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Pfeifer NM, Weber M, Wiegand E, Barth SA, Berens C, Menge C. Escherichia coli resistant to the highest priority critically important fluoroquinolone or 3rd and 4th generation cephalosporin antibiotics persist in pigsties. Appl Environ Microbiol 2025:e0138624. [PMID: 40338087 DOI: 10.1128/aem.01386-24] [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: 07/24/2024] [Accepted: 03/25/2025] [Indexed: 05/09/2025] Open
Abstract
Antimicrobial resistance threatens human and animal health, with antimicrobial usage being a key driver of selection, transmission, and spread of resistant bacteria. Livestock represents a potential reservoir for human transmission, leading authorities to restrict veterinary usage of fluoroquinolones and certain cephalosporins. However, growing evidence indicates that the corresponding resistance determinants can be retained even in the drugs' absence. To obtain data on the magnitude and dynamics of this phenomenon in pig farming, we quantitatively and qualitatively assessed fluoroquinolone- and cephalosporin-resistant Escherichia coli in Thuringian pigsties practicing a closed management system to minimize the impact of externally introduced strains. Pooled fecal samples from consecutive fattening runs at one conventional and two organic farms and from 25 piglet groups from another conventional farm were collected over 16 months and screened for E. coli on plates containing enrofloxacin, ceftiofur, or cefquinome. Resistant bacteria were isolated on all farms; their counts varied strongly but were generally higher in piglets and declined with increasing animal age. Phylogenetic comparison of 393 isolates was performed via multiple-locus variable number tandem repeat analysis (MLVA) to follow strain dynamics and persistence. The isolates displayed large phylogenetic heterogeneity, featuring 52 different MLVA patterns. Still, conserved MLVA patterns indicated long-term persistence of specific strains in each farm's environment. This suggests that resistant strains appear well-adapted to the particular farm and its management practices, implying that, beyond restricting usage, further measures, including, e.g., consideration of the type of resistance as well as its persistence and transmission dynamics, will be indispensable to reduce the antimicrobial resistance load in pork production.IMPORTANCEAntimicrobial resistance (AMR) represents a global threat to human and animal health, with animals considered a reservoir for transmission of AMR to humans. Because antimicrobial usage is a driver for resistance, one approach to decrease the AMR burden is to reduce its usage. However, this can, but does not necessarily, lead to lower AMR prevalence. German and EU legislation restrict the use of fluoroquinolones and certain cephalosporins, substance classes designated as highest priority critically important antimicrobials for human medicine, in animal husbandry. Longitudinal sampling of organic and conventional farms in Thuringia for resistance to these antibiotic classes revealed that certain resistant Escherichia coli strains can persist in the farm environment over extended time periods. These strains displayed farm specificity, indicating adaptation to the particular farm and its management practices, so that their elimination might be difficult, requiring either procedures acting generally against Enterobacterales or targeted action against the specific strains.
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Affiliation(s)
- Nicola M Pfeifer
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Michael Weber
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Elisabeth Wiegand
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Stefanie A Barth
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Christian Berens
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Christian Menge
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
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2
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Schmartz GP, Rehner J, Schuff MJ, Molano LAG, Becker SL, Krawczyk M, Tagirdzhanov A, Gurevich A, Francke R, Müller R, Keller V, Keller A. Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes. Nat Commun 2024; 15:8263. [PMID: 39327429 PMCID: PMC11427580 DOI: 10.1038/s41467-024-52669-9] [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: 12/18/2023] [Accepted: 09/13/2024] [Indexed: 09/28/2024] Open
Abstract
Understanding human, animal, and environmental microbiota is essential for advancing global health and combating antimicrobial resistance (AMR). We investigate the oral and gut microbiota of 48 animal species in captivity, comparing them to those of wildlife animals. Specifically, we characterize the microbiota composition, metabolic pathways, AMR genes, and biosynthetic gene clusters (BGCs) encoding the production of specialized metabolites. Our results reveal a high diversity of microbiota, with 585 novel species-level genome bins (SGBs) and 484 complete BGCs identified. Functional gene analysis of microbiomes shows diet-dependent variations. Furthermore, by comparing our findings to wildlife-derived microbiomes, we observe the impact of captivity on the animal microbiome, including examples of converging microbiome compositions. Importantly, our study identifies AMR genes against commonly used veterinary antibiotics, as well as resistance to vancomycin, a critical antibiotic in human medicine. These findings underscore the importance of the 'One Health' approach and the potential for zoonotic transmission of pathogenic bacteria and AMR. Overall, our study contributes to a better understanding of the complexity of the animal microbiome and highlights its BGC diversity relevant to the discovery of novel antimicrobial compounds.
