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O’Neill L, Manzanilla EG, Ekhlas D, Leonard FC. Antimicrobial Resistance in Commensal Escherichia coli of the Porcine Gastrointestinal Tract. Antibiotics (Basel) 2023; 12:1616. [PMID: 37998818 PMCID: PMC10669415 DOI: 10.3390/antibiotics12111616] [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: 09/18/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Antimicrobial resistance (AMR) in Escherichia coli of animal origin presents a threat to human health. Although animals are not the primary source of human infections, humans may be exposed to AMR E. coli of animal origin and their AMR genes through the food chain, direct contact with animals, and via the environment. For this reason, AMR in E. coli from food producing animals is included in most national and international AMR monitoring programmes and is the subject of a large body of research. As pig farming is one of the largest livestock sectors and the one with the highest antimicrobial use, there is considerable interest in the epidemiology of AMR in E. coli of porcine origin. This literature review presents an overview and appraisal of current knowledge of AMR in commensal E. coli of the porcine gastrointestinal tract with a focus on its evolution during the pig lifecycle and the relationship with antimicrobial use. It also presents an overview of the epidemiology of resistance to extended spectrum cephalosporins, fluoroquinolones, and colistin in pig production. The review highlights the widespread nature of AMR in the porcine commensal E. coli population, especially to the most-used classes in pig farming and discusses the complex interplay between age and antimicrobial use during the pig lifecycle.
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Affiliation(s)
- Lorcan O’Neill
- Pig Development Department, Teagasc, The Irish Food and Agriculture Authority, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (E.G.M.); (D.E.)
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland;
| | - Edgar García Manzanilla
- Pig Development Department, Teagasc, The Irish Food and Agriculture Authority, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (E.G.M.); (D.E.)
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland;
| | - Daniel Ekhlas
- Pig Development Department, Teagasc, The Irish Food and Agriculture Authority, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (E.G.M.); (D.E.)
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland;
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin D15 DY05, Ireland
| | - Finola C. Leonard
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland;
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Ozawa M, Shirakawa T, Moriya K, Furuya Y, Kawanishi M, Makita K, Sekiguchi H. Role of Plasmids in Co-Selection of Antimicrobial Resistances Among Escherichia coli Isolated from Pigs. Foodborne Pathog Dis 2023; 20:435-441. [PMID: 37540099 DOI: 10.1089/fpd.2023.0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
Co-selection is thought to occur when resistance genes are located on the same mobile genetic element. However, this mechanism is currently poorly understood. In this study, complete circular plasmids from swine-derived Escherichia coli were sequenced with short and long reads to confirm that resistance genes involved in co-resistance were co-transferred by the same plasmid. Conjugative transfer tests were performed, and multiple resistance genes were transmitted. The genes possessed by the donor, transconjugant, and plasmid of the donor were highly similar. In addition, the sequences of the plasmid of the donor and the plasmid of the transconjugant were almost identical. Resistance genes associated with statistically significant combinations of antimicrobial use and resistance were co-transmitted by the same plasmid. These results suggest that resistance genes may be involved in co-selection by their transfer between bacteria on the same plasmid.
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Affiliation(s)
- Manao Ozawa
- Assay Division II, National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan
| | - Takahiro Shirakawa
- Assay Division II, National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan
| | - Konomi Moriya
- Assay Division II, National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan
| | - Yukari Furuya
- Assay Division II, National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan
| | - Michiko Kawanishi
- Assay Division II, National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan
| | - Kohei Makita
- Veterinary Epidemiology Unit, Division of Health and Environmental Sciences, Department of Veterinary Medicine, School of Veterinary Medicine, Rakino Gakuen University, Hokkaido, Japan
| | - Hideto Sekiguchi
- Assay Division II, National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan
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Kobayashi S, Tamamura-Andoh Y, Yamane I, Kusumoto M, Katsuda K. The association between farm-level antimicrobial usage and resistance of Staphylococcus spp., as the major genus isolated from aerosol samples, in Japanese piggeries. Front Vet Sci 2023; 10:1127819. [PMID: 37565078 PMCID: PMC10411535 DOI: 10.3389/fvets.2023.1127819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/10/2023] [Indexed: 08/12/2023] Open
Abstract
Bacteria are the dominant particulate matter in livestock houses and can threaten animal and public health. Antimicrobial resistance (AMR) is a crucial concern worldwide, and nationwide measures established based on the One Health approach are being implemented in many countries. This requires multidisciplinary perspectives and collaboration among the human, animal, and environmental sectors. However, information on the AMR risk in livestock house aerosol is limited, especially its association with antimicrobial usage (AMU). Therefore, this study was conducted to reveal the AMR profile of Staphylococcus, the major bacterial genus in the aerosol of the piggeries of Japanese farms, and the association between farm-level AMU and AMR. The investigation at 10 farrow-to-finish pig farms revealed that regardless of the sampling season and the piggery group, the resistance rate of isolated staphylococci for oxacillin, erythromycin, and lincomycin was more than 40% of the median and tended to be higher than that for other antimicrobials. The AMU adjusted by the defined daily dose (DDD-adjusted AMU) in the fattening piggery group was significantly higher than that in the sow piggery group (p < 0.05). Finally, for the fattening piggery group, the generalized linear mixed model revealed that the AMR rate for oxacillin, erythromycin, tetracycline, and chloramphenicol was positively associated with the corresponding class-based DDD-adjusted AMU of penicillins (odds ratio (OR) = 2.63, p = 0.03), macrolides (OR = 6.89, p = 0.0001), tetracyclines (OR = 2.48, p = 0.04), and amphenicols (OR = 3.22, p = 0.03), respectively. These significant positive associations observed in this study imply that the resistance rate for these antimicrobials may decrease by reducing the corresponding antimicrobials' use. In addition, the resistance rates for erythromycin and chloramphenicol also displayed a positive association with the AMU of antimicrobial classes other than macrolides and amphenicols, respectively. The mechanism underlying these phenomena is unclear; therefore, further evaluation will be needed. As limited studies have reported staphylococci in piggery aerosol and its AMR with quantitative AMU, these results based on on-farm investigations are expected to aid in establishing countermeasures for AMR of aerosol bacteria in pig farms.
