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Silva A, Silva V, Dapkevicius MDLE, Azevedo M, Cordeiro R, Pereira JE, Valentão P, Falco V, Igrejas G, Caniça M, Poeta P. Unveiling Antibiotic Resistance, Clonal Diversity, and Biofilm Formation in E. coli Isolated from Healthy Swine in Portugal. Pathogens 2024; 13:305. [PMID: 38668260 PMCID: PMC11054063 DOI: 10.3390/pathogens13040305] [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: 02/26/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024] Open
Abstract
Escherichia coli, a commensal microorganism found in the gastrointestinal tract of human and animal hosts, plays a central role in agriculture and public health. Global demand for animal products has promoted increased pig farming, leading to growing concerns about the prevalence of antibiotic-resistant E. coli strains in swine populations. It should be noted that a significant portion of antibiotics deployed in swine management belong to the critically important antibiotics (CIA) class, which should be reserved for human therapeutic applications. This study aimed to characterize the prevalence of antibiotic resistance, genetic diversity, virulence characteristics, and biofilm formation of E. coli strains in healthy pigs from various farms across central Portugal. Our study revealed high levels of antibiotic resistance, with resistance to tetracycline, ampicillin, tobramycin, and trimethoprim-sulfamethoxazole. Multidrug resistance is widespread, with some strains resistant to seven different antibiotics. The ampC gene, responsible for broad-spectrum resistance to cephalosporins and ampicillin, was widespread, as were genes associated with resistance to sulfonamide and beta-lactam antibiotics. The presence of high-risk clones, such as ST10, ST101, and ST48, are a concern due to their increased virulence and multidrug resistance profiles. Regarding biofilm formation, it was observed that biofilm-forming capacity varied significantly across different compartments within pig farming environments. In conclusion, our study highlights the urgent need for surveillance and implementation of antibiotic management measures in the swine sector. These measures are essential to protect public health, ensure animal welfare, and support the swine industry in the face of the growing global demand for animal products.
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Affiliation(s)
- Adriana Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Maria de Lurdes Enes Dapkevicius
- IITAA—Institute of Agricultural and Environmental Research and Technology, University of the Azores (UAc), 9700-042 Angra do Heroísmo, Portugal
| | - Mónica Azevedo
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4049-021 Porto, Portugal; (M.A.)
- CIISA—Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR/HAI), Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
| | - Rui Cordeiro
- Intergados, SA, Av. de Olivença, S/N, 2870-108 Montijo, Portugal;
| | - José Eduardo Pereira
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
| | - Patrícia Valentão
- Laboratory for Green Chemistry (LAQV) of the Network of Chemistry and Technology (REQUIMTE), Universidade do Porto, 2829-516 Caparica, Portugal; (P.V.)
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, R. Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
| | - Virgílio Falco
- Laboratory for Green Chemistry (LAQV) of the Network of Chemistry and Technology (REQUIMTE), Universidade do Porto, 2829-516 Caparica, Portugal; (P.V.)
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Universidade of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Manuela Caniça
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4049-021 Porto, Portugal; (M.A.)
- CIISA—Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR/HAI), Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
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Silva A, Silva V, Pereira JE, Maltez L, Igrejas G, Valentão P, Falco V, Poeta P. Antimicrobial Resistance and Clonal Lineages of Escherichia coli from Food-Producing Animals. Antibiotics (Basel) 2023; 12:1061. [PMID: 37370379 DOI: 10.3390/antibiotics12061061] [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: 04/30/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Escherichia coli are one of the most important pathogenic bacteria readily found in the livestock and widely studied as an indicator that carries drug-resistant genes between humans, animals, and the environment. The use of antimicrobials in the food chain, particularly in food-producing animals, is recognized as a significant contributor to the development and spread of antimicrobial resistance (AMR) and resistance genes can be transferred from the farm through the food-chain. The objective of this review is to highlight the background of the antimicrobials use in food-producing animals, more specifically, to study clonal lineages and the resistance profiles observed in E. coli, as well as in extended spectrum beta-lactamases (ESBL) producing E. coli, in a set of food-production animals with greater relevance in food consumption, such as pigs, poultry, cattle, fish farming and rabbits. Regarding the prevalence of ESBL-producing E. coli among farm animals, high-to-moderate prevalence was observed, and the highest resistance rates to tetracycline and ampicillin was detected in different farms in all geographic regions. Worldwide pandemic clones and high-risk zoonotic E. coli clones have been identified in most food-producing animals, and some of these clones are already disseminated in different niches, such as the environment and humans. A better understanding of the epidemiology of E. coli and ESBL-producing E. coli in livestock is urgently needed. Animal production is one of the major causes of the antibiotic resistance problem worldwide and a One Health approach is needed.
