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Sun Y, Staley ZR, Woodbury B, Riethoven JJ, Li X. Composting reduces the risks of resistome in beef cattle manure at the transcriptional level. Appl Environ Microbiol 2024; 90:e0175223. [PMID: 38445903 PMCID: PMC11022583 DOI: 10.1128/aem.01752-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
Transcriptomic evidence is needed to determine whether composting is more effective than conventional stockpiling in mitigating the risk of resistome in livestock manure. The objective of this study is to compare composting and stockpiling for their effectiveness in reducing the risk of antibiotic resistance in beef cattle manure. Samples collected from the center and the surface of full-size manure stockpiling and composting piles were subject to metagenomic and metatranscriptomic analyses. While the distinctions in resistome between stockpiled and composted manure were not evident at the DNA level, the advantages of composting over stockpiling were evident at the transcriptomic level in terms of the abundance of antibiotic resistance genes (ARGs), the number of ARG subtypes, and the prevalence of high-risk ARGs (i.e., mobile ARGs associated with zoonotic pathogens). DNA and transcript contigs show that the pathogen hosts of high-risk ARGs included Escherichia coli O157:H7 and O25b:H4, Klebsiella pneumoniae, and Salmonella enterica. Although the average daily temperatures for the entire composting pile exceeded 55°C throughout the field study, more ARG and ARG transcripts were removed at the center of the composting pile than at the surface. This work demonstrates the advantage of composting over stockpiling in reducing ARG risk in active populations in beef cattle manure.IMPORTANCEProper treatment of manure before land application is essential to mitigate the spread of antibiotic resistance in the environment. Stockpiling and composting are two commonly used methods for manure treatment. However, the effectiveness of composting in reducing antibiotic resistance in manure has been debated. This work compared the ability of these two methods to reduce the risk of antibiotic resistance in beef cattle manure. Our results demonstrate that composting reduced more high-risk resistance genes at the transcriptomic level in cattle manure than conventional stockpiling. This finding not only underscores the effectiveness of composting in reducing antibiotic resistance in manure but also highlights the importance of employing RNA analyses alongside DNA analyses.
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Affiliation(s)
- Yuepeng Sun
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Zachery R. Staley
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Bryan Woodbury
- USDA-ARS U.S. Meat Animal Research Center, Clay Center, Clay Center, Nebraska, USA
| | - Jean-Jack Riethoven
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Xu Li
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Nohrborg S, Nguyen-Thi T, Xuan HN, Lindahl J, Boqvist S, Järhult JD, Magnusson U. Understanding Vietnamese chicken farmers' knowledge and practices related to antimicrobial resistance using an item response theory approach. Front Vet Sci 2024; 11:1319933. [PMID: 38645642 PMCID: PMC11027563 DOI: 10.3389/fvets.2024.1319933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/21/2024] [Indexed: 04/23/2024] Open
Abstract
Introduction Antimicrobial resistance (AMR) poses a threat to animal and human health, as well as food security and nutrition. Development of AMR is accelerated by over- and misuse of antimicrobials as seen in many livestock systems, including poultry production. In Vietnam, high AMR levels have been reported previously within poultry production, a sector which is dominated by small-scale farming, even though it is intensifying. This study focuses on understanding small- and medium-scale chicken farmers' knowledge and practices related to AMR by applying an item response theory (IRT) approach, which has several advantages over simpler statistical methods. Methods Farmers representing 305 farms in Thai Nguyen province were interviewed from November 2021 to January 2022, using a structured questionnaire. Results generated with IRT were used in regression models to find associations between farm characteristics, and knowledge and practice levels. Results Descriptive results showed that almost all farmers could buy veterinary drugs without prescription in the local community, that only one third of the farmers received veterinary professional advice or services, and that the majority of farmers gave antibiotics as a disease preventive measure. Regression analysis showed that multiple farm characteristics were significantly associated to farmers' knowledge and practice scores. Conclusion The study highlights the complexity when tailoring interventions to move towards more medically rational antibiotic use at farms in a setting with high access to over-the-counter veterinary drugs and low access to veterinary services, since many on-farm factors relevant for the specific context need to be considered.
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Affiliation(s)
- Sandra Nohrborg
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Thinh Nguyen-Thi
- International Livestock Research Institute, Regional Office for East and Southeast Asia, Hanoi, Vietnam
| | - Huyen Nguyen Xuan
- Department of Bacteriology, National Institute of Veterinary Research, Hanoi, Vietnam
| | - Johanna Lindahl
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, Uppsala, Sweden
| | - Sofia Boqvist
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Josef D. Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Ulf Magnusson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Hasan M, Talukder S, Mandal AK, Tasmim ST, Parvin S, Ali Y, Sikder MH, Callaghan TJ, Soares Magalhães RJ, Islam T. Antimicrobial Resistance Profiles of Campylobacter spp. Recovered from Chicken Farms in Two Districts of Bangladesh. Foodborne Pathog Dis 2024. [PMID: 38563794 DOI: 10.1089/fpd.2023.0079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
The rapid emergence of antimicrobial resistance (AMR) in Campylobacter has reinforced its status as a foodborne pathogen of significant public health concern. Resistant Campylobacter is typically transferred to humans via the consumption of contaminated animal products, particularly poultry. The genes associated with antimicrobial resistance in Campylobacter spp. are poorly understood. To address this knowledge gap, we conducted a prevalence survey of AMR Campylobacter across 84 chicken farms in two districts of Bangladesh. Pooled cloacal swabs were collected from chickens and underwent bacteriological testing for Campylobacter spp. with PCR confirmation. Antimicrobial susceptibility was tested against 14 antibiotics by disk diffusion method, and 12 resistance genes were screened in Campylobacter-positive isolates using multiplex PCR. A total of 34 (40.5%) farms were Campylobacter-positive of which 73.5% of isolates were resistant to at least 10 antibiotics. The antimicrobial susceptibility results indicate a high level of resistance against streptomycin (97.1%), clindamycin (97.1%), ampicillin (94.1%), tetracycline (94.1%), erythromycin (91.2%), ciprofloxacin (88.2%), nalidixic acid (85.3%), and imipenem (82.4%), and comparatively a low frequency of resistance to chloramphenicol (47.1%), ceftazidime (44.1%), and colistin (35.3%). Multidrug-resistant (MDR) and extensively drug-resistant Campylobacter were identified in 97.1%, and 50% of isolates, respectively. Ten resistance genes were identified including blaTEM (in 97.1% of isolates), strA-strB (85.9%), tetA (70.6%), tetB (32.4%), qnrS (23.5%), blaCTX-M-1 (20.6%), qnrB (20.6%), blaSHV (8.8%), aadB (5.9%), and qnrA (2.9%). Our findings demonstrate that resistance to ampicillin, tetracycline, and ceftazidime in Campylobacter isolates was significantly (p ≤ 0.05) associated with the presence of blaTEM, tetA, and blaSHV genes, respectively. The high rates of AMR in Campylobacter isolates from our study are not surprising given the liberal use of antimicrobials and incomplete biosecurity provisions on farms. Of particular concern are resistance rates to those classes of antibiotics that should be reserved for human use (azithromycin, ciprofloxacin, and colistin). AMR was more prevalent in chicken farms that used multiple antibiotics, engaged in prophylactic treatment of the birds, and improperly disposed of antibiotic packages. The high prevalence of MDR in chicken-derived Campylobacter isolates from the different regions of our study reinforces the need for more prudent use of antimicrobial compounds in Bangladeshi chicken farms.
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Affiliation(s)
- Mehedi Hasan
- Population Medicine and AMR Laboratory, Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Sudipta Talukder
- Population Medicine and AMR Laboratory, Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Amit Kumar Mandal
- Population Medicine and AMR Laboratory, Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Syeda Tanjina Tasmim
- Population Medicine and AMR Laboratory, Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Sonia Parvin
- Population Medicine and AMR Laboratory, Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Yamin Ali
- Population Medicine and AMR Laboratory, Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Department of Livestock Services, Dhaka, Bangladesh
| | - Mahmudul Hasan Sikder
- Department of Pharmacology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Thomas J Callaghan
- UQ Spatial Epidemiology Laboratory, School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Ricardo J Soares Magalhães
- UQ Spatial Epidemiology Laboratory, School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
- Children's Health and Environment Program, Child Health Research Centre, The University of Queensland, South Brisbane, Queensland, Australia
| | - Taohidul Islam
- Population Medicine and AMR Laboratory, Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
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Portal EAR, Sands K, Farley C, Boostrom I, Jones E, Barrell M, Carvalho MJ, Milton R, Iregbu K, Modibbo F, Uwaezuoke S, Akpulu C, Audu L, Edwin C, Yusuf AH, Adeleye A, Mukkadas AS, Maduekwe D, Gambo S, Sani J, Walsh TR, Spiller OB. Characterisation of colistin resistance in Gram-negative microbiota of pregnant women and neonates in Nigeria. Nat Commun 2024; 15:2302. [PMID: 38485761 PMCID: PMC10940312 DOI: 10.1038/s41467-024-45673-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/30/2024] [Indexed: 03/18/2024] Open
Abstract
A mobile colistin resistance gene mcr was first reported in 2016 in China and has since been found with increasing prevalence across South-East Asia. Here we survey the presence of mcr genes in 4907 rectal swabs from mothers and neonates from three hospital sites across Nigeria; a country with limited availability or history of colistin use clinically. Forty mother and seven neonatal swabs carried mcr genes in a range of bacterial species: 46 Enterobacter spp. and single isolates of; Shigella, E. coli and Klebsiella quasipneumoniae. Ninety percent of the genes were mcr-10 (n = 45) we also found mcr-1 (n = 3) and mcr-9 (n = 1). While the prevalence during this collection (2015-2016) was low, the widespread diversity of mcr-gene type and range of bacterial species in this sentinel population sampling is concerning. It suggests that agricultural colistin use was likely encouraging sustainment of mcr-positive isolates in the community and implementation of medical colistin use will rapidly select and expand resistant isolates.
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Affiliation(s)
- E A R Portal
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK.
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK.
| | - K Sands
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK.
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK.
| | - C Farley
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - I Boostrom
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - E Jones
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - M Barrell
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - M J Carvalho
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - R Milton
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Centre for Trials Research, Cardiff University, Cardiff, UK
| | - K Iregbu
- National Hospital Abuja, Abuja, Nigeria
| | - F Modibbo
- Murtala Muhammad Specialist Hospital, Kano, Nigeria
| | - S Uwaezuoke
- Federal Medical Centre -Jabi, Abuja, Nigeria
| | - C Akpulu
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
- National Hospital Abuja, Abuja, Nigeria
- Interdisciplinary Biosciences DTP, University of Oxford, Oxford, UK
| | - L Audu
- National Hospital Abuja, Abuja, Nigeria
| | - C Edwin
- Department of Medical Microbiology Aminu Kano Teaching Hospital, Kano, Nigeria
| | - A H Yusuf
- Department of Medical Microbiology Aminu Kano Teaching Hospital, Kano, Nigeria
| | - A Adeleye
- Department of Medical Microbiology Aminu Kano Teaching Hospital, Kano, Nigeria
| | - A S Mukkadas
- Department of Medical Microbiology Aminu Kano Teaching Hospital, Kano, Nigeria
| | - D Maduekwe
- Wuse General Hospital Abuja, Abuja, Nigeria
| | - S Gambo
- Department of Paediatrics, Murtala Muhammed Specialist Hospital, Kano, Nigeria
| | - J Sani
- Department of Paediatrics Abdullahi Wase Teaching Hospital, Kano, Nigeria
| | - T R Walsh
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - O B Spiller
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
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Zarske M, Luu HQ, Deneke C, Knüver MT, Thieck M, Hoang HTT, Bretschneider N, Pham NT, Huber I, Stingl K. Identification of knowledge gaps in whole-genome sequence analysis of multi-resistant thermotolerant Campylobacter spp. BMC Genomics 2024; 25:156. [PMID: 38331708 PMCID: PMC10851486 DOI: 10.1186/s12864-024-10014-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/14/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Campylobacter spp. is the most frequent cause of bacterial food-borne gastroenteritis and a high priority antibiotic resistant bacterium according to the World Health Organization (WHO). European monitoring of thermotolerant Campylobacter spp. does not reflect the global burden of resistances already circulating within the bacterial population worldwide. METHODS We systematically compared whole genome sequencing with comprehensive phenotypic antimicrobial susceptibility, analyzing 494 thermotolerant Campylobacter poultry isolates from Vietnam and Germany. Any discrepancy was checked by repeating the wet lab and improving the dry lab part. Selected isolates were additionally analyzed via long-read Oxford Nanopore technology, leading to closed chromosomes and plasmids. RESULTS Overall, 22 different resistance genes and gene variants (e. g. erm(B), aph(3')-IIIa, aph(2'')-If, catA, lnu(C), blaOXA, sat4) and point mutations in three distinct genes (gyrA, 23S rRNA, rpsL) associated with AMR were present in the Campylobacter isolates. Two AMR genes were missing in the database and one falsely associated with resistance. Bioinformatic analysis based on short-read data partly failed to identify tet(O) and aadE, when the genes were present as duplicate or homologous gene variants. Intriguingly, isolates also contained different determinants, redundantly conferring resistance to chloramphenicol, gentamicin, kanamycin, lincomycin and streptomycin. We found a novel tet(W) in tetracycline sensitive strains, harboring point mutations. Furthermore, analysis based on assemblies from short-read data was impaired to identify full length phase variable aad9, due to variations of the poly-C tract within the gene. The genetic determinant responsible for gentamicin resistance of one isolate from Germany could not be identified. GyrT86I, presenting the main determinant for (fluoro-)quinolone resistance led to a rare atypical phenotype of ciprofloxacin resistance but nalidixic acid sensitivity. Long-read sequencing predicted AMR genes were mainly located on the chromosome, and rarely on plasmids. Predictions from long- and short-read sequencing, respectively, often differed. AMR genes were often organized in multidrug resistance islands (MDRI) and partially located in proximity to transposase genes, suggesting main mobilization of resistance determinants is via natural transformation and transposition in Campylobacter. CONCLUSIONS The results of this study suggest that there is frequent resistance gene duplication, mosaicism, and mutation leading to gene variation and truncation in Campylobacter strains that have not been reported in previous studies and are missing from databases. Furthermore, there is a need for deciphering yet unknown resistance mechanisms and resistance spread in thermotolerant Campylobacter spp. that may pose a challenge to global food safety.