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Affiliation(s)
- Sota Kobayashi
- Enteric Pathogen Group, Division of Zoonosis Research, National Institute of Animal Health, NARO, Tsukuba, Ibaraki, Japan
| | - Yukino Tamamura-Andoh
- Enteric Pathogen Group, Division of Zoonosis Research, National Institute of Animal Health, NARO, Tsukuba, Ibaraki, Japan
| | - Itsuro Yamane
- Enteric Pathogen Group, Division of Zoonosis Research, National Institute of Animal Health, NARO, Tsukuba, Ibaraki, Japan
| | - Masahiro Kusumoto
- Enteric Pathogen Group, Division of Zoonosis Research, National Institute of Animal Health, NARO, Tsukuba, Ibaraki, Japan
| | - Ken Katsuda
- Division of Hygiene Management Research, National Institute of Animal Health, NARO, Tsukuba, Ibaraki, Japan
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Li M, Li Z, Zhong Q, Liu J, Han G, Li Y, Li C. Antibiotic resistance of fecal carriage of Escherichia coli from pig farms in China: a meta-analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:22989-23000. [PMID: 34797542 DOI: 10.1007/s11356-021-17339-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Fecal carriage of bacteria is a major source of antibiotic resistance genes (ARGs) and a public health risk, but the antibiotic resistance of Escherichia coli (E. coli) in Chinese pig farms remains a major gap in the available literature. Our goal was to conduct a meta-analysis of studies reporting antibiotic resistance of fecal carriage of E. coli from pig farms in China, calculating the pooled resistance rates and summarizing factors associated with it. We searched PubMed and Web of Science for studies published in English up to February 28, 2021. We also searched bibliographic indices and corresponded with the authors. We chose ciprofloxacin, gentamicin, tetracycline, ampicillin, and florfenicol from five major types of antibiotics to comprehensively evaluate the resistance rate of E. coli. We used a random-effects model and Freeman-Tukey double arcsine transformation to calculate the resistance rate and 95% confidence interval. Among the 120 retrieved manuscripts, 16 studies (1985 E. coli isolates) were deemed eligible for our analysis. The combined resistance rate of E. coli from feces was 58.8% (95% CI: 45.3-71.7%) to ciprofloxacin, 54.3% (95% CI: 35.3-72.6%) to gentamicin, 91.0% (95% CI: 83.1-96.7%) to tetracycline, 81.4% (95% CI: 62.0-95.1%) to ampicillin, and 65.4% (95% CI: 33.9-90.9%) to florfenicol. In conclusion, fecal carriage of E. coli in Chinese pig farms shows high resistance to ciprofloxacin, gentamicin, tetracycline, ampicillin, and florfenicol. Subgroup analysis showed that the resistance of E. coli to antibiotics was closely related to the sample size and the health condition of the pigs. Specifically, ESBL-producing E. coli has a higher ratio of resistance to other antibiotics. Future collection of antibiotic resistance and other information in pig farms should be more precise and depend on local surveys.
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Affiliation(s)
- Mingyang Li
- Research Center for livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Zhi Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei Province, China
| | - Qiuming Zhong
- Research Center for livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Junze Liu
- Research Center for livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Guofeng Han
- Research Center for livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Yansen Li
- Research Center for livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Chunmei Li
- Research Center for livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China.
