1
|
Xiao J, Cheng Y, Zhang W, Lu Q, Guo Y, Hu Q, Wen G, Shao H, Luo Q, Zhang T. Genetic characteristics, antimicrobial susceptibility, and virulence genes distribution of Campylobacter isolated from local dual-purpose chickens in central China. Front Cell Infect Microbiol 2023; 13:1236777. [PMID: 37743858 PMCID: PMC10517862 DOI: 10.3389/fcimb.2023.1236777] [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: 06/08/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023] Open
Abstract
Food-borne antibiotic-resistant Campylobacter poses a serious threat to public health. To understand the prevalence and genetic characteristics of Campylobacter in Chinese local dual-purpose (meat and eggs) chickens, the genomes of 30 Campylobacter isolates, including 13 C. jejuni and 17 C. coli from Jianghan-chickens in central China, were sequenced and tested for antibiotic susceptibility. The results showed that CC-354 and CC-828 were the dominant clonal complexes of C. jejuni and C. coli, respectively, and a phylogenetic analysis showed that three unclassified multilocus sequence types of C. coli were more closely genetically related to C. jejuni than to other C. coli in this study. Of the six antibiotics tested, the highest resistance rates were to ciprofloxacin and tetracycline (100%), followed by lincomycin (63.3%), erythromycin (30.0%), amikacin (26.7%), and cefotaxime (20.0%). The antibiotic resistance rate of C. coli was higher than that of C. jejuni. The GyrA T86I mutation and 15 acquired resistance genes were detected with whole-genome sequencing (WGS). Among those, the GyrA T86I mutation and tet(O) were most prevalent (both 96.7%), followed by the blaOXA-type gene (90.0%), ant(6)-Ia (26.7%), aac(6')-aph(3'') (23.3%), erm(B) (13.3%), and other genes (3.3%). The ciprofloxacin and tetracycline resistance phenotypes correlated strongly with the GyrA T86I mutation and tet(O)/tet(L), respectively, but for other antibiotics, the correlation between genes and resistance phenotypes were weak, indicating that there may be resistance mechanisms other than the resistance genes detected in this study. Virulence gene analysis showed that several genes related to adhesion, colonization, and invasion (including cadF, porA, ciaB, and jlpA) and cytolethal distending toxin (cdtABC) were only present in C. jejuni. Overall, this study extends our knowledge of the epidemiology and antibiotic resistance of Campylobacter in local Chinese dual-purpose chickens.
Collapse
Affiliation(s)
- Jia Xiao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yiluo Cheng
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wenting Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qin Lu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yunqing Guo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qiao Hu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Guoyuan Wen
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Huabin Shao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qingping Luo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Hubei Hongshan Laboratory, Wuhan, China
| | - Tengfei Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| |
Collapse
|
2
|
Liao X, Deng R, Warriner K, Ding T. Antibiotic resistance mechanism and diagnosis of common foodborne pathogens based on genotypic and phenotypic biomarkers. Compr Rev Food Sci Food Saf 2023; 22:3212-3253. [PMID: 37222539 DOI: 10.1111/1541-4337.13181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/22/2023] [Accepted: 05/06/2023] [Indexed: 05/25/2023]
Abstract
The emergence of antibiotic-resistant bacteria due to the overuse or inappropriate use of antibiotics has become a significant public health concern. The agri-food chain, which serves as a vital link between the environment, food, and human, contributes to the large-scale dissemination of antibiotic resistance, posing a concern to both food safety and human health. Identification and evaluation of antibiotic resistance of foodborne bacteria is a crucial priority to avoid antibiotic abuse and ensure food safety. However, the conventional approach for detecting antibiotic resistance heavily relies on culture-based methods, which are laborious and time-consuming. Therefore, there is an urgent need to develop accurate and rapid tools for diagnosing antibiotic resistance in foodborne pathogens. This review aims to provide an overview of the mechanisms of antibiotic resistance at both phenotypic and genetic levels, with a focus on identifying potential biomarkers for diagnosing antibiotic resistance in foodborne pathogens. Furthermore, an overview of advances in the strategies based on the potential biomarkers (antibiotic resistance genes, antibiotic resistance-associated mutations, antibiotic resistance phenotypes) for antibiotic resistance analysis of foodborne pathogens is systematically exhibited. This work aims to provide guidance for the advancement of efficient and accurate diagnostic techniques for antibiotic resistance analysis in the food industry.