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Affiliation(s)
- Michael Zarske
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany
| | - Huong Quynh Luu
- National Institute of Veterinary Research (NIVR), 86 Truong Chinh Street, Hanoi, Dong Da District, Vietnam
| | - Carlus Deneke
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany
| | - Marie-Theres Knüver
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany
| | - Maja Thieck
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany
| | - Ha Thi Thu Hoang
- Department of Bacteriology, National Institute of Hygiene and Epidemiology (NIHE), 1 Yersin Street, Hanoi, Trung District, Vietnam
| | - Nancy Bretschneider
- Department of Molecular Biology and Gene Technology, Bavarian Health and Food Safety Authority, Oberschleissheim, D-85764, Germany
| | - Ngoc Thi Pham
- National Institute of Veterinary Research (NIVR), 86 Truong Chinh Street, Hanoi, Dong Da District, Vietnam
| | - Ingrid Huber
- Department of Molecular Biology and Gene Technology, Bavarian Health and Food Safety Authority, Oberschleissheim, D-85764, Germany
| | - Kerstin Stingl
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany.
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Alvarez L, Carhuaricra D, Palomino-Farfan J, Calle S, Maturrano L, Siuce J. Genomic Profiling of Multidrug-Resistant Swine Escherichia coli and Clonal Relationship to Human Isolates in Peru. Antibiotics (Basel) 2023; 12:1748. [PMID: 38136782 PMCID: PMC10740509 DOI: 10.3390/antibiotics12121748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
The misuse of antibiotics is accelerating antimicrobial resistance (AMR) in Escherichia coli isolated from farm animals. The genomes of ten multidrug-resistant (MDR) E. coli isolates from pigs were analyzed to determine their sequence types, serotypes, virulence, and AMR genes (ARGs). Additionally, the relationship was evaluated adding all the available genomes of Peruvian E. coli from humans using the cgMLST + HierCC scheme. Two aEPEC O186:H11-ST29 were identified, of which H11 and ST29 are reported in aEPEC isolates from different sources. An isolate ETEC-O149:H10-ST100 was identified, considered a high-risk clone that is frequently reported in different countries as a cause of diarrhea in piglets. One ExPEC O101:H11-ST167 was identified, for which ST167 is an international high-risk clone related to urinary infections in humans. We identified many ARGs, including extended-spectrum β-lactamase genes, and one ETEC harboring the mcr-1 gene. CgMLST + HierCC analysis differentiated three clusters, and in two, the human isolates were grouped with those of swine in the same cluster. We observed that Peruvian swine MDR E. coli cluster with Peruvian E. coli isolates from healthy humans and from clinical cases, which is of great public health concern and evidence that AMR surveillance should be strengthened based on the One Health approach.
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Affiliation(s)
- Luis Alvarez
- Laboratory of Veterinary Bacteriology and Mycology, Faculty of Veterinary Medicine, National University of San Marcos, Lima 15021, Peru; (L.A.); (J.P.-F.); (S.C.)
| | - Dennis Carhuaricra
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation [SANIGEN], Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, National University of San Marcos, Lima 15021, Peru; (D.C.); (L.M.)
| | - Joel Palomino-Farfan
- Laboratory of Veterinary Bacteriology and Mycology, Faculty of Veterinary Medicine, National University of San Marcos, Lima 15021, Peru; (L.A.); (J.P.-F.); (S.C.)
| | - Sonia Calle
- Laboratory of Veterinary Bacteriology and Mycology, Faculty of Veterinary Medicine, National University of San Marcos, Lima 15021, Peru; (L.A.); (J.P.-F.); (S.C.)
| | - Lenin Maturrano
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation [SANIGEN], Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, National University of San Marcos, Lima 15021, Peru; (D.C.); (L.M.)
| | - Juan Siuce
- Laboratory of Veterinary Bacteriology and Mycology, Faculty of Veterinary Medicine, National University of San Marcos, Lima 15021, Peru; (L.A.); (J.P.-F.); (S.C.)
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Lemlem M, Aklilu E, Mohamed M, Kamaruzzaman NF, Zakaria Z, Harun A, Devan SS, Kamaruzaman INA, Reduan MFH, Saravanan M. Phenotypic and genotypic characterization of colistin-resistant Escherichia Coli with mcr-4, mcr-5, mcr-6, and mcr-9 genes from broiler chicken and farm environment. BMC Microbiol 2023; 23:392. [PMID: 38062398 PMCID: PMC10704802 DOI: 10.1186/s12866-023-03118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Colistin is an antibiotic used as a last-resort to treat multidrug-resistant Gram-negative bacterial infections. Colistin had been used for a long time in veterinary medicine for disease control and as a growth promoter in food-producing animals. This excessive use of colistin in food animals causes an increase in colistin resistance. This study aimed to determine molecular characteristics of colistin-resistant Escherichia coli in broiler chicken and chicken farm environments. RESULTS Four hundred fifty-three cloacal and farm environment samples were collected from six different commercial chicken farms in Kelantan, Malaysia. E. coli was isolated using standard bacteriological methods, and the isolates were tested for antimicrobial susceptibility using disc diffusion and colistin minimum inhibitory concentration (MIC) by broth microdilution. Multiplex PCR was used to detect mcr genes, and DNA sequencing was used to confirm the resistance genes. Virulence gene detection, phylogroup, and multilocus sequence typing (MLST) were done to further characterize the E. coli isolates. Out of the 425 (94%; 425/453) E. coli isolated from the chicken and farm environment samples, 10.8% (48/425) isolates were carrying one or more colistin-resistance encoding genes. Of the 48 colistin-resistant isolates, 54.2% (26/48) of the mcr positive isolates were genotypically and phenotypically resistant to colistin with MIC of colistin ≥ 4 μg/ml. The most prominent mcr gene detected was mcr-1 (47.9%; 23/48), followed by mcr-8 (18.8%; 9/48), mcr-7 (14.5%; 7/48), mcr-6 (12.5%; 6/48), mcr-4 (2.1%; 1/48), mcr-5 (2.1%; 1/48), and mcr-9 (2.1%; 1/48) genes. One E. coli isolate originating from the fecal sample was found to harbor both mcr-4 and mcr-6 genes and another isolate from the drinking water sample was carrying mcr-1 and mcr-8 genes. The majority of the mcr positive isolates were categorized under phylogroup A followed by phylogroup B1. The most prevalent sequence typing (ST) was ST1771 (n = 4) followed by ST206 (n = 3). 100% of the mcr positive E. coli isolates were multidrug resistant. The most frequently detected virulence genes among mcr positive E. coli isolates were ast (38%; 18/48) followed by iss (23%; 11/48). This is the first research to report the prevalence of mcr-4, mcr-5, mcr-6, mcr-7, and mcr-8 genes in E. coli from broiler chickens and farm environments in Malaysia. CONCLUSION Our findings suggest that broiler chickens and broiler farm environments could be reservoirs of colistin-resistant E. coli, posing a risk to public health and food safety.
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Affiliation(s)
- Mulu Lemlem
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, 16100, Malaysia.
- Department of Medical Microbiology and Immunology, College of Health Science, Mekelle University, 231, Mekelle, Tigray, Ethiopia.
| | - Erkihun Aklilu
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, 16100, Malaysia.
| | - Maizan Mohamed
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, 16100, Malaysia
| | | | - Zunita Zakaria
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, 43400, Malaysia
| | - Azian Harun
- School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Kelantan, 15200, Malaysia
| | - Susmita Seenu Devan
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, 16100, Malaysia
| | | | - Mohd Farhan Hanif Reduan
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, 16100, Malaysia
| | - Muthupandian Saravanan
- AMR and Nanotherapeutics Lab, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, 600077, India
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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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9
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Nhung NT, Dutta A, Higginson E, Kermack L, Yen NTP, Phu DH, Kiet BT, Choisy M, Geskus RB, Baker S, Carrique-Mas J. Impact of antimicrobial use on abundance of antimicrobial resistance genes in chicken flocks in Vietnam. JAC Antimicrob Resist 2023; 5:dlad090. [PMID: 37484028 PMCID: PMC10362913 DOI: 10.1093/jacamr/dlad090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/09/2023] [Indexed: 07/25/2023] Open
Abstract
Objectives We investigated longitudinally Vietnamese small-scale chicken flocks in order to characterize changes in antimicrobial resistance gene (ARG) content over their life cycle, and the impact of antimicrobial use (AMU) on an intervention consisting of veterinary advice provision. Methods AMU data and faecal samples were collected from 83 flocks (25 farms) at day-old, mid- and late-production (∼4 month cycle). Using high-throughput real-time PCR, samples were investigated for 94 ARGs. ARG copies were related to 16S rRNA and ng of DNA (ngDNA). Impact of AMU and ARGs in day-olds was investigated by mixed-effects models. Results Flocks received a mean (standard error, SE) animal daily dose (ADD) of 736.7 (83.0) and 52.1 (9.9) kg in early and late production, respectively. Overall, ARGs/16S rRNA increased from day-old (mean 1.47; SE 0.10) to mid-production (1.61; SE 0.16), further decreasing in end-production (1.60; SE 0.1) (all P > 0.05). In mid-production, ARGs/16S rRNA increased for aminoglycosides, phenicols, sulphonamides and tetracyclines, decreasing for polymyxins β-lactams and genes that confer resistance to mutiple classes (multi-drug resistance) (MDR). At end-production, aminoglycoside resistance decreased and polymyxin and quinolone resistance increased (all P < 0.05). Results in relation to ngDNA gave contradictory results. Neither AMU nor ARGs in day-olds had an impact on subsequent ARG abundance. The intervention resulted in 74.2% AMU reduction; its impact on ARGs depended on whether ARGs/ngDNA (+14.8%) or ARGs/16S rRNA metrics (-10.7%) (P > 0.05) were computed. Conclusions The flocks' environment (contaminated water, feed and residual contamination) is likely to play a more important role in transmission of ARGs to flocks than previously thought. Results highlight intriguing differences in the quantification of ARGs depending on the metric chosen.
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Affiliation(s)
- Nguyen Thi Nhung
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Avijit Dutta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
- Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh
| | - Ellen Higginson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
| | - Leanne Kermack
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
| | | | - Doan Hoang Phu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City, Vietnam
| | - Bach Tuan Kiet
- Sub-Department of Animal Health and Production, Dong Thap Province, Cao Lanh, Vietnam
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Ronald B Geskus
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Food and Agriculture Organization of the United Nations (FAO), Hanoi, Vietnam
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10
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Anyanwu MU, Jaja IF, Okpala COR, Njoga EO, Okafor NA, Oguttu JW. Mobile Colistin Resistance ( mcr) Gene-Containing Organisms in Poultry Sector in Low- and Middle-Income Countries: Epidemiology, Characteristics, and One Health Control Strategies. Antibiotics (Basel) 2023; 12:1117. [PMID: 37508213 PMCID: PMC10376608 DOI: 10.3390/antibiotics12071117] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023] Open
Abstract
Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) are plasmid-encoded genes that threaten the clinical utility of colistin (COL), one of the highest-priority critically important antibiotics (HP-CIAs) used to treat infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. For more than six decades, COL has been used largely unregulated in the poultry sector in low- and middle-income countries (LMICs), and this has led to the development/spread of mcr gene-containing bacteria (MGCB). The prevalence rates of mcr-positive organisms from the poultry sector in LMICs between January 1970 and May 2023 range between 0.51% and 58.8%. Through horizontal gene transfer, conjugative plasmids possessing insertion sequences (ISs) (especially ISApl1), transposons (predominantly Tn6330), and integrons have enhanced the spread of mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8, mcr-9, and mcr-10 in the poultry sector in LMICs. These genes are harboured by Escherichia, Klebsiella, Proteus, Salmonella, Cronobacter, Citrobacter, Enterobacter, Shigella, Providencia, Aeromonas, Raoultella, Pseudomonas, and Acinetobacter species, belonging to diverse clones. The mcr-1, mcr-3, and mcr-10 genes have also been integrated into the chromosomes of these bacteria and are mobilizable by ISs and integrative conjugative elements. These bacteria often coexpress mcr with virulence genes and other genes conferring resistance to HP-CIAs, such as extended-spectrum cephalosporins, carbapenems, fosfomycin, fluoroquinolone, and tigecycline. The transmission routes and dynamics of MGCB from the poultry sector in LMICs within the One Health triad include contact with poultry birds, feed/drinking water, manure, poultry farmers and their farm workwear, farming equipment, the consumption and sale of contaminated poultry meat/egg and associated products, etc. The use of pre/probiotics and other non-antimicrobial alternatives in the raising of birds, the judicious use of non-critically important antibiotics for therapy, the banning of nontherapeutic COL use, improved vaccination, biosecurity, hand hygiene and sanitization, the development of rapid diagnostic test kits, and the intensified surveillance of mcr genes, among others, could effectively control the spread of MGCB from the poultry sector in LMICs.
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Affiliation(s)
| | - Ishmael Festus Jaja
- Department of Livestock and Pasture Science, University of Fort Hare, Alice 5700, South Africa
| | - Charles Odilichukwu R Okpala
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland
- UGA Cooperative Extension, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA 30602, USA
| | - Emmanuel Okechukwu Njoga
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka 400001, Nigeria
| | | | - James Wabwire Oguttu
- Department of Agriculture and Animal Health, Florida Campus, University of South Africa, Johannesburg 1709, South Africa
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11
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Ali MW, Utsho KS, Karmakar S, Hoque MN, Rahman MT, Hassan J. First report on the molecular characteristics of mcr-1 colistin resistant E. coli isolated from retail broiler meat in Bangladesh. Int J Food Microbiol 2023; 388:110065. [PMID: 36610233 DOI: 10.1016/j.ijfoodmicro.2022.110065] [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: 10/21/2022] [Revised: 12/15/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022]
Abstract
Poultry meat is considered as a potential source of colistin resistant Escherichia coli (CREC). This study aimed to determine the prevalence and characteristics of CREC in broiler meat and ascertain their possible zoonotic potential(s). Broiler meat (n = 104) comprising 26 of each of the thigh, breast, liver, and proventriculus-gizzard was purchased from the retail outlets, Bangladesh. CREC was isolated from the meat samples on MacConkey agar plates containing colistin sulfate followed by PCR confirmation, mcr subtyping (mcr-1 to mcr-5), phylogenetic grouping and detailed molecular characterization through whole genome sequencing (WGS). Antimicrobial resistance of the CREC isolates were evaluated by disc diffusion method and MIC (minimum inhibitory concentration) of colistin sulfate was determined by broth microdilution. The investigation revealed 58 (55.77 %) of 104 samples as positive for CREC, and 53 (91.38 %) of CREC isolates carried mcr-1 gene with no other mcr subtypes evident. Most of the CREC belonged to commensal E. coli (66.04 %) with some pathogenic phylotypes (33.96 %) based on dichotomous decision tree. All the mcr-1 CREC isolates were multidrug-resistant (MDR) and had MICs of 4-8 μg/mL colistin sulfate. WGS of a commensal MDR mcr-1 CREC strain 1ChBEc2mcr revealed as a potential human pathogen belonging to ST162 that harbored 60 virulence factors associated genes (VFGs). The mcr-1 gene in 1ChBEc2mcr genome was located on a plasmid (p1ChBEc2mcr) and showed nucleotide similarities (>95 %) to another plasmid reported from human E. coli in Bangladesh. Beyond mcr-1 gene, this plasmid (p1ChBEc2mcr) also harbored genes related to aminoglycoside, beta-lactams, macrolides, and tetracycline resistance. Presence of similar mcr-1 carrying plasmids in broiler and human CREC denotes a threat of possibly human to avian (broiler) or vice-versa transfer of mcr-1 CREC through close contact as prevailing in the retail outlets of Bangladesh.