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Informing Stewardship Measures in Canadian Food Animal Species through Integrated Reporting of Antimicrobial Use and Antimicrobial Resistance Surveillance Data-Part I, Methodology Development. Pathogens 2021; 10:pathogens10111492. [PMID: 34832647 PMCID: PMC8618382 DOI: 10.3390/pathogens10111492] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022] Open
Abstract
This study explores methodologies for the data integration of antimicrobial use (AMU) and antimicrobial resistance (AMR) results within and across three food animal species, surveyed at the farm-level by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). The approach builds upon existing CIPARS methodology and principles from other AMU and AMR surveillance systems. Species level data integration involved: (1) standard CIPARS descriptive and temporal analysis of AMU/AMR, (2) synthesis of results, (3) selection of AMU and AMR outcomes for integration, (4) selection of candidate AMU indicators to enable comparisons of AMU levels between species and simultaneous assessment of AMU and AMR trends, (5) exploration of analytic options for studying associations between AMU and AMR, and (6) interpretation and visualization. The multi-species integration was also completed using the above approach. In addition, summarized reporting of internationally-recognized indicators of AMR (i.e., AMR adjusted for animal biomass) and AMU (mg/population correction unit, mg/kg animal biomass) is explored. It is envisaged that this approach for species and multi-species AMU-AMR data integration will be applied to the annual CIPARS farm-level data and progressively developed over time to inform AMU-AMR integrated surveillance best practices for further enhancement of AMU stewardship actions.
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Agunos A, Gow SP, Deckert AE, Léger DF. Informing Stewardship Measures in Canadian Food Animal Species through Integrated Reporting of Antimicrobial Use and Antimicrobial Resistance Surveillance Data-Part II, Application. Pathogens 2021; 10:pathogens10111491. [PMID: 34832646 PMCID: PMC8621420 DOI: 10.3390/pathogens10111491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 11/16/2022] Open
Abstract
Using the methodology developed for integrated analysis and reporting of antimicrobial use (AMU) and antimicrobial resistance (AMR) data, farm-level surveillance data were synthesized and integrated to assess trends and explore potential AMU and AMR associations. Data from broiler chicken flocks (n = 656), grower-finisher pig herds (n = 462) and turkey flocks (n = 339) surveyed by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) at the farm-level (2015-2019) were used. The analyses showed a reduction in mean flock/herd level number of defined daily doses using Canadian standards (nDDDvetCA) adjusted for kg animal biomass that coincided with the decline in % resistance in the three species. This was noted in most AMU-AMR pairs studied except for ciprofloxacin resistant Campylobacter where resistance continued to be detected (moderate to high levels) despite limited fluoroquinolone use. Noteworthy was the significantly negative association between the nDDDvetCA/kg animal biomass and susceptible Escherichia coli (multispecies data), an early indication that AMU stewardship actions are having an impact. However, an increase in the reporting of diseases in recent years was observed. This study highlighted the value of collecting high-resolution AMU surveillance data with animal health context at the farm-level to understand AMR trends, enable data integration and measure the impact of AMU stewardship actions.
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Affiliation(s)
- Agnes Agunos
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada; (A.E.D.); (D.F.L.)
- Correspondence: ; Tel.: +1-519-4007895
| | - Sheryl P. Gow
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Saskatoon, SK S7N 5B4, Canada;
| | - Anne E. Deckert
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada; (A.E.D.); (D.F.L.)
| | - David F. Léger
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada; (A.E.D.); (D.F.L.)
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Sali V, Nykäsenoja S, Heikinheimo A, Hälli O, Tirkkonen T, Heinonen M. Antimicrobial Use and Susceptibility of Indicator Escherichia coli in Finnish Integrated Pork Production. Front Microbiol 2021; 12:754894. [PMID: 34803978 PMCID: PMC8600236 DOI: 10.3389/fmicb.2021.754894] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022] Open
Abstract
In pigs, antimicrobial use (AMU) practices vary at different production phases between herds and between countries. Antimicrobial resistance (AMR) development is linked to AMU but recognized as a multi-factorial issue, and thus, any information increasing knowledge of AMU and AMR relationships is valuable. We described AMU and screened the carriage of different AMR phenotypes of indicator Escherichia coli in 25 selected Finnish piglet-producing and finishing herds that formed nine birth-to-slaughter production lines. Moreover, we studied associations between AMU and AMR in both herd types and throughout the production line. Treatment records were obtained from the national Sikava register for 1year, and AMU was quantified as mg/PCU (population correction unit) and TIs (treatment incidences). For phenotypic antimicrobial susceptibility testing, ten pen-level pooled feces samples (n=250) in each herd were collected from one room representing the oldest weaned piglets or the oldest finishing pigs. Majority of the medications (96.8%) was administered parenterally, and penicillin was the predominant antimicrobial in every herd. More different antimicrobial substances were used in piglet-producing than in finishing herds (median 5 and 1, respectively, p<0.001). As mg/PCU, sows had the highest AMU and suckling piglets had the highest TIs, whereas finishing pigs were the least treated age group. The proportion of susceptible indicator E. coli isolates of all studied isolates was 59.6%. Resistance was found most commonly against tetracycline, sulfamethoxazole, trimethoprim, and ampicillin, and multi-resistant (MR) isolates (46.5% of all resistant isolates) were resistant to a maximum of four different antimicrobials. Quinolone resistance was rare, and no resistance against 3rd-generation cephalosporins, meropenem, azithromycin, colistin, gentamicin, or tigecycline was detected. The main associations between AMU and AMR were found at antimicrobial group level when use was compared with the presence of AMR phenotypes. The proportion of resistant isolates was not associated with AMU, and herd size was not associated with either AMU or AMR. We suggest that the use of narrow-spectrum beta-lactams as a primary treatment option and lack of wide application of oral group medications potentially favors a good resistance pattern in integrated pork production.
