of the pentameric VirB5 co-evolves in sequence with VirB6, and the conserved N-terminal may act as a potential drug target to inhibit the plasmid transfer channel. This study will deepen the understanding of the pMCR epidemic patterns and provide additional insights for controlling the spread of resistant plasmids.
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Affiliation(s)
- Zhe Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenpeng Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yao Peng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mengke Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing, China
| | - Yuanxi Wen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xin Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Biao Kan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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16
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Lin J, Ni S, Li B, Guo Y, Gao X, Liu Y, Yi L, Wang P, Chen R, Yao J, Wood T, Wang X. A noncanonical intrinsic terminator in the HicAB toxin-antitoxin operon promotes the transmission of conjugative antibiotic resistance plasmids. Nucleic Acids Res 2025; 53:gkaf125. [PMID: 40036506 PMCID: PMC11878559 DOI: 10.1093/nar/gkaf125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 01/24/2025] [Accepted: 02/10/2025] [Indexed: 03/06/2025] Open
Abstract
Conjugative plasmids, major vehicles for the spread of antibiotic resistance genes, often contain multiple toxin-antitoxin (TA) systems. However, the physiological functions of TA systems remain obscure. By studying two TA families commonly found on colistin-resistant IncI2 mcr-1-bearing plasmids, we discovered that the HicAB TA, rather than the StbDE TA, acts as a crucial addiction module to increase horizontal plasmid-plasmid competition. In contrast to the canonical type II TA systems in which the TA genes are cotranscribed and/or the antitoxin gene has an additional promoter to allow for an increased antitoxin/toxin ratio, the HicAB TA system with the toxin gene preceding the antitoxin gene employs internal transcription termination to allow for a higher toxin production. This intrinsic terminator, featuring a G/C-rich hairpin with a UUU tract, lies upstream of the antitoxin gene, introducing a unique mechanism for the enhancing toxin/antitoxin ratio. Critically, the hicAB TA significantly contributes to plasmid competition and plasmid persistence in the absence of antibiotic selection, and deleting this intrinsic terminator alone diminishes this function. These findings align with the observed high occurrence of hicAB in IncI2 plasmids and the persistence of these plasmids after banning colistin as a feed additive. This study reveals how reprogramming the regulatory circuits of TA operons impacts plasmid occupancy in the microbial community and provides critical targets for combating antibiotic resistance.
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Affiliation(s)
- Jianzhong Lin
- Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songwei Ni
- Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Baiyuan Li
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425199 Hunan, China
| | - Yunxue Guo
- Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Xinyu Gao
- Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yabo Liu
- Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Lingxian Yi
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pengxia Wang
- Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Ran Chen
- Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Jianyun Yao
- Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-4400, United States
| | - Xiaoxue Wang
- Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
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17
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Kawabe H, Manfio L, Magana Pena S, Zhou NA, Bradley KM, Chen C, McLendon C, Benner SA, Levy K, Yang Z, Marchand JA, Fuhrmeister ER. Harnessing Non-standard Nucleic Acids for Highly Sensitive Icosaplex (20-Plex) Detection of Microbial Threats for Environmental Surveillance. ACS Synth Biol 2025; 14:470-484. [PMID: 39898969 PMCID: PMC11854376 DOI: 10.1021/acssynbio.4c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 01/13/2025] [Accepted: 01/17/2025] [Indexed: 02/04/2025]
Abstract
Environmental surveillance and clinical diagnostics heavily rely on the polymerase chain reaction (PCR) for target detection. A growing list of microbial threats warrants new PCR-based detection methods that are highly sensitive, specific, and multiplexable. Here, we introduce a PCR-based icosaplex (20-plex) assay for detecting 18 enteropathogen and two antimicrobial resistance genes. This multiplexed PCR assay leverages the self-avoiding molecular recognition system (SAMRS) to avoid primer dimer formation, the artificially expanded genetic information system (AEGIS) for amplification specificity, and next-generation sequencing for amplicon identification. Using parallelized multitarget TaqMan Array Cards (TAC) to benchmark performance of the 20-plex assay on wastewater, soil, and human stool samples, we found 90% agreement on positive calls and 89% agreement on negative calls. Additionally, we show how long-read and short-read sequencing information from the 20-plex can be used to further classify allelic variants of genes and distinguish subspecies. The strategy presented offers sensitive, affordable, and robust multiplex detection that can be used to support efforts in wastewater-based epidemiology, environmental monitoring, and human/animal diagnostics.
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Affiliation(s)
- Hinako Kawabe
- Chemical
Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Luran Manfio
- Foundation
for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, Florida 32615, United States
| | - Sebastian Magana Pena
- Foundation
for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, Florida 32615, United States
| | - Nicolette A. Zhou
- Department
of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Kevin M. Bradley
- Foundation
for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, Florida 32615, United States
- Firebird
Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, Florida 32615, United States
| | - Cen Chen
- Foundation
for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, Florida 32615, United States
- Firebird
Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, Florida 32615, United States
| | - Chris McLendon
- Firebird
Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, Florida 32615, United States
| | - Steven A. Benner
- Foundation
for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, Florida 32615, United States
- Firebird
Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, Florida 32615, United States
| | - Karen Levy
- Department
of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Zunyi Yang
- Foundation
for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, Florida 32615, United States
- Firebird
Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, Florida 32615, United States
| | - Jorge A. Marchand
- Chemical
Engineering, University of Washington, Seattle, Washington 98195, United States
- Molecular
Engineering and Science Institute, University
of Washington, Seattle, Washington 98195, United States
| | - Erica R. Fuhrmeister
- Department
of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195, United States
- Molecular
Engineering and Science Institute, University
of Washington, Seattle, Washington 98195, United States
- Civil and
Environmental Engineering, University of
Washington, Seattle, Washington 98195, United States
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18
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Zhang Y, Chen J, Yang X, Wu Y, Wang Z, Xu Y, Zhou L, Wang J, Jiao X, Sun L. Emerging Mobile Colistin Resistance Gene Mcr-1 and Mcr-10 in Enterobacteriaceae Isolates From Urban Sewage in China. Infect Drug Resist 2025; 18:1035-1048. [PMID: 39990786 PMCID: PMC11847452 DOI: 10.2147/idr.s502067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 02/08/2025] [Indexed: 02/25/2025] Open
Abstract
Purpose This study aimed to investigate the epidemiology and dissemination of mcr-positive Enterobacteriaceae in urban sewage in Yangzhou, China. Methods A total of 366 sewage samples were collected from the Yangzhou Wastewater Treatment Plant in Jiangsu Province. Colistin-resistant Enterobacteriaceae was identified through PCR targeting mcr-1 to mcr-10 genes. The isolates underwent antimicrobial susceptibility testing, and whole-genome sequencing was performed to analyze their genomic features. Additionally, conjugation experiments were conducted to assess the transferability of mcr-positive plasmids. Results Three mcr-positive Enterobacteriaceae isolates were identified, representing an isolation rate of 0.82%. These included one mcr-1-positive Escherichia coli (ST167) and two mcr-10-positive Klebsiella pneumoniae complex strains with novel sequence types ST6801 and ST6825. The mcr-1 gene was located on an IncI2 plasmid (pYZ22WS208_3) and successfully transferred to recipient strains. In contrast, the mcr-10 gene was carried on IncF plasmids (pYZ22WS067_1 and pYZ22WS223_1) but was not transferable in this study. Phylogenetic analysis revealed that the mcr-1-positive E. coli strain clustered within Clade II, alongside strains from various countries and sources. Phylogenomic analysis of mcr-10-positive isolates showed their sporadic distribution across 13 countries, with associations to diverse hosts and environments, indicating potential for widespread transmission. Conclusion This study demonstrates the presence of mcr-1 and mcr-10-positive Enterobacteriaceae in wastewater, emphasizing the importance of wastewater surveillance for tracking antibiotic resistance. The horizontal transfer of mcr-1 and potential spread of mcr-10 across various hosts underscore the need for ongoing monitoring and preventive measures.
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Affiliation(s)
- Yujing Zhang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
| | - Jiajie Chen
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
| | - Xinyu Yang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
| | - Yangshiyu Wu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
| | - Zhenyu Wang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
| | - Yawen Xu
- Yangzhou Center for Disease Control and Prevention, Yangzhou, People’s Republic of China
| | - Le Zhou
- Yangzhou Center for Disease Control and Prevention, Yangzhou, People’s Republic of China
| | - Jing Wang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
| | - Lin Sun
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
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19
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Mondol SM, Hossain MA, Haque FKM. Comprehensive genomic insights into a highly pathogenic clone ST656 of mcr8.1 containing multidrug-resistant Klebsiella pneumoniae from Bangladesh. Sci Rep 2025; 15:5909. [PMID: 39966674 PMCID: PMC11836182 DOI: 10.1038/s41598-025-90414-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Accepted: 02/12/2025] [Indexed: 02/20/2025] Open
Abstract
Antimicrobial resistance (AMR) is a pressing global health issue, intensified by the spread of resistant pathogens like Klebsiella pneumoniae (K. pneumoniae), which frequently causes hospital-acquired infections. This study focuses on a multidrug-resistant K. pneumoniae sequence type (ST) 656 strain, isolated from canal water in Bangladesh. Whole-genome sequencing and comparative genomic analysis revealed extensive resistance mechanisms and genetic elements underlying its adaptability. The strain exhibited resistance to colistin and multiple β-lactam antibiotics, containing key resistance genes such as mcr8.1, blaLAP-2, blaTEM-1, blaSHV-11 and blaOXA-1, alongside genes for copper, zinc, and silver resistance, indicating survival capability in metal-rich environments. Virulence factor analysis identified genes supporting adhesion, biofilm formation, and immune evasion, amplifying its pathogenic potential. Plasmid and phage analyses revealed mobile genetic elements, highlighting the role of horizontal gene transfer in AMR dissemination. The study included a pangenome analysis using a dataset of 32 publicly available K. pneumoniae sequence type (ST) 656 genomes, demonstrating evidence of an expanding pangenome for K. pneumoniae ST656. This study emphasized the role of environmental sources in AMR spread and the importance of continued surveillance, particularly in settings with intensive antibiotic usage, to mitigate the spread of high-risk, multidrug-resistant clones like K. pneumoniae ST656.
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Affiliation(s)
- Spencer Mark Mondol
- Microbiology Program, Department of Mathematics and Natural Sciences, Brac University, Dhaka, 1212, Bangladesh
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Mohammed Aziz Hossain
- Microbiology Program, Department of Mathematics and Natural Sciences, Brac University, Dhaka, 1212, Bangladesh
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Fahim Kabir Monjurul Haque
- Microbiology Program, Department of Mathematics and Natural Sciences, Brac University, Dhaka, 1212, Bangladesh.
