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Spets P, Ebert K, Dinnétz P. Spatial analysis of antimicrobial resistance in the environment. A systematic review. GEOSPATIAL HEALTH 2023; 18. [PMID: 37246541 DOI: 10.4081/gh.2023.1168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/20/2023] [Indexed: 05/30/2023]
Abstract
Antimicrobial resistance (AMR) is a global major health concern. Spatial analysis is considered an invaluable method in health studies. Therefore, we explored the usage of spatial analysis in Geographic Information Systems (GIS) in studies on AMR in the environment. This systematic review is based on database searches, a content analysis, ranking of the included studies according to the preference ranking organization method for enrichment evaluations (PROMETHEE) and estimation of data points per km2. Initial database searches resulted in 524 records after removal of duplicates. After the last stage of full text screening, 13 greatly heterogeneous articles with diverse study origins, methods and design remained. In the majority of studies, the data density was considerably less than one sampling site per km2 but exceeded 1,000 sites per km2 in one study. The results of the content analysis and ranking showed a variation between studies that primarily used spatial analysis and those that used spatial analysis as a sec ondary method. We identified two distinct groups of GIS methods. The first was focused on sample collection and laboratory testing, with GIS as supporting method. The second group used overlay analysis as the primary method to combine datasets in a map. In one case, both methods were combined. The low number of articles that met our inclusion criteria highlights a research gap. Based on the findings of this study we encourage application of GIS to its full potential in studies of AMR in the environment.
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Affiliation(s)
- Patrick Spets
- Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge.
| | - Karin Ebert
- Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge.
| | - Patrik Dinnétz
- Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge.
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2
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Daly M, Powell J, O'Connell NH, Murphy L, Dunne CP. Antimicrobial Resistance Is Prevalent in E. coli and Other Enterobacterales Isolated from Public and Private Drinking Water Supplies in the Republic of Ireland. Microorganisms 2023; 11:1224. [PMID: 37317198 DOI: 10.3390/microorganisms11051224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 06/16/2023] Open
Abstract
High levels of bacterial antimicrobial resistance (AMR) have been reported in many environmental studies conducted in Ireland and elsewhere. The inappropriate use of antibiotics in both human and animal healthcare as well as concentrations of residual antibiotics being released into the environment from wastewaters are thought to be contributing factors. Few reports of AMR in drinking water-associated microbes are available for Ireland or internationally. We analysed 201 enterobacterales from group water schemes and public and private water supplies, only the latter having been surveyed in Ireland previously. The organisms were identified using conventional or molecular techniques. Antimicrobial susceptibility testing for a range of antibiotics was performed using the ARIS 2X interpreted in accordance with EUCAST guidelines. A total of 53 Escherichia coli isolates, 37 Serratia species, 32 Enterobacter species and enterobacterales from seven other genera were identified. A total of 55% of isolates were amoxicillin resistant, and 22% were amoxicillin-clavulanic acid resistant. A lower level of resistance (<10%) was observed to aztreonam, chloramphenicol, ciprofloxacin, gentamicin, ceftriaxone and trimethoprim-sulfamethoxazole. No resistance to amikacin, piperacillin/tazobactam, ertapenem or meropenem was detected. The level of AMR detected in this study was low but not insignificant and justifies ongoing surveillance of drinking water as a potential source of antimicrobial resistance.
