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Wang G, Kang X, Wang S, Meng C, Gu D, Song L, Jiao X, Pan Z. Prevalence and Characteristics of Salmonella from Tibetan Pigs in Tibet, China. Foodborne Pathog Dis 2024. [PMID: 38995857 DOI: 10.1089/fpd.2024.0069] [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: 07/14/2024] Open
Abstract
This study aimed to understand the epidemiological characteristics of Salmonella in Tibetan pigs. We isolated, identified, and examined via antimicrobial susceptibility testing on Salmonella from Tibetan pigs breeder farms and slaughterhouses in Tibet, China. A genetic evolutionary tree was constructed on the basis of whole genome sequencing (WGS). A total of 81 Salmonella isolates were isolated from 987 samples. The main serovars were Salmonella Typhimurium and Salmonella London in Tibetan pigs. The isolated Salmonella Typhimurium isolates subjected to antimicrobial susceptibility testing showed varying degrees of resistance to β-lactams, aminoglycosides, fluoroquinolones, sulfonamides, tetracyclines, and amphenicols. WGS analysis was performed on 20 Salmonella Typhimurium isolates in Tibet (n = 10), Jiangsu (n = 10), and 205 genome sequences downloaded from the Enterobase database to reveal their epidemiological and genetic characteristics. They were divided into two clusters based on core genome single-nucleotide polymorphisms: Cluster A with 112 isolates from Tibet and other regions in China and Cluster B with 113 isolates from Jiangsu and other regions. The isolates in Cluster A were further divided into two subclusters: A-1 with 40 isolates including Tibet and A-2 with 72 isolates from other regions. Virulence factors analysis revealed that all isolates from Tibet carried adeG, but this observation was not as common in Salmonella isolates from Jiangsu and other regions of China. Antibiotic resistance genes (ARGs) analysis showed that all isolates from Tibet carried blaTEM-55 and rmtB, which were absent in Salmonella isolates from Jiangsu and other regions of China. Genetic characteristic analysis and biofilm determination indicated that the biofilm formation capabilities of the isolates from Tibet were stronger than those of the isolates from Jiangsu and other regions of China. Our research revealed the epidemic patterns and genomic characteristics of Salmonella in Tibetan pigs and provided theoretical guidance for the prevention and control of local salmonellosis.
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Affiliation(s)
- Gang Wang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xilong Kang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Shuangjuan Wang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Chuang Meng
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Dan Gu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Li Song
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
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Koutsoumanis K, Allende A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Fox E, Gosling R(B, Gil BM, Møretrø T, Stessl B, da Silva Felício MT, Messens W, Simon AC, Alvarez‐Ordóñez A. Persistence of microbiological hazards in food and feed production and processing environments. EFSA J 2024; 22:e8521. [PMID: 38250499 PMCID: PMC10797485 DOI: 10.2903/j.efsa.2024.8521] [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] [Indexed: 01/23/2024] Open
Abstract
Listeria monocytogenes (in the meat, fish and seafood, dairy and fruit and vegetable sectors), Salmonella enterica (in the feed, meat, egg and low moisture food sectors) and Cronobacter sakazakii (in the low moisture food sector) were identified as the bacterial food safety hazards most relevant to public health that are associated with persistence in the food and feed processing environment (FFPE). There is a wide range of subtypes of these hazards involved in persistence in the FFPE. While some specific subtypes are more commonly reported as persistent, it is currently not possible to identify universal markers (i.e. genetic determinants) for this trait. Common risk factors for persistence in the FFPE are inadequate zoning and hygiene barriers; lack of hygienic design of equipment and machines; and inadequate cleaning and disinfection. A well-designed environmental sampling and testing programme is the most effective strategy to identify contamination sources and detect potentially persistent hazards. The establishment of hygienic barriers and measures within the food safety management system, during implementation of hazard analysis and critical control points, is key to prevent and/or control bacterial persistence in the FFPE. Once persistence is suspected in a plant, a 'seek-and-destroy' approach is frequently recommended, including intensified monitoring, the introduction of control measures and the continuation of the intensified monitoring. Successful actions triggered by persistence of L. monocytogenes are described, as well as interventions with direct bactericidal activity. These interventions could be efficient if properly validated, correctly applied and verified under industrial conditions. Perspectives are provided for performing a risk assessment for relevant combinations of hazard and food sector to assess the relative public health risk that can be associated with persistence, based on bottom-up and top-down approaches. Knowledge gaps related to bacterial food safety hazards associated with persistence in the FFPE and priorities for future research are provided.
