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Ojha S, Thakur KK, Ojasanya RA, Saab ME. Retrospective study on the occurrence of Salmonella serotypes in veterinary specimens of Atlantic Canada (2012-2021). Vet Med Sci 2024; 10:e1530. [PMID: 38979670 PMCID: PMC11231644 DOI: 10.1002/vms3.1530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/14/2024] [Accepted: 06/14/2024] [Indexed: 07/10/2024] Open
Abstract
AIM This study aimed to summarize the frequency and the antimicrobial susceptibility profiles of the Salmonella serotypes identified from the specimens of companion animals, livestock, avian, wildlife and exotic species within Atlantic Canada. MATERIALS AND METHODS The retrospective electronic laboratory data of microbiological analyses of a selected subset of samples from 03 January 2012 to 29 December 2021 submitted from various animal species were retrieved. The frequency of Salmonella serotypes identified, and their antimicrobial susceptibility results obtained using the disk diffusion or broth method were analysed. The test results were interpreted according to the Clinical and Laboratory Standards Institute standard. The Salmonella serotypes were identified by slide agglutination (Kauffman-White-Le-Minor Scheme) and/or the Whole Genome Sequencing for the Salmonella in silico Serovar Typing Resource-based identification. RESULTS Of the cases included in this study, 4.6% (n = 154) had at least one Salmonella isolate, corresponding to 55 different serovars. Salmonella isolation was highest from exotic animal species (n = 40, 1.20%), followed by porcine (n = 26, 0.78%), and canine (n = 23, 0.69%). Salmonella subsp. enterica serovar Typhimurium was predominant among exotic mammals, porcine and caprine samples, whereas S. Enteritidis was mostly identified in bovine and canine samples. S. Typhimurium of porcine origin was frequently resistant (>70.0%) to ampicillin. In contrast, S. Typhimurium isolates from porcine and caprine samples were susceptible (>70.0%) to florfenicol. S. Oranienburg from equine samples was susceptible to chloramphenicol, but frequently resistant (>90.0%) to azithromycin. In avian samples, S. Copenhagen was susceptible (>90.0%) to florfenicol, whereas Muenchen was frequently resistant (>90.0%) to florfenicol. S. subsp. diarizonae serovar IIIb:61:k:1,5 of ovine origin was resistant (50.0% isolates) to sulfadimethoxine. No significant changes were observed in the antibiotic resistance profiles across the study years. CONCLUSIONS This report provides data for surveillance studies, distribution of Salmonella serotypes and their antimicrobial resistance among veterinary specimens of Atlantic Canada.
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Affiliation(s)
- Shivani Ojha
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
- Veterinary Diagnostic Services Laboratory, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Krishna K Thakur
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Rasaq A Ojasanya
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Matthew E Saab
- Veterinary Diagnostic Services Laboratory, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
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Li P, Zhan L, Wang H, Yan Y, Jia M, Gao L, Sun Y, Zhu G, Chen Z. Prevalence and Antimicrobial Resistance Diversity of Salmonella Isolates in Jiaxing City, China. Antibiotics (Basel) 2024; 13:443. [PMID: 38786171 PMCID: PMC11117378 DOI: 10.3390/antibiotics13050443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/11/2024] [Accepted: 05/12/2024] [Indexed: 05/25/2024] Open
Abstract
Nontyphoidal Salmonella (NTS) is a cause of foodborne diarrheal diseases worldwide. Important emerging NTS serotypes that have spread as multidrug-resistant high-risk clones include S. Typhimurium monophasic variant and S. Kentucky. In this study, we isolated Salmonella in 5019 stool samples collected from patients with clinical diarrhea and 484 food samples. Antibiotic susceptibility testing and whole-genome sequencing were performed on positive strains. The detection rates of Salmonella among patients with diarrhea and food samples were 4.0% (200/5019) and 3.1% (15/484), respectively. These 215 Salmonella isolates comprised five main serotypes, namely S. Typhimurium monophasic variant, S. Typhimurium, S. London, S. Enteritidis, and S. Rissen, and were mainly resistant to ampicillin, tetracycline, chloramphenicol, and trimethoprim/sulfamethoxazole. The MDR rates of five major serotypes were 77.4%, 56.0%, 66.7%, 53.3%, and 80.0%, respectively. The most commonly acquired extended-spectrum β-lactamase-encoding genes were blaTEM-1B, blaOXA-10, and blaCTX-M-65. The S. Typhimurium monophasic variant strains from Jiaxing City belonged to a unique clone with broad antibiotic resistance. S. Kentucky isolates showed the highest drug resistance, and all were MDR strains. The discovery of high antibiotic resistance rates in this common foodborne pathogen is a growing concern; therefore, ongoing surveillance is crucial to effectively monitor this pathogen.