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Affiliation(s)
- Maureen Daly
- Department of Clinical Microbiology, University Hospital Limerick, V94 F858 Limerick, Ireland
- Biomedical Sciences Research Institute, University of Ulster, Coleraine BT52 1SA, UK
| | - James Powell
- Department of Clinical Microbiology, University Hospital Limerick, V94 F858 Limerick, Ireland
- Centre for Interventions in Infection, Inflammation & Immunity (4i), School of Medicine, University of Limerick, V94 T9PX Limerick, Ireland
| | - Nuala H O'Connell
- Department of Clinical Microbiology, University Hospital Limerick, V94 F858 Limerick, Ireland
- Centre for Interventions in Infection, Inflammation & Immunity (4i), School of Medicine, University of Limerick, V94 T9PX Limerick, Ireland
| | - Liz Murphy
- Public Health Laboratory, Raheen Business Park, V94 H9YE Limerick, Ireland
| | - Colum P Dunne
- Centre for Interventions in Infection, Inflammation & Immunity (4i), School of Medicine, University of Limerick, V94 T9PX Limerick, Ireland
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Bueno I, Rodríguez A, Beaudoin A, Arnold WA, Wammer KH, de la Torre A, Singer RS. Identifying the spatiotemporal vulnerability of soils to antimicrobial contamination through land application of animal manure in Minnesota, United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 832:155050. [PMID: 35398123 DOI: 10.1016/j.scitotenv.2022.155050] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Antimicrobials may reach the soil environment from a variety of sources and pathways, including land application of human biosolids and animal manure. Once in soil, antimicrobials can affect the abundance and activity of soil microorganisms and exert selection pressures that enhance the emergence and spread of antimicrobial resistance (AMR). To mitigate the spread of AMR it is important to understand the spatial and temporal interactions between antimicrobials and soil. The goal of this study was to assess the vulnerability of Minnesota (U.S.) soil to contamination with specific antimicrobial compounds at temperatures experienced throughout the year. Soil contamination potential was estimated based upon specific antimicrobial drug binding and permanence, and average monthly temperature. Minnesota soil vulnerability was estimated by incorporating spatially explicit soil contamination potential, land cover type, and livestock density. Assessment of antimicrobials used in livestock production showed that soils are most vulnerable to antimicrobial contamination in southwestern Minnesota, to enrofloxacin, chlortetracycline, and oxytetracycline, and in the months of April and October. While the assessment herein was not based on actual on-farm antimicrobial use data and subsequent excretion of antimicrobial metabolites into the environment, this study provides an overview of the spatial and temporal potential for Minnesota soil to be contaminated by several antimicrobial drugs and demonstrates how specific vulnerability assessments might be conducted for geographic areas with known exposure (e.g., cropland fertilized with livestock manure and/or human biosolids). Such assessments might be used to identify best practices for mitigating antimicrobial exposure to soils and guide additional research to understand the role of environmental antimicrobial contamination in the problem of AMR.
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Affiliation(s)
- Irene Bueno
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Ave, Falcon Heights, MN 55108, United States.
| | - Antonio Rodríguez
- Animal Health Research Center, National Institute for Agricultural and Food Research and Technology (INIA/CISA-CSIC), Ctra Algete a El Casar s/n 28130 Valdeolmos, Madrid, Spain
| | - Amanda Beaudoin
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Ave, Falcon Heights, MN 55108, United States; Minnesota Department of Health. P.O. Box 64975, St. Paul, MN 55164-0975, United States
| | - William A Arnold
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota. 500, Pillsbury Drive S.E. Minneapolis, MN 55455-0116, United States
| | - Kristine H Wammer
- Department of Chemistry, College of Arts & Sciences, University of St. Thomas, 2115 Summit Ave., St. Paul, MN 55105, United States
| | - Ana de la Torre
- Animal Health Research Center, National Institute for Agricultural and Food Research and Technology (INIA/CISA-CSIC), Ctra Algete a El Casar s/n 28130 Valdeolmos, Madrid, Spain
| | - Randall S Singer
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Ave, Falcon Heights, MN 55108, United States
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Hooban B, Fitzhenry K, O'Connor L, Miliotis G, Joyce A, Chueiri A, Farrell ML, DeLappe N, Tuohy A, Cormican M, Morris D. A Longitudinal Survey of Antibiotic-Resistant Enterobacterales in the Irish Environment, 2019-2020. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154488. [PMID: 35278563 DOI: 10.1016/j.scitotenv.2022.154488] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The natural environment represents a complex reservoir of antibiotic-resistant bacteria as a consequence of different wastewater discharges including anthropogenic and agricultural. Therefore, the aim of this study was to examine sewage and waters across Ireland for the presence of antibiotic-resistant Enterobacterales. Samples were collected from the West, East and South of Ireland. Two periods of sampling took place between July 2019 and November 2020, during which 118 water (30 L) and 36 sewage samples (200 mL) were collected. Waters were filtered using the CapE method, followed by enrichment and culturing. Sewage samples were directly cultured on selective agars. Isolates were identified by MALDI-TOF and antibiotic susceptibility testing was performed in accordance with EUCAST criteria. Selected isolates were examined for blaCTX-M, blaVIM, blaIMP, blaOXA-48, blaNDM, and blaKPC by real time PCR and whole genome sequencing (n = 146). A total of 419 Enterobacterales (348 water, 71 sewage) were isolated from all samples. Hospital sewage isolates displayed the highest percentage resistance to many beta-lactam and aminoglycoside antibiotics. Extended-spectrum beta-lactamase-producers were identified in 78% of water and 50% of sewage samples. One or more carbapenemase-producing Enterobacterales were identified at 23 individual sampling sites (18 water, 5 sewage). This included the detection of blaOXA-48 (n = 18), blaNDM (n = 14), blaKPC (n = 4) and blaOXA-484 (n = 1). All NDM-producing isolates harbored the ble-MBL bleomycin resistance gene. Commonly detected sequence types included Klebsiella ST323, ST17, and ST405 as well as E. coli ST131, ST38 and ST10. Core genome MLST comparisons detected identical E. coli isolates from wastewater treatment plant (WWTP) influent and nursing home sewage, and the surrounding waters. Similarly, one Klebsiella pneumoniae isolated from WWTP influent and the surrounding estuarine water were identical. These results highlight the need for regular monitoring of the aquatic environment for the presence of antibiotic-resistant organisms to adequately inform public health policies.