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Affiliation(s)
- Adriana Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Lisbon, Portugal
| | - Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Lisbon, Portugal
| | - José Eduardo Pereira
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
| | - Luís Maltez
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Lisbon, Portugal
| | - Patrícia Valentão
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, R. Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
| | - Virgílio Falco
- Chemistry Research Centre (CQ-VR), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
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Martins JCL, Pintor-Cora A, Alegría Á, Santos JA, Herrera-Arias F. Characterization of ESBL-producing Escherichia spp. and report of an mcr-1 colistin-resistance Escherichia fergusonni strain from minced meat in Pamplona, Colombia. Int J Food Microbiol 2023; 394:110168. [PMID: 36931145 DOI: 10.1016/j.ijfoodmicro.2023.110168] [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: 10/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
Abstract
Foods of animal origin are increasingly considered a source of extended spectrum β-lactamase (ESBL) producing bacteria which can disseminate throughout the food chain and become a health concern for humans. This work aimed to evaluate the occurrence of ESBL-producing Escherichia coli in 100 retail minced meat samples taken in markets in Pamplona, Colombia. A total of 19 ESBL-producing isolates were obtained, 18 identified as E. coli and one as E. fergusonii. Fifteen isolates (78.9 %) carried blaCTX-M and blaTEM genes, one (5.2 %) blaSHV and blaTEM genes, one isolate (5.2 %) carried blaCTX-M and one (5.2 %) blaSHV alone. The majority of CTX-M-positive E. coli isolates carried the blaCTX-M-15 gene (13 isolates), being the blaCTX-M-9, blaCTX-M-2, and blaCTX-M-8 (one isolate each) also detected. Two SHV-positive isolates presented the blaSHV-5 and blaSHV-12 allele. The isolate identified as E. fergusonii was positive for blaCTX-M-65 gene and mcr-1 gene. Sixteen isolates (84.2 %) belonged to phylogroups A and B1 and grouped together in the phylogenetic tree obtained by MLST; phylogroups E and F were also detected. Transfer of ESBL resistance was demonstrated for the E. fergusonii isolate. Whole genome sequencing of this isolate revealed the presence of plasmids carrying additional resistance genes. This investigation showed the high prevalence of ESBL-producing E. coli in retail samples of minced meat. Also, the isolation of a strain of E. fergusonii is an additional concern, as some resistance genes are located in mobile elements, which can be transmitted to other bacteria. These evidences support the increasing public health concern considering the spreading of resistance genes through the food chain.
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Affiliation(s)
- Joana C L Martins
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain
| | - Alberto Pintor-Cora
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain.
| | - Ángel Alegría
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain.
| | - Jesús A Santos
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain.
| | - Fanny Herrera-Arias
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain; Departamento de Microbiología, Facultad de Ciencias Básicas, Universidad de Pamplona, Pamplona, Colombia.
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Evaluation of Antimicrobial Resistance of Different Phylogroups of Escherichia coli Isolates from Feces of Breeding and Laying Hens. Antibiotics (Basel) 2022; 12:antibiotics12010020. [PMID: 36671221 PMCID: PMC9854720 DOI: 10.3390/antibiotics12010020] [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: 10/27/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
Animal and food sources are seen as a potential transmission pathway of multi-drug resistance (MDR) micro-organisms to humans. Escherichia. coli is frequently used as an indicator of fecal contamination in the food industry and known as a reservoir of antimicrobial resistance genes (ARGs). Microbial contamination as a major outcome for the poultry and egg industry and is a serious public health problem. In the present study we performed the quantification of β-glucoronidase positive E. coli in 60 fecal samples of breeding and laying hens collected in Portugal in 2019. Phylogenetic and pathotypic characterization, antimicrobial susceptibility, and detection of resistant extended-spectrum β-lactamase (ESBL) genes were assessed. The phylogenetic and pathogenic characterization and detection of ESBL genes were assessed by real-time PCR and antimicrobial susceptibility was evaluated using the disk diffusion method. Overall, E. coli quantification was 6.03 log CFU/g in breeding hens and 6.02 log CFU/g in laying hens. The most frequent phylogroups were B1. None of the isolates was classified as diarrheagenic E. coli (DEC). In total, 57% of the isolates showed MDR and 3.8% were positive for ESBL. Our study highlights that consumers may be exposed to MDR E. coli, presenting a major hazard to food safety and a risk to public health.