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Prasertsee T, Pascoe B, Patchanee P. Colistin resistance and resistance determinants are mobile among Salmonella enterica isolates from diseased and healthy pigs in Thailand. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526471. [PMID: 36778303 PMCID: PMC9915662 DOI: 10.1101/2023.01.31.526471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Salmonella is an important enteric pathogen that poses a threat to human and livestock animal health, with emerging multidrug resistance (MDR) a major public health issue globally. We investigated the prevalence of Salmonella in healthy and diseased pigs from Thai pig farms and determined their phenotypic and genotypic antimicrobial resistance profiles. A total of 150 fecal samples were collected from pigs housed in pens from four separate pig farms in southern Thailand and tested for the presence of Salmonella. Confirmed Salmonella isolates were tested for their susceptibility to 11 antimicrobials, and PCR used to detect known antimicrobial resistance genes (ARGs). Salmonella isolates were cultured from 69% (103/150) of all fecal samples, with higher prevalence in disease pigs (12/15; 80%), compared with healthy pigs (91/135; 67%). Serotype Rissen was the most frequently identified serotype among the Salmonella isolates. Resistance to ampicillin (AMP) (97%), sulfonamide-trimethoprim (SXT) (97%), and tetracycline (TET) (94%) were the most common phenotypes observed. The most common ARGs identified were blaTEM gene (99.%), tetA (87%), sul1 (77%), and dfrA1 (74%), and more than 95% of the Salmonella isolates tested were MDR - based on resistance to three or more antimicrobial classes. The most common antimicrobial resistance pattern exhibited was AMP-TET-SXT (76%), and resistance to colistin (via the mcr-1 gene) was observed in both healthy and diseased pigs. The clonal groups of PFGE analysis in serotype Typhimurium revealed the genetic relationship among Salmonella isolated from healthy and diseased pigs from different pig farms.
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Affiliation(s)
- Teerarat Prasertsee
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla, Thailand
| | - Ben Pascoe
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Ineos Oxford Institute of Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Prapas Patchanee
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
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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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Eiamsam-ang T, Tadee P, Pascoe B, Patchanee P. Genome-based analysis of infrequent Salmonella serotypes through the Thai pork production chain. Front Microbiol 2022; 13:968695. [PMID: 36090074 PMCID: PMC9453559 DOI: 10.3389/fmicb.2022.968695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/05/2022] [Indexed: 12/05/2022] Open
Abstract
Salmonella is a prevalent zoonotic foodborne pathogen. Swine and pork are implicated as important sources of salmonellosis in humans. In Chiang Mai and Lamphun Provinces in northern Thailand, there has been a high prevalence of Salmonella persistence for over a decade. Infection is usually with dominant S. enterica serotypes, including serotypes Rissen and 1,4,[5],12:i:-. However, other serotypes also contribute to disease but are less well characterized. The whole genome sequencing data of 43 S. enterica serotypes isolated from pork production chain through 2011-2014, were used to evaluate genetic diversity and ascertain the possible source of Salmonella contamination based on Core Genome Multilocus Sequence Typing (cgMLST) approach. The Salmonella serotypes recovered from farms and slaughterhouses were re-circulating by swine environmental contamination. Conversely, the Salmonella contamination in the retail market represents cross-contamination from multiple sources, including contaminated foodstuffs. Salmonella contamination in the pork production chain has the competency for host cell adhesion, host cell invasion, and intracellular survival, which is enough for the pathogenicity of salmonellosis. In addition, all of these isolates were multi-drug resistant Salmonella, which contained at least 10 antimicrobial resistance genes. This result indicated that these S. enterica serotypes also pose a significant public health risk. Our findings support the need for appropriate surveillance of food-animal products going to market to reduce public exposure to highly pathogenic, multi-drug resistant Salmonella. Acquiring information would motivate all stakeholders to reinforce sanitation standards throughout the pork production chain in order to eradicate Salmonella contamination and reduce the risk of salmonellosis in humans.