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Affiliation(s)
- Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, 66421 Saarland University, Homburg, Germany
| | - Miriam J Schuff
- Institute of Medical Microbiology and Hygiene, 66421 Saarland University, Homburg, Germany
| | | | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, 66421 Saarland University, Homburg, Germany
| | - Marcin Krawczyk
- Department of Medicine II, 66421 Saarland University, Homburg, Germany
| | - Azat Tagirdzhanov
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany
| | - Alexey Gurevich
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany
- Department of Computer Science, Saarland University, 66123, Saarbrücken, Germany
| | | | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany
| | - Verena Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany.
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Guo ZF, Das K, Boeing WJ, Xu YY, Borgomeo E, Zhang D, Ao SC, Yang XR. Distance-decay equations of antibiotic resistance genes across freshwater reservoirs. WATER RESEARCH 2024; 258:121830. [PMID: 38823285 DOI: 10.1016/j.watres.2024.121830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/10/2024] [Accepted: 05/22/2024] [Indexed: 06/03/2024]
Abstract
Distance-decay (DD) equations can discern the biogeographical pattern of organisms and genes in a better way with advanced statistical methods. Here, we developed a data Compilation, Arrangement, and Statistics framework to advance quantile regression (QR) into the generation of DD equations for antibiotic resistance genes (ARGs) across various spatial scales using freshwater reservoirs as an illustration. We found that QR is superior at explaining dissemination potential of ARGs to the traditionally used least squares regression (LSR). This is because our model is based on the 'law of limiting factors', which reduces influence of unmeasured factors that reduce the efficacy of the LSR method. DD equations generated from the 99th QR model for ARGs were 'Sall = 90.03e-0.01Dall' in water and 'Sall = 92.31e-0.011Dall' in sediment. The 99th QR model was less impacted by uneven sample sizes, resulting in a better quantification of ARGs dissemination. Within an individual reservoir, the 99th QR model demonstrated that there is no dispersal limitation of ARGs at this smaller spatial scale. The QR method not only allows for construction of robust DD equations that better display dissemination of organisms and genes across ecosystems, but also provides new insights into the biogeography exhibited by key parameters, as well as the interactions between organisms and environment.
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Affiliation(s)
- Zhao-Feng Guo
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Kiranmoy Das
- Applied Statistics Division, Indian Statistical Institute, Kolkata 700108, India
| | - Wiebke J Boeing
- Department of Fish, Wildlife & Conservation Ecology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Yao-Yang Xu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China.