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Li C, Chen X, Ju Z, Li C, Xu Y, Ding J, Wang Y, Ma P, Gu K, Lei C, Tang Y, Wang H. Comparative Analysis of Phylogenetic Relationships and Virulence Factor Characteristics between Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Derived from Clinical Sites and Chicken Farms. Microbiol Spectr 2022; 10:e0255722. [PMID: 36374015 PMCID: PMC9769871 DOI: 10.1128/spectrum.02557-22] [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: 07/15/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance in bacteria is the most urgent global threat to public health, with extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) being one of the most documented examples. Nonetheless, the ESBL-E. coli transmission relationship among clinical sites and chicken farms remains unclear. Here, 408 ESBL-E. coli strains were isolated from hospitals and chicken farms in Sichuan Province and Yunnan Province in 2021. We detected blaCTX-M genes in 337 (82.62%) ESBL-E. coli strains. Although the isolation rate, prevalent sequence type (ST) subtypes, and blaCTX-M gene subtypes of ESBL-E. coli varied based on regions and sources, a few strains of CTX-ESBL-E. coli derived from clinical sites and chicken farms in Sichuan Province displayed high genetic similarity. This indicates a risk of ESBL-E. coli transmission from chickens to humans. Moreover, we found that the high-risk clonal strains ST131 and ST1193 primarily carried blaCTX-M-27. This indicates that drug-resistant E. coli from animal and human sources should be monitored. As well, the overuse of β-lactam antibiotics should be avoided in poultry farms to ensure public health and build an effective regulatory mechanism of "farm to fork" under a One Health perspective. IMPORTANCE Bacterial drug resistance has become one of the most significant threats to human health worldwide, especially for extended-spectrum β-lactamase-producing E. coli (ESBL-E. coli). Timely and accurate epidemiological surveys can provide scientific guidance for the adoption of treatments in different regions and also reduce the formation of drug-resistant bacteria. Our study showed that the subtypes of ESBL-E. coli strains prevalent in different provinces are somewhat different, so it is necessary to individualize treatment regimens in different regions, and it is especially important to limit and reduce antibiotic use in poultry farming since chicken-derived ESBL-E. coli serves as an important reservoir of drug resistance genes and has the potential to spread to humans, thus posing a threat to human health. The use of antibiotics in poultry farming should be particularly limited and reduced.
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Affiliation(s)
- Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xuan Chen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Zijing Ju
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Cui Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Ying Xu
- The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jiawei Ding
- Clinical Laboratory Department, Yan’an Hospital Affiliated with Kunming Medical University, Kunming, Yunnan, China
| | - Yuting Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Peng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Kui Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yizhi Tang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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Al-Mustapha AI, Alada SA, Raufu IA, Lawal AN, Eskola K, Brouwer MS, Adetunji V, Heikinheimo A. Co-occurrence of antibiotic and disinfectant resistance genes in extensively drug-resistant Escherichia coli isolated from broilers in Ilorin, North Central Nigeria. J Glob Antimicrob Resist 2022; 31:337-344. [PMID: 36375754 DOI: 10.1016/j.jgar.2022.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The occurrence of multidrug-resistant (MDR) bacteria in poultry poses the public health threat of zoonotic transmission to humans. Hence, this study assessed the occurrence of drug-resistant Escherichia coli in broilers in the largest live bird market in Kwara State, Nigeria in December 2020. METHODS Presumptive E. coli isolates were isolated using the European Union Reference Laboratory guideline of 2017 and confirmed via matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Broth microdilution was performed on confirmed E. coli isolates to determine the minimum inhibitory concentration. Five extensively drug-resistant (XDR) isolates were selected for Illumina whole genome sequencing to predict the resistome, phylotype, sequence type, serotype, and diversity of mobile genetic elements in these isolates. RESULTS Of the 181 broiler caecal samples, 73 E. coli isolates were obtained, of which 67 (82.0%) and 37 (50.6%) were determined as MDR (resistant to at least three classes of antibiotics) and XDR (resistant to at least five classes of antibiotics), respectively. Whole genome sequencing revealed diverse sequence types, phylogroups, and serotypes (ST165/B1 - O80:H19, ST115/A - Unknown: H7, ST901/B1 - O109:H4, ST4087/F - O117:H42, and ST8324/A - O127:H42). The XDR E. coli isolates encoded resistance to fluoroquinolones, fosfomycin, sulfamethoxazole, ampicillin and cephalosporins, trimethoprim, aminoglycosides, chloramphenicol, tetracycline, and macrolides. Mutations in the gyrA gene conferring resistance to fluoroquinolones were also detected. There was a positive correlation between phenotypic resistance patterns and the antibiotic resistance genes that were detected in the sequenced isolates. The XDR isolates also harbored two disinfectant resistance genes (qacE and sitABCD) that conferred resistance to hydrogen peroxide and quaternary ammonium compounds, respectively. The genome of the XDR isolates harbored several mobile genetic elements and virulence-associated genes, which were conserved in all sequenced XDR isolates. CONCLUSIONS This is the first report of co-carriage of antibiotic resistance genes and disinfectant resistance genes in E. coli isolated from broilers in Ilorin, Nigeria. Our findings suggest that poultry are potential carriers of clonally diverse, pathogenic, MDR/XDR E. coli, which may have detrimental zoonotic potentials on human health.