Collapse
Affiliation(s)
- Xinyu Liao
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- School of Mechanical and Energy Engineering, NingboTech University, Ningbo, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, China
| | - Keith Warriner
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Tian Ding
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
| |
Collapse
|
3
|
Takawira FT, Pitout JDD, Thilliez G, Mashe T, Gutierrez AV, Kingsley RA, Peirano G, Matheu J, Midzi SM, Mwamakamba LW, Gally DL, Tarupiwa A, Mukavhi L, Ehlers MM, Mtapuri-Zinyowera S, Kock MM. Faecal carriage of ESBL producing and colistin resistant Escherichia coli in avian species over a 2-year period (2017-2019) in Zimbabwe. Front Cell Infect Microbiol 2022; 12:1035145. [PMID: 36619741 PMCID: PMC9816332 DOI: 10.3389/fcimb.2022.1035145] [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: 09/02/2022] [Accepted: 10/31/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Extended spectrum beta-lactamase (ESBL) producing Escherichia coli have become widespread among food producing animals. These strains serve as a reservoir of antibiotic resistance genes (ARGs) and act as a possible source of infection to humans as transmission can occur by direct or indirect contact. Methods This study investigated the faecal carriage of ESBL producing and colistin resistant E. coli in poultry over a 2-year period (2017-2019) from Zimbabwe. A total of 21 ESBL positive isolates from poultry cloacal specimens were selected for whole genome sequencing from animal E. coli isolates bio-banked at the National Microbiology Reference laboratory using phenotypic susceptibility testing results from the National Escherichia coli Surveillance Program to provide representation of different geographical regions and year of isolation. Cloacal swabs were collected from 3000 broiler live birds from farm 1 and from farm 2, 40 backyard chickens and 10 ducks were sampled. Antimicrobial susceptibility and ESBL testing were performed as per Clinical Laboratory Standards Institute guidelines. Whole genome sequencing of ESBL producing isolates was used to determine sequence types (STs), ARGs, and phylogroups. Results Twenty-one of the included E. coli isolates were confirmed as ESBL producers. Three defined sequence type clonal complexes (CCs) were identified (ST10CC, ST155CC and ST23CC), with ST10CC associated with the most antibiotic resistant profile. The ESBL phenotype was linked to the presence of either cefotaximase-Munich-14 (CTX-M-14) or CTX-M-79. Plasmid mediated quinolone resistant determinants identified were qnrB19 and qnrS1 and one ST10CC isolate from farm 1 broiler chickens harbored a mobile colistin resistance gene (mcr-1). Phylogenetic groups most identified were B1, A and unknown. Discussions The avian ESBL producing E. coli belonged to a diverse group of strains. The detection of several ARGs highlights the importance of implementing enhanced control measures to limit the spread in animals, environment, and humans. This is the first report of mcr-1 in Zimbabwe, which further underscores the importance of the One Health approach to control the spread and development of AMR.