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Affiliation(s)
- Virpi Sali
- Department of Production Animal Medicine, University of Helsinki, Mäntsälä, Finland
| | - Suvi Nykäsenoja
- Microbiology Unit, Finnish Food Authority, Helsinki, Finland
| | - Annamari Heikinheimo
- Microbiology Unit, Finnish Food Authority, Helsinki, Finland
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Outi Hälli
- Department of Production Animal Medicine, University of Helsinki, Mäntsälä, Finland
| | | | - Mari Heinonen
- Department of Production Animal Medicine, University of Helsinki, Mäntsälä, Finland
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The First Report of mcr-1-Carrying Escherichia coli Originating from Animals in Serbia. Antibiotics (Basel) 2021; 10:antibiotics10091063. [PMID: 34572647 PMCID: PMC8467794 DOI: 10.3390/antibiotics10091063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/16/2021] [Accepted: 08/30/2021] [Indexed: 01/08/2023] Open
Abstract
The aim of this study was continuous monitoring of the presence of mcr-1 to mcr-5 genes in Enterobacterales isolated from cattle, pigs, and domestic poultry at intensive breeding facilities in Northern Vojvodina, Serbia, from 1 January 1 to 1 October 2020. Out of 2167 examined samples, mcr-1 was observed in five E. coli isolates originating from healthy turkeys. Four isolates belonged to the phylogenetic group B1, and one isolate to the phylogenetic group A. Detected E. coli serogenotypes (somatic O and flagellar H antigens) were O8:H25 and O29:H25. Core-genome multi-locus sequence typing (cgMLST) revealed three ST58 isolates clustering together in Clonal Complex (CC) 155 and two singletons of ST641-CC86 and ST410-CC23, respectively. Clonotyping revealed CH4-32 (n = 3), CH6-53 (n = 1) and CH4-24 (n = 1). In all isolates, the mcr-1 gene was located on a large IncX4 replicon type plasmid. Eight virulence-associated genes (VAGs) typical of avian pathogenic E. coli (APEC) (fyuA, fimH, hlyF, iss, ompT, sitA, traT, iroN) were detected in four isolates. These isolates were investigated for susceptibility to four biocides and revealed MIC values of 0.125% for glutardialdehyde, of 0.00003–0.00006% for chlorohexidine, of 4–6% for isopropanol and of 0.001–0.002% for benzalkonium chloride. All obtained MIC values of the tested biocides were comparable to the reference strain, with no indication of possible resistance. This is the first report of mcr-1.1-carrying E. coli from Serbia. Although only samples from turkeys were mcr-positive in this study, continuous monitoring of livestock samples is advised to prevent a spill-over from animals to humans.