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Affiliation(s)
- Ahmad Ibrahim Al-Mustapha
- Department of Veterinary Services, Kwara State Ministry of Agriculture and Rural Development, Ilorin, Kwara State, Nigeria; Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Ibadan, Oyo State, Nigeria; Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland.
| | - Shafi Abdullah Alada
- Veterinary Microbiology Laboratory, University of Ilorin Veterinary Teaching Hospital, Ilorin, Kwara State, Nigeria
| | - Ibrahim Adisa Raufu
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Ilorin, Kwara State, Nigeria
| | - Adedeji Nurudeen Lawal
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Ilorin, Kwara State, Nigeria; Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Katarina Eskola
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Michael Sm Brouwer
- Department of Bacteriology and Host-Pathogen Reaction, Wageningen University and Research, Lelystad, The Netherlands
| | - Victoria Adetunji
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Ibadan, Oyo State, Nigeria
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland; Finnish Food Authority, Seinäjoki, Finland
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Enciso-Martínez Y, González-Aguilar GA, Martínez-Téllez MA, González-Pérez CJ, Valencia-Rivera DE, Barrios-Villa E, Ayala-Zavala JF. Relevance of tracking the diversity of Escherichia coli pathotypes to reinforce food safety. Int J Food Microbiol 2022; 374:109736. [DOI: 10.1016/j.ijfoodmicro.2022.109736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/21/2022]
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Khalifeh OM, Obaidat MM. Urinary tract virulence genes in extended-spectrum beta-lactamase E. coli from dairy cows, beef cattle, and small ruminants. Acta Trop 2022; 234:106611. [PMID: 35850234 DOI: 10.1016/j.actatropica.2022.106611] [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: 06/02/2022] [Revised: 07/03/2022] [Accepted: 07/14/2022] [Indexed: 11/01/2022]
Abstract
Extended-spectrum β-lactamase Escherichia coli is an important cause of urinary tract infections in humans. ESBL producers E. coli were reported in food-producing animals, but no previous study reported the virulence potential of these isolates. Thus, this study determined the virulence potential of ESBL producers E. coli isolates from 518 beef feces, 610 dairy cow feces, 305 dairy cow milk, 503 sheep milk and 445 goat milk samples. A total of 278 isolates; specifically, 130 from beef feces, 39 from the cow's feces, 42 from cow's milk, 44 from sheep milk and 23 from goats' milk were isolated and then tested for 14 virulence genes by polymerase chain reaction. After that, the correlation of virulence genes presence among the isolates was determined statistically. Overall, 97% of the isolates carried fimH, 39% carried iroN E. coli and 32% carried papC. The kpsMT K1, cnf1, papAH, papG allele II & III, papG allele II, and kpsMT II were carried by 6 to 23% of the isolates, while less than 6% of the isolates carried papG allele III, papG allele I, Univcnf, iutA and hlyA. About 68.2% of the isolates carried two or more virulence genes and 41.8% carried three or more. Moreover, the isolates had 71 different profiles of virulence genes, where the most common profiles were fimH alone (86 isolate), fimH + iroN E. coli (35 isolate), fimH + papC (20 isolate), and fimH + papC + iroN E. coli (13 isolate). The adhesion, capsule synthesis and toxins secretion genes were significantly associated (p ˂ 0.01) with each other. These results call for awareness about the risk of food animals as reservoirs of ESBL uropathogenic E. coli that would threaten public health and limits the treatment options for urinary tract infections.