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Affiliation(s)
- Md Wohab Ali
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Kishor Sosmith Utsho
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Susmita Karmakar
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Nazmul Hoque
- Department of Gynecology, Obstetrics & Reproductive Health, Faculty of Veterinary Medicine & Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Md Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Jayedul Hassan
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
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12
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Nguyen PV, Le CT, Nguyen XH, Nguyen TM, Nguyen KCT. First study on capsular serotypes and virulence factors of Pasteurella multocida isolates from Phan Rang sheep in Vietnam. Vet World 2023; 16:281-290. [PMID: 37042011 PMCID: PMC10082718 DOI: 10.14202/vetworld.2023.281-290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/05/2023] [Indexed: 02/16/2023] Open
Abstract
Background and Aim: Pasteurella multocida is considered as a main factor mediating pneumonic pasteurellosis in ruminants, including sheep. It is also a current threat to Phan Rang sheep in Vietnam. This study aimed to characterize P. multocida isolated from Phan Rang sheep, their antibiotic resistance profile, and the prevalence of some virulence-associated genes of these strains.
Materials and Methods: Bacteria were isolated on brain heart infusion, 10% sheep blood agar plates, and screened by biochemical tests. The polymerase chain reaction technique was used with specific primers to identify P. multocida, the presence of virulence-associated genes, and serotypes of isolates. Antimicrobial susceptibility and biofilm formation of isolates were examined using the disk diffusion method and crystal violet-based method, respectively.
Results: A total of 41 P. multocida strains were isolated from 485 samples from clinically sick and healthy sheep. Of the isolates, 58.53% were serotype A, 9.75% were serotype B, and 31.71% were serotype D. Healthy animals were infected with serotype D only. All 15 virulence genes were identified in all strains isolated from clinically sick sheep, while strains isolated from healthy sheep carried 11/15 virulence genes tested. Among virulence-associated genes exbB, exbD, tonB, ompA, oma87, fimA, hgbA, and nanB were detected in over 90% of isolates, whereas hgbB, nanH, tbpA and pfhA were less frequent. Interestingly, pmHAS and tadD were highly prevalent in capsular type A strains, whereas the toxA gene was detected in capsular type D strains only. All of the isolated strains were fully susceptible to enrofloxacin, ciprofloxacin, neomycin, and ofloxacin. About 92.68% were susceptible to chloramphenicol and 90.24% to amikacin, but there was high resistance to erythromycin, tetracycline, and amoxicillin. Our results reveal that 53.65% of 41 isolates could produce biofilm, whereas 46.34% could not.
Conclusion: Pasteurella multocida from Phan Rang sheep possess many virulence genes and resistance to several common antibiotics such as erythromycin, tetracycline, and amoxicillin. The results are an important warning regarding antibiotic resistance of P. multocida.
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Affiliation(s)
- Phu Van Nguyen
- Institute of Biotechnology, Hue University, Road 10, Phu Thuong, Thua Thien Hue, Vietnam
| | - Cong Tuan Le
- Department of Environmental Science, University of Sciences, Hue University, Thua Thien Hue, Vietnam
| | - Xuan Huy Nguyen
- Department of Science, Technology and International Relations, Hue University, Thua Thien Hue, Vietnam
| | - Tuan Manh Nguyen
- Institute of Life Science, Thai Nguyen University of Agriculture and Forestry, Quyet Thang, Thai Nguyen, Vietnam
| | - Kim Cuc Thi Nguyen
- Institute of Biotechnology, Hue University, Road 10, Phu Thuong, Thua Thien Hue, Vietnam
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13
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Phu DH, Wongtawan T, Truong DB, Van Cuong N, Carrique-Mas J, Thomrongsuwannakij T. A systematic review and meta-analysis of integrated studies on antimicrobial resistance in Vietnam, with a focus on Enterobacteriaceae, from a One Health perspective. One Health 2022; 15:100465. [PMID: 36561710 PMCID: PMC9767812 DOI: 10.1016/j.onehlt.2022.100465] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/21/2022] Open
Abstract
Vietnam is a low- and middle-income country (LMIC), a primary food producer, and an antimicrobial resistance (AMR) hotspot. AMR is recognized as a One Health challenge since it may transfer between humans, animals and the environment. This study aimed to apply systematic review and meta-analysis to investigate the phenotypic profiles and correlations of antimicrobial-resistant Enterobacteriaceae across three compartments: humans, animals and the environment in Vietnam. A total of 89 articles found in PubMed, Science Direct, and Google Scholar databases were retrieved for qualitative synthesis. E. coli and non-typhoidal Salmonella (NTS) were the most common bacterial species in studies of all compartments (60/89 studies). Among antimicrobials classified as critically important, the resistance levels were observed to be highest to quinolones, 3rd generation of cephalosporins, penicillins, and aminoglycosides. Of 89 studies, 55 articles reported the resistance prevalence of E. coli and NTS in healthy humans, animals and the environment against ciprofloxacin, ceftazidime, ampicillin, gentamicin, sulfamethoxazole-trimethoprim, chloramphenicol was used for meta-analysis. The pooled prevalence was found highest in E. coli against ampicillin 84.0% (95% CI 73.0-91.0%) and sulfamethoxazole-trimethoprim 66.0% (95% CI 56.0-75.0%) while in NTS they were 34.0% (95% CI 24.0-46.0%), 33.0% (95% CI 25.0-42.0%), respectively. There were no significant differences in the pooled prevalence of E. coli and NTS to these antimicrobials across healthy humans, animals and the environment, except for ceftazidime-resistant E. coli (χ2 = 8.29, p = 0.02), chloramphenicol-resistant E.coli (χ2 = 9.65, p < 0.01) and chloramphenicol-resistant NTS (χ2 = 7.51, p = 0.02). Findings from the multiple meta-regression models indicated that the AMR levels in E. coli (β = 1.887, p < 0.001) and the North (β = 0.798, p = 0.047) had a higher fraction of AMR than NTS and other regions of Vietnam. The outcomes of this study play an important role as the baseline information for further investigation and follow-up intervention strategies to tackle AMR in Vietnam, and more generally, can be adapted to other LMICs.
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Affiliation(s)
- Doan Hoang Phu
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand,College of Graduate Studies, Walailak University, Nakhon Si Thammarat 80160, Thailand,Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City 70000, Viet Nam
| | - Tuempong Wongtawan
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand,Centre for One Health, Walailak University, Nakhon Si Thammarat 80160, Thailand,Centre of Excellence Research for Melioidosis and other Microorganism, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Dinh Bao Truong
- Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City 70000, Viet Nam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, Ho Chi Minh City 70000, Viet Nam,Ausvet PTY LTD, Bruce ACT 2617, Canberra, Australia
| | - Juan Carrique-Mas
- Food and Agriculture Organization of the United Nations, Ha Noi 10000, Viet Nam
| | - Thotsapol Thomrongsuwannakij
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand,Centre for One Health, Walailak University, Nakhon Si Thammarat 80160, Thailand,Corresponding author at: Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand.
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14
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Kittiwan N, Calland JK, Mourkas E, Hitchings MD, Murray S, Tadee P, Tadee P, Duangsonk K, Meric G, Sheppard SK, Patchanee P, Pascoe B. Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs. Microb Genom 2022; 8:mgen000882. [PMID: 36326658 PMCID: PMC9836093 DOI: 10.1099/mgen.0.000882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Streptococcus suis is a leading cause of bacterial meningitis in South-East Asia, with frequent zoonotic transfer to humans associated with close contact with pigs. A small number of invasive lineages are responsible for endemic infection in the swine industry, causing considerable global economic losses. A lack of surveillance and a rising trend in clinical treatment failure has raised concerns of growing antimicrobial resistance (AMR) among invasive S. suis. Gene flow between healthy and disease isolates is poorly understood and, in this study, we sample and sequence a collection of isolates predominantly from healthy pigs in Chiang Mai province, Northern Thailand. Pangenome characterization identified extensive genetic diversity and frequent AMR carriage in isolates from healthy pigs. Multiple AMR genes were identified, conferring resistance to aminoglycosides, lincosamides, tetracycline and macrolides. All isolates were non-susceptible to three or more different antimicrobial classes, and 75 % of non-serotype 2 isolates were non-susceptible to six or more classes (compared to 37.5 % of serotype 2 isolates). AMR genes were found on integrative and conjugative elements previously observed in other species, suggesting a mobile gene pool that can be accessed by invasive disease isolates. This article contains data hosted by Microreact.
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Affiliation(s)
- Nattinee Kittiwan
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Veterinary Research and Development Center (Upper Northern Region), Hang Chat, Lampang 52190, Thailand
| | - Jessica K. Calland
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Evangelos Mourkas
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK
| | - Matthew D. Hitchings
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, UK
| | - Susan Murray
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, UK,Present address: Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, UK
| | - Pakpoom Tadee
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Phacharaporn Tadee
- Faculty of Animal Science and Technology, Maejo University, Chiang Mai 50290, Thailand
| | - Kwanjit Duangsonk
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Guillaume Meric
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK,Present address: Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Samuel K. Sheppard
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK,Faculty of Allied Medical Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Prapas Patchanee
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,*Correspondence: Prapas Patchanee,
| | - Ben Pascoe
- Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK,Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK,*Correspondence: Ben Pascoe,
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15
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Nguyen PTL, Ngo THH, Tran TMH, Vu TNB, Le VT, Tran HA, Pham DT, Nguyen HT, Tran DL, Nguyen TPL, Nguyen TTT, Tran ND, Dang DA, Bañuls AL, Choisy M, van Doorn HR, Suzuki M, Tran HH. Genomic epidemiological analysis of mcr-1-harboring Escherichia coli collected from livestock settings in Vietnam. Front Vet Sci 2022; 9:1034610. [PMID: 36387375 PMCID: PMC9643773 DOI: 10.3389/fvets.2022.1034610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/05/2022] [Indexed: 09/19/2023] Open
Abstract
Livestock has been implicated as a reservoir for antimicrobial resistance (AMR) genes that can spread to humans when antimicrobials are used in animals for food production to treat clinical diseases and prevent and control common disease events. In Vietnam, mcr-1-harboring Escherichia coli (MCRPEC) strains have been isolated from humans, animals (chickens, pigs, and dogs) feces, flies, foods, and the environment (rainwater, well water, and irrigation water) in communities and from clinical specimens in hospitals. The relationship between levels of AMR in livestock and its occurrence in humans is complex and is driven by many factors. We conducted whole genome sequencing of MCRPEC to analyze the molecular epidemiological characteristics, history, and relatedness of 50 isolates obtained in 2019 from different reservoirs in farms and markets in Ha Nam province, Vietnam. 34 sequence types (STs) with 3 new STs were identified in multilocus sequence typing analysis: ST12945 and ST12946 from chicken feces, and ST12947 from flies. The AMR phenotypes of 50 MCRPEC isolates were as follows: ampicillin (100%, 50/50), cefotaxime (10%, 5/50), gentamicin (60%, 30/50), amikacin (8%, 4/50), meropenem (6%, 3/50), ceftazidime (18%, 9/50), colistin (24%, 12/50) and ciprofloxacin (80%, 40/50). All 50 MCRPEC isolates were identified as MDR. 100% (50/50) isolates carried AMR genes, ranging from 5 to 22 genes. The most prevalent plasmid replicon types carrying mcr-1 were IncP-1 (17/37, 45.9%), IncX4 (7/37, 18.9%), and IncHI2/IncHI2A (6/37, 16.2%). These data suggest that the epidemiology of the mcr-1 gene is mostly determined by plasmid spreading instead of clonal dissemination of MCRPE strains. The co-occurrence of several STs such as ST10, ST48, ST155, ST206, ST2705 in various sample types, joined to the higher prevalence of a few types of Inc plasmids, confirms the dissemination of the mcr-1 carrying plasmids in E. coli clones established in livestock. 5 over 8 STs identified in flies (ST206, ST2705, ST155, ST10, and ST48) suggested the fly contribution in the transmission of AMR bacteria in environments. These popular STs also occur in human samples and 100% of the human samples were positive for the mcr-1 gene.
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Affiliation(s)
| | | | | | | | - Viet Thanh Le
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | | | - Duy Thai Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Ha Thanh Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Dieu Linh Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | | | - Nhu Duong Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Anne-Laure Bañuls
- MIVEGEC (IRD-CNRS-Université de Montpellier), LMI DRISA, Center IRD, Montpellier, France
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Masato Suzuki
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Huy Hoang Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
- Hanoi Medical University, Hanoi, Vietnam
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16
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Genome-associations of extended-spectrum ß-lactamase producing (ESBL) or AmpC producing E. coli in small and medium pig farms from Khon Kaen province, Thailand. BMC Microbiol 2022; 22:253. [PMID: 36266637 PMCID: PMC9585832 DOI: 10.1186/s12866-022-02646-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022] Open
Abstract
Thailand is undergoing rapid intensification of livestock production where small subsistence farms and medium sized commercial farms coexist. In medium farms, antimicrobials are prescribed by a veterinarian, whereas in small farms antimicrobial use remains largely unsupervised. The impact of these differences as well as other farming practices on the emergence and composition of antimicrobial resistance genes (ARGs) remains largely unknown. We analyzed 363 genomes of extended-spectrum ß-lactamase producing (ESBL) and/or AmpC producing Escherichia coli recovered from humans and pigs at small and medium farms from the Khon Kaen province, Thailand. We tested for genome-wide associations to identify links between ARGs, host, and farm size. Pig isolates from small farms were associated with mcr and qnr genes conferring resistance to colistin and fluoroquinolones, respectively. In contrast, pig isolates from medium farms were associated with ARGs conferring resistance to drugs commonly used on medium farms (i.e., streptomycin). ESBL plasmids from small farms co-carried ARGs conferring resistance to critically important antimicrobials more frequently compared to plasmid from medium farms. Frequent ARG combinations included blaCTX-M-55 + qnrS1 (29.8% vs 17.5% in small and medium farms, respectively), blaCTX-M-55 + qnrS1 + mcr-3.19 (5% vs 0%), blaCTX-M-14 + qnrS1 (9.3% vs 6.2%), and blaCTX-M-14 + qnrS1 + mcr-1.1 (3.1% vs 0%). The co-location on plasmids of ARGs conferring resistance to critically important antimicrobials as defined by the World Health Organization is concerning, and actions to curb their spread are urgently needed. Legislation on limiting antimicrobial sales and initiatives to better inform farmers and veterinarians on appropriate antimicrobial usage and farm biosecurity could help reduce antimicrobial use on farms.