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20
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Ortega-Paredes D, Del Canto F, Rios R, Diaz L, Reyes J, Arias CA, Zurita J. Genomic Insights into Colistin and Tigecycline Resistance in ESBL-Producing Escherichia coli and Klebsiella pneumoniae Harboring blaKPC Genes in Ecuador. Antibiotics (Basel) 2025; 14:206. [PMID: 40001449 PMCID: PMC11851850 DOI: 10.3390/antibiotics14020206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Revised: 11/22/2024] [Accepted: 12/03/2024] [Indexed: 02/27/2025] Open
Abstract
Introduction: Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) are resistant to third-generation cephalosporins (3GCs), carbapenems, colistin, and tigecycline, making them a major public health priority, mainly within the developing world. However, their genomic epidemiology and possible determinants of resistance remain to be elucidated. Thus, this study aimed to perform a genomic characterization of E. coli and K. pneumoniae, both of which are resistant to last-line antibiotics, isolated from humans, poultry, and a dairy farm environment within Ecuador. Methods: This study analyzed nine 3GC-resistant E. coli isolates harboring the mcr-1 gene (six from poultry farms, two from human infections, and one from dairy farm compost), together with ten isolated colistin- and carbapenem-resistant K. pneumoniae clinical samples. Results: The E. coli isolates of human origin belonged to ST609 and phylogroup A, while the poultry and compost isolates belonged to phylogroups A, B1, E, and F. Diverse STs of the K. pneumoniae isolates included ST13 (five isolates), ST258 (four isolates), and ST86 (one isolate). Within the E. coli isolates, blaCTX-M-55, blaCTX-M-65, blaCTX-M-15, and blaCTX-M-2 genes were identified. This study also identified blaCMY-2 and blaKPC-3 (the latter in a carbapenem-susceptible isolate). In E. coli, the plasmid-borne mcr-1.1 gene was identified across all E. coli isolates within an IncI2 plasmid. Tigecycline-reduced susceptibility or resistance was related to missense amino acid substitutions coded in the marA and acrA genes. Within K. pneumoiae, blaCTX-M-15 and blaCTX-M-65, on the one hand, and blaKPC-2 and blaKPC-3, on the other, were associated with 3GC and carbapenem resistance, respectively. The blaKPC-2 allele was identified in a ~10 kb Tn4401 transposon (tnpR-tnpA-istA-istB-blaKPC-2-tnpA). In K pneumoniae, sequence data and phenotypic analysis linked a nonsense amino acid substitution coded in the mgrB (K3*) gene and missense amino acid substitutions coded in the marA, acrA, arnB, eptA, pmrB, pmrJ, and phoQ genes to colistin resistance. Meanwhile, tigecycline resistance was linked to nonsense and missense amino acid substitutions coded within the ramR sequence. Additionally, this study identified several integron structures, including Int191 (5'CS-dfrA14-3'CS), which was the most prevalent integron (Int) among E. coli and K. pneumoniae isolates in this study, followed by Int0 (5'CS-3'CS) and Int18 (5'CS-dfrA1-3'CS). Conclusions: These results contribute to the genomic epidemiology of MDR E. coli and K. pneumoniae in our setting and to the worldwide epidemiology in the One Health approach.
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Affiliation(s)
- David Ortega-Paredes
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Samborondón 092301, Ecuador;
| | - Felipe Del Canto
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 9170022, Chile
| | - Rafael Rios
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Bacterial Genomics, Universidad El Bosque, Bogotá 111321, Colombia
| | - Lorena Diaz
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Bacterial Genomics, Universidad El Bosque, Bogotá 111321, Colombia
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Bacterial Genomics, Universidad El Bosque, Bogotá 111321, Colombia
| | - Cesar A. Arias
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Bacterial Genomics, Universidad El Bosque, Bogotá 111321, Colombia
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jeannete Zurita
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
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21
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Machado M, Panzenhagen P, Aburjaile FF, Brenig B, Costa MMD, Azevedo VADC, Figueiredo EEDS, Conte-Junior CA. Evolution of pathogenic Escherichia coli harboring the transmissible locus of stress tolerance: from food sources to clinical environments. Sci Rep 2025; 15:5014. [PMID: 39934272 PMCID: PMC11814101 DOI: 10.1038/s41598-025-89066-1] [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: 05/12/2024] [Accepted: 02/03/2025] [Indexed: 02/13/2025] Open
Abstract
Escherichia coli (E. coli) carrying the transmissible locus of stress tolerance (tLST) are able to overcome numerous environmental challenges. In our in-silico study, we aimed to characterize tLST in terms of its variants in 793 genomes of E. coli from Brazil originating from food, environmental and clinical (animal and human) sources, and to perform a temporal analysis in order to identify the historical moment of its emergence. We also analyzed the presence of two Yersinia high pathogenicity island (HPI) variants in E. coli genomes, describing other genes and accessory for resistance, persistence, mobile elements (plasmids) and sequence types. The prevalence of the tLST was 10% in E. coli from Brazil, predominantly observed in milk-originating genomes, within the prevalent tLSTCP010237 variant. In E. coli from other sources (clinical/environmental), only part of the tLST was present. Remarkably, our temporal analysis pinpointed the emergence of tLST back to around 1914, coinciding with major societal events. Regarding virulence genes, we found a prevalence of 38.5% for HPI of Y. pestis across genomes from all sources. Our global analysis also showed a high diversity of other virulence genes for milk E. coli (+ 100 genes). These genomes also stood out from the overall metadata for presenting a greater variety of resistance genes to other stresses, such as metals, biocides and acids, as well as persistence genes (biofilm formation). This study demonstrated the historical background of E. coli with tLST genes dating back more than 100 years, and the acquisition of a wide range of virulence and resistance genes that allow it to circulate in different environments: from food to clinic or from clinic to food, making this bacterium a pathogen that requires rigorous surveillance and strategic interventions to mitigate potential risks.
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Affiliation(s)
- Maxsueli Machado
- Food Science Program (PPGCAL), Chemistry Institute (IQ), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, 21941-909, Brazil
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
- Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - Flávia Figueira Aburjaile
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, 31270- 901, Minas Gerais, Brazil
| | | | - Mateus Matiuzzi da Costa
- Animal Science Program, Federal University of Vale do São Francisco (UNIVASF), Pernambuco, 56300-000, Brazil
| | - Vasco Ariston de Carvalho Azevedo
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, 31270- 901, Minas Gerais, Brazil
| | - Eduardo Eustáquio de Souza Figueiredo
- Animal Science Program (PPGCA), Federal University of Mato Grosso (UFMT), Cuiabá, 78060-900, Mato Grosso, Brazil
- Nutrition, Food and Metabolism Program (PPGNAM), Federal University of Mato Grosso (UFMT), Cuiabá, 78060-900, Mato Grosso, Brazil
| | - Carlos Adam Conte-Junior
- Food Science Program (PPGCAL), Chemistry Institute (IQ), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, 21941-909, Brazil.
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
- Horacio Macedo. Avenue, Cidade Universitária, Ilha do Fundão, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-598, RJ, Brazil.
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22
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Cui XD, Liu SB, Wang RY, He DD, Pan YS, Yuan L, Zhai YJ, Hu GZ. Investigation on the reversal effect of closantel on colistin resistance in MCR-1 positive Escherichia coli based on dose-response relationship. J Antimicrob Chemother 2025; 80:528-537. [PMID: 39658100 DOI: 10.1093/jac/dkae441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 11/26/2024] [Indexed: 12/12/2024] Open
Abstract
BACKGROUND The lack of research on the dose-response relationship of adjuvants in reversing colistin resistance will lead to a lack of scientific theoretical basis for determining the dosage of adjuvants in clinical combination therapy plans or their compound formulations. OBJECTIVES This study investigates the dose-response relationship of the deworming drug closantel (CST) on the reversal of colistin resistance in mcr-1-positive Escherichia coli (E. coli). METHODS Firstly, the reversal effect of different concentrations of CST on colistin resistance in mcr-1-positive E. coli was analysed using broth microdilution method, checkerboard method and time-killing curves. Then, the inhibitory effect of CST on the development of colistin resistance, as well as the haemolytic and cytotoxic properties of CST, was analysed. Finally, the in vivo efficacy of the combination of CST and colistin was evaluated. RESULTS Both the checkerboard assays and the time-killing curves indicate that there is a special dose-response relationship between CST and its reversal effect on colistin resistance, which is not concentration-dependent. High reversal efficiency can be achieved within a low concentration range. However, as the CST concentration increases, the ability to reverse colistin resistance remains unchanged or decreases, which resulted in a gradual decrease in reversal efficiency. Additionally, CST can inhibit the development of colistin resistance and reduce the cytotoxicity of colistin. Importantly, in a mouse model of E. coli infection, the combination of CST and colistin showed a significant therapeutic effect. CONCLUSIONS This study indicates a special dose-response relationship between CST and its reversal effect on colistin resistance, which was not concentration-dependent.
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Affiliation(s)
- Xiao-Die Cui
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Shuo-Bo Liu
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Rui-Yun Wang
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Dan-Dan He
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Yu-Shan Pan
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Li Yuan
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Ya-Jun Zhai
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Gong-Zheng Hu
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China
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23
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Cheng Q, Cheung Y, Xu C, Chan EWC, Chan KF, Chen S. Overall mutational scanning unveils the essential active residues for the mechanistic action of MCR-1. Microbiol Res 2025; 291:127982. [PMID: 39608179 DOI: 10.1016/j.micres.2024.127982] [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: 09/12/2024] [Revised: 11/11/2024] [Accepted: 11/20/2024] [Indexed: 11/30/2024]
Abstract
Polymyxins, including colistin and polymyxin B, serve as crucial last-resort antibiotics for managing infections caused by carbapenem-resistant Enterobacterales (CRE). However, the rapid spread of the mobilized colistin resistance gene (mcr-1) challenged the efficacy of treatment by polymyxins. The mcr-1 gene encoded a transmembrane phosphoethanolamine (PEA) transferase enzyme, MCR-1. MCR-1 could catalyze the transfer of PEA moiety of phosphatidylethanolamine (PE) to the 1' (or 4')-phosphate group of the lipid A. Despite the determination of several structures of the soluble domain of MCR-1, the structural and biochemical mechanisms of integral MCR-1 remain less understood. In this study, we utilized an alanine scanning mutagenesis approach to systematically investigate the functional attributes of distinct regions within MCR-1. We identified fifteen critical residues that are indispensable for the enzymatic activity of MCR-1 and are pivotal for its ability to confer resistance to colistin. Furthermore, molecular docking of MCR-1 complexed with the phosphoethanolamine (PE) substrate revealed the presence of a channel-shaped cavity, a characteristic feature shared with other phosphoethanolamine transferases. Despite MCR-1 exhibiting a low sequence identity with both MCR homologues and other phosphoethanolamine (PEA) transferases, several conserved sites were identified, including Y97, M105, K333, H395, L477, and H478, suggesting a potentially shared catalytic mechanism among them for modifying LPS-lipid A. Overall, these findings provide a deep understanding of the catalytic mechanism of MCR-1 for colistin resistance. Moreover, these findings provide a robust structural and functional foundation, enabling the rational design of targeted inhibitors and restoring colistin activity against serious infections with carbapenem-resistant Enterobacterales (CRE).