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Affiliation(s)
- Omar Mohammad Khalifeh
- Faculty of Medicine, Jordan University of Science and Technology, Ar-Ramtha, Irbid, Jordan
| | - Mohammad M Obaidat
- Faculty of Veterinary Medicine, Jordan University of Science and Technology, Ar-Ramtha, Irbid 22110, Jordan.
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Li Y, Tang M, Dai X, Zhou Y, Zhang Z, Qiu Y, Li C, Zhang L. Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China. Infect Drug Resist 2021; 14:4427-4440. [PMID: 34737583 PMCID: PMC8559237 DOI: 10.2147/idr.s330787] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/24/2021] [Indexed: 12/17/2022] Open
Abstract
Purpose Three NDM-5-producing Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae, and Citrobacter braakii, one each) were isolated during a screening study for the presence of carbapenemase-producing Enterobacteriaceae (CPE) strains in urban rivers in China. The aim of the present study was to characterize these NDM-5-producing isolates by using whole-genome analysis. Methods In vitro susceptibility testing was performed using the broth microdilution method. Conjugation assay was carried out to investigate the transferability of blaNDM-5-harboring plasmids. Whole-genome sequencing was performed using an Illumina HiSeq combined with the PacBio RSII system. The genetic characteristics of the blaNDM-5-harboring plasmids were analyzed. Antimicrobial resistance genes and virulence genes were identified from the genome sequences. Phylogenetic analysis was performed based on core genome. Results Antimicrobial susceptibility testing showed that all three isolates were resistant to carbapenems, cephalosporins, quinolones, and aminoglycosides, and susceptible to colistin. Whole-genome sequencing showed that each isolate carried multiple antibiotic resistance genes mediating multidrug resistance, and harbored numerous virulence genes, some of which were located on plasmids. In these isolates, blaNDM-5 was carried by an IncX3 plasmid in K. pneumoniae and C. braakii, and on an IncR/IncX1 plasmid in E. coli. Conjugation experiments showed that these blaNDM-5-haboring plasmids were successfully transferred to E. coli J53. Phylogenetic analysis revealed that E. coli SCLZR49 was present in a cluster with isolates of different origin, K. pneumoniae SCLZR50 was mainly clustered with clinical isolates, and C. braakii SCLZR53 had closely genetic relationship with environmental isolates. Conclusion This study revealed contamination of the urban river ecosystems by clinically significant carbapenemase gene blaNDM-5, raising the possibility of plasmid transmission into the environmental from humans and highlighting the need for a constant surveillance of CPE in the environment under the “One-Health” perspective.
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Affiliation(s)
- Ying Li
- Department of Immunology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Immunological Technology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Min Tang
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Xiaoyi Dai
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Pathogen Biology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Yingshun Zhou
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Pathogen Biology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Zhikun Zhang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Pathogen Biology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Yichuan Qiu
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Pathogen Biology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Chengwen Li
- Department of Immunology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Immunological Technology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Luhua Zhang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Pathogen Biology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
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Loayza-Villa F, Torres A, Zhang L, Trueba G. Removal of antimicrobial prophylaxis and its effect on swine carriage of antimicrobial-resistant coliforms. Sci Prog 2021; 104:368504211050279. [PMID: 34872396 PMCID: PMC10466387 DOI: 10.1177/00368504211050279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The use of antimicrobials in the food animal industry has caused an increased prevalence of antimicrobial-resistant bacteria and antimicrobial resistance genes, which can be transferred to the microbiota of humans through the food chain or the environment. To reduce the development and spread of antimicrobial resistance, restrictions on antimicrobial use in food animals have been implemented in different countries. We investigated the impact of an antimicrobial restriction intervention during two generations of pigs. Fecal samples were collected in five growth phases. The frequency of antimicrobial-resistant coliforms and antimicrobial-resistant bacteria or antimicrobial resistance genes was analyzed. No differences in the richness or abundance of antimicrobial-resistant coliforms or antimicrobial resistance genes were found when animals fed with or without prophylactic antimicrobials were compared. Withholding antimicrobial supplementation did not negatively affect weight gain in pigs. Withdrawal of prophylactic antimicrobial consumption during two generations of pigs was not enough to reduce the prevalence of antimicrobial resistance genes, as measured by richness and abundance markers. This study indicates that the fitness costs associated with bacterial carriage of some antimicrobial resistance genes are low.