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Prevalence of mobile colistin resistance (mcr) genes in extended-spectrum β-lactamase-producing Escherichia coli isolated from retail raw foods in Nha Trang, Vietnam. Int J Food Microbiol 2021; 346:109164. [PMID: 33813365 DOI: 10.1016/j.ijfoodmicro.2021.109164] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 12/15/2022]
Abstract
The aim of the study was to assess the presence of genes in ESBL-producing E. coli (ESBL-Ec) isolated from retail raw food in Nha Trang, Vietnam. A total of 452 food samples comprising chicken (n = 116), pork (n = 112), fish (n = 112) and shrimp (n = 112) collected between 2015 and 2017 were examined for the prevalence of ESBL-Ec. ESBL-Ec were detected in 46.0% (208/452) of retail food samples, particularly in 66.4% (77/116), 55.4% (62/112), 42.0% (47/112) 19.6% (22/112) of chicken, pork, fish and shrimp, respectively. Sixty-five out of the 208 (31.3%) ESBL-Ec isolates were positive for mcr genes including mcr-1, mcr-3 and both mcr-1 and mcr-3 genes in 56/208 (26.9%), 1/208 (0.5%) and 8/208 (3.9%) isolates, respectively. Particularly, there was higher prevalence of mcr-1 in ESBL-Ec isolates from chicken (53.2%, 41/77) in comparison to shrimp (22.7%, 5/22), pork (11.3%, 7/62) and fish (6.4%, 3/47). mcr-3 gene was detected in co-existence with mcr-1 in ESBL-Ec isolates from shrimp (9.1%, 2/22), pork (8.1%, 5/62) and fish (2.1%, 1/47) but not chicken. The 65 mcr-positive ESBL-Ec (mcr-ESBL-Ec) were colistin-resistant with the MICs of 4-8 μg/mL. All mcr-3 gene-positive isolates belonged to group A, whereas phylogenetic group distribution of isolates harboring only mcr-1 was B1 (44.6%), A (28.6%) and D (26.8%). PFGE analysis showed diverse genotypes, although some isolates demonstrated nearly clonal relationships. S1-PFGE and Southern hybridization illustrated that the mcr-1 and mcr-3 genes were located either on chromosomes or on plasmids. However, the types of mcr genes were harbored on different plasmids with varied sizes of 30-390 kb. Besides, the ESBL genes of CTX-M-1 or CTX-M-9 were also detected to be located on plasmids. Noteworthy, co-location of CTX-M-1 with mcr-1 or mcr-3 genes on the same plasmid was identified. The conjugation experiment indicated that the mcr-1 or mcr-3 was horizontally transferable. All mcr-ESBL-Ec isolates were multidrug resistance (resistance to ≥3 antimicrobial classes). Moreover, β-Lactamase-encoding genes of the CTX-M-1 (78.5%), CTX-M-9 (21.5%), TEM (61.5%) groups were found in mcr-ESBL-Ec. The astA gene was detected in 27 (41.5%) mcr-ESBL-Ec isolates demonstrating their potential virulence. In conclusion, mcr-1 and mcr-3 genes existed individually or concurrently in ESBL-Ec isolates recovered from retail raw food in Nha Trang city, which might further complicate the antimicrobial-resistant situation in Vietnam, and is a possible health risk for human.
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Misumi W, Funamori T, Hamada K, Iwamoto J, Fujisono S, Chitose K, Kusumoto M. Association between antimicrobial treatment and resistance of pathogenic Escherichia coli isolated from diseased swine in Kagoshima Prefecture, Japan. J Vet Med Sci 2021; 83:358-369. [PMID: 33431756 PMCID: PMC8025414 DOI: 10.1292/jvms.20-0338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Pathogenic Escherichia coli is an important cause of diarrhea, edema disease, and septicemia in swine. In Japan, the volume of antimicrobial drugs used for animals is highest in swine, but information about the prevalence of antimicrobial-resistant bacteria is confined to apparently healthy animals. In the present study, we determined the O serogroups, virulence factors, and antimicrobial resistance of 360 E. coli isolates from swine that died of disease in Kagoshima Prefecture, Japan, between 1999 and 2017. The isolates of the predominant serogroups O139, OSB9, O149, O8, and O116 possessed virulence factor genes typically found in diarrheagenic E. coli. We further found five strains of third-generation cephalosporin-resistant E. coli that each produced an extended-spectrum β-lactamase encoded by blaCTX-M-14, blaCTX-M-15, blaCTX-M-24, blaCTX-M-61, or blaSHV-12. In 218 swine with a clear history of antimicrobial drug use, we further analyzed associations between the use of antimicrobials for the treatment of diseased swine and the isolation of resistant E. coli. We found significant associations between antimicrobial use and selection of resistance to the same class of antimicrobials, such as the use of ceftiofur and resistance to cefotaxime, cefazolin, or ampicillin, the use of aminoglycosides and resistance to streptomycin, and the use of phenicols and resistance to chloramphenicol. A significant association between antimicrobial use and the resistance of E. coli isolates to structurally unrelated antimicrobials, such as the use of ceftiofur and resistance to chloramphenicol, was also observed.