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Affiliation(s)
- Qipeng Cheng
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China; State Key Laboratory of Chemical Biology and Drug Discovery, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Yanchu Cheung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Chen Xu
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Edward Wai Chi Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Kin Fai Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
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24
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Bustamante M, Mei S, Daras IM, van Doorn G, Falcao Salles J, de Vos MG. An eco-evolutionary perspective on antimicrobial resistance in the context of One Health. iScience 2025; 28:111534. [PMID: 39801834 PMCID: PMC11719859 DOI: 10.1016/j.isci.2024.111534] [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: 01/16/2025] Open
Abstract
The One Health approach musters growing concerns about antimicrobial resistance due to the increased use of antibiotics in healthcare and agriculture, with all of its consequences for human, livestock, and environmental health. In this perspective, we explore the current knowledge on how interactions at different levels of biological organization, from genetic to ecological interactions, affect the evolution of antimicrobial resistance. We discuss their role in different contexts, from natural systems with weak selection, to human-influenced environments that impose a strong pressure toward antimicrobial resistance evolution. We emphasize the need for an eco-evolutionary approach within the One Health framework and highlight the importance of horizontal gene transfer and microbiome interactions for increased understanding of the emergence and spread of antimicrobial resistance.
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Affiliation(s)
| | - Siyu Mei
- University of Groningen – GELIFES, Groningen, the Netherlands
| | - Ines M. Daras
- University of Groningen – GELIFES, Groningen, the Netherlands
| | - G.S. van Doorn
- University of Groningen – GELIFES, Groningen, the Netherlands
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25
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Castañeda-Barba S, Ridenhour BJ, Top EM, Stalder T. Detection of rare plasmid hosts using a targeted Hi-C approach. ISME COMMUNICATIONS 2025; 5:ycae161. [PMID: 40161467 PMCID: PMC11950669 DOI: 10.1093/ismeco/ycae161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 11/21/2024] [Accepted: 12/12/2024] [Indexed: 04/02/2025]
Abstract
Despite the significant role plasmids play in microbial evolution, there is limited knowledge of their ecology, evolution, and transfer in microbial communities. This is partly due to the limitations of current methods in associating a plasmid with its host in microbiomes. To address this knowledge gap, we developed and implemented a novel approach to identify rare plasmid hosts by combining Hi-C, a proximity ligation method, with enrichment for plasmid-specific DNA. We hereafter refer to this approach as Hi-C+. We applied Hi-C and Hi-C+ to soil microbial communities in which we mimicked increasingly rare transfer of an antimicrobial resistance plasmid from a donor to a recipient. This was achieved by inoculating agricultural soil with mixtures of known plasmid-containing and plasmid-free cells at different proportions. We demonstrated that Hi-C can link a plasmid to its host in soil when the relative abundance of that plasmid-host pair is as low as 0.001%. Hi-C+ further improved the detection limit of Hi-C 100-fold and allowed the identification of plasmid hosts at the genus level. As a culture-independent approach, Hi-C+ will significantly improve our understanding of the range and frequency of spread of antibiotic resistance and other genes that are introduced into soil and other microbiomes.
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Affiliation(s)
- Salvador Castañeda-Barba
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, United States
- Bioinformatics and Computational Biology Graduate Program (BCB), University of Idaho, Moscow, ID 83844, United States
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, United States
| | - Benjamin J Ridenhour
- Bioinformatics and Computational Biology Graduate Program (BCB), University of Idaho, Moscow, ID 83844, United States
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, United States
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, United States
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID 83844, United States
| | - Eva M Top
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, United States
- Bioinformatics and Computational Biology Graduate Program (BCB), University of Idaho, Moscow, ID 83844, United States
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, United States
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, United States
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, United States
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, United States
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, United States
- Université de Limoges, INSERM, CHU Limoges, RESINFIT, U1092, F-87000, Limoges, France
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26
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Harris SL, Dutta S, Liu N, Wollenberg T, Wang X. Extended structure-activity relationship studies of the [1,2,5]oxadiazolo[3,4-b]pyrazine-containing colistin adjuvants. Bioorg Med Chem Lett 2025; 115:130008. [PMID: 39481690 DOI: 10.1016/j.bmcl.2024.130008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Revised: 10/22/2024] [Accepted: 10/23/2024] [Indexed: 11/02/2024]
Abstract
Antimicrobial resistance (AMR) is a formidable global health challenge. Multidrug-resistant (MDR) Gram-negative bacterial infections are of primary concern due to diminishing treatment options and high morbidity and mortality. Colistin, a polymyxin family antibiotic, is a last-resort treatment for MDR Gram-negative infections, but its wider use has resulted in escalating resistance. In 2022, using a screening approach, we discovered that a [1,2,5]oxadiazolo[3,4-b]pyrazine (ODP)-containing compound selectively re-sensitized various MDR Gram-negative bacteria to colistin. Initial structure-activity relationship (SAR) studies confirmed that bisanilino ODP compounds are colistin adjuvants with low mammalian toxicity. Herein, we report our extended SAR studies on a wide range of ODP analogs bearing alkyl- or arylalkylamines. Specifically, we discovered two new compounds, 5q and 8g, with potent colistin-potentiating activity and low mammalian toxicity in a wide range of clinically relevant pathogens.
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Affiliation(s)
| | | | - Nianzi Liu
- Department of Chemistry, Boulder, CO 80309, USA
| | | | - Xiang Wang
- Department of Chemistry, Boulder, CO 80309, USA.
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27
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Ben Selma W, Ferjeni S, Farouk A, Marzouk M, Boukadida J. Antimicrobial activity of Cinnamomum zeylanicum essential oil against colistin-resistant gram-negative bacteria. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2025; 35:169-181. [PMID: 38695857 DOI: 10.1080/09603123.2024.2348094] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 01/02/2025]
Abstract
In the current study, we evaluated the antimicrobial activity of Cinnamomum zeylanicum Blume essential oil (Cinn-EO) against a group of thirteen clinical colistin-resistant Gram-negative bacteria, including Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The GCMS analysis showed that cinnamaldehyde was the major compound (94.29%) of the Cinn-EO. The diameter of the inhibition zone by Cinn-EO varied from 24 to 37 mm. The minimum inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) values ranged between 0.625 and 5 mg/mL. Interestingly, the MBC/MIC was equal to 1 for most tested bacterial strains, indicating an advanced bactericidal effect of Cinn-EO against colistin-resistant Gram-negative bacteria. The absorption, distribution, metabolism, elimination, and toxicity (ADMET) prediction showed good pharmacokinetic properties of the tested cinnamaldehyde. The results suggest that cinnamaldehyde could be a potential alternative to treat infection caused by colistin-resistant Gram-negative bacteria.
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Affiliation(s)
- Walid Ben Selma
- Laboratory of biological and genetic markers studying for early diagnosis and follow-up of neurological diseases (LR18ES47), Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Higher Institute of Applied Sciences and Technology, University of Monastir, Mahdia, Tunisia
| | - Sana Ferjeni
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Amr Farouk
- Flavor and Aroma Chemistry Department, National Research Center, Cairo, Egypt
| | - Manel Marzouk
- Laboratory of Microbiology, Farhat Hached University Hospital, Sousse, Tunisia
| | - Jalel Boukadida
- Laboratory of Microbiology, Farhat Hached University Hospital, Sousse, Tunisia
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28
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Schumann A, Gaballa A, Wiedmann M. The multifaceted roles of phosphoethanolamine-modified lipopolysaccharides: from stress response and virulence to cationic antimicrobial resistance. Microbiol Mol Biol Rev 2024; 88:e0019323. [PMID: 39382292 DOI: 10.1128/mmbr.00193-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2024] Open
Abstract
SUMMARYLipopolysaccharides (LPS) are an integral part of the outer membrane of Gram-negative bacteria and play essential structural and functional roles in maintaining membrane integrity as well as in stress response and virulence. LPS comprises a membrane-anchored lipid A group, a sugar-based core region, and an O-antigen formed by repeating oligosaccharide units. 3-Deoxy-D-manno-octulosonic acid-lipid A (Kdo2-lipid A) is the minimum LPS component required for bacterial survival. While LPS modifications are not essential, they play multifaceted roles in stress response and host-pathogen interactions. Gram-negative bacteria encode several distinct LPS-modifying phosphoethanolamine transferases (PET) that add phosphoethanolamine (pEtN) to lipid A or the core region of LPS. The pet genes differ in their genomic locations, regulation mechanisms, and modification targets of the encoded enzyme, consistent with their various roles in different growth niches and under varied stress conditions. The discovery of mobile colistin resistance genes, which represent lipid A-modifying pet genes that are encoded on mobile elements and associated with resistance to the last-resort antibiotic colistin, has led to substantial interest in PETs and pEtN-modified LPS over the last decade. Here, we will review the current knowledge of the functional diversity of pEtN-based LPS modifications, including possible roles in niche-specific fitness advantages and resistance to host-produced antimicrobial peptides, and discuss how the genetic and structural diversities of PETs may impact their function. An improved understanding of the PET group will further enhance our comprehension of the stress response and virulence of Gram-negative bacteria and help contextualize host-pathogen interactions.