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Affiliation(s)
- Ping Li
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; (P.L.)
| | - Li Zhan
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China;
| | - Henghui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; (P.L.)
| | - Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; (P.L.)
| | - Miaomiao Jia
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; (P.L.)
| | - Lei Gao
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; (P.L.)
| | - Yangming Sun
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; (P.L.)
| | - Guoying Zhu
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; (P.L.)
| | - Zhongwen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; (P.L.)
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Vázquez X, Fernández J, Heinisch JJ, Rodicio R, Rodicio MR. Insights into the Evolution of IncR Plasmids Found in the Southern European Clone of the Monophasic Variant of Salmonella enterica Serovar Typhimurium. Antibiotics (Basel) 2024; 13:314. [PMID: 38666990 PMCID: PMC11047700 DOI: 10.3390/antibiotics13040314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024] Open
Abstract
Salmonella enterica subspecies enterica serovar 4,[5],12:i:- is a monophasic variant of S. Typhimurium which has emerged as a world-wide distributed pathogen in the last decades. Several clones have been identified within this variant, the European clone, the Spanish clone, the Southern European clone and the U.S./American clone. The present study focused on isolates of the Southern European clone that were obtained from clinical samples at Spanish hospitals. The selected isolates were multidrug resistant, with most resistance genes residing on IncR plasmids that also carried virulence genes. These plasmids had a mosaic structure, comprising a highly reduced IncR backbone, which has acquired a large amount of exogenous DNA mostly derived from pSLT and IncI1-I(alfa) plasmids. Although composed of approximately the same elements, the investigated plasmids displayed a high diversity, consistent with active evolution driven by a wealth of mobile genetic elements. They comprise multiple intact or truncated insertion sequences, transposons, pseudo-compound transposons and integrons. Particularly relevant was the role of IS26 (with six to nine copies per plasmid) in generating insertions, deletions and inversions, with many of the rearrangements uncovered by tracking the patterns of eight bp target site duplications. Most of the resistance genes detected in the analyzed isolates have been previously associated with the Southern European clone. However, erm(B), lnu(G) and blaTEM-1B are novel, with the last two carried by a second resistance plasmid found in one of the IncR-positive isolates. Thus, evolution of resistance in the Southern European clone is not only mediated by diversification of the IncR plasmids, but also through acquisition of additional plasmids. All isolates investigated in the present study have the large deletion affecting the fljBA region previously found to justify the monophasic phenotype in the Southern European and U.S./American clones. An SNP-based phylogenetic analysis revealed the close relationship amongst our isolates, and support that those sharing the large fljBA deletion could be more heterogeneous than previously anticipated.
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Affiliation(s)
- Xenia Vázquez
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain; (X.V.); (J.F.)
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| | - Javier Fernández
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain; (X.V.); (J.F.)
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain
- Centro de Investigación Biomédica en Red-Enfermedades Respiratorias, 30627 Madrid, Spain
- Research & Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, 33001 Oviedo, Spain
| | - Jürgen J. Heinisch
- Department of Genetics, Faculty of Biology and Chemistry, University of Osnabrück, Barbarastrasse 11, D-49076 Osnabrück, Germany;
| | - Rosaura Rodicio
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo (UO), 33006 Oviedo, Spain
| | - M. Rosario Rodicio
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain; (X.V.); (J.F.)
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
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Zhao QY, Zhang L, Yang JT, Wei HJ, Zhang YH, Wang JY, Liu WZ, Jiang HX. Diversity of evolution in MDR monophasic S. Typhimurium among food animals and food products in Southern China from 2011 to 2018. Int J Food Microbiol 2024; 412:110572. [PMID: 38237416 DOI: 10.1016/j.ijfoodmicro.2024.110572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/02/2024] [Accepted: 01/06/2024] [Indexed: 01/28/2024]
Abstract
The monophasic variant of Salmonella enterica serovar Typhimurium with the antigenic formula 1,4,[5],12:i:- is one of the most common pathogenic bacteria causing global food-borne outbreaks. However, the research on molecular characteristics and evolution of monophasic S. typhimurium in China is still lacking. In the current study, 59 monophasic S. typhimurium strains were isolated from food animals and food products in South China between 2011 and 2018. A total of 87.5 % of monophasic S. typhimurium isolates were grouped into one independent clade with other monophasic S. typhimurium strains in China distinct from other countries by phylogenomic analysis. These isolates possess variable genotypes, including multiple ARGs on plasmid IncHI2, diverse evolutions at the fljAB locus, and virulence factors. Our results suggest that the monophasic S. typhimurium isolates currently circulating in China might be an independent epidemic subtype.