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Affiliation(s)
- Thanaporn Eiamsam-ang
- Graduate Program in Veterinary Science, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pakpoom Tadee
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Ben Pascoe
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- The Milner Center for Evolution, University of Bath, Bath, United Kingdom
| | - Prapas Patchanee
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
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Vogt NA, Hetman BM, Vogt AA, Pearl DL, Reid-Smith RJ, Parmley EJ, Kadykalo S, Ziebell K, Bharat A, Mulvey MR, Janecko N, Ricker N, Allen SE, Bondo KJ, Jardine CM. Using whole-genome sequence data to examine the epidemiology of antimicrobial resistance in Escherichia coli from wild meso-mammals and environmental sources on swine farms, conservation areas, and the Grand River watershed in southern Ontario, Canada. PLoS One 2022; 17:e0266829. [PMID: 35395054 PMCID: PMC8993012 DOI: 10.1371/journal.pone.0266829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/28/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) threatens the health of humans and animals and has repeatedly been detected in wild animal species across the world. This cross-sectional study integrates whole-genome sequence data from Escherichia coli isolates with demonstrated phenotypic resistance that originated from a previous longitudinal wildlife study in southern Ontario, as well as phenotypically resistant E. coli water isolates previously collected as part of a public health surveillance program. The objective of this work was to assess for evidence of possible transmission of antimicrobial resistance determinants between wild meso-mammals, swine manure pits, and environmental sources on a broad scale in the Grand River watershed, and at a local scale—for the subset of samples collected on both swine farms and conservation areas in the previous wildlife study. Logistic regression models were used to assess potential associations between sampling source, location type (swine farm vs. conservation area), and the occurrence of select resistance genes and predicted plasmids. In total, 200 isolates from the following sources were included: water (n = 20), wildlife (n = 73), swine manure pit (n = 31), soil (n = 73), and dumpsters (n = 3). Several genes and plasmid incompatibility types were significantly more likely to be identified on swine farms compared to conservation areas. Conversely, internationally distributed sequence types (e.g., ST131), extended-spectrum beta-lactamase- and AmpC-producing E. coli were isolated in lower prevalences (<10%) and were almost exclusively identified in water sources, or in raccoon and soil isolates obtained from conservation areas. Differences in the odds of detecting resistance genes and predicted plasmids among various sources and location types suggest different primary sources for individual AMR determinants, but, broadly, our findings suggest that raccoons, skunks and opossums in this region may be exposed to AMR pollution via water and agricultural sources, as well as anthropogenic sources in conservation areas.
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Affiliation(s)
- Nadine A. Vogt
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Benjamin M. Hetman
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Adam A. Vogt
- Independent Researcher, Mississauga, Ontario, Canada
| | - David L. Pearl
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Richard J. Reid-Smith
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - E. Jane Parmley
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Stefanie Kadykalo
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nicol Janecko
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Samantha E. Allen
- Wyoming Game and Fish Department, Laramie, Wyoming, United States of America
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, United States of America
| | - Kristin J. Bondo
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Claire M. Jardine
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, Guelph, Ontario, Canada
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Wang Z, Zhang Y, Xu H, Chu C, Wang J, Jiao X, Li Q. Whole-genome sequencing analysis reveals pig as the main reservoir for persistent evolution of Salmonella enterica serovar Rissen causing human salmonellosis. Food Res Int 2022; 154:111007. [DOI: 10.1016/j.foodres.2022.111007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/15/2022] [Accepted: 02/10/2022] [Indexed: 11/30/2022]
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Vogt NA, Hetman BM, Pearl DL, Vogt AA, Reid-Smith RJ, Parmley EJ, Janecko N, Bharat A, Mulvey MR, Ricker N, Bondo KJ, Allen SE, Jardine CM. Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada. PLoS One 2021; 16:e0260234. [PMID: 34793571 PMCID: PMC8601536 DOI: 10.1371/journal.pone.0260234] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/04/2021] [Indexed: 11/19/2022] Open
Abstract
To better understand the contribution of wildlife to the dissemination of Salmonella and antimicrobial resistance in Salmonella and Escherichia coli, we examined whole-genome sequence data from Salmonella and E. coli isolates collected from raccoons (Procyon lotor) and environmental sources on farms in southern Ontario. All Salmonella and phenotypically resistant E. coli collected from raccoons, soil, and manure pits on five swine farms as part of a previous study were included. We assessed for evidence of potential transmission of these organisms between different sources and farms utilizing a combination of population structure assessments (using core-genome multi-locus sequence typing), direct comparisons of multi-drug resistant isolates, and epidemiological modeling of antimicrobial resistance (AMR) genes and plasmid incompatibility (Inc) types. Univariable logistic regression models were fit to assess the impact of source type, farm location, and sampling year on the occurrence of select resistance genes and Inc types. A total of 159 Salmonella and 96 resistant E. coli isolates were included. A diversity of Salmonella serovars and sequence types were identified, and, in some cases, we found similar or identical Salmonella isolates and resistance genes between raccoons, soil, and swine manure pits. Certain Inc types and resistance genes associated with source type were consistently more likely to be identified in isolates from raccoons than swine manure pits, suggesting that manure pits are not likely a primary source of those particular resistance determinants for raccoons. Overall, our data suggest that transmission of Salmonella and AMR determinants between raccoons and swine manure pits is uncommon, but soil-raccoon transmission appears to be occurring frequently. More comprehensive sampling of farms, and assessment of farms with other livestock species, as well as additional environmental sources (e.g., rivers) may help to further elucidate the movement of resistance genes between these various sources.