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Affiliation(s)
- Anna Schumann
- Department of Food Science, Cornell University, Ithaca, New York, USA
- Graduate Field of Biomedical and Biological Sciences, Cornell University, Ithaca, New York, USA
| | - Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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29
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Tanzin AZ, Nath C, Nayem MRK, Sayeed MA, Khan SA, Magalhaes RS, Alawneh JI, Hassan MM. Detection and Characterisation of Colistin-Resistant Escherichia coli in Broiler Meats. Microorganisms 2024; 12:2535. [PMID: 39770738 PMCID: PMC11676989 DOI: 10.3390/microorganisms12122535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 12/04/2024] [Accepted: 12/05/2024] [Indexed: 01/11/2025] Open
Abstract
The irrational use of antimicrobials has led to the emergence of resistance, impacting not only pathogenic bacteria but also commensal bacteria. Resistance against colistin, a last-resort antibiotic, mediated by globally disseminated plasmid-borne mobile colistin resistance (mcr) genes, has raised significant global concerns. This cross-sectional study aimed to investigate the antimicrobial resistance patterns of colistin-resistant Escherichia coli (E. coli) and mobilised colistin resistance (mcr 1-5) genes from broiler meat. A total of 570 broiler samples (285 liver and 285 muscle) were collected from 7 supermarkets and 11 live bird markets (LBMs) in Chattogram metropolitan areas of Bangladesh. The isolation and identification of E. coli were carried out using standard bacteriological and molecular techniques. Antimicrobial susceptibility testing (AST) was performed using the Kirby-Bauer disc diffusion method, and colistin's minimum inhibitory concentration (MIC) was determined by the broth microdilution (BMD) method. Colistin-resistant isolates were further tested for the presence of mcr (1-5) genes using polymerase chain reaction (PCR). Out of the 570 samples, 311 (54.56%; 95% confidence interval: 50.46-58.60) were positive for E. coli. AST results showed the highest resistance to sulphamethoxazole-trimethoprim (89.39%), while the highest susceptibility was observed for cefalexin (62.70%). A total of 296 isolates (95.18%) were found to be multidrug-resistant (MDR), with the multiple antibiotic resistance (MAR) index ranging from 0.38 to 1. Additionally, 41 isolates (13.18%) exhibited resistance to five antimicrobial classes, with resistance patterns of CIP + SXT + AMP + DO + TE + CT. A total of 233 isolates (74.92%) were resistant to colistin (MIC > 2 mg/L). A strong correlation between colistin resistance and the presence of the mcr-1 gene was observed (r = 1). All phenotypic colistin-resistant E. coli isolates carried the mcr-1 gene, while no isolates were positive for mcr (2-5). The detection of mcr genes in E. coli strains from poultry sources poses a significant risk, as these resistance genes can be transferred to humans through the food chain. The prevalence of multidrug-resistant Escherichia coli and the mcr-1 gene in poultry products in Bangladesh presents a significant public health and food safety concern.
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Affiliation(s)
- Abu Zubayer Tanzin
- Remount Veterinary and Farm Corps, Bangladesh Army, Savar, Dhaka 1341, Bangladesh; (A.Z.T.); (M.R.K.N.)
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh; (C.N.); (S.A.K.)
| | - Chandan Nath
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh; (C.N.); (S.A.K.)
| | - Md. Raihan Khan Nayem
- Remount Veterinary and Farm Corps, Bangladesh Army, Savar, Dhaka 1341, Bangladesh; (A.Z.T.); (M.R.K.N.)
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh; (C.N.); (S.A.K.)
| | - Md Abu Sayeed
- National Centre for Epidemiology and Population Health (NCEPH), College of Health and Medicine, The Australian National University, Canberra, ACT 2601, Australia
| | - Shahneaz Ali Khan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh; (C.N.); (S.A.K.)
| | - Ricardo Soares Magalhaes
- Queensland Alliance for One Health Sciences, School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia;
| | - John I. Alawneh
- Plant Biosecurity and Product Integrity, Biosecurity Queensland, Department of Agriculture and Fisheries, Brisbane, QLD 4000, Australia;
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh; (C.N.); (S.A.K.)
- Queensland Alliance for One Health Sciences, School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia;
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30
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Furlan JPR, Rosa RDS, Ramos MS, Lopes R, Dos Santos LDR, Savazzi EA, Stehling EG. Convergence of mcr-1 and broad-spectrum β-lactamase genes in Escherichia coli strains from the environmental sector. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 362:124937. [PMID: 39260544 DOI: 10.1016/j.envpol.2024.124937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 08/30/2024] [Accepted: 09/08/2024] [Indexed: 09/13/2024]
Abstract
The mcr-type gene encodes the main plasmid-mediated mechanism of colistin resistance and has been reported in several bacterial species obtained from different sources. Anthropogenic activities in the environment favor the evolution of antimicrobial resistance. Indeed, mcr-1-positive Escherichia coli strains were susceptible to non-polymyxins antimicrobials, but now emerging as multidrug-resistant (MDR) lineages. In this regard, hundreds of surface water and agricultural soil samples were screened for the presence of E. coli carrying the mcr-type genes and mcr-1-positive strains were subjected to in-depth genomic analysis. Almost all colistin-resistant strains were classified as MDR, highlighting those obtained from soils that showed resistance to extended-spectrum cephalosporins and carbapenems. International and high-risk clones of E. coli were identified, with ST10 and ST1720 shared between water and soil samples. Resistome analysis showed a broad resistome (AMR, metal tolerance, and biocide resistance). The mcr-1.1 and mcr-1.26 allelic variants were detected on IncX4 and IncI2 plasmids. Curiously, mcr-1-positive E. coli strains from agricultural soils harbored plasmid-mediated blaCTX-M-1, blaCTX-M-8, or blaKPC-2 genes. Virulome analysis demonstrated traits of a high putative virulence potential, with the presence of extraintestinal pathogenic E. coli. Comparative analysis revealed the persistence and dissemination of plasmid-mediated antimicrobial resistance genes in genetically diversity E. coli strains at the human-animal-environmental interface. These findings demonstrate a possible emerging AMR trend with the convergence of resistance to colistin and broad-spectrum β-lactams in environmental-derived E. coli strains.
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rafael da Silva Rosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ralf Lopes
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Lucas David Rodrigues Dos Santos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
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31
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Echegorry M, Marchetti P, Sanchez C, Olivieri L, Faccone D, Martino F, Sarkis Badola T, Ceriana P, Rapoport M, Lucero C, Albornoz E, RECAPT-AR Group, Corso A, Pasteran F. National Multicenter Study on the Prevalence of Carbapenemase-Producing Enterobacteriaceae in the Post-COVID-19 Era in Argentina: The RECAPT-AR Study. Antibiotics (Basel) 2024; 13:1139. [PMID: 39766529 PMCID: PMC11672406 DOI: 10.3390/antibiotics13121139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 11/16/2024] [Accepted: 11/19/2024] [Indexed: 01/04/2025] Open
Abstract
The COVID-19 pandemic has exacerbated the global antimicrobial resistance (AMR) crisis. Consequently, it is more urgent than ever to prioritize AMR containment and support countries in improving the detection, characterization, and rapid response to emerging AMR threats. We conducted a prospective, multicenter study to assess the prevalence of carbapenemase-producing Enterobacterales in infectious processes in Argentina during the post-COVID-19 pandemic period and explore therapeutic alternatives for their treatment (RECAPT-AR study). METHODS A total of 182 hospitals participated by submitting Enterobacterales clinical isolates to the National Reference Laboratory (NRL) during the first three weeks of November 2021. Inclusion criteria were defined as an ertapenem MIC ≥ 0.5 mg/L, a zone diameter ≤ 22 mm. Carbapenemase genes and those coding for major extended-spectrum β-lactamases were molecularly characterized using multiplex PCR at the NRL. Antibiotic susceptibility testing followed international standards (CLSI and EUCAST). RESULTS The NRL analyzed 821 Enterobacterales isolates. Metallo-β-lactamase (MBL, 42.0%) and KPC (39.8%) accounted for 81.8% of carbapenemases, followed by OXA-163 (7.4%), a variant of OXA-48 with additional activity against extended-spectrum cephalosporins, and enzyme combinations (8.3%). These combinations included NDM plus KPC (3.4%), OXA-163 plus KPC (2.4%), and OXA-163 plus NDM (2.1%). Klebsiella pneumoniae was the main species recovered, representing 76% of the isolates. According to the carbapenemase classes or combinations, tigecycline exhibited a susceptibility range of 33-83%, fosfomycin 59-81%, colistin 27-78%, and amikacin 17-81%. Ceftazidime-avibactam (CZA) and imipenem-relebactam (IMR) showed 92% and 98% susceptibility against serine carbapenemases, respectively. Meanwhile, aztreonam-avibactam (AZA) exhibited 96-98% susceptibility against all carbapenemase classes. CONCLUSIONS A new epidemiological landscape has emerged, characterized by the equivalent circulation of NDM and KPC. K. pneumoniae remains the primary species responsible for their dissemination. The co-production of carbapenemase combinations, particularly KPC plus NDM, was confirmed, mainly in K. pneumoniae. High activity was observed for AZA against MBLs and for CZA and IMR against KPC and OXA-163 carbapenemases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Fernando Pasteran
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistant, National Institute of Infectious Diseases (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G Malbrán”, Ave. Velez Sarsfield 563, Buenos Aires City 1281, Argentina; (M.E.)
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32
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Zou P, Huang L, Li Y, Liu D, Che J, Zhao T, Li H, Li J, Cui YN, Yang G, Li Z, Li LL, Gao C. Phase-Separated Nano-Antibiotics Enhanced Survival in Multidrug-Resistant Escherichia coli Sepsis by Precise Periplasmic EcDsbA Targeting. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2407152. [PMID: 39279551 DOI: 10.1002/adma.202407152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 08/27/2024] [Indexed: 09/18/2024]
Abstract
Disulfide bond (Dsb) proteins, especially DsbA, represent a promising but as-yet-unrealized target in combating multidrug-resistant (MDR) bacteria because their precise subcellular targeting through multibarrier remains a significant challenge. Here, a novel heterogenization-phase-separated nano-antibiotics (NCefoTs) is proposed, through the co-assembly of enzyme-inhibiting lipopeptides (ELp component), membrane-recognizing and disrupting lipopeptides (MLp component), and cefoperazone. The self-sorting components of MLp "concentrated island-liked clusters" on the surface of NCefoTs promote the efficient penetration of NCefoTs through the outer membrane. Triggered by the DsbA, the precisely spatiotemporal engineered NCefoTs transform to nanofibers in situ and further significantly enhance the inhibition of DsbA. The hydrolytic activity of β-lactamase and the motility function of flagella are thereby impeded, confirming the efficacy of NCefoTs in restoring susceptibility to antibiotics and inhibiting infection dissemination. By these synergistic effects of NCefoTs, the minimum inhibitory concentration of antibiotics decreases from over 300 µM to 1.56 µM for clinically isolated E. coli MDR. The survival rate of sepsis-inflicted mice is significantly enhanced from 0% to 92% upon encapsulation of cefoperazone in NCefoTs, which rapidly eliminates invading pathogens and mitigates inflammation. The universally applicable delivery system, based on an "on demands" strategy, presents a promising prospect for undruggable antibiotic targets in the periplasm to combat MDR bacteria.