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Affiliation(s)
- Qiu-Yun Zhao
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou 311300, China
| | - Lin Zhang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jin-Tao Yang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Hai-Jing Wei
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yu-Hua Zhang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jiang-Yang Wang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Wen-Zi Liu
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Hong-Xia Jiang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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Pereira GDN, Seribelli AA, Campioni F, Gomes CN, Tiba-Casas MR, Medeiros MIC, Rodrigues DDP, Falcão JP. High levels of multidrug-resistant isolates of genetically similar Salmonella 1,4, [5],12:I:- from Brazil between 1983 and 2020. J Med Microbiol 2024; 73. [PMID: 38375878 DOI: 10.1099/jmm.0.001792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
Introduction. Salmonella 1,4, [5],12:i:- strains with different antimicrobial resistance profiles have been associated with foodborne disease outbreaks in several countries. In Brazil, S. 1,4, [5],12:i:- was identified as one of the most prevalent serovars in São Paulo State during 2004-2020.Gap Statement. However, few studies have characterized this serovar in Brazil.Aim. This study aimed to determine the antimicrobial resistance profiles of S. 1,4, [5],12:i:- strains isolated from different sources in Southeast Brazil and compare their genetic diversity.Methodology. We analysed 113 S. 1,4, [5],12:i:- strains isolated from humans (n=99), animals (n=7), food (n=5) and the environment (n=2) between 1983 and 2020. Susceptibility testing against 13 antimicrobials was performed using the disc diffusion method for all the strains. Plasmid resistance genes and mutations in the quinolone resistance-determining regions were identified in phenotypically fluoroquinolone-resistant strains. Molecular typing was performed using enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) for all strains and multilocus sequence typing (MLST) for 40 selected strains.Results. Of the 113 strains, 54.87 % were resistant to at least one antimicrobial. The highest resistance rates were observed against ampicillin (51.33 %), nalidixic acid (39.82 %) and tetracycline (38.05 %). Additionally, 39 (34.51 %) strains were classified as multidrug-resistant (MDR). Nine fluoroquinolone-resistant strains exhibited the gyrA mutation (Ser96→Tyr96) and contained the qnrB gene. The 113 strains were grouped into two clusters using ERIC-PCR, and most of strains were present in one cluster, with a genetic similarity of ≥80 %. Finally, 40 strains were typed as ST19 using MLST.Conclusion. The prevalence of MDR strains is alarming because antimicrobial treatment against these strains may lead to therapeutic failure. Furthermore, the ERIC-PCR and MLST results suggested that most strains belonged to one main cluster. Thus, a prevalent subtype of Salmonella 1,4, [5],12:i:- strains has probably been circulating among different sources in São Paulo, Brazil, over decades.
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Affiliation(s)
- Giovana do Nascimento Pereira
- Universidade de São Paulo (USP), Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Departamento de Análises Clínicas, Toxicológicas e Bromatológicas (DACTB), Ribeirão Preto, SP, Brazil
| | - Amanda Aparecida Seribelli
- Universidade de São Paulo (USP), Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Departamento de Análises Clínicas, Toxicológicas e Bromatológicas (DACTB), Ribeirão Preto, SP, Brazil
- Universidade de São Paulo (USP), Faculdade de Medicina de Ribeirão Preto, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Ribeirão Preto, SP, Brazil
| | - Fábio Campioni
- Universidade de São Paulo (USP), Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Departamento de Análises Clínicas, Toxicológicas e Bromatológicas (DACTB), Ribeirão Preto, SP, Brazil
- Universidade de São Paulo (USP), Instituto de Física de São Carlos, Departamento de Física e Ciência Interdisciplinar, São Carlos, SP, Brazil
| | - Carolina Nogueira Gomes
- Universidade de São Paulo (USP), Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Departamento de Análises Clínicas, Toxicológicas e Bromatológicas (DACTB), Ribeirão Preto, SP, Brazil
| | | | | | | | - Juliana Pfrimer Falcão
- Universidade de São Paulo (USP), Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Departamento de Análises Clínicas, Toxicológicas e Bromatológicas (DACTB), Ribeirão Preto, SP, Brazil
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Wang Z, Gu D, Hong Y, Hu Y, Gu J, Tang Y, Zhou X, Zhang Y, Jiao X, Li Q. Microevolution of Salmonella 4,[5],12:i:- derived from Salmonella enterica serovar Typhimurium through complicated transpositions. Cell Rep 2023; 42:113227. [PMID: 37837619 DOI: 10.1016/j.celrep.2023.113227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/28/2023] [Accepted: 09/21/2023] [Indexed: 10/16/2023] Open