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Mmatli M, Mbelle NM, Osei Sekyere J. Global epidemiology, genetic environment, risk factors and therapeutic prospects of mcr genes: A current and emerging update. Front Cell Infect Microbiol 2022; 12:941358. [PMID: 36093193 PMCID: PMC9462459 DOI: 10.3389/fcimb.2022.941358] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/01/2022] [Indexed: 12/28/2022] Open
Abstract
Background Mobile colistin resistance (mcr) genes modify Lipid A molecules of the lipopolysaccharide, changing the overall charge of the outer membrane. Results and discussion Ten mcr genes have been described to date within eleven Enterobacteriaceae species, with Escherichia coli, Klebsiella pneumoniae, and Salmonella species being the most predominant. They are present worldwide in 72 countries, with animal specimens currently having the highest incidence, due to the use of colistin in poultry for promoting growth and treating intestinal infections. The wide dissemination of mcr from food animals to meat, manure, the environment, and wastewater samples has increased the risk of transmission to humans via foodborne and vector-borne routes. The stability and spread of mcr genes were mediated by mobile genetic elements such as the IncHI2 conjugative plasmid, which is associated with multiple mcr genes and other antibiotic resistance genes. The cost of acquiring mcr is reduced by compensatory adaptation mechanisms. MCR proteins are well conserved structurally and via enzymatic action. Thus, therapeutics found effective against MCR-1 should be tested against the remaining MCR proteins. Conclusion The dissemination of mcr genes into the clinical setting, is threatening public health by limiting therapeutics options available. Combination therapies are a promising option for managing and treating colistin-resistant Enterobacteriaceae infections whilst reducing the toxic effects of colistin.
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Affiliation(s)
- Masego Mmatli
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN, United States
- Department of Dermatology, School of Medicine, University of Pretoria, Pretoria, South Africa
- *Correspondence: John Osei Sekyere, ;
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Nguyen PTL, Tran HTM, Tran HA, Pham TD, Luong TM, Nguyen TH, Nguyen LTP, Nguyen TTT, Hoang HTA, Nguyen C, Tran DN, Dang AD, Suzuki M, Le TV, Bañuls AL, Choisy M, Van Doorn RH, Tran HH. Carriage of Plasmid-Mediated Colistin Resistance-1-Positive Escherichia coli in Humans, Animals, and Environment on Farms in Vietnam. Am J Trop Med Hyg 2022; 107:65-71. [PMID: 35895375 PMCID: PMC9294698 DOI: 10.4269/ajtmh.21-1203] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/27/2022] [Indexed: 07/30/2023] Open
Abstract
Plasmid-Mediated Colistin Resistance 1 (mcr-1) was first reported in 2015 and is a great concern to human health. In this study, we investigated the prevalence of mcr-1 and mcr-1-positive Escherichia coli (MCRPEC) and the association in infection status among various reservoirs connected to livestock. The study was conducted in 70 poultry and swine farms in a commune in Ha Nam province, northern Vietnam. Samples were collected from farmers, food animals, domestic animals, and farm environments (flies and wastewater) for polymerase chain reaction (PCR) screening for mcr-1 gene and species identification of PCR positive isolates. Among 379 obtained mcr-1 positives isolates, Escherichia coli was the major identified, varying from 50% (2/4) in dog feces to 100% (31/31) in humans feces isolates. The prevalence of MCRPEC was 14.4% (20/139), 49.7% (96/193), 31.3% (25/80), 36.7% (40/109), 26.9% (18/67), and 3.9% (2/51) in humans, chickens, pigs, flies, wastewater, and dogs, respectively. The study identified association between MCRPEC infection status in humans and flies (OR = 3.4), between flies and chickens (OR = 5.3), and between flies and pigs (OR = 9.0). Farmers' age and farm livestock unit were also associated factors of MCRPEC infection status in humans (OR = 5.1 and 1.05, respectively). These findings bring new knowledge on antibiotic resistance in livestock setting and important suggestions on potential role of flies in the transmission of mcr-1 resistance gene.
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Affiliation(s)
| | | | | | - Thai Duy Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Tan Minh Luong
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Thanh Ha Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | | | | | - Chi Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
- Association of Public Health Laboratories, Silver Spring, Maryland
| | - Duong Nhu Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Anh Duc Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Masato Suzuki
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Thanh Viet Le
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Anne-Laure Bañuls
- MIVEGEC (IRD-CNRS-Université de Montpellier), LMI DRISA, Centre IRD, Montpellier, France
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Rogier H. Van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Huy Hoang Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
- Hanoi Medical University, Hanoi, Vietnam
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Worldwide Prevalence of mcr-mediated Colistin-Resistance Escherichia coli in Isolates of Clinical Samples, Healthy Humans, and Livestock-A Systematic Review and Meta-Analysis. Pathogens 2022; 11:pathogens11060659. [PMID: 35745513 PMCID: PMC9230117 DOI: 10.3390/pathogens11060659] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Antimicrobial resistance is a serious public-health problem throughout the world. Escherichia coli, the most common Gram-negative microorganism, has developed different resistance mechanisms, making treating infections difficult. Colistin is considered a last-resort drug in the treatment of infections caused by E. coli. Plasmid-mediated mobile-colistin-resistant (mcr) genes in E. coli, now disseminated globally, are considered a major public-health threat. Humans, chickens, and pigs are the main reservoirs for E. coli and the sources of antibiotic resistance. Hence, an up-to-date and precise estimate of the global prevalence of mcr resistance genes in these reservoirs is necessary to understand more precisely the worldwide spread and to more effectively implement control and prevention strategies. Methodology: Publications were identified in the PubMed database on the basis of the PRISMA guidelines. English full-text articles were selected from December 2014 to March 2021. Descriptive statistics and a meta-analysis were performed in Excel and R software, respectively. Colistin resistance was defined as the molecular-genetic detection of the mcr genes. The crude and estimated prevalence were calculated for each host and continent. The studies were divided into two groups; community-based when they involved isolates from healthy humans, chickens, or pigs, and clinical studies when they involved only hospital, outpatient, or laboratory isolates. Results: A total of 1278 studies were identified and 218 were included in this systematic review and meta-analysis, divided into community studies (159 studies) and clinical studies (59 studies). The general prevalence of mcr-mediated colistin-resistant E. coli (mcrMCRE) was 6.51% (n = 11,583/177,720), reported in 54 countries and on five continents; Asia with 119 studies followed by Europe with 61 studies registered the most articles. Asia reported the major diversity of mcr-variants (eight of nine, except mcr-2). Worldwide, chickens and pigs proved to be the principal reservoir of mcr with an estimated prevalence of 15.8% and 14.9%, respectively. Healthy humans and clinical isolates showed a lower prevalence with 7.4% and 4.2% respectively. Conclusions: In this systematic review and meta-analysis, the worldwide prevalence of mcr in E. coli isolated from healthy humans, chickens, and pigs was investigated. A wide prevalence and distribution of mcr genes was demonstrated on all continents in E. coli isolates from the selected reservoirs. Understanding the epidemiology and occurrence in the reservoirs of mcr in E. coli on different continents of the world facilitates tracing how mcr genes are transmitted and determining the infection risks for humans. This knowledge can be used to reduce the incidence of zoonotic transmission by implementing the appropriate control programs.
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Nhung NT, Yen NTP, Dung NTT, Nhan NTM, Phu DH, Kiet BT, Thwaites G, Geskus RB, Baker S, Carrique-Mas J, Choisy M. Antimicrobial resistance in commensal Escherichia coli from humans and chickens in the Mekong Delta of Vietnam is driven by antimicrobial usage and potential cross-species transmission. JAC Antimicrob Resist 2022; 4:dlac054. [PMID: 35663829 PMCID: PMC9154321 DOI: 10.1093/jacamr/dlac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/28/2022] [Indexed: 11/14/2022] Open
Abstract
Objectives To investigate phenotypic antimicrobial resistance (AMR) in relation to antimicrobial use (AMU) and potential inter-species transmission among Escherichia coli from humans and chickens located in the same households in the Mekong Delta of Vietnam. Methods We collected data on AMU and faecal swabs from humans (N = 426) and chickens (N = 237) from 237 small-scale farms. From each sample, one E. coli strain was isolated and tested for its susceptibility against 11 antimicrobials by Sensititre AST. The association between AMR and AMU was investigated by logistic regression modelling. Using randomization, we compared the degree of similarity in AMR patterns between human and chicken E. coli from the same farms compared with isolates from different farms. Results The AMU rate was ∼19 times higher in chickens (291.1 per 1000 chicken-days) than in humans (15.1 per 1000 person-days). Isolates from chickens also displayed a higher prevalence of multidrug resistance (63.3%) than those of human origin (55.1%). AMU increased the probability of resistance in isolates from human (ORs between 2.1 and 5.3) and chicken (ORs between 1.9 and 4.8). E. coli from humans and chickens living on same farms had a higher degree of similarity in their AMR patterns than isolates from humans and chicken living on different farms. Conclusions We demonstrated the co-influence of AMU and potential transmission on observed phenotypic AMR patterns among E. coli isolates from food-producing animals and in-contact humans. Restricting unnecessary AMU alongside limiting interspecies contact (i.e. increasing hygiene and biocontainment) are essential for reducing the burden of AMR.
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Affiliation(s)
- Nguyen Thi Nhung
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | | | - Doan Hoang Phu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City, Vietnam
| | - Bach Tuan Kiet
- Sub-Department of Animal Health and Production, Dong Thap Province, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Ronald B. Geskus
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
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21
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Epidemiological Prevalence of Phenotypical Resistances and Mobilised Colistin Resistance in Avian Commensal and Pathogenic E. coli from Denmark, France, The Netherlands, and the UK. Antibiotics (Basel) 2022; 11:antibiotics11050631. [PMID: 35625275 PMCID: PMC9137498 DOI: 10.3390/antibiotics11050631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 01/10/2023] Open
Abstract
Colistin has been used for the treatment of non-invasive gastrointestinal infections caused by avian pathogenic E. coli (APEC). The discovery of mobilised colistin resistance (mcr) in E. coli has instigated a One Health approach to minimise colistin use and the spread of resistance. The aim of this study was to compare colistin susceptibility of APECs (collected from Denmark n = 25 and France n = 39) versus commensal E. coli (collected from the Netherlands n = 51 and the UK n = 60), alongside genetic (mcr-1−5) and phenotypic resistance against six other antimicrobial classes (aminoglycosides, cephalosporins, fluoroquinolones, penicillins, sulphonamides/trimethoprim, tetracyclines). Minimum inhibitory concentration (MIC) values were determined using a broth microdilution method (EUCAST guidelines), and phenotypic resistance was determined using disk diffusion. Colistin MIC values of APEC were significantly lower than those for commensals by 1 dilution (p < 0.0001, Anderson-Darling test), and differences in distributions were observed between countries. No isolate carried mcr-1−5. Three phenotypically resistant isolates were identified in 2/62 APEC and 1/111 commensal isolates. Gentamicin or gentamicin−ceftriaxone co-resistance was observed in two of these isolates. This study showed a low prevalence of phenotypic colistin resistance, with no apparent difference in colistin resistance between commensal E. coli strains and APEC strains.
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22
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Chah JM, Nwankwo SC, Uddin IO, Chah KF. Knowledge and practices regarding antibiotic use among small-scale poultry farmers in Enugu State, Nigeria. Heliyon 2022; 8:e09342. [PMID: 35520608 PMCID: PMC9062671 DOI: 10.1016/j.heliyon.2022.e09342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 11/03/2021] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
This study examined the knowledge and practices regarding antibiotic use among small-scale poultry farmers in Enugu State, Nigeria. A multistage sampling technique was employed to select 88 poultry farmers. The interview schedule was used for data collection. Respondents' indices of knowledge of antibiotic use (KABU), antibiotic resistance (KABR) and antibiotic use practices (PABU) were determined. Binary logistic regression was performed to ascertain the effect of socio-demographics of respondents, knowledge of antibiotic use and knowledge of antibiotic resistance on the likelihood that farmers use antibiotics inappropriately. All poultry farmers studied used antibiotics for growth promotion, disease prevention, and treatment. The mean index of KABU was 0.54 with 48 % of the respondents having good KABU while the mean index of KABR was 0.65 and 70.5 % of the farmers had good KABR. The farmers' mean index of PABU was 0.47 and 83 % of them used antibiotics inappropriately. Farmers with good KABU (OR = 4.2; 95% CI = 1.030-17.222) and KABR (OR = 4.5; 95% CI = 1.258-15.791) were more likely to misuse antibiotics than those with poor knowledge. Antibiotics are routinely, and on many occasions inappropriately, used in small-scale poultry production in Enugu State, Nigeria. Antibiotics are valuable agents whose efficacy can only be preserved if they are handled with care. Training small-scale farmers will allow them to improve their knowledge and practices regarding antibiotic use.