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Affiliation(s)
- Pengfei Zou
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- School of Material Science and Engineering, Beijing Institute of Technology, Beijing, 100081, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Lin Huang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Yi Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Dan Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- School of Chemical and Pharmaceutical Engineering, Hebei University of Science and Technology, Shijiazhuang, Hebei, 050018, China
| | - Junwei Che
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Te Zhao
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- School of Chemical and Pharmaceutical Engineering, Hebei University of Science and Technology, Shijiazhuang, Hebei, 050018, China
| | - Hui Li
- Department of Pharmacy, Peking University Third Hospital, Beijing, 100083, China
| | - Jiaxin Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Ya-Nan Cui
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Guobao Yang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Zhiping Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Li-Li Li
- School of Material Science and Engineering, Beijing Institute of Technology, Beijing, 100081, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Chunsheng Gao
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
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Nuske MR, Zhong J, Huang R, Sarojini V, Chen JLY, Squire CJ, Blaskovich MAT, Leung IKH. Adjuvant strategies to tackle mcr-mediated polymyxin resistance. RSC Med Chem 2024:d4md00654b. [PMID: 39539347 PMCID: PMC11556429 DOI: 10.1039/d4md00654b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 11/01/2024] [Indexed: 11/16/2024] Open
Abstract
The emergence of the mobile colistin resistance (mcr) gene is a demonstrable threat contributing to the worldwide antibiotic resistance crisis. The gene is encoded on plasmids and can easily spread between different bacterial strains. mcr encodes a phosphoethanolamine (pEtN) transferase, which catalyses the transfer of the pEtN moiety from phosphatidylethanolamine to lipid A, the head group of lipopolysaccharides (LPS). This neutralises the overall negative charge of the LPS and prevents the binding of polymyxins to bacterial membranes. We believe that the development of polymyxin adjuvants could be a promising approach to prolong the use of this important class of last-resort antibiotics. This review discusses recent progress in the identification, design and development of adjuvants to restore polymyxin sensitivity in these resistant bacteria, and focuses on both MCR inhibitors as well as alternative approaches that modulate polymyxin resistance.
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Affiliation(s)
- Madison R Nuske
- School of Chemistry, The University of Melbourne Parkville Victoria 3010 Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne Parkville Victoria 3010 Australia
| | - Junlang Zhong
- School of Chemistry, The University of Melbourne Parkville Victoria 3010 Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne Parkville Victoria 3010 Australia
| | - Renjie Huang
- School of Chemical Sciences, The University of Auckland Auckland 1010 New Zealand
| | | | - Jack L Y Chen
- Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology Auckland 1010 New Zealand
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences, Università degli Studi di Siena 53100 Siena Italy
| | - Christopher J Squire
- School of Biological Sciences, The University of Auckland Auckland 1010 New Zealand
| | - Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland St. Lucia Queensland 4072 Australia
| | - Ivanhoe K H Leung
- School of Chemistry, The University of Melbourne Parkville Victoria 3010 Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne Parkville Victoria 3010 Australia
- School of Chemical Sciences, The University of Auckland Auckland 1010 New Zealand
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Souque C, González Ojeda I, Baym M. From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance. Annu Rev Microbiol 2024; 78:361-382. [PMID: 39141706 DOI: 10.1146/annurev-micro-041522-102707] [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] [Indexed: 08/16/2024]
Abstract
Tackling the challenge created by antibiotic resistance requires understanding the mechanisms behind its evolution. Like any evolutionary process, the evolution of antimicrobial resistance (AMR) is driven by the underlying variation in a bacterial population and the selective pressures acting upon it. Importantly, both selection and variation will depend on the scale at which resistance evolution is considered (from evolution within a single patient to the host population level). While laboratory experiments have generated fundamental insights into the mechanisms underlying antibiotic resistance evolution, the technological advances in whole genome sequencing now allow us to probe antibiotic resistance evolution beyond the lab and directly record it in individual patients and host populations. Here we review the evolutionary forces driving antibiotic resistance at each of these scales, highlight gaps in our current understanding of AMR evolution, and discuss future steps toward evolution-guided interventions.
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Affiliation(s)
- Célia Souque
- Departments of Biomedical Informatics and Microbiology, Harvard Medical School, Boston, Massachusetts, USA; ,
| | - Indra González Ojeda
- Departments of Biomedical Informatics and Microbiology, Harvard Medical School, Boston, Massachusetts, USA; ,
| | - Michael Baym
- Departments of Biomedical Informatics and Microbiology, Harvard Medical School, Boston, Massachusetts, USA; ,
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Gyraitė G, Kataržytė M, Espinosa RP, Kalvaitienė G, Lastauskienė E. Microbiome and Resistome Studies of the Lithuanian Baltic Sea Coast and the Curonian Lagoon Waters and Sediments. Antibiotics (Basel) 2024; 13:1013. [PMID: 39596708 PMCID: PMC11591088 DOI: 10.3390/antibiotics13111013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 10/17/2024] [Accepted: 10/26/2024] [Indexed: 11/29/2024] Open
Abstract
BACKGROUND the widespread use of antibiotics in human and veterinary medicine has contributed to the global challenge of antimicrobial resistance, posing significant environmental and public health risks. OBJECTIVES this study aimed to examine the microbiome and resistome dynamics across a salinity gradient, analyzing water and sediment samples from the Baltic Sea coast and the Curonian Lagoon between 2017 and 2023. METHODS the composition of the water and sediment bacterial community was determined by Full-Length Amplicon Metagenomics Sequencing, while ARG detection and quantification were performed using the SmartChipTM Real-Time PCR system. RESULTS the observed differences in bacterial community composition between the Baltic Sea coast and the Curonian Lagoon were driven by variations in salinity and chlorophyll a (chl a) concentration. The genera associated with infectious potential were observed in higher abundances in sediment than in water samples. Over 300 genes encoding antibiotic resistance (ARGs), such as aminoglycosides, beta-lactams, and multidrug resistance genes, were identified. Of particular interest were those ARGs that have previously been detected in pathogens and those currently classified as a potential future threat. Furthermore, our findings reveal a higher abundance and a distinct profile of ARGs in sediment samples from the lagoon compared to water. CONCLUSIONS these results suggest that transitional waters such as lagoons may serve as reservoirs for ARGs, and might be influenced by anthropogenic pressures and natural processes such as salinity fluctuation and nutrient cycling.
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Affiliation(s)
- Greta Gyraitė
- Bioscience Institute, Life Science Center, Vilnius University, 10257 Vilnius, Lithuania;
| | - Marija Kataržytė
- Marine Research Institute, Klaipeda University, 92295 Klaipėda, Lithuania; (M.K.); (R.P.E.); (G.K.)
| | - Rafael Picazo Espinosa
- Marine Research Institute, Klaipeda University, 92295 Klaipėda, Lithuania; (M.K.); (R.P.E.); (G.K.)
| | - Greta Kalvaitienė
- Marine Research Institute, Klaipeda University, 92295 Klaipėda, Lithuania; (M.K.); (R.P.E.); (G.K.)
| | - Eglė Lastauskienė
- Bioscience Institute, Life Science Center, Vilnius University, 10257 Vilnius, Lithuania;
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Yap PSX, Yeo LF, Teh CSJ, Dhanoa A, Phipps ME. Plasmid-Mediated Co-Occurrence of mcr-1.1 in Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli Isolated From the Indigenous Seminomadic Community in Malaysia. Transbound Emerg Dis 2024; 2024:9223696. [PMID: 40303148 PMCID: PMC12017022 DOI: 10.1155/2024/9223696] [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: 11/22/2023] [Revised: 07/07/2024] [Accepted: 08/24/2024] [Indexed: 05/02/2025]
Abstract
The growing prevalence of commensal antibiotic resistant Escherichia coli poses a significant concern for the global spread of antibiotic resistance. Stool samples (n = 35) from a seminomadic indigenous community in Malaysia, the Jehai, were screened for multidrug-resistant bacteria, specifically the extended-spectrum β-lactamase (ESBL) producers. Subsequently, whole-genome sequencing was used to provide genomic insights into eight ESBL-producing E. coli that colonised eight individuals. The ESBL E. coli isolates carry resistance genes from various antibiotic classes such as the β-lactams (bla TEM, bla CTX-M-15 and bla CTX-M-55), quinolones (gyrA, qnrS and qnrS1) and aminoglycosides (aph(3')-Ia, aph(6)-Id and aac(3)-IId). Three concerning convergence of ESBL, colistin and metal resistance determinants, with three plasmids from H-type lineage harbouring bla CTX-M and mcr-1.1 genes were identified. Using the Oxford Nanopore Technology (ONT) Native Barcoding Kit (SQK-NBD114.24) in conjunction with the R10.4.1 flow cell, which achieved an average read accuracy (Q > 10) of 99.84%, we further characterised the mcr-1.1-bearing plasmids, ranging in size from 25 to 28 kb, from three strains of E. coli. This report represents the first whole genome analysis of multidrug-resistant bacteria, specifically those resistant to colistin, found within the indigenous population in Malaysia. It strongly indicates that the pertinent issue of colistin resistance in the country is far more significant than previously estimated.