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Affiliation(s)
- Nadine A. Vogt
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Benjamin M. Hetman
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
| | - David L. Pearl
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Adam A. Vogt
- Independent Researcher, Mississauga, Ontario, Canada
| | - Richard J. Reid-Smith
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - E. Jane Parmley
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Nicol Janecko
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Kristin J. Bondo
- Department of Pathobiology, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Samantha E. Allen
- Department of Pathobiology, Ontario Veterinary College, Guelph, Ontario, Canada
- Wyoming Game and Fish Department, Laramie, Wyoming, United States of America
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, United States of America
| | - Claire M. Jardine
- Department of Pathobiology, Ontario Veterinary College, Guelph, Ontario, Canada
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, Guelph, Ontario, Canada
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Elbediwi M, Shi D, Biswas S, Xu X, Yue M. Changing Patterns of Salmonella enterica Serovar Rissen From Humans, Food Animals, and Animal-Derived Foods in China, 1995-2019. Front Microbiol 2021; 12:702909. [PMID: 34394048 PMCID: PMC8358327 DOI: 10.3389/fmicb.2021.702909] [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: 04/30/2021] [Accepted: 06/25/2021] [Indexed: 12/04/2022] Open
Abstract
Salmonellosis represents a growing threat to global public health. Salmonella enterica remains the leading cause of bacterial foodborne diseases in China. Salmonella enterica serovar Rissen (S. Rissen) has been recognized as one of the emerging serovars among humans in different countries worldwide. However, knowledge on the prevalence of S. Rissen in China is largely lacking. To address essential epidemiological information for S. Rissen in China, a total of 1,182 S. Rissen isolates recovered from samples across the food chain were collected from 16 provinces or province-level cities between 1995 and 2019. Risk factors due to the consumption of animal-derived food products were also analyzed. We found S. Rissen is widely distributed, especially in the Eastern and Southern parts of China, and there is an increasing frequency in recent years as evidenced by the greater number of isolates recovered in 2016, 2017, and 2018. Interestingly, the majority of S. Rissen isolates recovered in this study were from human samples (63.4%; 749/1182), remarkably, 58.4% (438/749) were from asymptomatic carriers. We obtained most of the S. Rissen isolates from humans from Guangxi (59.5%; 446/749) and Shanghai (29.5%; 221/749). Among 302 human diarrheal isolates (40.3%; 302/749), we found 44.6% (139/311) of S. Rissen in children with diarrhea (age below 10 years old). This is of clinical significance as diarrhea is one of the crucial causes of child mortality globally and our findings here highlighted the importance of Salmonella infections in Chinese children. Additionally, S. Rissen isolates were also found to be associated with pork and poultry products in China. This study projected the most updated national-wide study of S. Rissen isolates obtained from different sources in China over the past two decades. Continued surveillance is warranted to further monitor this emerging serovar in China and elsewhere over the world.
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Affiliation(s)
- Mohammed Elbediwi
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China.,Agriculture Research Center, Animal Health Research Institute, Cairo, Egypt
| | - Daiwei Shi
- National Institutes for Food and Drug Control, Beijing, China
| | - Silpak Biswas
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Xuebin Xu
- Department of Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Min Yue
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China.,Hainan Institute of Zhejiang University, Sanya, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
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10
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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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11
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Khare M, Sinha D, Zgheib R, Traore SI, Lagier JC, Raoult D, Edouard FP. Genomic description and characterization of Nigeribacterium massiliense gen. nov., sp. nov., isolated from the human gut. Microbes Infect 2021; 23:104842. [PMID: 34020025 DOI: 10.1016/j.micinf.2021.104842] [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: 02/12/2021] [Revised: 04/23/2021] [Accepted: 05/08/2021] [Indexed: 02/07/2023]
Abstract
Strain Marseille-P1302 was isolated from the stool of a 2-year-old Nigerian boy suffering from Kwashiorkor, a form of severe acute malnutrition. The strain grows in aerobic atmosphere and bacterial cells are Gram-positive cocci ranging in diameter from 0.8 to 1 μm. Strain Marseille-P1302 exhibits a 16S rRNA sequence similarity of 94.97% with Brevilactibacter flavus strain VG341T, but phylogenetically-closest species with standing in nomenclature is Brevilactibacter sinopodophylli strains KCTC 33808Twith the sequence similarity of 93.41%. The draft genome of strain Marseille-P1302 is 2,934,258bp-long with a 70.38% G+C content, and contains 2,704 protein-coding genes and 55 RNAs that includes 9 rRNA genes. On the basis of these data, we propose the creation of the new genus Nigeribacterium gen. nov., with strain Marseille-P1302T (= CSUR P1302 = DSM 29084) being the type strain of new species Nigeribacterium. massiliense gen. nov., sp. nov.