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Affiliation(s)
- Jane M. Chah
- Department of Agricultural Extension, University of Nigeria Nsukka, Nigeria
| | - Sandra C. Nwankwo
- Department of Agricultural Extension, University of Nigeria Nsukka, Nigeria
| | - Irenonsen O. Uddin
- Department of Agricultural Economics and Extension, Ambrose Alli University, Ekpoma, Nigeria
| | - Kennedy F. Chah
- Department of Veterinary Pathology and Microbiology, University of Nigeria Nsukka, Nigeria
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23
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Conjugative transfer of mcr-1-bearing plasmid from Salmonella to Escherichia coli in vitro on chicken meat and in mouse gut. Food Res Int 2022; 157:111263. [DOI: 10.1016/j.foodres.2022.111263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 11/23/2022]
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Khine NO, Lugsomya K, Niyomtham W, Pongpan T, Hampson DJ, Prapasarakul N. Longitudinal Monitoring Reveals Persistence of Colistin-Resistant Escherichia coli on a Pig Farm Following Cessation of Colistin Use. Front Vet Sci 2022; 9:845746. [PMID: 35372535 PMCID: PMC8964308 DOI: 10.3389/fvets.2022.845746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/17/2022] [Indexed: 12/25/2022] Open
Abstract
Colistin-resistant bacteria harboring plasmid-mediated mcr genes are of concern as they may be a cause of serious nosocomial infections. It is hypothesized that cessation of colistin use as a feed additive for pigs will reduce the occurrence and distribution of mcr genes in farms. The aim of this study was to investigate this hypothesis by longitudinal monitoring and characterizing of mcr positive Escherichia coli (MCRPE) isolates after colistin was withdrawn on a central Thailand pig farm that previously had a high frequency of MCRPE. Colistin use ceased at the beginning of 2017, and subsequently 170 samples were collected from farrowing sows and suckling piglets (n = 70), wastewater (n = 50) and farm workers (n = 50) over a 3.5-year period. Bacteria were identified by MALDI-TOF mass spectrometry and minimal inhibitory concentrations were determined by broth microdilution. The antibiogram of mcr positive E. coli isolates was determined using the Vitek2 automated susceptibility machine, and multiplex and simplex PCRs were performed for mcr-1-8 genes. MCRPE containing either mcr-1 or mcr-3 were isolated from pigs throughout the investigation period, but with a declining trend, whereas MCRPE isolates were recovered from humans only in 2017. MCRPE were still being recovered from wastewater in 2020. Most MCRPE isolates possessed the virulence genes Stap, Stb, or Stx2e, reflecting pathogenic potential in pigs, and showed high rates of resistance to ampicillin, gentamicin and tetracycline. Pulsed-field gel electrophoresis and multi-locus sequence typing showed that diverse MCRPE clones were distributed on the farm. The study identified a decline of pathogenic MCRPE following withdrawal of colistin, with pigs being the primary source, followed by wastewater. However, short-term therapeutic usage of other antibiotics could enhance the re-occurrence of mcr-carrying bacteria. Factors including the environment, management, and gene adaptations that allow maintenance of colistin resistance require further investigation, and longer-term studies are needed.
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Affiliation(s)
- Nwai Oo Khine
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Kittitat Lugsomya
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, China
| | - Waree Niyomtham
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Tawat Pongpan
- Center of Excellence in Diagnosis and Monitoring of Animal Pathogens (DMAP), Bangkok, Thailand
| | - David J. Hampson
- School of Veterinary Medicine, Murdoch University, Perth, WA, Australia
| | - Nuvee Prapasarakul
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Diagnosis and Monitoring of Animal Pathogens (DMAP), Bangkok, Thailand
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Antimicrobial Resistance Surveillance of Pigs and Chickens in the Lao People’s Democratic Republic, 2018–2021. Antibiotics (Basel) 2022; 11:antibiotics11020177. [PMID: 35203780 PMCID: PMC8868105 DOI: 10.3390/antibiotics11020177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/17/2022] [Accepted: 01/27/2022] [Indexed: 02/01/2023] Open
Abstract
The use of antimicrobials in the livestock sector has been identified as a driver for the emergence of antimicrobial resistance (AMR), and AMR has become a growing public health and economic threat in the Lao PDR. We conducted surveillance for AMR in five provinces of the Lao PDR, in order to determine the antimicrobial susceptibility of Escherichia coli and Salmonella spp. isolated from caecal samples from slaughtered pigs at slaughterhouses and from slaughtered chickens at markets during two different time periods: 2018/2019 and 2020/2021. Antimicrobial susceptibility was determined using a panel of 14 antimicrobials using the broth microdilution technique. E. coli and Salmonella from chickens (62% and 33%, respectively) and pigs (88% and 81%, respectively) exhibited resistance to ≥3 classes of antimicrobials. Of important public health concern was the detection of Salmonella resistant to cefotaxime/ceftazidime, ciprofloxacin, and colistin, deemed as critically important antimicrobials in human medicine. This study aimed to evaluate a national sampling strategy at slaughterhouses and wet markets, and to pilot the laboratory methodologies for bacterial recovery and AMR testing. Experiences from this study will inform capacity development for a national AMR surveillance program, and these early data could serve as reference points for monitoring the impact of the Lao PDR’s national action plan to contain AMR.
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Antibiotic Resistance in Salmonella Isolated from Ho Chi Minh City (Vietnam) and Difference of Sulfonamide Resistance Gene Existence in Serovars. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, a total of 228 raw meat samples (pork: 76, beef: 76, chicken: 76) and 301 raw seafood samples (fish: 199, shrimp: 67, squid: 35) were collected randomly at traditional markets in Ho Chi Minh City (Vietnam). In meat, the ratio of Salmonella spp. was 70.61% (161/228). Among the contaminated meat samples, pork was infected with a ratio of 90.79 % (69/76) while the contamination ratios in beef and chicken were 43.42% (33/76) and 77.63% (59/76), respectively. Salmonella contamination was detected in fish (40.20%), shrimp (7.46%) and squid (17.14%). Because of sulfonamide group is used in Salmonella treatment, the study focused on sulfonamide resistance. In fresh seafood comparison, there were 32.56%, 40% and 10% Salmonella showing resistance to sulfamethoxazol in fish, squid and shrimp, respectively. In fresh meat comparison, there were 31.58%, 16.67% and 55.56% Salmonella showing resistance to sulfamethoxazol in pork, beef and chicken, respectively. Interestingly, there were 21 serovars including 19 identified serovars including S. Kentucky (8), S. Agona (2), S. Infanis (4), S. Saintpaul (1), S. Indiana (1), S. Braenderup (1), S. Potsman (2) and 2 unidentified serovars showing different phenotype to this antibiotic. Among the 21 serovars, only 23.81% strains carried both genes (sul1, sul2). For the sul1 gene, 61.9% strains were presented while sul2 occupied at a lower rate than sul1 with the rate of 52.38%. The study is very interesting and useful to go more functional analysis in sulfonamide resistance.
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Freire CMADS, Taunay-Rodrigues A, Gonzatti MB, Fonseca FMP, Freire JEDC. New insights about the EptA protein and its correlation with the pmrC gene in polymyxin resistance in Pseudomonas aeruginosa. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100042. [PMID: 34841333 PMCID: PMC8610356 DOI: 10.1016/j.crmicr.2021.100042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/30/2021] [Accepted: 06/06/2021] [Indexed: 11/19/2022] Open
Abstract
Computational biology. Bacterial resistance. Pseudomonas aeruginosa. Gram-negative bacteria. Polymyxin.
Nowadays, clinical and scientific interest in antibiotics, as polymyxin, has increased due to the large number of reports of multiresistant Gram-negative bacteria, as Pseudomonas aeruginosa. The aim of this study was to investigate a related group of proteins for resistance to polymyxins, encoded by P. aeruginosa genome, through in silico analysis. The mobilized colistin resistance 1 (MCR1) protein from Escherichia coli was used for comparison. Similar sequences to the protein MCR1 in P. aeruginosa were analysed for physicochemical properties. 31 protein isoforms in P. aeruginosa (EptA) were found able to confer resistance to polymyxin showing protein lengths between 551 and 572 amino acids, with molecular mass values between 61.36 - 62. 80 kDa, isoelectric point between 6.10 to 7.17, instability index between 33.76 to 41.87, aliphatic index between 98.67 to 102.63 and the hydropathyindex between - 0.008 to 0.094. These proteins belong to the DUF1705 superfamily with bit-score values between 559.81 and 629.78. A high degree of similarity between EpTAs in P. aeruginosa was observed in relation to other proteins that confer resistance to polymyxins, present in Gram-negative bacteria species of clinical interest. Although, further studies are needed to identify the actual contribution of EptAs in P. aeruginosa species.
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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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29
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Valiakos G, Kapna I. Colistin Resistant mcr Genes Prevalence in Livestock Animals (Swine, Bovine, Poultry) from a Multinational Perspective. A Systematic Review. Vet Sci 2021; 8:265. [PMID: 34822638 PMCID: PMC8619609 DOI: 10.3390/vetsci8110265] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 12/23/2022] Open
Abstract
The objective of this review is to collect and present the results of relevant studies on an international level, on the subject of colistin resistance due to mcr genes prevalence in livestock animals. After a literature search, and using PRISMA guidelines principles, a total of 40 swine, 16 bovine and 31 poultry studies were collected concerning mcr-1 gene; five swine, three bovine and three poultry studies referred to mcr-2 gene; eight swine, one bovine, two poultry studies were about mcr-3 gene; six swine, one bovine and one poultry manuscript studied mcr-4 gene; five swine manuscripts studied mcr-5 gene; one swine manuscript was about mcr-6, mcr-7, mcr-8, mcr-9 genes and one poultry study about mcr-10 gene was found. Information about colistin resistance in bacteria derived from animals and animal product foods is still considered limited and that should be continually enhanced; most of the information about clinical isolates are relative to enteropathogens Escherichia coli and Salmonella spp. This review demonstrates the widespread dispersion of mcr genes to livestock animals, indicating the need to further increase measures to control this important threat for public health issue.
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Affiliation(s)
- George Valiakos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece;
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30
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Truong DTQ, Hounmanou YMG, Dang STT, Olsen JE, Truong GTH, Tran NT, Scheutz F, Dalsgaard A. Genetic Comparison of ESBL-Producing Escherichia coli from Workers and Pigs at Vietnamese Pig Farms. Antibiotics (Basel) 2021; 10:1165. [PMID: 34680746 PMCID: PMC8532784 DOI: 10.3390/antibiotics10101165] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
We analyzed and compared genomes of Extended Spectrum Beta-Lactamase (ESBL)-producing Escherichia coli from pigs and pig farm workers at 116 farms in Vietnam. Analyses revealed the presence of blaCTX-M-55, blaCTX-M-27, blaCTX-M-15, blaCTX-M-14, blaCTX-M-3, blaCTX-M-65, blaCTX-M-24, blaDHA-1, and blaCMY2 in both hosts. Most strains from pigs contained quinolones (qnr) and colistin resistance genes (mcr-1 and mcr-3). Isolates predominantly harbored more than one plasmid replicon and some harbored plasmid replicons on the same contigs as the ESBL genes. Five strains from farm workers of ST38 (2), ST69 (1), and ST1722 (2) were classified as either uropathogenic E. coli (UPECHM)/extraintestinal pathogenic E. coli (ExPECJJ) or UPECHM, and the remaining were genetically distinct commensals. A high heterogeneity was found among the ESBL-producing E. coli from pigs and workers, with most isolates belonging to unrelated phylogroups, serogroups, and sequence types with >4046 Single-Nucleotide Polymorphisms-(SNPs). In comparing the genomes of pig isolates to those from humans, it appeared that ESBL-producing E. coli in workers did not predominantly originate from pigs but were rather host-specific. Nevertheless, the occurrence of ESBL-producing E. coli carrying plasmid-mediated colistin and quinolone resistance genes in pigs could represent a potential source for horizontal transmission to humans through food rather than direct contact.
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Affiliation(s)
- Duong Thi Quy Truong
- National Institute of Veterinary Research, Hanoi 10000, Vietnam; (D.T.Q.T.); (S.T.T.D.); (G.T.H.T.); (N.T.T.)
| | | | - Son Thi Thanh Dang
- National Institute of Veterinary Research, Hanoi 10000, Vietnam; (D.T.Q.T.); (S.T.T.D.); (G.T.H.T.); (N.T.T.)
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark;
| | - Giang Thi Huong Truong
- National Institute of Veterinary Research, Hanoi 10000, Vietnam; (D.T.Q.T.); (S.T.T.D.); (G.T.H.T.); (N.T.T.)
| | - Nhat Thi Tran
- National Institute of Veterinary Research, Hanoi 10000, Vietnam; (D.T.Q.T.); (S.T.T.D.); (G.T.H.T.); (N.T.T.)
| | - Flemming Scheutz
- Department of Bacteria, Parasites and Fungi, Statens Serum Institute, 2300 Copenhagen S, Denmark;
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark;
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31
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Cuong NV, Ly NPC, Van NTB, Phu DH, Kiet BT, Hien VB, Padungtod P, Thwaites G, Choisy M, Carrique-Mas J. Feasibility study of a field survey to measure antimicrobial usage in humans and animals in the Mekong Delta region of Vietnam. JAC Antimicrob Resist 2021; 3:dlab107. [PMID: 34396120 PMCID: PMC8360299 DOI: 10.1093/jacamr/dlab107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/30/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Development of antimicrobial use (AMU) surveillance systems in humans and animals is a priority for many low- and middle-income countries; however accurate estimations are hampered by a diversity of animal production systems and metrics. The Mekong Delta region of Vietnam is a 'hotspot' of antimicrobial resistance and is home to a high density of humans and animal populations. OBJECTIVES To measure and compare AMU using different metrics (standing population, biomass and population correction unit) in the Mekong Delta, and to explore the potential of field-based data collection methods in the design of AMU surveillance systems. METHODS We collected AMU data from humans and animals (chickens, ducks, Muscovy ducks, pigs) from 101 small-scale farms in the Mekong Delta over a fixed period (90 days in humans, 7 days in animals). RESULTS Humans used 7.1 DDDkg, or 175.9 mg of antimicrobial active ingredients (AAIs) per kg of standing body mass annually; animals consumed 60.9 ADDkg or 1324 mg. In the Mekong Delta humans represented 79.3% of the total body mass but consumed 29.6% of AAIs by weight. AAIs regarded of critical importance by WHO represented 56.9% and 50.2% of doses consumed by animals and humans, respectively. CONCLUSIONS Using a One Health approach, we show that AMU can potentially be estimated from cross-sectional surveys, although results are hypothetical due to small sample size and are sensitive to the chosen population denominator. The methodology proposed here can potentially be scaled up be applied to design AMU surveillance in low-resource settings, allowing AMU reduction efforts to be focused on particular animal species.