Abstract
Salmonella enterica subsp. enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-), derived from S. Typhimurium, has become the dominant serotype causing human salmonellosis. In this study, we define the genetic mechanism of the generation of Salmonella 4,[5],12:i:- from S. Typhimurium through complicated transpositions and demonstrate that Salmonella 4,[5],12:i:- displays more efficient colonization and survival abilities in mice than its parent S. Typhimurium strain. We identified intermediate strains carrying both resistance regions (RRs) and the fljAB operon for the generation of Salmonella 4,[5],12:i:-. The insertion of RR3 into the chromosomal hin-iroB site of S. Typhimurium produced RR3-S. Typhimurium as a primary intermediate. Salmonella 4,[5],12:i:- was then produced by replacing the fljAB operon and/or its flanking sequences through intramolecular transpositions mediated by IS26 and/or IS1R elements in RR3-S. Typhimurium, which was further confirmed both in vitro and in vivo. Overall, we demonstrate the molecular mechanism underlying the origin, generation, and advantage of RRs-Salmonella 4,[5],12:i:- from S. Typhimurium.
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Affiliation(s)
- Zhenyu Wang
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China
| | - Dan Gu
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China
| | - Yaming Hong
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China
| | - Yachen Hu
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China
| | - Jiaojie Gu
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China
| | - Yuanyue Tang
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China
| | - Xiaohui Zhou
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT 06269, USA; School of Public Health and Emergency Management, Southern University of Science and Technology, 1088 Xueyuan Road, Nanshan District, Shenzhen 518055, Guangdong, China
| | - Yunzeng Zhang
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China.
| | - Xinan Jiao
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China.
| | - Qiuchun Li
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety, Yangzhou University, 48 Wenhui East Road, Yangzhou 225000, Jiangsu, China.
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Soliani L, Rugna G, Prosperi A, Chiapponi C, Luppi A. Salmonella Infection in Pigs: Disease, Prevalence, and a Link between Swine and Human Health. Pathogens 2023; 12:1267. [PMID: 37887782 PMCID: PMC10610219 DOI: 10.3390/pathogens12101267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
Salmonella is one of the most spread foodborne pathogens worldwide, and Salmonella infections in humans still represent a global health burden. The main source of Salmonella infections in humans is represented by contaminated animal-derived foodstuffs, with pork products being one of the most important players. Salmonella infection in swine is critical not only because it is one of the main causes of economic losses in the pork industry, but also because pigs can be infected by several Salmonella serovars, potentially contaminating the pig meat production chain and thus posing a significant threat to public health globally. As of now, in Europe and in the United States, swine-related Salmonella serovars, e.g., Salmonella Typhimurium and its monophasic variant Salmonella enterica subsp. enterica 1,4,[5],12:i:-, are also frequently associated with human salmonellosis cases. Moreover, multiple outbreaks have been reported in the last few decades which were triggered by the consumption of Salmonella-contaminated pig meat. Throughout the years, changes and evolution across the pork industry may have acted as triggers for new issues and obstacles hindering Salmonella control along the food chain. Gathered evidence reinforces the importance of coordinating control measures and harmonizing monitoring programs for the efficient control of Salmonella in swine. This is necessary in order to manage outbreaks of clinical disease in pigs and also to protect pork consumers by controlling Salmonella subclinical carriage and shedding. This review provides an update on Salmonella infection in pigs, with insights on Salmonella ecology, focusing mainly on Salmonella Choleraesuis, S. Typhimurium, and S. 1,4,[5],12:i:-, and their correlation to human salmonellosis cases. An update on surveillance methods for epidemiological purposes of Salmonella infection in pigs and humans, in a "One Health" approach, will also be reported.
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Affiliation(s)
- Laura Soliani
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna (IZSLER), 25124 Brescia, Italy; (G.R.); (A.P.); (C.C.); (A.L.)