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Affiliation(s)
- Wakako Misumi
- Kagoshima Central Livestock Hygiene Service Center, 1678 Yuda, Higashiichiki, Hioki, Kagoshima 899-2201, Japan
| | - Taruho Funamori
- Hiroshima Western Livestock Hygiene Service Center, 1-15 Saijogojo, Higashi-Hiroshima, Hiroshima 739-0013, Japan
| | - Kyohei Hamada
- Fukuoka Chuo Livestock Hygiene Service Center, 4-14-5 Hakozakifuto, Higashi-ku, Fukuoka 812-0051, Japan
| | - Jiro Iwamoto
- Kagoshima Central Livestock Hygiene Service Center, 1678 Yuda, Higashiichiki, Hioki, Kagoshima 899-2201, Japan
| | - Shoichiro Fujisono
- Kagoshima Central Livestock Hygiene Service Center, 1678 Yuda, Higashiichiki, Hioki, Kagoshima 899-2201, Japan
| | - Kenichi Chitose
- Kagoshima Central Livestock Hygiene Service Center, 1678 Yuda, Higashiichiki, Hioki, Kagoshima 899-2201, Japan
| | - Masahiro Kusumoto
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
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Gozi KS, Froes JR, Deus Ajude LPT, da Silva CR, Baptista RS, Peiró JR, Marinho M, Mendes LCN, Nogueira MCL, Casella T. Dissemination of Multidrug-Resistant Commensal Escherichia coli in Feedlot Lambs in Southeastern Brazil. Front Microbiol 2019; 10:1394. [PMID: 31293542 PMCID: PMC6603138 DOI: 10.3389/fmicb.2019.01394] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/04/2019] [Indexed: 12/31/2022] Open
Abstract
Antimicrobial resistance (AR) is a public health issue since it limits the choices to treat infections by Escherichia coli in humans and animals. In Brazil, the ovine meat market has grown in recent years, but studies about AR in sheep are still scarce. Thus, this study aims to investigate the presence of AR in E. coli isolated from lambs during feedlot. To this end, feces from 112 lambs with 2 months of age, after weaning, were collected on the first day of the animals in the feedlot (day 0), and on the last day before slaughtering (day 42). Isolates were selected in MacConkey agar supplemented with 4 mg/L of ceftiofur and identified by biochemical methods. Isolates were submitted to an antimicrobial susceptibility test by disc-diffusion and PCR to investigate genes for phylogenetic group, virulence determinants and resistance to the several antimicrobial classes tested. The genetic localization of the bla genes detected was elucidated by S1-PFGE followed by Southern blot-hybridizations. The isolates were typed by XbaI-PFGE and MLST methods. Seventy-eight E. coli were isolated from 8/112 (7.1%) animals on day 0, and from 55/112 (49.1%) animals on day 42. Since only fimH was present in almost all E. coli (97.4%) as a virulence gene, and also 88.5% belonged to phylogroups B1 or A, we consider that isolates represent intestinal commensal bacteria. The dendrogram separated the 78 non-virulent isolates in seven clusters, two of which comprised 50 E. coli belonging to ST/CC 1727/446 or ST 3994 recovered on day 42 commonly harboring the genotype bla CMY -2-aac(3)-IIa -tetA-sul1-sul2-floR-cmlA. Special attention should be given to the presence of bla CTX-M-15, a worldwide gene spread, and bla CTX-M-14, a hitherto undetected gene in Enterobacteriaceae from food-producing animals in Brazil. Importantly, E. coli lineages and plasmids carrying bla genes detected here have already been reported as sources of infection in humans either from animals, food, or the environment, which raises public health concerns. Hence, two types of commensal E. coli carrying important AR genes clearly prevailed during feedlot, but lambs are also reservoirs of bacteria carrying important AR genes such as bla CTX-M-14 and bla CTX-M-15, mostly related to antimicrobial treatment failure.
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Affiliation(s)
- Katia Suemi Gozi
- Centro de Investigação e Microrganismos, FAMERP, São José do Rio Preto, Brazil
| | | | | | | | | | - Juliana Regina Peiró
- Faculdade de Medicina Veterinária, São Paulo State University (UNESP), Araçatuba, Brazil
| | - Marcia Marinho
- Faculdade de Medicina Veterinária, São Paulo State University (UNESP), Araçatuba, Brazil
| | | | | | - Tiago Casella
- Centro de Investigação e Microrganismos, FAMERP, São José do Rio Preto, Brazil
- Hospital de Base, São José do Rio Preto, Brazil
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12
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Gay E, Bour M, Cazeau G, Jarrige N, Martineau C, Madec JY, Haenni M. Antimicrobial Usages and Antimicrobial Resistance in Commensal Escherichia coli From Veal Calves in France: Evolution During the Fattening Process. Front Microbiol 2019; 10:792. [PMID: 31031738 PMCID: PMC6473463 DOI: 10.3389/fmicb.2019.00792] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 03/27/2019] [Indexed: 11/13/2022] Open
Abstract
Extended-Spectrum-Cephalosporin (ESC)-resistant Enterobacteriaceae have widely spread in all settings worldwide. In animals, Extended-Spectrum Beta-Lactamase (ESBL) producers have been frequently identified in veal calves. The objectives of this study were to investigate the trends in the ESBL load and antimicrobial resistance (AMR) proportions, and antimicrobial usages (AMU) in veal calves during the fattening process. Ten fattening farms were selected and 50 animals per farm were sampled. AMR was assessed in bacteria from the dominant flora (collected on non-selective MacConckey agar) and in ESBL/AmpC-carrying bacteria from the subdominant flora (selected on ChromID ESBL selective plates) upon arrival and 5-6 months later before slaughter. The number and types of treatments during fattening were also collected. Rates of ESBL-producing E. coli from the subdominant flora significantly decreased in all farms (arrival: 67.7%; departure: 20.4%) whereas rates of multidrug-resistant E. coli from the dominant flora have significantly increased (arrival: 60.2%; departure: 67.2%; p = 0.025). CTX-M-1 was the most frequently identified ESBL enzyme (arrival: 59.3%; departure: 52.0%). The plasmid-mediated mcr-1 gene was also identified occasionally. In parallel, levels of resistances to non-critically important antimicrobials were already high upon arrival but have still further increased over time until slaughter. Our study also highlighted that if only ESBL-producing isolates were monitored, it might have led to a partial (and partly false) picture of AMR rates globally decreasing during the fattening period. The mean number of antimicrobial treatments per calf (NTPC) was 8.75 but no association between AMU and AMR was evidenced. Most ESBL producers were clonally unrelated suggesting multiple sources and not cross-contaminations among calves during transportation. Feeding milk containing antimicrobial residues to veal calves is hypothesized to explain the high ESBL loads in animals at the entrance on farms.