| | - Edoardo Borgomeo
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
| | - Dong Zhang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Si-Cheng Ao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
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Zeng JY, Li W, Su JQ, Wang YZ, Li Y, Yao H. Manure application amplified the co-selection of quaternary ammonium disinfectant and antibiotic on soil antibiotic resistome. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133792. [PMID: 38368685 DOI: 10.1016/j.jhazmat.2024.133792] [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: 10/13/2023] [Revised: 01/17/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Disinfectants and antibiotics are widely used for the prevention and control of bacterial infectious diseases. Frequent disinfection is thought to exacerbate antibiotic resistance. However, little is known about how disinfectants and antibiotics co-induce changes in the soil antibiotic resistance genes (ARGs). This study determined the ARG profiles and bacterial community dynamics between unamended soil and manure-amended soil exposed to benzalkonium chloride (C12) (BC, 10 mg kg-1) disinfectant and sulfamethazine (SMZ, 1 mg kg-1), using high-throughput quantitative PCR and 16 S rRNA gene sequencing. Manure application enriched the soil in terms of ARGs abundance and diversity, which synergistically amplified the co-selection effect of BC and SMZ on soil antibiotic resistome. Compared with the control treatment, BC and SMZ exposure had a smaller impact on the bacterial infectious diseases and antimicrobial resistance-related functions in manure-amended soil, in which bacterial communities with greater tolerance to antimicrobial substances were constructed. Manure application increased the proportion of rank I ARGs and potential human pathogenic bacteria, while BC and SMZ exposure increased the drug-resistant pathogens transmission risk. This study validated that BC and SMZ aggravated the antimicrobial resistance under manure application, providing a reference for managing the spread risk of antimicrobial resistance in agricultural activities.
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Affiliation(s)
- Jie-Yi Zeng
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Wei Li
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China.
| | - Yan-Zi Wang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China.
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Merenstein D, Pot B, Leyer G, Ouwehand AC, Preidis GA, Elkins CA, Hill C, Lewis ZT, Shane AL, Zmora N, Petrova MI, Collado MC, Morelli L, Montoya GA, Szajewska H, Tancredi DJ, Sanders ME. Emerging issues in probiotic safety: 2023 perspectives. Gut Microbes 2023; 15:2185034. [PMID: 36919522 PMCID: PMC10026873 DOI: 10.1080/19490976.2023.2185034] [Citation(s) in RCA: 143] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/22/2023] [Indexed: 03/16/2023] Open
Abstract
Probiotics are used for both generally healthy consumers and in clinical settings. However, theoretical and proven adverse events from probiotic consumption exist. New probiotic strains and products, as well as expanding use of probiotics into vulnerable populations, warrants concise, and actionable recommendations on how to work toward their safe and effective use. The International Scientific Association for Probiotics and Prebiotics convened a meeting to discuss and produce evidence-based recommendations on potential acute and long-term risks, risks to vulnerable populations, the importance for probiotic product quality to match the needs of vulnerable populations, and the need for adverse event reporting related to probiotic use. The importance of whole genome sequencing, which enables determination of virulence, toxin, and antibiotic resistance genes, as well as clear assignment of species and strain identity, is emphasized. We present recommendations to guide the scientific and medical community on judging probiotic safety.
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Affiliation(s)
- Daniel Merenstein
- Department of Family Medicine, Georgetown University Medical Center, Washington, DCUSA
| | - Bruno Pot
- Yakult Europe BV, Almere, Netherlands
| | | | - Arthur C. Ouwehand
- Global Health & Nutrition Sciences, International Flavors & Fragrances, Kantvik, Finland
| | - Geoffrey A. Preidis
- Division of Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA
| | - Christopher A. Elkins
- Clinical and Environmental Microbiology Branch, Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Andi L. Shane
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Emory Children’s Center, Atlanta, Georgia
| | - Niv Zmora
- Scientific consultant, Elinav Lab, Immunology Department, Weizmann Institute of Science, Department of Gastroenterology and Liver Diseases, Tel Aviv, Israel
| | | | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain
| | - Lorenzo Morelli
- Department of Food Science and Technology, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Gina A. Montoya
- Department of Chemical Risk Assessment, Nestlé S.A., Lausanne, Switzerland
| | - Hania Szajewska
- Department of Paediatrics, The Medical University of Warsaw, Warsaw, Poland
| | - Daniel J. Tancredi
- Department of Pediatrics, UC Davis School of Medicine, Sacramento, CA, USA
| | - Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, Centennial, CO, USA
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