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8
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Luo Q, Wu Y, Bao D, Xu L, Chen H, Yue M, Draz MS, Kong Y, Ruan Z. Genomic epidemiology of mcr carrying multidrug-resistant ST34 Salmonella enterica serovar Typhimurium in a one health context: The evolution of a global menace. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165203. [PMID: 37406695 DOI: 10.1016/j.scitotenv.2023.165203] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
The rapid global dissemination of Salmonella enterica sequence type 34 (ST34) has sparked significant concern due to its resistance to critical antimicrobials and its ability to spread across various sectors. In order to investigate the evolution and transmission dynamics of this epidemic clonal lineage, as well as the horizontal transfer of mcr-carrying plasmids within the One Health framework, we conducted a comprehensive genomic epidemiological study. This study focused on the 11 mcr-carrying S. enterica isolates obtained from clinical settings in China, while also considering 2337 publicly available genomes of mcr-carrying S. enterica collected from 20 countries and diverse sources spanning over a 22-year period. Among the mcr-positive Salmonella isolates, ST34 was found to be the predominant lineage, comprising 30.12 % (704/2337) of the total collection. These isolates were identified as either serovar Typhimurium or its monophasic variant, which were obtained from both clinical and non-clinical sources. Phylogeographic analyses traced the global spread of the mcr-carrying ST34 lineage, which was divided into three distinct clusters, with 83.10 % of them carrying mcr-1 or/and mcr-9 genes. Notably, the mcr-1 positive ST34 isolates were primarily found in China (190/298, 63.76 %), with only four from the United States. Conversely, mcr-9 positive ST34 isolates were predominantly identified in the United States (261/293, 89.08 %), while none were observed in China. The mcr-1 positive ST34 isolates was predicted to have originated from clinical sources in United Kingdom, whereas mcr-9 positive ST34 isolates was likely derived from environmental sources in Germany. The most recent common ancestor for mcr-1 and mcr-9 carrying ST34 S. enterica was estimated to have emerged around 1983 and 1951. These findings provided thorough and intuitive insights into the intercontinental spread of mcr-carrying S. enterica ST34 lineage in a One Health context. Ongoing surveillance is crucial for effectively monitoring the worldwide dissemination of this multidrug-resistant high-risk clone.
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Affiliation(s)
- Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuye Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Danni Bao
- Department of Clinical Laboratory, Sanmen People's Hospital, Taizhou, China
| | - Linna Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; School of Laboratory Medicine and Biotechnology, Hangzhou Medical College, Hangzhou, China
| | - Hangfei Chen
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Meina Yue
- Department of Clinical Laboratory, Hangzhou Children's Hospital, Hangzhou, China
| | - Mohamed S Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biomedical Engineering, Cleveland Clinic, Cleveland, OH, USA
| | - Yingying Kong
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China.
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9
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Napoleoni M, Villa L, Barco L, Lucarelli C, Tiengo A, Baggio G, Dionisi AM, Angellotti A, Ferretti E, Ruggeri S, Staffolani M, Rocchegiani E, Silenzi V, Morandi B, Blasi G. Monophasic Variant of Salmonella Typhimurium 4,[5],12:i:- (ACSSuGmTmpSxt Type) Outbreak in Central Italy Linked to the Consumption of a Roasted Pork Product (Porchetta). Microorganisms 2023; 11:2567. [PMID: 37894225 PMCID: PMC10609469 DOI: 10.3390/microorganisms11102567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
The monophasic variant of S. Typhimurium 4,[5],12:i:- (MVST) is the third most commonly reported Salmonella serovar involved in human infections (8.8%) in the EU and ranks after S. Enteritidis (54.6%) and S. Typhimurium (11.4%). In Italy, in contrast, the MVST has achieved peculiar epidemiological and ecological success which has allowed it to be, since 2011, the serovar most frequently isolated from humans. In the summer of 2022, a foodborne outbreak of the MVST involving 63 people occurred in the Marche Region (Central Italy). A common food exposure source among some human cases was a roasted, ready-to-eat (RTE) pork product, porchetta, which is a typical product of Central Italy. This paper describes the results of investigations conducted to clarify this outbreak. The porchetta was produced by a local manufacturing plant and distributed to at least two local retail stores, one of which was the retail outlet for the manufacturing plant. The MVST was isolated from surface samples collected at the porchetta manufacturing plant and at both local retail stores via bacterial analysis, and the porchetta sampled at one store contained the MVST. These data confirm this type of RTE pork product can be a source of Salmonella infection in humans.