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Affiliation(s)
- Emilie Gay
- Université de Lyon - ANSES, Laboratoire de Lyon, Unité Épidémiologie et Appui à la Surveillance, Lyon, France
| | - Maxime Bour
- Université de Lyon - ANSES, Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France.,Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Géraldine Cazeau
- Université de Lyon - ANSES, Laboratoire de Lyon, Unité Épidémiologie et Appui à la Surveillance, Lyon, France
| | - Nathalie Jarrige
- Université de Lyon - ANSES, Laboratoire de Lyon, Unité Épidémiologie et Appui à la Surveillance, Lyon, France
| | | | - Jean-Yves Madec
- Université de Lyon - ANSES, Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- Université de Lyon - ANSES, Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
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13
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Lugsomya K, Chatsuwan T, Niyomtham W, Tummaruk P, Hampson DJ, Prapasarakul N. Routine Prophylactic Antimicrobial Use Is Associated with Increased Phenotypic and Genotypic Resistance in Commensal Escherichia coli Isolates Recovered from Healthy Fattening Pigs on Farms in Thailand. Microb Drug Resist 2017; 24:213-223. [PMID: 28604274 DOI: 10.1089/mdr.2017.0042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study examined antimicrobial resistance (AMR) profiles in commensal Escherichia coli derived from healthy fattening pigs in Thai farms that used prophylactic antimicrobials (in-feed tiamulin fumarate and amoxicillin) [PAs], therapeutic antimicrobials (injectable enrofloxacin or gentamicin) [TAs], or no antimicrobials [NAs]. Commensal E. coli were used as a proxy for overall AMR on the farms. There was a high level of multidrug resistance in all three categories of farm, with isolates showing resistance to β-lactams (amoxicillin, ampicillin, and piperacillin) and tetracyclines (tetracycline), and commonly possessing tetA, blaTEM, and plasmid replicons FIB and F. On the other hand, isolates with an extended-spectrum beta-lactamase phenotype (ESBLP) and with resistance to aminoglycosides, chloramphenicol, fluoroquinolones, nitrofurantoin, tiamulin, and trimethoprim/sulfamethoxazole were significantly more common among the PA farms (p < 0.05) than in the other two farm categories. In the PA farms, ESBLP E. coli commonly contained the blaCTX-M-1 group, blaCTX-M-9 group, or both gene groups, and were shown to transfer blaCTX-M genes in a conjugation experiment. E. coli containing N, FIC and A/C replicons were found only in PA farms. In summary, although E. coli isolates from all farms contained a core set of resistance to β-lactams and tetracyclines, the routine use of PA increased resistance rates to other important antimicrobials.
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Affiliation(s)
- Kittitat Lugsomya
- 1 Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University , Bangkok, Thailand
| | - Thanitta Chatsuwan
- 2 Department of Microbiology, Faculty of Medicine, Chulalongkorn University , Bangkok, Thailand
| | - Waree Niyomtham
- 1 Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University , Bangkok, Thailand
| | - Padet Tummaruk
- 3 Department of Obstetrics Gynecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University , Bangkok, Thailand
| | - David J Hampson
- 4 School of Veterinary and Life Sciences, Murdoch University , Perth, Western Australia, Australia
| | - Nuvee Prapasarakul
- 1 Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University , Bangkok, Thailand
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14
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Kempf I, Jouy E, Chauvin C. Colistin use and colistin resistance in bacteria from animals. Int J Antimicrob Agents 2016; 48:598-606. [PMID: 27836380 DOI: 10.1016/j.ijantimicag.2016.09.016] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 08/04/2016] [Accepted: 09/15/2016] [Indexed: 11/28/2022]
Abstract
Colistin has been used in veterinary medicine for decades, mainly for the prevention and treatment of Enterobacteriaceae infections. However, data regarding colistin resistance in bacteria from animals and food of animal origin are relatively scarce, partly because there are methodological difficulties hampering the analysis of susceptibility to colistin. Most data regarding clinical isolates are related to enteropathogenic Escherichia coli and Salmonella. The resistance percentages are sometimes high for pathogenic strains, and the mcr-1 gene has been detected in pathogenic E. coli isolates from pigs, cattle and poultry in different countries. The prevalence of colistin resistance in Salmonella from healthy animals is usually low but depends on the proportion of intrinsically colistin-resistant serotypes. For indicator E. coli, the resistance levels are often very low, although higher levels have been observed in Asia. The mcr-1 gene has been detected in indicator E. coli from pigs, cattle, poultry and their products. Thus, there is an urgent need to re-assess the use of colistin in livestock throughout the world to ensure a global strategy for preserving this last-resort antimicrobial.