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Affiliation(s)
- Polly Soo Xi Yap
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Subang Jaya, Selangor, Malaysia
| | - Li-Fang Yeo
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Subang Jaya, Selangor, Malaysia
- Cancer Research Malaysia, Sime Darby Medical Centre Subang Jaya, 2nd Floor, Outpatient Centre, Subang Jaya 47500, Selangor, Malaysia
| | - Cindy Shuan Ju Teh
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya 50603, Kuala Lumpur, Malaysia
| | - Amreeta Dhanoa
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Subang Jaya, Selangor, Malaysia
| | - Maude Elvira Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Subang Jaya, Selangor, Malaysia
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Li S, Liu X, Zhao H, Zhang Y, Lu Z, Wang J, Li R, Xie P, Hu Y, Zhou C, Mao Q, Sun L, Li S, Wang W, Wang F, Liu X, Liu T, Pan W, Wang C. Genome-Based Molecular Diversity of Extended-Spectrum β-Lactamase-Producing Escherichia coli From Pigeons in China. Transbound Emerg Dis 2024; 2024:1828830. [PMID: 40303011 PMCID: PMC12017244 DOI: 10.1155/2024/1828830] [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: 03/27/2024] [Revised: 06/05/2024] [Accepted: 08/29/2024] [Indexed: 05/02/2025]
Abstract
Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) strains present a significant menace to the well-being of both animals and humans. However, limited information is available regarding their profiles in pigeons. Using a combination of whole genome sequencing, drug susceptibility testing, and bioinformatics analysis, we examined the genomic features and epidemiology of 95 ESBL-EC strains (41 racing and 54 meat pigeons) that were isolated from 11 Chinese cities. These strains belonged to seven phylogenetic groups (A, B1, B2, C, D, E, and F). Moreover, these isolates have 51 serotypes, including several pathogenic ones (e.g., O51, O8, O4, O25, and O6). Notably, two high-risk clones, ST131 O25:H4, were found in racing pigeons and were responsible for the worldwide outbreaks of highly pathogenic and multidrug-resistant (MDR) E. coli infections. In addition, we found 41 multilocus sequence typing types, of which the dominant types were ST155, ST20, ST1011, and ST1196. In total, 91 isolates (95.79%) showed MDR, while eight isolates (8.42%) showed resistance to up to eight classes of antibiotics. Furthermore, we identified a series of ESBL genes in these isolates, including bla CTX-M, bla TEM, bla OXA, bla LAP, and bla CMY. Also, 50 other antibiotic resistance genes (ARGs) were accompanied by the carriage of 33 plasmid replicon types, facilitating the horizontal spread of ARGs. Interestingly, three mcr-1, four mcr-1.1, and one tet(X4) were found in isolates of meat pigeons, and it was possible to successfully transfer the plasmids containing tet(X4) and mcr-1.1 to E. coli C600. In summary, this work presents the complexity of MDR profiles, plasmid profiles, and multiple typing profiles of Chinese ESBL-EC isolates of pigeon origin for the first time. The thorough investigation of ESBL-EC in pigeons presented in this work suggests that racing and meat pigeons are significant ARGs reservoirs.
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Affiliation(s)
- Shuangyu Li
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | | | - Haoyu Zhao
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Yuhua Zhang
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Zheng Lu
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Juan Wang
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Ruichao Li
- College of Veterinary MedicineYangzhou University, Yangzhou 225009, Jiangsu, China
| | - Peng Xie
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Yibin Hu
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Caiyuan Zhou
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Qian Mao
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Leilei Sun
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Shanshan Li
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Wenhui Wang
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Fang Wang
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Xinyu Liu
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Tiantian Liu
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
| | - Wei Pan
- Jiangsu Key Laboratory of Immunity and MetabolismJiangsu International Laboratory of Immunity and MetabolismDepartment of Pathogen Biology and ImmunologyXuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Chengbao Wang
- College of Veterinary MedicineNorthwest A&F University, Yangling 712100, Shaanxi, China
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Song K, Jin L, Cai M, Wang Q, Wu X, Wang S, Sun S, Wang R, Chen F, Wang H. Decoding the origins, spread, and global risks of mcr-9 gene. EBioMedicine 2024; 108:105326. [PMID: 39260038 PMCID: PMC11416231 DOI: 10.1016/j.ebiom.2024.105326] [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: 04/10/2024] [Revised: 08/23/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND The global spread of the plasmid-mediated mcr (mobilized colistin resistance) gene family presents a significant threat to the efficacy of colistin, a last-line defense against numerous Gram-negative pathogens. The mcr-9 is the second most prevalent variant after mcr-1. METHODS A dataset of 698 mcr-9-positive isolates from 44 countries is compiled. The historical trajectory of the mcr-9 gene is reconstructed using Bayesian analysis. The effective reproduction number is used innovatively to study the transmission dynamics of this mobile-drug-resistant gene. FINDINGS Our investigation traces the origins of mcr-9 back to the 1960s, revealing a subsequent expansion from Western Europe to the America and East Asia in the late 20th century. Currently, its transmissibility remains high in Western Europe. Intriguingly, mcr-9 likely emerged from human-associated Salmonella and exhibits a unique propensity for transmission within the Enterobacter. Our research provides a new perspective that this host preference may be driven by codon usage biases in plasmids. Specifically, mcr-9-carrying plasmids prefer the nucleotide C over T compared to mcr-1-carrying plasmids among synonymous codons. The same bias is seen in Enterobacter compared to Escherichia (respectively as their most dominant genus). Furthermore, we uncovered fascinating patterns of coexistence between different mcr-9 subtypes and other resistance genes. Characterized by its low colistin resistance, mcr-9 has used this seemingly benign feature to silently circumnavigate the globe, evading conventional detection methods. However, colistin-resistant Enterobacter strains with high mcr-9 expression have emerged clinically, implying a strong risk of mcr-9 evolving into a global "true-resistance-gene". INTERPRETATION This study explores the mcr-9 gene, emphasizing its origin, adaptability, and dissemination potential. Given the high mcr-9 expression colistin-resistant strains was observed in clinically the prevalence of mcr-9 poses a significant challenge to drug resistance prevention and control within the One Health framework. FUNDING This work was partially supported by the National Natural Science Foundation of China (Grant No. 32141001 and 81991533).
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Affiliation(s)
- Kaiwen Song
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Longyang Jin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Meng Cai
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Qi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Xingyu Wu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shuyi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shijun Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Fengning Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China.
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Schmartz GP, Rehner J, Gund MP, Keller V, Molano LAG, Rupf S, Hannig M, Berger T, Flockerzi E, Seitz B, Fleser S, Schmitt-Grohé S, Kalefack S, Zemlin M, Kunz M, Götzinger F, Gevaerd C, Vogt T, Reichrath J, Diehl L, Hecksteden A, Meyer T, Herr C, Gurevich A, Krug D, Hegemann J, Bozhueyuek K, Gulder TAM, Fu C, Beemelmanns C, Schattenberg JM, Kalinina OV, Becker A, Unger M, Ludwig N, Seibert M, Stein ML, Hanna NL, Martin MC, Mahfoud F, Krawczyk M, Becker SL, Müller R, Bals R, Keller A. Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics. Nat Commun 2024; 15:8261. [PMID: 39327438 PMCID: PMC11427559 DOI: 10.1038/s41467-024-52598-7] [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: 12/18/2023] [Accepted: 09/13/2024] [Indexed: 09/28/2024] Open
Abstract
The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies.
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Affiliation(s)
- Georges P Schmartz
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421, Homburg, Germany
| | - Madline P Gund
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66421, Homburg, Germany
| | - Verena Keller
- Department of Medicine II, Saarland University Medical Center, 66421, Homburg, Germany
| | | | - Stefan Rupf
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66421, Homburg, Germany
- Synoptic Dentistry, Saarland University, 66421, Homburg, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66421, Homburg, Germany
| | - Tim Berger
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Elias Flockerzi
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Sara Fleser
- Department of General Pediatrics and Neonatology, Saarland University, 66421, Homburg, Germany
| | - Sabina Schmitt-Grohé
- Department of General Pediatrics and Neonatology, Saarland University, 66421, Homburg, Germany
| | - Sandra Kalefack
- Department of General Pediatrics and Neonatology, Saarland University, 66421, Homburg, Germany
| | - Michael Zemlin
- Department of General Pediatrics and Neonatology, Saarland University, 66421, Homburg, Germany
| | - Michael Kunz
- Department of Internal Medicine III, Cardiology, Angiology, Intensive Care Medicine, Saarland University Hospital, 66421, Homburg, Germany
| | - Felix Götzinger
- Department of Internal Medicine III, Cardiology, Angiology, Intensive Care Medicine, Saarland University Hospital, 66421, Homburg, Germany
| | - Caroline Gevaerd
- Clinic for Dermatology, Venereology, and Allergology, 66421, Homburg, Germany
| | - Thomas Vogt
- Clinic for Dermatology, Venereology, and Allergology, 66421, Homburg, Germany
| | - Jörg Reichrath
- Clinic for Dermatology, Venereology, and Allergology, 66421, Homburg, Germany
| | - Lisa Diehl
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Anne Hecksteden
- Institute for Sport and Preventive Medicine, Saarland University, 66123, Saarbrücken, Germany
- Chair of Sports Medicine, Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Tim Meyer
- Institute for Sport and Preventive Medicine, Saarland University, 66123, Saarbrücken, Germany
| | - Christian Herr
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Saarbrücken, Germany
| | - Alexey Gurevich
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
- Center for Bioinformatics Saar and Saarland University, Saarland Informatics Campus, 66123, Saarbrücken, Germany
| | - Daniel Krug
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Julian Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Kenan Bozhueyuek
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Tobias A M Gulder
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Chengzhang Fu
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Christine Beemelmanns
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Jörn M Schattenberg
- Department of Medicine II, Saarland University Medical Center, 66421, Homburg, Germany
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Anouck Becker
- Department for Neurology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Marcus Unger
- Department for Neurology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Nicole Ludwig
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Martina Seibert
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Marie-Louise Stein
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Nikolas Loka Hanna
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Saarbrücken, Germany
| | - Marie-Christin Martin
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Felix Mahfoud
- Department of Internal Medicine III, Cardiology, Angiology, Intensive Care Medicine, Saarland University Hospital, 66421, Homburg, Germany
| | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Center, 66421, Homburg, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421, Homburg, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
- PharmaScienceHub, 66123, Saarbrücken, Germany
| | - Robert Bals
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Saarbrücken, Germany
- PharmaScienceHub, 66123, Saarbrücken, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany.
- PharmaScienceHub, 66123, Saarbrücken, Germany.
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Cifuentes SG, Graham J, Trueba G, Cádenas PA. Detection of mobile colistin resistance genes mcr-9.1 and mcr-10.1 in Enterobacter asburiae from Ecuadorian children. Microbiol Resour Announc 2024; 13:e0031324. [PMID: 39162443 PMCID: PMC11384748 DOI: 10.1128/mra.00313-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/10/2024] [Indexed: 08/21/2024] Open
Abstract
Colistin is one of the last-line treatments for multi-drug resistant Gram-negative bacterial infections. The emergence of mobile colistin resistance genes has driven global concern and triggered the need for surveillance. Our report reveals the identification of mcr-9.1 and mcr-10.1 in Ecuador by employing a proximity ligation technique.