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Affiliation(s)
- Fernanda Loayza-Villa
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Alejandro Torres
- Escuela de Veterinaria, Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Lixin Zhang
- Department of Microbiology and Molecular Genetics, Michigan State University, Michigan, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
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Song J, Kim J, Oh SS, Shin J. Multidrug-Resistant Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Vegetable Farm Soil in South Korea. Microb Drug Resist 2021; 27:1489-1494. [PMID: 33926223 DOI: 10.1089/mdr.2020.0542] [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] [Indexed: 12/20/2022] Open
Abstract
The populations of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) have increasingly disseminated in humans, animals, and the environment. This study aimed to determine the prevalence, antimicrobial susceptibilities, and molecular characteristics of ESBL-EC isolates obtained from vegetable farm soil. In total, 200 soil samples were collected from vegetable farms in Incheon, South Korea, between 2018 and 2019 and cultured on MacConkey screening plates supplemented with 2 μg/mL cefotaxime. Cefotaxime-resistant ESBL-EC isolates were recovered from 4.0% (8/200) of the soil samples. All eight isolates were nonsusceptible to ampicillin, piperacillin, cefazolin, cefotaxime, and cefepime and harbored blaCTX-M-type ESBL genes, including blaCTX-M-15 (50.0%), blaCTX-M-55 (25.0%), and blaCTX-M-14 (25.0%). Phylogenetic analysis showed that the B1 lineage was predominant (75.0%), followed by A (12.5%) and B2 (12.5%) lineages. Multilocus sequence typing revealed eight different E. coli sequence types (STs), including ST10, ST73, ST155, ST847, ST2521, ST3285, ST5173, and ST9479. Notably, ST10 and ST73 belong to the global extraintestinal pathogenic E. coli lineages. Our findings demonstrated that the farm soil environment may serve as a reservoir of human-associated multidrug-resistant ESBL-producing pathogens.
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Affiliation(s)
- Jihyun Song
- Department of Microbiology, Inha University College of Medicine, Incheon, South Korea
| | - Junghee Kim
- Incheon Research Institute of Public Health and Environment, Incheon, South Korea
| | - Sung-Suck Oh
- Incheon Research Institute of Public Health and Environment, Incheon, South Korea
| | - Jinwook Shin
- Department of Microbiology, Inha University College of Medicine, Incheon, South Korea
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Genetic Features of Extended-Spectrum β-Lactamase-Producing Escherichia coli from Poultry in Mayabeque Province, Cuba. Antibiotics (Basel) 2021; 10:antibiotics10020107. [PMID: 33499392 PMCID: PMC7910960 DOI: 10.3390/antibiotics10020107] [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: 12/04/2020] [Revised: 01/13/2021] [Accepted: 01/17/2021] [Indexed: 02/07/2023] Open
Abstract
A total of 434 poultry cloacal samples were collected from seven different farms in different years (2013–2015) in the Cuban province of Mayabeque and analyzed for the presence of third-generation cephalosporin-resistant Escherichia coli (3GC-R-Ec). Sixty-two 3GC-R-Ec isolates were recovered in total from the farms, with detection rates of 2.9% in 2013, 10.3% in 2014, and 28.7% in 2015. Characterization of 32 3GC-R-Ec isolates revealed the presence of the extended-spectrum β-lactamase (ESBL) genes blaCTX-M-1 (n = 27), blaCTX-M-15 (n = 4), and blaCTX-M-1 together with blaLAP-2 (n = 1). The isolates also contained different proportions of genes conferring decreased susceptibility to sulfonamides (sul1, sul2, sul3), trimethoprim (dfrA1, dfrA7, dfrA12, dfrA14, dfrA17), tetracyclines (tet(A), tet(B)), aminoglycosides (aac(6′)-Ib-cr, strA, strB), chloramphenicol (cmlA1, floR), macrolides (mph(A), mph(D)), and quinolones (qnrS, qnrB, aac(6′)-Ib-cr) as well as mutations in the fluoroquinolone-resistance determining regions of GyrA (S83L, D87N, D87Y) and ParC (S80I, E84G). The isolates belonged to 23 different sequence types and to phylogroups A (n = 25), B1 (n = 5), and D (n = 2), and they contained plasmid-associated incompatibility groups FII, X1, HI1, HI2, N, FIA, and FIB. These findings reveal a genetically diverse population of multiresistant ESBL-producing E. coli in poultry farms in Cuba, which suggests multiple sources of contamination and the acquisition of antibiotic resistance genes.
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