Collapse
Affiliation(s)
- Faustinos Tatenda Takawira
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa,National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Johann D. D. Pitout
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa,Department of Microbiology, Alberta Precision Laboratories, Department Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Tapfumanei Mashe
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa,National Microbiology Reference Laboratory, Harare, Zimbabwe
| | | | | | - Gisele Peirano
- Department of Microbiology, Alberta Precision Laboratories, Department Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jorge Matheu
- World Health Organization (WHO), Geneva, Switzerland
| | | | | | - David L. Gally
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Andrew Tarupiwa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Leckson Mukavhi
- University of Zimbabwe College of Health Sciences, Health Professions Education, Harare, Zimbabwe
| | - Marthie M. Ehlers
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa,Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa
| | | | - Marleen M. Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa,Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa,*Correspondence: Marleen M. Kock,
| |
Collapse
|
4
|
High Genetic Diversity and Antimicrobial Resistance in Escherichia coli Highlight Arapaima gigas (Pisces: Arapaimidae) as a Reservoir of Quinolone-Resistant Strains in Brazilian Amazon Rivers. Microorganisms 2022; 10:microorganisms10040808. [PMID: 35456858 PMCID: PMC9030826 DOI: 10.3390/microorganisms10040808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/03/2022] [Accepted: 03/06/2022] [Indexed: 12/10/2022] Open
Abstract
The increasing prevalence of multi-drug resistant (MDR) Escherichia coli in distinct ecological niches, comprising water sources and food-producing animals, such as fish species, has been widely reported. In the present study, quinolone-resistant E. coli isolates from Arapirama gigas, a major fish species in the Brazilian Amazon rivers and fish farms, were characterized regarding their antimicrobial susceptibility, virulence, and genetic diversity. A total of forty (40) specimens of A. gigas, including 20 farmed and 20 wild fish, were included. Thirty-four quinolone-resistant E. coli isolates were phenotypically tested by broth microdilution, while resistance and virulence genes were detected by PCR. Molecular epidemiology and genetic relatedness were analyzed by MLST and PFGE typing. The majority of isolates were classified as MDR and detected harboring blaCTX-M, qnrA and qnrB genes. Enterotoxigenic E. coli pathotype (ETEC) isolates were presented in low prevalence among farmed animals. MLST and PFGE genotyping revealed a wide genetic background, including the detection of internationally spread clones. The obtained data point out A. gigas as a reservoir in Brazilian Amazon aquatic ecosystems and warns of the interference of AMR strains in wildlife and environmental matrices.
Collapse
|
5
|
Thomson NM, Gilroy R, Getino M, Foster-Nyarko E, van Vliet AH, La Ragione RM, Pallen MJ. Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens. PeerJ 2022; 10:e12935. [PMID: 35251780 PMCID: PMC8896058 DOI: 10.7717/peerj.12935] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/23/2022] [Indexed: 01/11/2023] Open
Abstract
The genus Escherichia has been extensively studied and it is known to encompass a range of commensal and pathogenic bacteria that primarily inhabit the gastrointestinal tracts of warm-blooded vertebrates. However, the presence of E. coli as a model organism and potential pathogen has diverted attention away from commensal strains and other species in the genus. To investigate the diversity of Escherichia in healthy chickens, we collected fecal samples from antibiotic-free Lohmann Brown layer hens and determined the genome sequences of 100 isolates, 81 of which were indistinguishable at the HC0 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing scheme. Despite initial selection on CHROMagar Orientation medium, which is considered selective for E. coli, in silico phylotyping and core genome single nucleotide polymorphism analysis revealed the presence of at least one representative of all major clades of Escherichia, except for E. albertii, Shigella, and E. coli phylogroup B2 and cryptic clade I. The most frequent phylogenomic groups were E. coli phylogroups A and B1 and E. ruysiae (clades III and IV). We compiled a collection of reference strains isolated from avian sources (predominantly chicken), representing every Escherichia phylogroup and species, and used it to confirm the phylogeny and diversity of our isolates. Overall, the isolates carried low numbers of the virulence and antibiotic resistance genes typically seen in avian pathogenic E. coli. Notably, the clades not recovered are ones that have been most strongly associated with virulence by other studies.