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Affiliation(s)
- Maira Napoleoni
- Centro di Riferimento Regionale Patogeni Enterici Marche, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Maestri del Lavoro, 7, 62029 Tolentino, Macerata, Italy; (M.S.); (E.R.); (V.S.); (G.B.)
| | - Laura Villa
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Roma, Italy; (L.V.); (C.L.); (A.M.D.)
| | - Lisa Barco
- Centro di Referenza Nazionale e Laboratorio di Referenza WOAH per le Salmonellosi, Istituto Zooprofilattico Sperimentale Delle Venezie, Viale dell’Università, 10, 35020 Legnaro, Padova, Italy; (L.B.); (A.T.); (G.B.)
| | - Claudia Lucarelli
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Roma, Italy; (L.V.); (C.L.); (A.M.D.)
| | - Alessia Tiengo
- Centro di Referenza Nazionale e Laboratorio di Referenza WOAH per le Salmonellosi, Istituto Zooprofilattico Sperimentale Delle Venezie, Viale dell’Università, 10, 35020 Legnaro, Padova, Italy; (L.B.); (A.T.); (G.B.)
| | - Giulia Baggio
- Centro di Referenza Nazionale e Laboratorio di Referenza WOAH per le Salmonellosi, Istituto Zooprofilattico Sperimentale Delle Venezie, Viale dell’Università, 10, 35020 Legnaro, Padova, Italy; (L.B.); (A.T.); (G.B.)
| | - Anna Maria Dionisi
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Roma, Italy; (L.V.); (C.L.); (A.M.D.)
| | - Antonio Angellotti
- UOC Igiene degli Alimenti di Origine Animale, Azienda Sanitaria Territoriale Fermo—Marche, Via Zeppilli, 22A, 63900 Fermo, Italy; (A.A.); (E.F.); (S.R.)
| | - Ezio Ferretti
- UOC Igiene degli Alimenti di Origine Animale, Azienda Sanitaria Territoriale Fermo—Marche, Via Zeppilli, 22A, 63900 Fermo, Italy; (A.A.); (E.F.); (S.R.)
| | - Simonetta Ruggeri
- UOC Igiene degli Alimenti di Origine Animale, Azienda Sanitaria Territoriale Fermo—Marche, Via Zeppilli, 22A, 63900 Fermo, Italy; (A.A.); (E.F.); (S.R.)
| | - Monica Staffolani
- Centro di Riferimento Regionale Patogeni Enterici Marche, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Maestri del Lavoro, 7, 62029 Tolentino, Macerata, Italy; (M.S.); (E.R.); (V.S.); (G.B.)
| | - Elena Rocchegiani
- Centro di Riferimento Regionale Patogeni Enterici Marche, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Maestri del Lavoro, 7, 62029 Tolentino, Macerata, Italy; (M.S.); (E.R.); (V.S.); (G.B.)
| | - Valentina Silenzi
- Centro di Riferimento Regionale Patogeni Enterici Marche, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Maestri del Lavoro, 7, 62029 Tolentino, Macerata, Italy; (M.S.); (E.R.); (V.S.); (G.B.)
| | - Benedetto Morandi
- Laboratorio di Diagnostica Animale, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Maestri del Lavoro, 7, 62029 Tolentino, Macerata, Italy;
| | - Giuliana Blasi
- Centro di Riferimento Regionale Patogeni Enterici Marche, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Maestri del Lavoro, 7, 62029 Tolentino, Macerata, Italy; (M.S.); (E.R.); (V.S.); (G.B.)
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10
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Chung The H, Pham P, Ha Thanh T, Phuong LVK, Yen NP, Le SNH, Vu Thuy D, Chau TTH, Le Phuc H, Ngoc NM, Vi LL, Mather AE, Thwaites GE, Thomson NR, Baker S, Pham DT. Multidrug resistance plasmids underlie clonal expansions and international spread of Salmonella enterica serotype 1,4,[5],12:i:- ST34 in Southeast Asia. Commun Biol 2023; 6:1007. [PMID: 37789208 PMCID: PMC10547704 DOI: 10.1038/s42003-023-05365-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023] Open
Abstract
Salmonella enterica serotype 1,4,[5],12:i:- (Typhimurium monophasic variant) of sequence type (ST) 34 has emerged as the predominant pandemic genotype in recent decades. Despite increasing reports of resistance to antimicrobials in Southeast Asia, Salmonella ST34 population structure and evolution remained understudied in the region. Here we performed detailed genomic investigations on 454 ST34 genomes collected from Vietnam and diverse geographical sources to elucidate the pathogen's epidemiology, evolution and antimicrobial resistance. We showed that ST34 has been introduced into Vietnam in at least nine occasions since 2000, forming five co-circulating major clones responsible for paediatric diarrhoea and bloodstream infection. Most expansion events were associated with acquisitions of large multidrug resistance plasmids of IncHI2 or IncA/C2. Particularly, the self-conjugative IncA/C2 pST34VN2 (co-transferring blaCTX-M-55, mcr-3.1, and qnrS1) underlies local expansion and intercontinental spread in two separate ST34 clones. At the global scale, Southeast Asia was identified as a potential hub for the emergence and dissemination of multidrug resistant Salmonella ST34, and mutation analysis suggests of selection in antimicrobial responses and key virulence factors.