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Affiliation(s)
- Nguyen Van Cuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Doan Hoang Phu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Ho Chi Minh City, Vietnam
| | - Bach Tuan Kiet
- Sub-Department of Animal Health and Production (SDAHP), Cao Lanh, Dong Thap, Vietnam
| | - Vo Be Hien
- Sub-Department of Animal Health and Production (SDAHP), Cao Lanh, Dong Thap, Vietnam
| | - Pawin Padungtod
- Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, UK
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, UK
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32
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Rodríguez-Santiago J, Cornejo-Juárez P, Silva-Sánchez J, Garza-Ramos U. Polymyxin resistance in Enterobacterales: overview and epidemiology in the Americas. Int J Antimicrob Agents 2021; 58:106426. [PMID: 34419579 DOI: 10.1016/j.ijantimicag.2021.106426] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/07/2021] [Accepted: 08/15/2021] [Indexed: 12/30/2022]
Abstract
The worldwide spread of carbapenem- and polymyxin-resistant Enterobacterales represents an urgent public-health threat. However, for most countries in the Americas, the available data are limited, although Latin America has been suggested as a silent spreading reservoir for isolates carrying plasmid-mediated polymyxin resistance mechanisms. This work provides an overall update on polymyxin and polymyxin resistance and focuses on uses, availability and susceptibility testing. Moreover, a comprehensive review of the current polymyxin resistance epidemiology in the Americas is provided. We found that reports in the English and Spanish literature show widespread carbapenemase-producing and colistin-resistant Klebsiella pneumoniae in the Americas determined by the clonal expansion of the pandemic clone ST258 and mgrB-mediated colistin resistance. In addition, widespread IncI2 and IncX4 plasmids carrying mcr-1 in Escherichia coli come mainly from human sources; however, plasmid-mediated colistin resistance in the Americas is underreported in the veterinary sector. These findings demonstrate the urgent need for the implementation of polymyxin resistance surveillance in Enterobacterales as well as appropriate regulatory measures for antimicrobial use in veterinary medicine.
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Affiliation(s)
- J Rodríguez-Santiago
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, Morelos, México; Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - P Cornejo-Juárez
- Departamento de Infectología, Instituto Nacional de Cancerología (INCan), Ciudad de México, México
| | - J Silva-Sánchez
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, Morelos, México
| | - U Garza-Ramos
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, Morelos, México.
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33
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Cama J, Leszczynski R, Tang PK, Khalid A, Lok V, Dowson CG, Ebata A. To Push or To Pull? In a Post-COVID World, Supporting and Incentivizing Antimicrobial Drug Development Must Become a Governmental Priority. ACS Infect Dis 2021; 7:2029-2042. [PMID: 33606496 PMCID: PMC7931625 DOI: 10.1021/acsinfecdis.0c00681] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The COVID-19 pandemic has refocused attention worldwide on the dangers of infectious diseases, in terms of both global health and the effects on the world economy. Even in high income countries, health systems have been found wanting in dealing with the new infectious agent. However, the even greater long-term danger of antimicrobial resistance in pathogenic bacteria and fungi is still under-appreciated, especially among the general public. Although antimicrobial drug development faces significant scientific challenges, the gravest challenge at the moment appears to be economic, where the lack of a viable market has led to a collapse in drug development pipelines. There is therefore a critical need for governments across the world to further incentivize the development of antimicrobials. Most incentive strategies over the past decade have focused on so-called "push" incentives that bridge the costs of antimicrobial research and development, but these have been insufficient for reviving the pipeline. In this Perspective, we analyze the current incentive strategies in place for antimicrobial drug development, and focus on "pull" incentives, which instead aim to improve revenue generation and thereby resolve the antimicrobial market failure challenge. We further analyze these incentives in a broader "One Health" context and stress the importance of developing and enforcing strict protocols to ensure appropriate manufacturing practices and responsible use. Our analysis reiterates the importance of international cooperation, coordination across antimicrobial research, and sustained funding in tackling this significant global challenge. A failure to invest wisely and continuously to incentivize antimicrobial pipelines will have catastrophic consequences for global health and wellbeing in the years to come.
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Affiliation(s)
- J. Cama
- Living
Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K.
- College
of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter EX4 4QF, U.K.
- ,
| | - R. Leszczynski
- Polygeia,
Global Health Student Think Tank, London, U.K.https://www.polygeia.com/
| | - P. K. Tang
- Polygeia,
Global Health Student Think Tank, London, U.K.https://www.polygeia.com/
- Faculty
of Life Sciences and Medicine, King’s
College London, Great
Maze Pond, London SE1 1UK, U.K.
| | - A. Khalid
- Polygeia,
Global Health Student Think Tank, London, U.K.https://www.polygeia.com/
- School
of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, U.K.
| | - V. Lok
- Polygeia,
Global Health Student Think Tank, London, U.K.https://www.polygeia.com/
- School of
Biological and Chemical Sciences, Queen
Mary University of London, Mile End Road, London E1 4NS, U.K.
| | - C. G. Dowson
- School
of Life Sciences, Gibbet Hill Campus, University
of Warwick, Coventry CV4 7AL, U.K.
- Antibiotic
Research U.K., Genesis 5, York Science Park, Heslington, York YO10 5DQ, U.K.
| | - A. Ebata
- Institute
of Development Studies, Library Road, Brighton BN1 9RE, U.K.
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Sirichokchatchawan W, Apiwatsiri P, Pupa P, Saenkankam I, Khine NO, Lekagul A, Lugsomya K, Hampson DJ, Prapasarakul N. Reducing the Risk of Transmission of Critical Antimicrobial Resistance Determinants From Contaminated Pork Products to Humans in South-East Asia. Front Microbiol 2021; 12:689015. [PMID: 34385984 PMCID: PMC8353453 DOI: 10.3389/fmicb.2021.689015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 01/10/2023] Open
Abstract
Antimicrobial resistance (AMR) is a critical challenge worldwide as it impacts public health, especially via contamination in the food chain and in healthcare-associated infections. In relation to farming, the systems used, waste management on farms, and the production line process are all determinants reflecting the risk of AMR emergence and rate of contamination of foodstuffs. This review focuses on South East Asia (SEA), which contains diverse regions covering 11 countries, each having different levels of development, customs, laws, and regulations. Routinely, here as elsewhere antimicrobials are still used for three indications: therapy, prevention, and growth promotion, and these are the fundamental drivers of AMR development and persistence. The accuracy of detection of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) depends on the laboratory standards applicable in the various institutes and countries, and this affects the consistency of regional data. Enterobacteriaceae such as Escherichia coli and Klebsiella pneumoniae are the standard proxy species used for indicating AMR-associated nosocomial infections and healthcare-associated infections. Pig feces and wastewater have been suspected as one of the hotspots for spread and circulation of ARB and ARG. As part of AMR surveillance in a One Health approach, clonal typing is used to identify bacterial clonal transmission from the production process to consumers and patients - although to date there have been few published definitive studies about this in SEA. Various alternatives to antibiotics are available to reduce antibiotic use on farms. Certain of these alternatives together with improved disease prevention methods are essential tools to reduce antimicrobial usage in swine farms and to support global policy. This review highlights evidence for potential transfer of resistant bacteria from food animals to humans, and awareness and understanding of AMR through a description of the occurrence of AMR in pig farm food chains under SEA management systems. The latter includes a description of standard pig farming practices, detection of AMR and clonal analysis of bacteria, and AMR in the food chain and associated environments. Finally, the possibility of using alternatives to antibiotics and improving policies for future strategies in combating AMR in a SEA context are outlined.
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Affiliation(s)
- Wandee Sirichokchatchawan
- College of Public Health Sciences, Chulalongkorn University, Bangkok, Thailand
- Diagnosis and Monitoring of Animal Pathogen Research Unit, Chulalongkorn University, Bangkok, Thailand
| | - Prasert Apiwatsiri
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Pawiya Pupa
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Imporn Saenkankam
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Nwai Oo Khine
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Angkana Lekagul
- International Health Policy Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Kittitat Lugsomya
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - David J. Hampson
- School of Veterinary Medicine, Murdoch University, Perth, WA, Australia
| | - Nuvee Prapasarakul
- Diagnosis and Monitoring of Animal Pathogen Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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35
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Zhou L, Alcalde RE, Deng J, Zuniga B, Sanford RA, Fouke BW, Werth CJ. Impact of antibiotic concentration gradients on nitrate reduction and antibiotic resistance in a microfluidic gradient chamber. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146503. [PMID: 34030234 DOI: 10.1016/j.scitotenv.2021.146503] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
In order to explore the impact of antibiotics on the bacterial metabolic cycling of nitrate within contaminated soil and groundwater environments, we compared the effects of polymyxin B (PMB) and ciprofloxacin (CIP) concentration gradients on the distribution and activity of a wild type (WT) and a flagella deficient mutant (Δflag) of Shewanella oneidensis MR-1 in a microfluidic gradient chamber (MGC). Complementary batch experiments were performed to measure bacteriostatic versus bactericidal concentrations of the two antibiotics, as well as their effect on nitrate reduction. Prior work demonstrated that PMB disrupts cell membranes while CIP inhibits DNA synthesis. Consistent with these modes of action, batch results from this work show that PMB is bactericidal at lower concentrations than CIP relative to their respective minimum inhibitory concentrations (MICs) (≥5× MICPMB vs. ≥20× MICCIP). Concentration gradients from 0 to 50× the MIC of both antibiotics were established in the MGC across a 2-cm interconnected pore network, with nutrients injected at both concentration boundaries. The WT cells could only access and reduce nitrate in regions of the MGC with PMB at <18× MICPMB, whereas this occurred with CIP up to 50× MICCIP; and cells extracted from these MGCs showed no antibiotic resistance. The distribution of Δflag cells was further limited to lower antibiotic concentrations (≤1× MICPMB, ≤43× MICCIP) due to inability of movement. These results indicate that S. oneidensis access and reduce nitrate in bactericidal regions via chemotactic migration without development of antibiotic resistance, and that this migration is inhibited by acutely lethal bactericidal levels of antibiotics.
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Affiliation(s)
- Lang Zhou
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Reinaldo E Alcalde
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Jinzi Deng
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Baltazar Zuniga
- College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Bruce W Fouke
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Charles J Werth
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA.
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Wakabayashi Y, Sekizuka T, Yamaguchi T, Fukuda A, Suzuki M, Kawahara R, Taguchi M, Kuroda M, Semba K, Shinomiya H, Kawatsu K. Isolation and plasmid characterisation of Salmonella enterica serovar Albany harbouring mcr-5 from retail chicken meat in Japan. FEMS Microbiol Lett 2021; 367:5881302. [PMID: 32756977 DOI: 10.1093/femsle/fnaa127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/28/2020] [Indexed: 11/13/2022] Open
Abstract
The emergence of plasmid-mediated colistin resistance genes (mcr), which is occurring in numerous countries, is a worldwide concern, primarily because colistin is a last-resort antibiotic. Compared to E. coli, prevalence of mcr genes in Salmonella is unclear in Japan. Here we screened for mcr-1-5 genes in our collection of Salmonella strains isolated from retail meat products collected in Japan from 2012 through 2016. We found that Salmonella Albany strain 27A-368 encodes mcr-5 and that mcr genes were undetectable among the remaining 202 isolates. The resistance plasmid p27A-368 was transferred by conjugation to S. Infantis and was stably retained as a transconjugant. Whole-genome sequencing revealed that mcr-5 resided on a 115 kb plasmid (p27A-368). The plasmid backbone of p27A-368 is more similar to that of pCOV27, an ESBL-encoding plasmid recovered from avian pathogenic E. coli, rather than pSE13-SA01718 of S. Paratyphi B that encodes mcr-5. Further, mcr-5 is located on a transposon, and its sequence is similar to that of pSE13-SA01718. A phylogenetic tree based on single nucleotide variants implies a relationship between 27A-368 and S. Albany isolated in Southeast Asian countries.
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Affiliation(s)
- Yuki Wakabayashi
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Centre, National Institute of Infectious Diseases, 1-3-21 Toyama Shinjuku-ku, Tokyo, Japan
| | - Takahiro Yamaguchi
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka, Japan
| | - Akira Fukuda
- Microbiology Section, Division of Microbiology, Osaka Institute of Public Health, 8-34 Toujyo-cho, Tennouji-ku, Osaka, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Centre, National Institute of Infectious Diseases, 4-2-1 Aoba-cho, Higashimurayama-shi, Tokyo, Japan
| | - Ryuji Kawahara
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka, Japan
| | - Masumi Taguchi
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka, Japan
| | - Makoto Kuroda
- Pathogen Genomics Centre, National Institute of Infectious Diseases, 1-3-21 Toyama Shinjuku-ku, Tokyo, Japan
| | - Keiko Semba
- Ehime Prefectural Institute of Public Health and Environmental Science, 8-234 Sanban-cho, Matsuyama-shi, Ehime, Japan
| | - Hiroto Shinomiya
- Ehime Prefectural Institute of Public Health and Environmental Science, 8-234 Sanban-cho, Matsuyama-shi, Ehime, Japan
| | - Kentaro Kawatsu
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka, Japan
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37
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Tuat CV, Hue PT, Loan NTP, Thuy NT, Hue LT, Giang VN, Erickson VI, Padungtod P. Antimicrobial Resistance Pilot Surveillance of Pigs and Chickens in Vietnam, 2017-2019. Front Vet Sci 2021; 8:618497. [PMID: 34307512 PMCID: PMC8298034 DOI: 10.3389/fvets.2021.618497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 04/14/2021] [Indexed: 11/30/2022] Open
Abstract
Antimicrobial use (AMU) and antimicrobial resistance (AMR) are a growing public health and economic threat in Vietnam. We conducted a pilot surveillance programme in five provinces of Vietnam, two in the south and three in the north, to identify antimicrobial resistance (AMR) in rectal swab samples from pigs and fecal samples from chickens at slaughter points during three different points in time from 2017 to 2019. Escherichia coli (E. coli) and non-typhoidal Salmonella (NTS) isolates were tested for antimicrobial susceptibility using disk diffusion assay for 19 antimicrobial agents belonging to nine antimicrobial classes and Etest for colistin (polymyxin). Almost all E. coli (99%; 1029/1042) and NTS (96%; 208/216) isolates were resistant to at least one antimicrobial agent; 94% (981/1042) of E. coli and 89% (193/216) of NTS isolates were multidrug-resistant (MDR). Higher proportions of E. coli and NTS isolated from chickens were resistant to all antimicrobial classes than those isolates from pigs. There was a significantly higher proportion of MDR NTS isolates from the southern provinces of Ho Chi Minh City and Long An (p = 0.008). Although there were increasing trends of NTS in proportion of resistance to fluoroquinolone over the three surveillance rounds, there was a significant decreasing trend of NTS in proportion of resistance to polymyxin (p = 0.002). It is important to establish an annual AMR surveillance program for livestock in Vietnam to assess the impact of interventions, observe trends and drive decision making that ultimately contributes to reducing AMR public health threat.