Collapse
Affiliation(s)
| | - Rachel Gilroy
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom,Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom,Department of Infection Biology, London School of Hygiene & Tropical Medicine, University of London, London, United Kingdom
| | - Arnoud H.M. van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Roberto M. La Ragione
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom,Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom,Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
| |
Collapse
|
6
|
Peng Z, Maciel-Guerra A, Baker M, Zhang X, Hu Y, Wang W, Rong J, Zhang J, Xue N, Barrow P, Renney D, Stekel D, Williams P, Liu L, Chen J, Li F, Dottorini T. Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming. PLoS Comput Biol 2022; 18:e1010018. [PMID: 35333870 PMCID: PMC8986120 DOI: 10.1371/journal.pcbi.1010018] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/06/2022] [Accepted: 03/14/2022] [Indexed: 01/26/2023] Open
Abstract
Anthropogenic environments such as those created by intensive farming of livestock, have been proposed to provide ideal selection pressure for the emergence of antimicrobial-resistant Escherichia coli bacteria and antimicrobial resistance genes (ARGs) and spread to humans. Here, we performed a longitudinal study in a large-scale commercial poultry farm in China, collecting E. coli isolates from both farm and slaughterhouse; targeting animals, carcasses, workers and their households and environment. By using whole-genome phylogenetic analysis and network analysis based on single nucleotide polymorphisms (SNPs), we found highly interrelated non-pathogenic and pathogenic E. coli strains with phylogenetic intermixing, and a high prevalence of shared multidrug resistance profiles amongst livestock, human and environment. Through an original data processing pipeline which combines omics, machine learning, gene sharing network and mobile genetic elements analysis, we investigated the resistance to 26 different antimicrobials and identified 361 genes associated to antimicrobial resistance (AMR) phenotypes; 58 of these were known AMR-associated genes and 35 were associated to multidrug resistance. We uncovered an extensive network of genes, correlated to AMR phenotypes, shared among livestock, humans, farm and slaughterhouse environments. We also found several human, livestock and environmental isolates sharing closely related mobile genetic elements carrying ARGs across host species and environments. In a scenario where no consensus exists on how antibiotic use in the livestock may affect antibiotic resistance in the human population, our findings provide novel insights into the broader epidemiology of antimicrobial resistance in livestock farming. Moreover, our original data analysis method has the potential to uncover AMR transmission pathways when applied to the study of other pathogens active in other anthropogenic environments characterised by complex interconnections between host species. Livestock have been suggested as an important source of antimicrobial-resistant (AMR) Escherichia coli, capable of infecting humans and carrying resistance to drugs used in human medicine. China has a large intensive livestock farming industry, poultry being the second most important source of meat in the country, and is the largest user of antibiotics for food production in the world. Here we studied antimicrobial resistance gene overlap between E. coli isolates collected from humans, livestock and their shared environments in a large-scale Chinese poultry farm and associated slaughterhouse. By using a computational approach that integrates machine learning, whole-genome sequencing, gene sharing network and mobile genetic elements analysis we characterized the E. coli community structure, antimicrobial resistance phenotypes and the genetic relatedness of non-pathogenic and pathogenic E. coli strains. We uncovered the network of genes, associated with AMR, shared across host species (animals and workers) and environments (farm and slaughterhouse). Our approach opens up new avenues for the development of a fast, affordable and effective computational solutions that provide novel insights into the broader epidemiology of antimicrobial resistance in livestock farming.
Collapse
Affiliation(s)
- Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Alexandre Maciel-Guerra
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Xibin Zhang
- Qingdao Tian run Food Co., Ltd, New Hope, Beijing, People’s Republic of China
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Jia Rong
- Qingdao Tian run Food Co., Ltd, New Hope, Beijing, People’s Republic of China
| | - Jing Zhang
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Ning Xue
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Paul Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - David Renney
- Nimrod Veterinary Products Limited, Moreton-in-Marsh, United Kingdom
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
| | - Paul Williams
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Longhai Liu
- Qingdao Tian run Food Co., Ltd, New Hope, Beijing, People’s Republic of China
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
- * E-mail: (FL); (TD)
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
- * E-mail: (FL); (TD)
| |
Collapse
|
7
|
Tartor YH, Abd El-Aziz NK, Gharieb RMA, El Damaty HM, Enany S, Soliman EA, Abdellatif SS, Attia ASA, Bahnass MM, El-Shazly YA, Elbediwi M, Ramadan H. Whole-Genome Sequencing of Gram-Negative Bacteria Isolated From Bovine Mastitis and Raw Milk: The First Emergence of Colistin mcr- 10 and Fosfomycin fosA5 Resistance Genes in Klebsiella pneumoniae in Middle East. Front Microbiol 2021; 12:770813. [PMID: 34956131 PMCID: PMC8692987 DOI: 10.3389/fmicb.2021.770813] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/01/2021] [Indexed: 01/10/2023] Open