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Affiliation(s)
- Sara G Cifuentes
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Pichincha, Ecuador
| | - Jay Graham
- Berkeley School of Public Health, University of California, Berkeley, California, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Pichincha, Ecuador
| | - Paúl A Cádenas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Pichincha, Ecuador
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Kawabe H, Manfio L, Pena SM, Zhou NA, Bradley KM, Chen C, McLendon C, Benner SA, Levy K, Yang Z, Marchand JA, Fuhrmeister ER. Harnessing non-standard nucleic acids for highly sensitive icosaplex (20-plex) detection of microbial threats. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.09.24313328. [PMID: 39314929 PMCID: PMC11419210 DOI: 10.1101/2024.09.09.24313328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Environmental surveillance and clinical diagnostics heavily rely on the polymerase chain reaction (PCR) for target detection. A growing list of microbial threats warrants new PCR-based detection methods that are highly sensitive, specific, and multiplexable. Here, we introduce a PCR-based icosaplex (20-plex) assay for detecting 18 enteropathogen and two antimicrobial resistance genes. This multiplexed PCR assay leverages the self-avoiding molecular recognition system (SAMRS) to avoid primer dimer formation, the artificially expanded genetic information system (AEGIS) for amplification specificity, and next-generation sequencing for amplicon identification. We benchmarked this assay using a low-cost, portable sequencing platform (Oxford Nanopore) on wastewater, soil, and human stool samples. Using parallelized multi-target TaqMan Array Cards (TAC) to benchmark performance of the 20-plex assay, there was 74% agreement on positive calls and 97% agreement on negative calls. Additionally, we show how sequencing information from the 20-plex can be used to further classify allelic variants of genes and distinguish sub-species. The strategy presented offers sensitive, affordable, and robust multiplex detection that can be used to support efforts in wastewater-based epidemiology, environmental monitoring, and human/animal diagnostics.
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Affiliation(s)
- Hinako Kawabe
- Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Luran Manfio
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
| | - Sebastian Magana Pena
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
| | - Nicolette A. Zhou
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Seattle, WA, 98195, USA
| | - Kevin M. Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Cen Chen
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Chris McLendon
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Seattle, WA, 98195, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Jorge A. Marchand
- Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
- Molecular Engineering and Science Institute, University of Washington, Seattle, Seattle, WA, 98195, USA
| | - Erica R. Fuhrmeister
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Seattle, WA, 98195, USA
- Civil and Environmental Engineering, University of Washington, Seattle, Seattle, WA, 98195, USA
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Lo CKF, Ritchie G, Bilawka J, Gowland L, Chorlton SD, Jang W, Matic N, Romney MG, Stefanovic A, Lowe CF. Evaluating the accuracy of the MBT Lipid Xtract Kit for assessing colistin resistance in comparison to broth microdilution. J Med Microbiol 2024; 73:001881. [PMID: 39222340 PMCID: PMC11368154 DOI: 10.1099/jmm.0.001881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 08/04/2024] [Indexed: 09/04/2024] Open
Abstract
Colistin resistance testing methods such as broth microdilution (BMD) are time-consuming and labour intensive for clinical laboratories. MBT Lipid Xtract Kit on MALDI Biotyper Sirius System (Bruker, Billerica, MA, USA) utilizes lipidomic analysis to identify specific cell wall modifications associated with colistin resistance. We compared MBT to BMD (ComASP Colistin, Liofilchem) across 36 Gram-negative isolates (non-resistant MIC ≤2 µg ml-1, resistant MIC ≥4 µg ml-1). All samples were tested twice on MBT with discrepant results repeated before assessing categorical agreement between MBT and BMD. 44.4% (16/36) of isolates were colistin resistant via BMD. MBT Lipid Xtract had 80.6% agreement (29/36) with BMD, with 5/7 discrepancies corrected to match upon repeat testing. There was 100% agreement for Escherichia coli isolates (n=16). The whole-genome sequencing was completed on the two discrepant Klebsiella pneumoniae isolates, with variants within colistin resistance-associated loci identified (MIC 0.5 µg ml-1: arnC S30T, pmrB T246A, lapB N212T, lpxM S253G, crrB Q287K and MIC >16 µg ml-1: arnC S30T, pmrB R90insRN, pmrB T246A, pmrA E57G, lpxM S253G). Further evaluation, particularly for non-E. coli, of MBT is required prior to implementation in clinical laboratories.
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Affiliation(s)
- Calvin Ka-Fung Lo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gordon Ritchie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Jennifer Bilawka
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Leah Gowland
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | | | - Willson Jang
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Nancy Matic
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Marc G. Romney
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Aleksandra Stefanovic
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Christopher F. Lowe
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
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Sheng Q, Wang X, Hou Z, Liu B, Jiang M, Ren M, Fu J, He M, Zhang J, Xiang Y, Zhang Q, Zhou L, Deng Y, Shen X. Novel functions of o-cymen-5-ol nanoemulsion in reversing colistin resistance in multidrug-resistant Klebsiella pneumoniae infections. Biochem Pharmacol 2024; 227:116384. [PMID: 38909787 DOI: 10.1016/j.bcp.2024.116384] [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: 02/21/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Multidrug resistance (MDR) Klebsiella pneumoniae (K. pneumoniae) is a major emerging threat to human health, and leads to very high mortality rate. The effectiveness of colistin, the last resort against MDR Gram-negative bacteria, is significantly compromised due to the widespread presence of plasmid- or chromosome-mediated resistance genes. In this study, o-cymen-5-ol has been found to greatly restore colistin sensitivity in MDR K. pneumoniae. Importantly, this compound does not impact bacterial viability, induce resistance, or cause any noticeable cell toxicity. Various routes disclosed the potential mechanism of o-cymen-5-ol potentiating colistin activity against MDR K. pneumoniae. These include inhibiting the activity of plasmid-mediated mobile colistin resistance gene (mcr-1), accelerating lipopolysaccharide (LPS) - mediated membrane damage, and promoting the ATP-binding cassette (ABC) transporter pathway. To enhance the administration and bioavailability of o-cymen-5-ol, a nanoemulsion has been designed, which significantly improves the loading efficiency and solubility of o-cymen-5-ol, resulting in antimicrobial potentiation of colistin against K. pneumoniae infection. This study has revealed a new understanding of the o-cymen-5-ol nanoemulsion as a means to enhance the effectiveness of colistin against resistant factors. The finding also suggests that o-cymen-5-ol nanoemulsion could be a promising approach in the development of potential treatments for multidrug-resistant Gram-negative bacterial infections.
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Affiliation(s)
- Qiushuang Sheng
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Xiao Wang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Zhaoyan Hou
- Changchun Center for Disease Control and Prevention, Changchun, China
| | - Bin Liu
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Mingquan Jiang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Mingyue Ren
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Jingchao Fu
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Miao He
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Jingchen Zhang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Yue Xiang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Qingbo Zhang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Lanying Zhou
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Yanhong Deng
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Xue Shen
- Department of Food Science, College of Food Science and Engineering, Jilin University, Changchun 130062, China; State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
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Garcias B, Flores MA, Fernández M, Monteith W, Pascoe B, Sheppard SK, Martín M, Cortey M, Darwich L. Global Variation in Escherichia coli mcr-1 Genes and Plasmids from Animal and Human Genomes Following Colistin Usage Restrictions in Livestock. Antibiotics (Basel) 2024; 13:759. [PMID: 39200059 PMCID: PMC11350921 DOI: 10.3390/antibiotics13080759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/09/2024] [Accepted: 08/10/2024] [Indexed: 09/01/2024] Open
Abstract
Antimicrobial resistance (AMR) is a significant global health threat, with multidrug-resistant (MDR) bacterial clones becoming a major concern. Polymyxins, especially colistin, have reemerged as last-resort treatments for MDR Gram-negative infections. However, colistin use in livestock has spread mobile colistin resistance (mcr) genes, notably mcr-1, impacting human health. In consequence, its livestock use was banned in 2017, originating a natural experiment to study bacterial adaptation. The aim of this work was to analyse the changes in the mcr-1 genetic background after colistin restriction across the world. This study analyses 3163 Escherichia coli genomes with the mcr-1 gene from human and livestock hosts, mainly from Asia (n = 2621) and Europe (n = 359). Genetic characterisation identifies IncI2 (40.4%), IncX4 (26.7%), and multidrug-resistant IncHI2 (18.8%) as the most common plasmids carrying mcr-1. There were differences in plasmids between continents, with IncX4 (56.6%) being the most common in Europe, while IncI2 (44.8%) was predominant in Asia. Promoter variants related to reduced fitness costs and ISApl1 showed a distinct pattern of association that appears to be associated with adaptation to colistin restriction, which differed between continents. Thus, after the colistin ban, Europe saw a shift to specialised mcr-1 plasmids as IncX4, while ISApl1 decreased in Asia due to changes in the prevalence of the distinct promoter variants. These analyses illustrate the evolution of mcr-1 adaptation following colistin use restrictions and the need for region-specific strategies against AMR following colistin restrictions.
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Affiliation(s)
- Biel Garcias
- Department Sanitat i Anatomia Animals, Veterinary Faculty, Universitat Autònoma de Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
| | - Mayra Alejandra Flores
- Department Sanitat i Anatomia Animals, Veterinary Faculty, Universitat Autònoma de Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
| | - Mercedes Fernández
- Department Sanitat i Anatomia Animals, Veterinary Faculty, Universitat Autònoma de Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
| | - William Monteith
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ben Pascoe
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Samuel K. Sheppard
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Marga Martín
- Department Sanitat i Anatomia Animals, Veterinary Faculty, Universitat Autònoma de Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
| | - Martí Cortey
- Department Sanitat i Anatomia Animals, Veterinary Faculty, Universitat Autònoma de Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
| | - Laila Darwich
- Department Sanitat i Anatomia Animals, Veterinary Faculty, Universitat Autònoma de Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
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45
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Fernández-García M. Understanding the evolutionary potential of mcr-1: growing evidence on costless colistin resistance. THE LANCET. MICROBE 2024; 5:100888. [PMID: 38870983 DOI: 10.1016/s2666-5247(24)00111-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 06/15/2024]
Affiliation(s)
- Miguel Fernández-García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia and Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Madrid 28660, Spain.