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Affiliation(s)
- C V Tuat
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - P T Hue
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - N T P Loan
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - N T Thuy
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - L T Hue
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - V N Giang
- Food and Agriculture Organization of the United Nations Country Office for Vietnam, Hanoi, Vietnam
| | - Vera I Erickson
- Food and Agriculture Organization of the United Nations Country Office for Vietnam, Hanoi, Vietnam
| | - Pawin Padungtod
- Food and Agriculture Organization of the United Nations Country Office for Vietnam, Hanoi, Vietnam
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Jibril AH, Okeke IN, Dalsgaard A, Olsen JE. Association between antimicrobial usage and resistance in Salmonella from poultry farms in Nigeria. BMC Vet Res 2021; 17:234. [PMID: 34215271 PMCID: PMC8254292 DOI: 10.1186/s12917-021-02938-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 06/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a global health threat affecting treatment outcome in animals and humans. A pre-requisite for development of AMR reduction strategies is knowledge of antimicrobial use patterns, and how these affect resistance development. The aim of this study was to determine antimicrobial usage (AMU) and whether such usage was associated with AMR in Salmonella from poultry farms in Northwest Nigeria. RESULTS Fifteen (37%) of antimicrobial products observed contained compounds that are of highest priority and critically important for human medicine. Broilers chicken consumed higher (28 ± 14 mg/kg active ingredients) amounts of antimicrobials compared to layers (13 ± 8 mg/kg) per week (p = 0.0009). Surprisingly, chickens raised under backyard system consumed higher amounts of antimicrobials (34 ± 7 mg/kg) than poultry in other systems (p = 0.02). High levels of resistance to tetracycline (58%), sulphonamides (65%), ciprofloxacin (46%) and gentamicin (42%) correlated with high farm level usage of these antimicrobials, and there was a strong correlation (r = 0.9) between farm usage and resistance of isolates to the same antimicrobials (p = 0.03). CONCLUSION High AMU, including use of highest priority critically important antimicrobials was observed at poultry farms in Northwest Nigeria. AMU correlated with high levels of resistance. Communication of prudent use of antimicrobials to farmers and regulation to obtain reduction in AMU should be a priority.
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Affiliation(s)
- Abdurrahman Hassan Jibril
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Usmanu Danfodiyo University Sokoto, Sokoto, Nigeria
| | - Iruka N. Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Di KN, Pham DT, Tee TS, Binh QA, Nguyen TC. Antibiotic usage and resistance in animal production in Vietnam: a review of existing literature. Trop Anim Health Prod 2021; 53:340. [PMID: 34089130 DOI: 10.1007/s11250-021-02780-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 05/23/2021] [Indexed: 01/21/2023]
Abstract
Inappropriate use of antibiotics in animal production system is one of the major factors leading to the antibiotic resistance (ABR) development. In Vietnam, the ABR situation is crucial as antibiotics have been used indiscriminately for disease prevention and as growth promoters in animals. Thus, a thorough understanding on the ABR in veterinary settings would be beneficial to the Vietnam public health authority in formulating timely interventions. This review aimed to provide information on the current status of antibiotic usage in animal husbandry in Vietnam, identified gaps in research, and suggested possible solutions to tackle ABR. To this end, data on ABR in animals were extracted from 3 major electronic databases (PubMed, Web of Science, and ScienceDirect) in the period of January 2013-December 2020. The review findings were reported according to PRISMA, which highlighted the emergence and persistence of ABR in bacterial isolates, including Escherichia coli, Enterococcus spp., and Salmonella species, obtained from pigs and poultry. The lack of awareness of Vietnamese farmers on the antibiotic utilization guidelines was one of the main causes driving the animal ABR. Hence, this paper calls for interventions to restrict antibiotics use in food-producing animals by national action plan and antibiotics control programs. Additionally, studies to evaluate knowledge, attitude, and practice (KAP) of the community are required to promote rational use of antibiotics in all sectors.
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Affiliation(s)
- Khanh Nguyen Di
- Department of Academic Affairs - Testing, Dong Nai Technology University, Nguyen Khuyen Street, Trang Dai Ward, Bien Hoa City, Dong Nai, 810000, Vietnam. .,Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Duy Toan Pham
- Department of Chemistry, College of Natural Sciences, Can Tho University, Can Tho, 900000, Vietnam.
| | - Tay Sun Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Quach An Binh
- Department of Academic Affairs - Testing, Dong Nai Technology University, Nguyen Khuyen Street, Trang Dai Ward, Bien Hoa City, Dong Nai, 810000, Vietnam
| | - Thanh Cong Nguyen
- Faculty of Applied Science and Health, Dong Nai Technology University, Nguyen Khuyen Street, Trang Dai Ward, Bien Hoa City, Dong Nai, 810000, Vietnam
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Resistance to widely-used disinfectants and heavy metals and cross resistance to antibiotics in Escherichia coli isolated from pigs, pork and pig carcass. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107892] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Cuong NV, Kiet BT, Hien VB, Truong BD, Phu DH, Thwaites G, Choisy M, Carrique-Mas J. Antimicrobial use through consumption of medicated feeds in chicken flocks in the Mekong Delta of Vietnam: A three-year study before a ban on antimicrobial growth promoters. PLoS One 2021; 16:e0250082. [PMID: 33886626 PMCID: PMC8061946 DOI: 10.1371/journal.pone.0250082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/30/2021] [Indexed: 12/30/2022] Open
Abstract
Antimicrobials are included in commercial animal feed rations in many low- and middle-income countries (LMICs). We measured antimicrobial use (AMU) in commercial feed products consumed by 338 small-scale chicken flocks in the Mekong Delta of Vietnam, before a gradual nationwide ban on prophylactic use of antimicrobials (including in commercial feeds) to be introduced in the country over the coming five years. We inspected the labels of commercial feeds and calculated amounts of antimicrobial active ingredients (AAIs) given to flocks. We framed these results in the context of overall AMU in chicken production, and highlighted those products that did not comply with Government regulations. Thirty-five of 99 (35.3%) different antimicrobial-containing feed products included at least one AAI. Eight different AAIs (avilamycin, bacitracin, chlortetracycline, colistin, enramycin, flavomycin, oxytetracycline, virginamycin) belonging to five classes were identified. Brooding feeds contained antimicrobials the most (60.0%), followed by grower (40.9%) and finisher feeds (20.0%). Quantitatively, chlortetracycline was consumed most (42.2 mg/kg SEM ±0.34; 50.0% of total use), followed by enramycin (18.4 mg/kg SEM ±0.03, 21.8%), bacitracin (16.4 mg/kg SEM ±0.20, 19.4%) and colistin (6.40 mg/kg SEM ± 4.21;7.6%). Other antimicrobials consumed were virgianamycin, avilamycin, flavomycin and oxytetracycline (each ≤0.50 mg/kg). Antimicrobials in commercial feeds were more commonly given to flocks in the earlier part of the production cycle. A total of 10 (9.3%) products were not compliant with existing Vietnamese regulation (06/2016/TT-BNNPTNT) either because they included a non-authorised AAI (4), had AAIs over the permitted limits (4), or both (2). A number of commercial feed formulations examined included colistin (polymyxin E), a critically important antimicrobial of highest priority for human medicine. These results illustrate the challenges for effective implementation and enforcement of restrictions of antimicrobials in commercial feeds in LMICs. Results from this study should help encourage discussion about policies on medicated feeds in LMICs.
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Affiliation(s)
- Nguyen Van Cuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Bach Tuan Kiet
- Sub-Department of Animal Health and Production (SDAHP), Cao Lanh, Dong Thap, Vietnam
| | - Vo Be Hien
- Sub-Department of Animal Health and Production (SDAHP), Cao Lanh, Dong Thap, Vietnam
| | - Bao Dinh Truong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, HCMC, Ho Chi Minh City, Vietnam
| | - Doan Hoang Phu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, HCMC, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
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Barbieri NL, Pimenta RL, de Melo DA, Nolan LK, de Souza MMS, Logue CM. mcr-1 Identified in Fecal Escherichia coli and Avian Pathogenic E. coli (APEC) From Brazil. Front Microbiol 2021; 12:659613. [PMID: 33959114 PMCID: PMC8093808 DOI: 10.3389/fmicb.2021.659613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/19/2021] [Indexed: 01/13/2023] Open
Abstract
Colisitin-associated resistance in bacteria of food producing animals has gained significant attention with the mcr gene being linked with resistance. Recently, newer variants of mcr have emerged with more than nine variants currently recognized. Reports of mcr associated resistance in Escherichia coli of poultry appear to be relatively limited, but its prevalence requires assessment since poultry is one of the most important and cheapest sources of the world’s protein and the emergence of resistance could limit our ability to treat disease outbreaks. Here, 107 E. coli isolates from production poultry were screened for the presence of mcr 1–9. The isolates were collected between April 2015 and June 2016 from broiler chickens and free-range layer hens in Rio de Janeiro, Brazil. All isolates were recovered from the trachea and cloaca of healthy birds and an additional two isolates were recovered from sick birds diagnosed with colibacillosis. All isolates were screened for the presence of mcr-1 to 9 using PCR and Sanger sequencing for confirmation of positive genes. Additionally, pulse field gel electrophoresis (PFGE) analysis, avian fecal E. coli (APEC) virulence associated gene screening, plasmid replicon typing and antimicrobial resistance phenotype and resistance gene screening, were also carried out to further characterize these isolates. The mcr-1 gene was detected in 62 (57.9%) isolates (61 healthy and 1 APEC) and the mcr-5 gene was detected in 3 (2.8%) isolates; mcr-2, mcr-3, mcr-4, mcr-6, mcr-7, mcr-8, and mcr-9 were not detected in any isolate. In addition, mcr 1 and 5 positive isolates were phenotypically resistant to colistin using the agar dilution assay (> 8ug/ml). PFGE analysis found that most of the isolates screened had unique fingerprints suggesting that the emergence of colistin resistance was not the result of clonal dissemination. Plasmid replicon types IncI2, FIB, and B/O were found in 38, 36, and 34% of the mcr positive isolates and were the most prevalent replicon types detected; tetA and tetB (32 and 26%, respectively) were the most prevalent antimicrobial resistance genes detected and iutA, was the most prevalent APEC virulence associated gene, detected in 50% of the isolates. Approximately 32% of the isolates examined could be classified as APEC-like, based on the presence of 3 or more genes of APEC virulence associated path panel (iroN, ompT, hlyF, iss, iutA). This study has identified a high prevalence of mcr-1 in poultry isolates in Brazil, suggesting that animal husbandry practices could result in a potential source of resistance to the human food chain in countries where application of colistin in animal health is practiced. Emergence of the mcr gene and associated colisitin resistance in production poultry warrants continued monitoring from the animal health and human health perspective.
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Affiliation(s)
- Nicolle Lima Barbieri
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Ramon Loureiro Pimenta
- Department of Veterinary Science, Universidade Federal Rural do Rio de Janeiro, Seropedica, Brazil
| | - Dayanne Araujo de Melo
- Department of Veterinary Science, Universidade Federal Rural do Rio de Janeiro, Seropedica, Brazil
| | - Lisa K Nolan
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | | | - Catherine M Logue
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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Hickman RA, Leangapichart T, Lunha K, Jiwakanon J, Angkititrakul S, Magnusson U, Sunde M, Järhult JD. Exploring the Antibiotic Resistance Burden in Livestock, Livestock Handlers and Their Non-Livestock Handling Contacts: A One Health Perspective. Front Microbiol 2021; 12:651461. [PMID: 33959112 PMCID: PMC8093850 DOI: 10.3389/fmicb.2021.651461] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/16/2021] [Indexed: 01/14/2023] Open
Abstract
Antibiotics are freqeuently used in the livestock sector in low- and middle-income countries for treatment, prophylaxis, and growth promotion. However, there is limited information into the zoonotic prevalence and dissemination patterns of antimicrobial resistance (AMR) within these environments. In this study we used pig farming in Thailand as a model to explore AMR; 156 pig farms were included, comprising of small-sized (<50 sows) and medium-sized (≥100 sows) farms, where bacterial isolates were selectively cultured from animal rectal and human fecal samples. Bacterial isolates were subjected to antimicrobial susceptibility testing (AST), and whole-genome sequencing. Our results indicate extensive zoonotic sharing of antibiotic resistance genes (ARGs) by horizontal gene transfer. Resistance to multiple antibiotics was observed with higher prevalence in medium-scale farms. Zoonotic transmission of colistin resistance in small-scale farms had a dissemination gradient from pigs to handlers to non-livestock contacts. We highly recommend reducing the antimicrobial use in animals’ feeds and medications, especially the last resort drug colistin.
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Affiliation(s)
- Rachel A Hickman
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | | | - Kamonwan Lunha
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jatesada Jiwakanon
- Research Group for Animal Health Technology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sunpetch Angkititrakul
- Research Group for Animal Health Technology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Ulf Magnusson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marianne Sunde
- Section for Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Josef D Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
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Bastard J, Haenni M, Gay E, Glaser P, Madec JY, Temime L, Opatowski L. Drivers of ESBL-producing Escherichia coli dynamics in calf fattening farms: A modelling study. One Health 2021; 12:100238. [PMID: 33851002 PMCID: PMC8022845 DOI: 10.1016/j.onehlt.2021.100238] [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: 09/17/2020] [Revised: 03/14/2021] [Accepted: 03/14/2021] [Indexed: 01/30/2023] Open
Abstract
The contribution of bacteria in livestock to the global burden of antimicrobial resistance raises concerns worldwide. However, the dynamics of selection and diffusion of antimicrobial resistance in farm animals are not fully understood. Here, we used veal calf fattening farms as a model system, as they are a known reservoir of Extended Spectrum β-Lactamase-producing Escherichia coli (ESBL-EC). Longitudinal data of ESBL-EC carriage and antimicrobial use (AMU) were collected from three veal calf farms during the entire fattening process. We developed 18 agent-based mechanistic models to assess different hypotheses regarding the main drivers of ESBL-EC dynamics in calves. The models were independently fitted to the longitudinal data using Markov Chain Monte Carlo and the best model was selected. Within-farm transmission between individuals and sporadic events of contamination were found to drive ESBL-EC dynamics on farms. In the absence of AMU, the median carriage duration of ESBL-EC was estimated to be 19.6 days (95% credible interval: [12.7; 33.3]). In the best model, AMU was found to influence ESBL-EC dynamics, by affecting ESBL-EC clearance rather than acquisition. This effect of AMU was estimated to decrease gradually after the end of exposure and to disappear after 62.5 days [50.0; 76.9]. Moreover, using a simulation study, we quantified the efficacy of ESBL-EC mitigation strategies. Decreasing ESBL-EC prevalence by 50% on arrival at the fattening farm reduced prevalence at slaughter age by 33.3%. Completely eliminating the use of selective antibiotics on arrival had a strong effect on average ESBL-EC prevalence (relative reduction of 77.0%), but the effect was mild if this use was only decreased by 50% compared to baseline (relative reduction of 3.3%).