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Affiliation(s)
- Brigid Hooban
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland.
| | - Kelly Fitzhenry
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Louise O'Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Aoife Joyce
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Alexandra Chueiri
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Maeve Louise Farrell
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Niall DeLappe
- National Salmonella, Shigella and Listeria Reference Laboratory, Galway University Hospitals, Galway, Ireland
| | - Alma Tuohy
- National Salmonella, Shigella and Listeria Reference Laboratory, Galway University Hospitals, Galway, Ireland
| | - Martin Cormican
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland; National Salmonella, Shigella and Listeria Reference Laboratory, Galway University Hospitals, Galway, Ireland; Health Service Executive, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
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Jadeja NB, Worrich A. From gut to mud: dissemination of antimicrobial resistance between animal and agricultural niches. Environ Microbiol 2022; 24:3290-3306. [PMID: 35172395 DOI: 10.1111/1462-2920.15927] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/11/2022]
Abstract
With increasing reports on antimicrobial resistance (AMR) in humans, animals and the environment, we are at risk of returning to a pre-antibiotic era. Therefore, AMR is recognized as one of the major global health threats of this century. Antibiotics are used extensively in farming systems to treat and prevent infections in food animals or to increase their growth. Besides the risk of a transfer of AMR between the human and the animal sector, there is another yet largely overlooked sector in the One Health triad. Human-dominated ecosystems such as agricultural soils are a major sink for antibiotics and AMR originating from livestock farming. This review summarizes current knowledge on the prevalence of AMR at the interface of animal and agricultural production and discusses the potential implications for human health. Soil resistomes are augmented by the application of manure from treated livestock. Subsequent transfer of AMR into plant microbiomes may likely play a critical role in human exposure to antibiotic resistance in the environment. Based on the knowledge that is currently available we advocate that more attention should be paid to the role of environmental resistomes in the AMR crisis.
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Affiliation(s)
- Niti B Jadeja
- Ashoka Trust for Research in Ecology and the Environment, PO, Royal Enclave, Srirampura, Jakkur, Bengaluru, Karnataka, 560064, India
| | - Anja Worrich
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Permoserstr. 15, Leipzig, 04318, Germany
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Bueno I, Beaudoin A, Arnold WA, Kim T, Frankson LE, LaPara TM, Kanankege K, Wammer KH, Singer RS. Quantifying and predicting antimicrobials and antimicrobial resistance genes in waterbodies through a holistic approach: a study in Minnesota, United States. Sci Rep 2021; 11:18747. [PMID: 34548591 PMCID: PMC8455696 DOI: 10.1038/s41598-021-98300-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/03/2021] [Indexed: 11/25/2022] Open
Abstract
The environment plays a key role in the spread and persistence of antimicrobial resistance (AMR). Antimicrobials and antimicrobial resistance genes (ARG) are released into the environment from sources such as wastewater treatment plants, and animal farms. This study describes an approach guided by spatial mapping to quantify and predict antimicrobials and ARG in Minnesota’s waterbodies in water and sediment at two spatial scales: macro, throughout the state, and micro, in specific waterbodies. At the macroscale, the highest concentrations across all antimicrobial classes were found near populated areas. Kernel interpolation provided an approximation of antimicrobial concentrations and ARG abundance at unsampled locations. However, there was high uncertainty in these predictions, due in part to low study power and large distances between sites. At the microscale, wastewater treatment plants had an effect on ARG abundance (sul1 and sul2 in water; blaSHV, intl1, mexB, and sul2 in sediment), but not on antimicrobial concentrations. Results from sediment reflected a long-term history, while water reflected a more transient record of antimicrobials and ARG. This study highlights the value of using spatial analyses, different spatial scales, and sampling matrices, to design an environmental monitoring approach to advance our understanding of AMR persistence and dissemination.