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Affiliation(s)
- Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
| | - Phuong Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Son-Nam H Le
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Duong Vu Thuy
- Children's Hospital No. 1, Ho Chi Minh City, Vietnam
| | | | - Hoang Le Phuc
- Children's Hospital No. 1, Ho Chi Minh City, Vietnam
| | | | - Lu Lan Vi
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen Baker
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases (CITIID), University of Cambridge, Cambridge, UK
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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11
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Yang M, Dong Q, Niu H, Li J, Lin Z, Aslam MZ, Wang X, Li Z, Liu Y, Ma Y, Qin X. Exposure of Salmonella enterica serovar 1,4,[5],12:i:- to benzalkonium chloride leads to acquired resistance to this disinfectant and antibiotics. J Appl Microbiol 2023; 134:lxad177. [PMID: 37587011 DOI: 10.1093/jambio/lxad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/24/2023] [Accepted: 08/15/2023] [Indexed: 08/18/2023]
Abstract
AIMS Disinfectants such as benzalkonium chloride (BC), extensively used in animal farms and food-processing industries, contribute to the development of adaptive and cross-resistance in foodborne pathogens, posing a serious threat to food safety and human health. The purpose of this study is to explore whether continuous exposure of Salmonella enterica serovar 1,4,[5],12:i:- (S. 1,4,[5],12:i:-) to sublethal concentrations of BC could result in acquired resistance to this agent and other environmental stresses (e.g. antibiotics, heat, and acid). METHODS AND RESULTS BC tolerance increased in all tested strains after exposure to gradually increasing concentrations of BC, with increases in minimum inhibitory concentrations between two and sixfold. The survival rate of BC-adapted strains was significantly (P < 0.05) higher than that of their wild-type (non-adapted) counterparts in lethal concentrations of BC. In addition, significant reductions (P < 0.05) in zeta potential were observed in BC-adapted strains compared to wild-type ones, indicating that a reduction in cell surface charge was a cause of adaptative resistance. More importantly, two BC-adapted strains exhibited increased antibiotic resistance to levofloxacin, ceftazidime, and tigecycline, while gene mutations (gyrA, parC) and antibiotic efflux-related genes (acrB, mdsA, mdsB) were detected by genomic sequencing analysis. Moreover, the tolerance of BC-adapted strains to heat (50, 55, and 60°C) and acid (pH 2.0, 2.5) was strain-dependent and condition-dependent. CONCLUSIONS Repeated exposure to sublethal concentrations of BC could result in the emergence of BC- and antibiotic-resistant S. 1,4,[5],12:i:- strains.
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Affiliation(s)
- Mingzhe Yang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Qingli Dong
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Hongmei Niu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Jiaming Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zijie Lin
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Muhammad Zohaib Aslam
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xiang Wang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zhuosi Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yangtai Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yue Ma
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xiaojie Qin
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
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12
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Wang Z, Jiang Z, Xu H, Jiao X, Li Q. Prevalence and molecular characterization of mcr-1-positive foodborne ST34-Salmonella isolates in China. Microbiol Res 2023; 274:127441. [PMID: 37356255 DOI: 10.1016/j.micres.2023.127441] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) and S. 4,[5],12:i:- have become the most common serovars associated with human salmonellosis worldwide. Moreover, the emergence of mcr-carrying S. Typhimurium and S. 4,[5],12:i:- with multidrug resistance (MDR) patterns has posed a threat to public health. In this study, we retrospectively screened 2009-2022 laboratory-preserved strains for the presence of mcr genes. We obtained 16 mcr-1-positive S. Typhimurium and S. 4,[5],12:i:- strains with MDR that belonged to sequence type 34 (ST34). Whole-genome sequencing analysis revealed that the mcr-1 was located on the IncI2 or IncHI2 plasmids. The ISApl1 element downstream of mcr-1 was present in all pig-derived strains. Conjugation experiments confirmed that nine mcr-1-carrying IncHI2 plasmids could not be transferred to Escherichia coli due to loss of the conjugation region. Finally, core genome single nucleotide polymorphism (cgSNP) analyses of the 16 mcr-1-carrying strains and 77 mcr-carrying ST34-Salmonella genome sequences from the NCBI and ENA databases showed that five out of eight clusters contained strains from pig and pig products, revealing pigs and pig products as key reservoirs of mcr-1-positive ST34-Salmonella strains. The transmission of mcr-carrying ST34 Salmonella strains to humans via the pig food chain is a potential cause for public health concern in controlling human salmonellosis.