Abstract
Antimicrobial resistance is a major concern in the dairy industry. This study investigated the prevalence, antimicrobial resistance phenotypes, and genome sequencing of Gram-negative bacteria isolated from clinical (n = 350) and subclinical (n = 95) bovine mastitis, and raw unpasteurized milk (n = 125). Klebsiella pneumoniae, Aeromonas hydrophila, Enterobacter cloacae (100% each), Escherichia coli (87.78%), and Proteus mirabilis (69.7%) were the most prevalent multidrug-resistant (MDR) species. Extensive drug-resistance (XDR) phenotype was found in P. mirabilis (30.30%) and E. coli (3.33%) isolates. Ten isolates (four E. coli, three Klebsiella species and three P. mirabilis) that displayed the highest multiple antibiotic resistance (MAR) indices (0.54–0.83), were exposed to whole-genome sequencing (WGS). Two multilocus sequence types (MLST): ST2165 and ST7624 were identified among the sequenced E. coli isolates. Three E. coli isolates (two from clinical mastitis and one from raw milk) belonging to ST2165 showed similar profile of plasmid replicon types: IncFIA, IncFIB, IncFII, and IncQ1 with an exception to an isolate that contained IncR, whereas E. coli ST7624 showed a different plasmid profile including IncHI2, IncHI2A, IncI1α, and IncFII replicon types. ResFinder findings revealed the presence of plasmid-mediated colistin mcr-10 and fosfomycin fosA5 resistance genes in a K. pneumoniae (K1) isolate from bovine milk. Sequence analysis of the reconstructed mcr-10 plasmid from WGS of K1 isolate, showed that mcr-10 gene was bracketed by xerC and insertion sequence IS26 on an IncFIB plasmid. Phylogenetic analysis revealed that K1 isolate existed in a clade including mcr-10-harboring isolates from human and environment with different STs and countries [United Kingdom (ST788), Australia (ST323), Malawi (ST2144), Myanmar (ST705), and Laos (ST2355)]. This study reports the first emergence of K. pneumoniae co-harboring mcr-10 and fosA5 genes from bovine milk in the Middle East, which constitutes a public health threat and heralds the penetration of the last-resort antibiotics. Hence, prudent use of antibiotics in both humans and animals and antimicrobial surveillance plans are urgently required.
Collapse
Affiliation(s)
- Yasmine H Tartor
- Microbiology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Norhan K Abd El-Aziz
- Microbiology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Rasha M A Gharieb
- Zoonoses Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Hend M El Damaty
- Animal Medicine Department (Infectious Diseases), Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Shymaa Enany
- Microbiology and Immunology Department, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Enas A Soliman
- Bacteriology, Immunology and Mycology Department, Faculty of Veterinary Medicine, Benha University, Benha, Egypt
| | - Samah S Abdellatif
- Food Control Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Amira S A Attia
- Veterinary Public Health Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Mosa M Bahnass
- Animal Medicine Department (Infectious Diseases), Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Yousry A El-Shazly
- Veterinary Hospital, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Mohammed Elbediwi
- Animal Health Research Institute, Agriculture Research Center, Cairo, Egypt.,Institute of Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hazem Ramadan
- Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt.,Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US National Poultry Research Center, US Department of Agriculture, Agricultural Research Service (USDA-ARS), Athens, GA, United States
| |
Collapse
|
8
|
Luo L, Wang H, Payne MJ, Liang C, Bai L, Zheng H, Zhang Z, Zhang L, Zhang X, Yan G, Zou N, Chen X, Wan Z, Xiong Y, Lan R, Li Q. Comparative genomics of Chinese and international isolates of Escherichia albertii: population structure and evolution of virulence and antimicrobial resistance. Microb Genom 2021; 7. [PMID: 34882085 PMCID: PMC8767325 DOI: 10.1099/mgen.0.000710] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Escherichia albertii is a recently recognized species in the genus Escherichia that causes diarrhoea. The population structure, genetic diversity and genomic features have not been fully examined. Here, 169 E. albertii isolates from different sources and regions in China were sequenced and combined with 312 publicly available genomes (from additional 14 countries) for genomic analyses. The E. albertii population was divided into two clades and eight lineages, with lineage 3 (L3), L5 and L8 more common in China. Clinical isolates were observed in all clades/lineages. Virulence genes were found to be distributed differently among lineages: subtypes of the intimin encoding gene eae and the cytolethal distending toxin gene cdtB were lineage associated, and the second type three secretion system (ETT2) island was truncated in L3 and L6. Seven new eae subtypes and one new cdtB subtype (cdtB-VI) were identified. Alarmingly, 85.9 % of the Chinese E. albertii isolates were predicted to be multidrug-resistant (MDR) with 35.9 % harbouring genes capable of conferring resistance to 10 to 14 different drug classes. The majority of the MDR isolates were of poultry source from China and belonged to four sequence types (STs) [ST4638, ST4479, ST4633 and ST4488]. Thirty-four plasmids with some carrying MDR and virulence genes, and 130 prophages were identified from 17 complete E. albertii genomes. The 130 intact prophages were clustered into five groups, with group five prophages harbouring more virulence genes. We further identified three E. albertii specific genes as markers for the identification of this species. Our findings provided fundamental insights into the population structure, virulence variation and drug resistance of E. albertii.