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Affiliation(s)
- Mudra Khare
- Aix Marseille University, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, UMR Vecteurs Infections Tropicales et Méditerranéennes. (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Dhiraj Sinha
- Aix Marseille University, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, UMR Vecteurs Infections Tropicales et Méditerranéennes. (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Rita Zgheib
- Aix Marseille University, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, UMR Vecteurs Infections Tropicales et Méditerranéennes. (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Sory Ibrahima Traore
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Jean-Christophe Lagier
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Fournier Pierre Edouard
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.
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12
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Xu X, Biswas S, Gu G, Elbediwi M, Li Y, Yue M. Characterization of Multidrug Resistance Patterns of Emerging Salmonella enterica Serovar Rissen along the Food Chain in China. Antibiotics (Basel) 2020; 9:antibiotics9100660. [PMID: 33007986 PMCID: PMC7600917 DOI: 10.3390/antibiotics9100660] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 11/25/2022] Open
Abstract
Salmonella spp. are recognized as important foodborne pathogens globally. Salmonella enterica serovar Rissen is one of the important Salmonella serovars linked with swine products in numerous countries and can transmit to humans by food chain contamination. Worldwide emerging S. Rissen is considered as one of the most common pathogens to cause human salmonellosis. The objective of this study was to determine the antimicrobial resistance properties and patterns of Salmonella Rissen isolates obtained from humans, animals, animal-derived food products, and the environment in China. Between 2016 and 2019, a total of 311 S. Rissen isolates from different provinces or province-level cities in China were included here. Bacterial isolates were characterized by serotyping and antimicrobial susceptibility testing. Minimum inhibitory concentration (MIC) values of 14 clinically relevant antimicrobials were obtained by broth microdilution method. S. Rissen isolates from humans were found dominant (67%; 208/311). S. Rissen isolates obtained from human patients were mostly found with diarrhea. Other S. Rissen isolates were acquired from food (22%; 69/311), animals (8%; 25/311), and the environment (3%; 9/311). Most of the isolates were resistant to tetracycline, trimethoprim-sulfamethoxazole, chloramphenicol, streptomycin, sulfisoxazole, and ampicillin. The S. Rissen isolates showed susceptibility against ceftriaxone, ceftiofur, gentamicin, nalidixic acid, ciprofloxacin, and azithromycin. In total, 92% of the S. Rissen isolates were multidrug-resistant and ASSuT (27%), ACT (25%), ACSSuT (22%), ACSSuTAmc (11%), and ACSSuTFox (7%) patterns were among the most prevalent antibiotic resistance patterns found in this study. The widespread dissemination of antimicrobial resistance could have emerged from misuse of antimicrobial agents in animal husbandry in China. These findings could be useful for rational antimicrobial usage against Salmonella Rissen infections.
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Affiliation(s)
- Xuebin Xu
- Department of Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China;
| | - Silpak Biswas
- Institute of Veterinary Sciences & Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (S.B.); (M.E.); (Y.L.)
| | - Guimin Gu
- Guangxi Institute for Product Quality Inspection, Nanning 530007, China;
| | - Mohammed Elbediwi
- Institute of Veterinary Sciences & Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (S.B.); (M.E.); (Y.L.)
- Animal Health Research Institute, Agriculture Research Centre, Cairo 11435, Egypt
| | - Yan Li
- Institute of Veterinary Sciences & Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (S.B.); (M.E.); (Y.L.)
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
| | - Min Yue
- Institute of Veterinary Sciences & Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (S.B.); (M.E.); (Y.L.)
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
- Correspondence: ; Tel./Fax: +86-0571-8898-2832
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