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Affiliation(s)
- Jonathan Bastard
- Université Paris-Saclay, UVSQ, Univ. Paris-Sud, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, F-78180 Montigny-le-Bretonneux, France
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion unit, F-75015 Paris, France
- MESuRS laboratory, Conservatoire national des arts et métiers, 292 rue Saint-Martin, 75003 Paris, France
- PACRI unit, Institut Pasteur, Conservatoire national des arts et métiers, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Corresponding author at: Institut Pasteur, EMEA unit, 25 rue du Docteur Roux, 75015 Paris, France.
| | - Marisa Haenni
- Université de Lyon - Anses, Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Emilie Gay
- Université de Lyon - Anses, Laboratoire de Lyon, Unité EAS, Lyon, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotics Resistance (EERA) unit, CNRS UMR 3525, Institut Pasteur, AP-HP, Université Paris-Sud, Paris, France
| | - Jean-Yves Madec
- Université de Lyon - Anses, Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Laura Temime
- MESuRS laboratory, Conservatoire national des arts et métiers, 292 rue Saint-Martin, 75003 Paris, France
- PACRI unit, Institut Pasteur, Conservatoire national des arts et métiers, Paris, France
| | - Lulla Opatowski
- Université Paris-Saclay, UVSQ, Univ. Paris-Sud, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, F-78180 Montigny-le-Bretonneux, France
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion unit, F-75015 Paris, France
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Ashokan A, Hanson J, Aung NM, Kyi MM, Taylor SL, Choo JM, Flynn E, Mobegi F, Warner MS, Wesselingh SL, Boyd MA, Rogers GB. Investigating potential transmission of antimicrobial resistance in an open-plan hospital ward: a cross-sectional metagenomic study of resistome dispersion in a lower middle-income setting. Antimicrob Resist Infect Control 2021; 10:56. [PMID: 33736699 PMCID: PMC7977308 DOI: 10.1186/s13756-021-00915-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 02/26/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) represents a profound global health threat. Reducing AMR spread requires the identification of transmission pathways. The extent to which hospital wards represent a venue for substantial AMR transmission in low- and middle-income countries settings is poorly understood. METHODS Rectal swabs were obtained from adult male inpatients in a "Nightingale" model general medicine ward in Yangon, Myanmar. Resistome characteristics were characterised by metagenomic sequencing. AMR gene carriage was related to inter-patient distance (representing inter-patient interaction) using distance-based linear models. Clinical predictors of AMR patterns were identified through univariate and multivariate regression. RESULTS Resistome similarity showed a weak but significant positive correlation with inter-patient distance (r = 0.12, p = 0.04). Nineteen AMR determinants contributed significantly to this relationship, including those encoding β-lactamase activity (OXA-1, NDM-7; adjusted p < 0.003), trimethoprim resistance (dfrA14, adjusted p = 0.0495), and chloramphenicol resistance (catB3, adjusted p = 0.002). Clinical traits of co-located patients carrying specific AMR genes were not random. Specifically, AMR genes that contributed to distance-resistome relationships (OXA-1, catB3, dfrA14) mapped to tuberculosis patients, who were placed together according to ward policy. In contrast, patients with sepsis were not placed together, and carried AMR genes that were not spatially significant or consistent with shared antibiotic exposure. CONCLUSIONS AMR dispersion patterns primarily reflect the placement of particular patients by their condition, rather than AMR transmission. The proportion of AMR determinants that varied with inter-patient distance was limited, suggesting that nosocomial transmission is a relatively minor contributor to population-level carriage.
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Affiliation(s)
- Anushia Ashokan
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide, SA, 5001, Australia
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Josh Hanson
- Cairns Hospital, Cairns, QLD, Australia
- Insein General Hospital, Insein, Yangon, Myanmar
| | - Ne Myo Aung
- Insein General Hospital, Insein, Yangon, Myanmar
- University of Medicine 2, Yangon, Myanmar
| | - Mar Mar Kyi
- Insein General Hospital, Insein, Yangon, Myanmar
- University of Medicine 2, Yangon, Myanmar
| | - Steven L Taylor
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide, SA, 5001, Australia
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Jocelyn M Choo
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide, SA, 5001, Australia
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Erin Flynn
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide, SA, 5001, Australia
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Fredrick Mobegi
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide, SA, 5001, Australia
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Morgyn S Warner
- Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
- South Australia (SA) Pathology, Adelaide, SA, Australia
| | - Steve L Wesselingh
- South Australia Health and Medical Research Institute, Adelaide, SA, Australia
| | - Mark A Boyd
- Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Geraint B Rogers
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide, SA, 5001, Australia.
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia.
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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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Azam M, Gaind R, Yadav G, Sharma A, Upmanyu K, Jain M, Singh R. Colistin Resistance Among Multiple Sequence Types of Klebsiella pneumoniae Is Associated With Diverse Resistance Mechanisms: A Report From India. Front Microbiol 2021; 12:609840. [PMID: 33692764 PMCID: PMC7937630 DOI: 10.3389/fmicb.2021.609840] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/22/2021] [Indexed: 12/25/2022] Open
Abstract
Background: The resistance to colistin and carbapenems in Klebsiella pneumoniae infections have been associated with increased morbidity and mortality worldwide. A retrospective observational study was conducted to determine the prevalence and molecular events contributing to colistin resistance. Methods: Clinical samples were screened for colistin resistance and underlying mechanisms were studied by PCR-based amplification and sequence analysis of genes of two-component regulatory system (phoPQ and pmrAB), regulatory transmembrane protein-coding mgrB, and mobilized colistin resistance genes (mcr-1-8). Gene expression of pmrC and pmrK was analyzed by qRT-PCR, and the genetic relationship was assessed by MLST. The putative effect of amino-acid substitutions was predicted by a combination of bioinformatics tools. Results: Of 335 Klebsiella spp. screened, 11 (3.2%) were identified as colistin-resistant (MIC range, 8 to >128 μg/ml). K. pneumoniae isolates belonged to clonal complex-11 (CC11) with sequence types (STs): 14, 16, 43, 54, 147 and 395, whereby four isolates conferred three novel STs (3986, 3987 and 3988) profiles. Sequence analysis revealed non-synonymous potentially deleterious mutations in phoP (T151A), phoQ (del87–90, del263–264, L30Q, and A351D), pmrA (G53S), pmrB (D150V, T157P, L237R, G250C, A252G, R315P, and Q331H), and mgrB (C28G) genes. The mgrB gene in three strains was disrupted by insertion sequences encoding IS1-like and IS5/IS1182 family-like transposase genes. All 11 isolates showed an elevation in the transcription level of pmrC gene. Mobilized colistin-resistance (mcr) genes were not detected. All but one of the colistin-resistant isolates was also resistant to carbapenems; β-lactamase genes blaNDM-1-like, blaOXA-48-like, and blaCTX-M-like were detected in eight, five, and nine isolates, respectively. Conclusion: All the studied colistin- and carbapenem-resistant K. pneumoniae isolates were genetically distinct, and various mechanisms of colistin resistance were detected, indicating its spontaneous emergence in this bacterial species.
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Affiliation(s)
- Mudsser Azam
- ICMR-National Institute of Pathology, New Delhi, India
| | - Rajni Gaind
- Department of Microbiology, VMMC and Safdarjung Hospital, New Delhi, India
| | - Gulshan Yadav
- ICMR-National Institute of Pathology, New Delhi, India
| | - Amit Sharma
- Department of Microbiology, VMMC and Safdarjung Hospital, New Delhi, India
| | - Kirti Upmanyu
- ICMR-National Institute of Pathology, New Delhi, India
| | - Manisha Jain
- Department of Microbiology, VMMC and Safdarjung Hospital, New Delhi, India
| | - Ruchi Singh
- ICMR-National Institute of Pathology, New Delhi, India
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Quantitative Analysis of Colistin-Resistant Escherichia coli in Retail Meat from Local Vietnamese Markets. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6678901. [PMID: 33681373 PMCID: PMC7910070 DOI: 10.1155/2021/6678901] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/01/2021] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
The spread of drug-resistant bacteria via food has contributed to the dissemination of resistant bacteria among humans. However, the status of food contamination with resistant bacteria, particularly the quantitative level of resistant bacteria in food, has not yet been well elucidated. In this study, the abundance of colistin-resistant Escherichia coli in meat samples was quantified to understand the origin of the contamination of meat available in local Vietnamese markets. Fifteen samples each of chicken and pork meat purchased from local Vietnamese markets were assessed for the presence of colistin-resistant E. coli with the mobile colistin resistance gene, mcr. The results showed that 40% (6/15) and 66% (10/15) of the pork and chicken meat samples, respectively, were contaminated with colistin-resistant E. coli. The median quantitative levels of colistin-resistant E. coli in the contaminated pork and chicken samples were 1.8 × 104 and 4.2 × 103 CFU/g, respectively. The results of phylogenetic analysis of isolates from a chicken meat sample showed that the contaminated colistin-resistant E. coli was a mix of multiple phylogenetical clones of bacteria that may have multiplied during sale. This is the first study to quantify the abundance of colistin-resistant E. coli in meat samples.
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A novel method for measuring phenotypic colistin resistance in Escherichia coli populations from chicken flocks. Appl Environ Microbiol 2021; 87:AEM.02597-20. [PMID: 33355096 PMCID: PMC8090885 DOI: 10.1128/aem.02597-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Colistin is extensively used in animal production in many low- and middle-income countries. There is a need to develop methodologies to benchmark and monitor changes in resistance among mixed commensal bacterial populations in farms. We aimed to evaluate the performance of a broth microdilution method based on culturing a pooled Escherichia coli suspension (30-50 organisms) obtained from each sample. To confirm the biological basis and sensitivity of the method, we cultured 16 combinations of one colistin-susceptible and one mcr-1 encoded colistin-resistant E. coli in the presence of 2mg/L colistin. Optical density (OD600nm) readings over time were used to generate a growth curve, and these values were adjusted to the values obtained in the absence of colistin (adjusted Area Under the Curve, AUCadj). The median limit of detection was 1 resistant in 104 susceptible colonies [1st - 3rd quartile, 102:1 -105:1]. We applied this method to 108 pooled faecal samples from 36 chicken flocks from the Mekong Delta (Vietnam), and determined the correlation between this method and the prevalence of colistin resistance in individual colonies harvested from field samples, determined by the Minimum Inhibitory Concentration. The overall prevalence of colistin resistance at sample and isolate level (estimated from the AUCadj) was 38.9% [95%CI, 29.8-48.8%] and 19.4% (SD± 26.3%), respectively. Increased colistin resistance was associated with recent (2 weeks) use of colistin (OR=3.67) and other, non-colistin antimicrobials (OR=1.84). Our method is a sensitive and affordable approach to monitor changes in colistin resistance in E. coli populations from faecal samples over time.IMPORTANCE Colistin (polymyxin E) is an antimicrobial with poor solubility in agar-based media, and therefore broth microdilution is the only available method for phenotypic resistance. However, estimating colistin resistance in mixed Escherichia coli populations is laborious since it requires individual colony isolation, identification and susceptibility testing. We developed a growth-based microdilution method suitable for pooled faecal samples. We validated the method by comparing it with individual MIC of 909 E. coli isolates; we then tested 108 pooled faecal samples from 36 healthy chicken flocks collected over their production cycle. A higher level of resistance was seen in flocks recently treated with colistin in water, although the observed generated resistance was short-lived. Our method is affordable, and may potentially be integrated into surveillance systems aiming at estimating the prevalence of resistance at colony level in flocks/herds. Furthermore, it may also be adapted to other complex biological systems, such as farms and abattoirs.
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Luu QH, Nguyen TLA, Pham TN, Vo NG, Padungtod P. Antimicrobial use in household, semi-industrialized, and industrialized pig and poultry farms in Viet Nam. Prev Vet Med 2021; 189:105292. [PMID: 33621709 DOI: 10.1016/j.prevetmed.2021.105292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 11/28/2022]
Abstract
The use and misuse of antimicrobials in livestock production contributes to increasing antimicrobial resistance (AMR). Antimicrobial use (AMU), has been identified as a problem in Viet Nam. There were many identified drivers of AMU in Viet Nam such as lack of access to veterinary services, easy access to cheap over-the-counter antimicrobials, and insufficient farm biosecurity. This study included chicken farmers (n = 540) and pig farmers (n = 540) from household, semi-industrialized, and industrialized farms in the North, Central, and South of Viet Nam. The objective of this study was to determine farmers rationale behind AMU on their farms and their usage patterns. On pig farms, 98.1% of the farmers reported use of antimicrobials in their production. On chicken farms, 87.9% reported use of antimicrobials in their production. The results of the survey showed that the three main purposes of AMU were treatment of sick animals, disease prevention, and weight gain. Treatment accounted for 81.3% in pig farming and 62.1% in chicken farming. The main reason to start antimicrobial therapy in pig and chicken production was observation of the first clinical signs of disease (73.9% of the pig farmers and 74.9% of chicken farmers). The proportion of industrial pig farms performing diagnostic tests before using antimicrobials was singnificantly (p < 0.05) higher than household farms (OR = 45.3). The proportion of chicken farmers who used diagnostic tests before using antimicrobials on semi-industrial (OR = 4.1) and industrial farms (OR = 26.7) were significantly higher compared with household farms. Through encouraging the prudent use of antimicrobials in animal husbandry we can reduce the use of antimicrobials at the primary production level and thereby lowering the risk of AMR.
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Affiliation(s)
- Quynh Huong Luu
- National Institute of Veterinary Research, No. 86, Truong Chinh road, Phuong Mai ward, Dong Da district, Ha Noi, Viet Nam.
| | - Thi Lan Anh Nguyen
- National Institute of Veterinary Research, No. 86, Truong Chinh road, Phuong Mai ward, Dong Da district, Ha Noi, Viet Nam.
| | - Thi Ngoc Pham
- National Institute of Veterinary Research, No. 86, Truong Chinh road, Phuong Mai ward, Dong Da district, Ha Noi, Viet Nam.
| | - Ngan Giang Vo
- Food and Agriculture Organization of the United Nations Country Office for Viet Nam Green One UN House Building, No. 304, Kim Ma Street, Hanoi, Viet Nam.
| | - Pawin Padungtod
- Food and Agriculture Organization of the United Nations Country Office for Viet Nam Green One UN House Building, No. 304, Kim Ma Street, Hanoi, Viet Nam.
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