Collapse
Affiliation(s)
- Lijuan Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Hong Wang
- Zigong Center for Disease Control and Prevention, Zigong, Sichuan, PR China
| | - Michael J Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Chelsea Liang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Li Bai
- Division I of Risk Assessment, National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, PR China
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Zhengdong Zhang
- Zigong Center for Disease Control and Prevention, Zigong, Sichuan, PR China
| | - Ling Zhang
- Zigong Center for Disease Control and Prevention, Zigong, Sichuan, PR China
| | - Xiaomei Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Guodong Yan
- Zigong Center for Disease Control and Prevention, Zigong, Sichuan, PR China
| | - Nianli Zou
- Zigong Center for Disease Control and Prevention, Zigong, Sichuan, PR China
| | - Xi Chen
- Zigong Center for Disease Control and Prevention, Zigong, Sichuan, PR China
| | - Ziting Wan
- Zigong Center for Disease Control and Prevention, Zigong, Sichuan, PR China
| | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Qun Li
- Zigong Center for Disease Control and Prevention, Zigong, Sichuan, PR China
| |
Collapse
|
9
|
Takawira FT, Pitout JD, Thilliez G, Mashe T, Gutierrez AV, Kingsley RA, Peirano G, Matheu J, Midzi SM, Mwamakamba LW, Gally DL, Tarupiwa A, Mukavhi L, Ehlers MM, Mtapuri-Zinyowera S, Kock MM. Molecular epidemiology of extended-spectrum beta-lactamase-producing extra-intestinal pathogenic Escherichia coli strains over a 2-year period (2017-2019) from Zimbabwe. Eur J Clin Microbiol Infect Dis 2021:10.1007/s10096-021-04379-z. [PMID: 34779943 DOI: 10.1007/s10096-021-04379-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/20/2021] [Indexed: 10/19/2022]
Abstract
This study was designed to characterize extended-spectrum beta-lactamase (ESBL)-producing extra-intestinal pathogenic Escherichia coli (E.coli) (ExPEC) associated with urinary tract infections in nine different geographic regions of Zimbabwe over a 2-year period (2017-2019). A total of 48 ESBL-positive isolates from urine specimen were selected for whole-genome sequencing from 1246 Escherichia coli isolates biobanked at the National Microbiology Reference laboratory using phenotypic susceptibility testing results from the National Escherichia coli Surveillance Programme to provide representation of different geographical regions and year of isolation. The majority of ESBL E. coli isolates produced cefotaximase-Munich (CTX-M)-15, CTX-M-27, and CTX-M-14. In this study, sequence types (ST) 131 and ST410 were the most predominant antimicrobial-resistant clones and responsible for the increase in ESBL-producing E. coli strains since 2017. Novel ST131 complex strains were recorded during the period 2017 to 2018, thus showing the establishment and evolution of this antimicrobial-resistant ESBL clone in Zimbabwe posing an important public health threat. Incompatibility group F plasmids were predominant among ST131 and ST410 isolates with the following replicons recorded most frequently: F1:A2:B20 (9/19, 47%), F2:A1: B (5/19, 26%), and F1:A1:B49 (8/13, 62%). The results indicate the need for continuous tracking of different ESBL ExPEC clones on a global scale, while targeting specific STs (e.g. ST131 and ST410) through control programs will substantially decrease the spread of ESBLs among ExPEC.