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46
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Liu CSC, Pandey R. Integrative genomics would strengthen AMR understanding through ONE health approach. Heliyon 2024; 10:e34719. [PMID: 39816336 PMCID: PMC11734142 DOI: 10.1016/j.heliyon.2024.e34719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 01/18/2025] Open
Abstract
Emergence of drug-induced antimicrobial resistance (AMR) forms a crippling health and economic crisis worldwide, causing high mortality from otherwise treatable diseases and infections. Next Generation Sequencing (NGS) has significantly augmented detection of culture independent microbes, potential AMR in pathogens and elucidation of mechanisms underlying it. Here, we review recent findings of AMR evolution in pathogens aided by integrated genomic investigation strategies inclusive of bacteria, virus, fungi and AMR alleles. While AMR monitoring is dominated by data from hospital-related infections, we review genomic surveillance of both biotic and abiotic components involved in global AMR emergence and persistence. Identification of pathogen-intrinsic as well as environmental and/or host factors through robust genomics/bioinformatics, along with monitoring of type and frequency of antibiotic usage will greatly facilitate prediction of regional and global patterns of AMR evolution. Genomics-enabled AMR prediction and surveillance will be crucial - in shaping health and economic policies within the One Health framework to combat this global concern.
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Affiliation(s)
- Chinky Shiu Chen Liu
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110007, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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47
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Li X, Hu H, Zhu Y, Wang T, Lu Y, Wang X, Peng Z, Sun M, Chen H, Zheng J, Tan C. Population structure and antibiotic resistance of swine extraintestinal pathogenic Escherichia coli from China. Nat Commun 2024; 15:5811. [PMID: 38987310 PMCID: PMC11237156 DOI: 10.1038/s41467-024-50268-2] [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: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024] Open
Abstract
Extraintestinal Pathogenic Escherichia coli (ExPEC) pose a significant threat to human and animal health. However, the diversity and antibiotic resistance of animal ExPEC, and their connection to human infections, remain largely unexplored. The study performs large-scale genome sequencing and antibiotic resistance testing of 499 swine-derived ExPEC isolates from China. Results show swine ExPEC are phylogenetically diverse, with over 80% belonging to phylogroups B1 and A. Importantly, 15 swine ExPEC isolates exhibit genetic relatedness to human-origin E. coli strains. Additionally, 49 strains harbor toxins typical of enteric E. coli pathotypes, implying hybrid pathotypes. Notably, 97% of the total strains are multidrug resistant, including resistance to critical human drugs like third- and fourth-generation cephalosporins. Correspondingly, genomic analysis unveils prevalent antibiotic resistance genes (ARGs), often associated with co-transfer mechanisms. Furthermore, analysis of 20 complete genomes illuminates the transmission pathways of ARGs within swine ExPEC and to human pathogens. For example, the transmission of plasmids co-harboring fosA3, blaCTX-M-14, and mcr-1 genes between swine ExPEC and human-origin Salmonella enterica is observed. These findings underscore the importance of monitoring and controlling ExPEC infections in animals, as they can serve as a reservoir of ARGs with the potential to affect human health or even be the origin of pathogens infecting humans.
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Affiliation(s)
- Xudong Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huifeng Hu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Yongwei Zhu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
| | - Taiquan Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Youlan Lu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiangru Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
| | - Zhong Peng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
| | - Ming Sun
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
| | - Jinshui Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Chen Tan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China.
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Bhushan G, Castano V, Wong Fok Lung T, Chandler C, McConville TH, Ernst RK, Prince AS, Ahn D. Lipid A modification of colistin-resistant Klebsiella pneumoniae does not alter innate immune response in a mouse model of pneumonia. Infect Immun 2024; 92:e0001624. [PMID: 38771050 PMCID: PMC11237409 DOI: 10.1128/iai.00016-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024] Open
Abstract
Polymyxin resistance in carbapenem-resistant Klebsiella pneumoniae bacteria is associated with high morbidity and mortality in vulnerable populations throughout the world. Ineffective antimicrobial activity by these last resort therapeutics can occur by transfer of mcr-1, a plasmid-mediated resistance gene, causing modification of the lipid A portion of lipopolysaccharide (LPS) and disruption of the interactions between polymyxins and lipid A. Whether this modification alters the innate host immune response or carries a high fitness cost in the bacteria is not well established. To investigate this, we studied infection with K. pneumoniae (KP) ATCC 13883 harboring either the mcr-1 plasmid (pmcr-1) or the vector control (pBCSK) ATCC 13883. Bacterial fitness characteristics of mcr-1 acquisition were evaluated. Differentiated human monocytes (THP-1s) were stimulated with KP bacterial strains or purified LPS from both parent isolates and isolates harboring mcr-1. Cell culture supernatants were analyzed for cytokine production. A bacterial pneumonia model in WT C57/BL6J mice was used to monitor immune cell recruitment, cytokine induction, and bacterial clearance in the bronchoalveolar lavage fluid (BALF). Isolates harboring mcr-1 had increased colistin MIC compared to the parent isolates but did not alter bacterial fitness. Few differences in cytokines were observed with purified LPS from mcr-1 expressing bacteria in vitro. However, in a mouse pneumonia model, no bacterial clearance defect was observed between pmcr-1-harboring KP and parent isolates. Consistently, no differences in cytokine production or immune cell recruitment in the BALF were observed, suggesting that other mechanisms outweigh the effect of these lipid A mutations in LPS.
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Affiliation(s)
- Gitanjali Bhushan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Victor Castano
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Tania Wong Fok Lung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Courtney Chandler
- Department of Microbial Pathogenesis, University of Maryland, School of Dentistry, Baltimore, Maryland, USA
| | - Thomas H. McConville
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland, School of Dentistry, Baltimore, Maryland, USA
| | - Alice S. Prince
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Danielle Ahn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
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49
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Sarker S, Neeloy RM, Habib MB, Urmi UL, Al Asad M, Mosaddek ASM, Khan MRK, Nahar S, Godman B, Islam S. Mobile Colistin-Resistant Genes mcr-1, mcr-2, and mcr-3 Identified in Diarrheal Pathogens among Infants, Children, and Adults in Bangladesh: Implications for the Future. Antibiotics (Basel) 2024; 13:534. [PMID: 38927200 PMCID: PMC11200974 DOI: 10.3390/antibiotics13060534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Colistin is a last-resort antimicrobial for treating multidrug-resistant Gram-negative bacteria. Phenotypic colistin resistance is highly associated with plasmid-mediated mobile colistin resistance (mcr) genes. mcr-bearing Enterobacteriaceae have been detected in many countries, with the emergence of colistin-resistant pathogens a global concern. This study assessed the distribution of mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5 genes with phenotypic colistin resistance in isolates from diarrheal infants and children in Bangladesh. Bacteria were identified using the API-20E biochemical panel and 16s rDNA gene sequencing. Polymerase chain reactions detected mcr gene variants in the isolates. Their susceptibilities to colistin were determined by agar dilution and E-test by minimal inhibitory concentration (MIC) measurements. Over 31.6% (71/225) of isolates showed colistin resistance according to agar dilution assessment (MIC > 2 μg/mL). Overall, 15.5% of isolates carried mcr genes (7, mcr-1; 17, mcr-2; 13, and mcr-3, with co-occurrence occurring in two isolates). Clinical breakout MIC values (≥4 μg/mL) were associated with 91.3% of mcr-positive isolates. The mcr-positive pathogens included twenty Escherichia spp., five Shigella flexneri, five Citrobacter spp., two Klebsiella pneumoniae, and three Pseudomonas parafulva. The mcr-genes appeared to be significantly associated with phenotypic colistin resistance phenomena (p = 0.000), with 100% colistin-resistant isolates showing MDR phenomena. The age and sex of patients showed no significant association with detected mcr variants. Overall, mcr-associated colistin-resistant bacteria have emerged in Bangladesh, which warrants further research to determine their spread and instigate activities to reduce resistance.
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Affiliation(s)
- Shafiuzzaman Sarker
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (S.S.); (R.M.N.); (M.B.H.); (U.L.U.); (M.A.A.); (S.N.)
| | - Reeashat Muhit Neeloy
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (S.S.); (R.M.N.); (M.B.H.); (U.L.U.); (M.A.A.); (S.N.)
| | - Marnusa Binte Habib
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (S.S.); (R.M.N.); (M.B.H.); (U.L.U.); (M.A.A.); (S.N.)
| | - Umme Laila Urmi
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (S.S.); (R.M.N.); (M.B.H.); (U.L.U.); (M.A.A.); (S.N.)
- School of Optometry and Vision Science, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Mamun Al Asad
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (S.S.); (R.M.N.); (M.B.H.); (U.L.U.); (M.A.A.); (S.N.)
| | | | | | - Shamsun Nahar
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (S.S.); (R.M.N.); (M.B.H.); (U.L.U.); (M.A.A.); (S.N.)
| | - Brian Godman
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK;
- Division of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
| | - Salequl Islam
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (S.S.); (R.M.N.); (M.B.H.); (U.L.U.); (M.A.A.); (S.N.)
- School of Optometry and Vision Science, UNSW Sydney, Sydney, NSW 2052, Australia
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Padhy I, Dwibedy SK, Mohapatra SS. A molecular overview of the polymyxin-LPS interaction in the context of its mode of action and resistance development. Microbiol Res 2024; 283:127679. [PMID: 38508087 DOI: 10.1016/j.micres.2024.127679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
With the rising incidences of antimicrobial resistance (AMR) and the diminishing options of novel antimicrobial agents, it is paramount to decipher the molecular mechanisms of action and the emergence of resistance to the existing drugs. Polymyxin, a cationic antimicrobial lipopeptide, is used to treat infections by Gram-negative bacterial pathogens as a last option. Though polymyxins were identified almost seventy years back, their use has been restricted owing to toxicity issues in humans. However, their clinical use has been increasing in recent times resulting in the rise of polymyxin resistance. Moreover, the detection of "mobile colistin resistance (mcr)" genes in the environment and their spread across the globe have complicated the scenario. The mechanism of polymyxin action and the development of resistance is not thoroughly understood. Specifically, the polymyxin-bacterial lipopolysaccharide (LPS) interaction is a challenging area of investigation. The use of advanced biophysical techniques and improvement in molecular dynamics simulation approaches have furthered our understanding of this interaction, which will help develop polymyxin analogs with better bactericidal effects and lesser toxicity in the future. In this review, we have delved deeper into the mechanisms of polymyxin-LPS interactions, highlighting several models proposed, and the mechanisms of polymyxin resistance development in some of the most critical Gram-negative pathogens.
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Affiliation(s)
- Indira Padhy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India.
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