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Affiliation(s)
- Isabelle Kempf
- Ploufragan-Plouzané Laboratory, ANSES (French Agency for Food, Environmental and Occupational Health & Safety), Université Bretagne Loire, Ploufragan, France.
| | - Eric Jouy
- Ploufragan-Plouzané Laboratory, ANSES (French Agency for Food, Environmental and Occupational Health & Safety), Université Bretagne Loire, Ploufragan, France
| | - Claire Chauvin
- Ploufragan-Plouzané Laboratory, ANSES (French Agency for Food, Environmental and Occupational Health & Safety), Université Bretagne Loire, Ploufragan, France
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15
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Wyrsch ER, Roy Chowdhury P, Chapman TA, Charles IG, Hammond JM, Djordjevic SP. Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis. Front Microbiol 2016; 7:843. [PMID: 27379026 PMCID: PMC4908116 DOI: 10.3389/fmicb.2016.00843] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/22/2016] [Indexed: 11/18/2022] Open
Abstract
Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.
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Affiliation(s)
- Ethan R Wyrsch
- The ithree Institute, University of Technology Sydney, Sydney NSW, Australia
| | - Piklu Roy Chowdhury
- The ithree Institute, University of Technology Sydney, SydneyNSW, Australia; NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, SydneyNSW, Australia
| | - Toni A Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney NSW, Australia
| | - Ian G Charles
- Institute of Food Research, Norwich Research Park Norwich, UK
| | - Jeffrey M Hammond
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney NSW, Australia
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, Sydney NSW, Australia
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16
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Rhouma M, Beaudry F, Letellier A. Resistance to colistin: what is the fate for this antibiotic in pig production? Int J Antimicrob Agents 2016; 48:119-26. [PMID: 27234675 DOI: 10.1016/j.ijantimicag.2016.04.008] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/25/2016] [Accepted: 04/02/2016] [Indexed: 01/12/2023]
Abstract
Colistin, a cationic polypeptide antibiotic, has reappeared in human medicine as a last-line treatment option for multidrug-resistant Gram-negative bacteria (MDR-GNB). Colistin is widely used in veterinary medicine for the treatment of gastrointestinal infections caused by Enterobacteriaceae. GNB resistant to colistin owing to chromosomal mutations have already been reported both in human and veterinary medicine, however several recent studies have just identified a plasmid-mediated mcr-1 gene encoding for colistin resistance in Escherichia coli colistin resistance. The discovery of a non-chromosomal mechanism of colistin resistance in E. coli has led to strong reactions in the scientific community and to concern among physicians and veterinarians. Colistin use in food animals and particularly in pig production has been singled out as responsible for the emergence of colistin resistance. The present review will focus mainly on the possible link between colistin use in pigs and the spread of colistin resistance in Enterobacteriaceae. First we demonstrate a possible link between Enterobacteriaceae resistance emergence and oral colistin pharmacokinetics/pharmacodynamics and its administration modalities in pigs. We then discuss the potential impact of colistin use in pigs on public health with respect to resistance. We believe that colistin use in pig production should be re-evaluated and its dosing and usage optimised. Moreover, the search for competitive alternatives to using colistin with swine is of paramount importance to preserve the effectiveness of this antibiotic for the treatment of MDR-GNB infections in human medicine.
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Affiliation(s)
- Mohamed Rhouma
- Chaire de recherche en salubrité des viandes (CRSV), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Groupe de recherche et d'enseignement en salubrité alimentaire (GRESA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Centre de recherche en infectiologie porcine et avicole (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Francis Beaudry
- Groupe de recherche en pharmacologie animale du Québec (GREPAQ), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Ann Letellier
- Chaire de recherche en salubrité des viandes (CRSV), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Groupe de recherche et d'enseignement en salubrité alimentaire (GRESA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Centre de recherche en infectiologie porcine et avicole (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Groupe de recherche en pharmacologie animale du Québec (GREPAQ), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada.
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