Collapse
Affiliation(s)
- Faustinos Tatenda Takawira
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Johann Dd Pitout
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Microbiology, Alberta Precision Laboratories, Department Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Tapfumanei Mashe
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | | | | | - Gisele Peirano
- Department of Microbiology, Alberta Precision Laboratories, Department Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jorge Matheu
- World Health Organization (WHO), Geneva, Switzerland
| | | | | | - David L Gally
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Edinburgh, Scotland
| | - Andrew Tarupiwa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Leckson Mukavhi
- University of Zimbabwe College of Health Sciences, Health Professions Education, Harare, Zimbabwe
| | - Marthie M Ehlers
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- National Health Laboratory Service, Academic Division, Pretoria, South Africa
| | | | - Marleen M Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.
- National Health Laboratory Service, Academic Division, Pretoria, South Africa.
| |
Collapse
|
10
|
Athanasakopoulou Z, Tsilipounidaki K, Sofia M, Chatzopoulos DC, Giannakopoulos A, Karakousis I, Giannakis V, Spyrou V, Touloudi A, Satra M, Galamatis D, Diamantopoulos V, Mpellou S, Petinaki E, Billinis C. Poultry and Wild Birds as a Reservoir of CMY-2 Producing Escherichia coli: The First Large-Scale Study in Greece. Antibiotics (Basel) 2021; 10:antibiotics10030235. [PMID: 33652621 PMCID: PMC7996950 DOI: 10.3390/antibiotics10030235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/16/2022] Open
Abstract
Resistance mediated by β-lactamases is a globally spread menace. The aim of the present study was to determine the occurrence of Escherichia coli producing plasmid-encoded AmpC β-lactamases (pAmpC) in animals. Fecal samples from chickens (n = 159), cattle (n = 104), pigs (n = 214), and various wild bird species (n = 168), collected from different Greek regions during 2018-2020, were screened for the presence of pAmpC-encoding genes. Thirteen E. coli displaying resistance to third-generation cephalosporins and a positive AmpC confirmation test were detected. blaCMY-2 was the sole pAmpC gene identified in 12 chickens' and 1 wild bird (Eurasian magpie) isolates and was in all cases linked to an upstream ISEcp1-like element. The isolates were classified into five different sequence types: ST131, ST117, ST155, ST429, and ST1415. Four chickens' stains were assigned to ST131, while five chickens' strains and the one from the Eurasian magpie belonged to ST117. Seven pAmpC isolates co-harbored genes conferring resistance to tetracyclines (tetM, tetB, tetC, tetD), 3 carried sulfonamide resistance genes (sulI and sulII), and 10 displayed mutations in the quinolone resistance-determining regions of gyrA (S83L+D87N) and parC (S80I+E84V). This report provides evidence of pAmpC dissemination, describing for the first time the presence of CMY-2 in chickens and wild birds from Greece.
Collapse
Affiliation(s)
- Zoi Athanasakopoulou
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.); (A.T.)
| | | | - Marina Sofia
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.); (A.T.)
| | - Dimitris C. Chatzopoulos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.); (A.T.)
| | - Alexios Giannakopoulos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.); (A.T.)
| | | | | | - Vassiliki Spyrou
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece;
| | - Antonia Touloudi
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.); (A.T.)
| | - Maria Satra
- Faculty of Public and Integrated Health, University of Thessaly, 43100 Karditsa, Greece;
| | - Dimitrios Galamatis
- Hellenic Agricultural Organization DIMITRA (ELGO DIMITRA), 57001 Thessaloniki, Greece;
| | | | - Spyridoula Mpellou
- Bioefarmoges Eleftheriou LP-Integrated Mosquito Control, 19007 Marathon, Greece;
| | - Efthymia Petinaki
- Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (K.T.); (E.P.)
| | - Charalambos Billinis
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.); (A.T.)
- Faculty of Public and Integrated Health, University of Thessaly, 43100 Karditsa, Greece;
- Correspondence:
| |
Collapse
|