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Affiliation(s)
- Irene Bueno
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, USA.
| | - Amanda Beaudoin
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, USA.,Minnesota Department of Health, P.O. Box 64975, St. Paul, MN, 55164-0975, USA
| | - William A Arnold
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, MN, 55455, USA.,Water Resources Science Program, University of Minnesota, 1985 Buford Ave., St. Paul, MN, 55108, USA
| | - Taegyu Kim
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, MN, 55455, USA
| | - Lara E Frankson
- Water Resources Science Program, University of Minnesota, 1985 Buford Ave., St. Paul, MN, 55108, USA
| | - Timothy M LaPara
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, MN, 55455, USA
| | - Kaushi Kanankege
- Center for Animal Health and Food Safety, College of Veterinary Medicine, University of Minnesota, 1354 Eckles Ave., St. Paul, MN, 55108, USA
| | - Kristine H Wammer
- College of Arts & Sciences, University of St. Thomas, 2115 Summit Ave., St. Paul, MN, 55105, USA
| | - Randall S Singer
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, USA
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Hooban B, Fitzhenry K, Cahill N, Joyce A, O' Connor L, Bray JE, Brisse S, Passet V, Abbas Syed R, Cormican M, Morris D. A Point Prevalence Survey of Antibiotic Resistance in the Irish Environment, 2018-2019. ENVIRONMENT INTERNATIONAL 2021; 152:106466. [PMID: 33706038 DOI: 10.1016/j.envint.2021.106466] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
Water bodies worldwide have proven to be vast reservoirs of clinically significant antibiotic resistant organisms. Contamination of waters by anthropogenic discharges is a significant contributor to the widespread dissemination of antibiotic resistance. The aim of this research was to investigate multiple different anthropogenic sources on a national scale for the role they play in the environmental propagation of antibiotic resistance. A total of 39 water and 25 sewage samples were collected across four local authority areas in the West, East and South of Ireland. In total, 211 Enterobacterales were isolated (139 water, 72 sewage) and characterised. A subset of isolates (n=60) were chosen for whole genome sequencing. Direct comparisons of the water versus sewage isolate collections revealed a higher percentage of sewage isolates displayed resistance to cefoxitin (46%) and ertapenem (32%), while a higher percentage of water isolates displayed resistance to tetracycline (55%) and ciprofloxacin (71%). Half of all isolates displayed extended spectrum beta-lactamase (ESBL) production phenotypically (n = 105/211; 50%), with blaCTX-M detected in 99/105 isolates by PCR. Carbapenemase genes were identified in 11 isolates (6 sewage, 5 water). The most common variant was blaOXA-48 (n=6), followed by blaNDM-5 (n=2) and blaKPC-2 (n=2). Whole genome sequencing analysis revealed numerous different sequence types in circulation in both waters and sewage including E. coli ST131 (n=15), ST38 (n=8), ST10 (n=4) along with Klebsiella ST405 (n=3) and ST11 (n=2). Core genome MLST (cgMLST) comparisons uncovered three highly similar Klebsiella isolates originating from hospital sewage and two nearby waters. The Klebsiella isolates from an estuary and seawater displayed 99.1% and 98.8% cgMLST identity to the hospital sewage isolate respectively. In addition, three pairs of E. coli isolates from different waters also revealed cgMLST similarities, indicating widespread dissemination and persistence of certain strains in the aquatic environment. These findings highlight the need for routine monitoring of water bodies used for recreational and drinking purposes for the presence of multi-drug resistant organisms.
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Affiliation(s)
- Brigid Hooban
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway.
| | - Kelly Fitzhenry
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway
| | - Niamh Cahill
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway
| | - Aoife Joyce
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway
| | - Louise O' Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway
| | - James E Bray
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Virginie Passet
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Raza Abbas Syed
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway
| | - Martin Cormican
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway; Health Service Executive, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway
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