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Affiliation(s)
- Zhenyu Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, 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 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China
| | - Zhongyi Jiang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, 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 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China
| | - Haiyan Xu
- Nantong Center for Disease Control and Prevention, Nantong 226007, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, 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 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China.
| | - Qiuchun Li
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, 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 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China.
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13
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Lopez-Garcia AV, AbuOun M, Nunez-Garcia J, Nale JY, Gaylov EE, Phothaworn P, Sukjoi C, Thiennimitr P, Malik DJ, Korbsrisate S, Clokie MRJ, Anjum MF. Pathogen genomics and phage-based solutions for accurately identifying and controlling Salmonella pathogens. Front Microbiol 2023; 14:1166615. [PMID: 37234523 PMCID: PMC10206635 DOI: 10.3389/fmicb.2023.1166615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/03/2023] [Indexed: 05/28/2023] Open
Abstract
Salmonella is a food-borne pathogen often linked to poultry sources, causing gastrointestinal infections in humans, with the numbers of multidrug resistant (MDR) isolates increasing globally. To gain insight into the genomic diversity of common serovars and their potential contribution to disease, we characterized antimicrobial resistance genes, and virulence factors encoded in 88 UK and 55 Thai isolates from poultry; the presence of virulence genes was detected through an extensive virulence determinants database compiled in this study. Long-read sequencing of three MDR isolates, each from a different serovar, was used to explore the links between virulence and resistance. To augment current control methods, we determined the sensitivity of isolates to 22 previously characterized Salmonella bacteriophages. Of the 17 serovars included, Salmonella Typhimurium and its monophasic variants were the most common, followed by S. Enteritidis, S. Mbandaka, and S. Virchow. Phylogenetic analysis of Typhumurium and monophasic variants showed poultry isolates were generally distinct from pigs. Resistance to sulfamethoxazole and ciprofloxacin was highest in isolates from the UK and Thailand, respectively, with 14-15% of all isolates being MDR. We noted that >90% of MDR isolates were likely to carry virulence genes as diverse as the srjF, lpfD, fhuA, and stc operons. Long-read sequencing revealed the presence of global epidemic MDR clones in our dataset, indicating they are possibly widespread in poultry. The clones included MDR ST198 S. Kentucky, harboring a Salmonella Genomic Island-1 (SGI)-K, European ST34 S. 1,4,[5],12:i:-, harboring SGI-4 and mercury-resistance genes, and a S. 1,4,12:i:- isolate from the Spanish clone harboring an MDR-plasmid. Testing of all isolates against a panel of bacteriophages showed variable sensitivity to phages, with STW-77 found to be the most effective. STW-77 lysed 37.76% of the isolates, including serovars important for human clinical infections: S. Enteritidis (80.95%), S. Typhimurium (66.67%), S. 1,4,[5],12:i:- (83.3%), and S. 1,4,12: i:- (71.43%). Therefore, our study revealed that combining genomics and phage sensitivity assays is promising for accurately identifying and providing biocontrols for Salmonella to prevent its dissemination in poultry flocks and through the food chain to cause infections in humans.
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Affiliation(s)
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Javier Nunez-Garcia
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Janet Y. Nale
- Department of Veterinary and Animal Science, Scotland's Rural College, Inverness, United Kingdom
| | - Edouard E. Gaylov
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Preeda Phothaworn
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chutikarn Sukjoi
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Danish J. Malik
- Department of Chemical Engineering, Loughborough University, Loughborough, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
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14
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Inflammatory Responses Induced by the Monophasic Variant of Salmonella Typhimurium in Pigs Play a Role in the High Shedder Phenotype and Fecal Microbiota Composition. mSystems 2023; 8:e0085222. [PMID: 36629432 PMCID: PMC9948705 DOI: 10.1128/msystems.00852-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Pigs infected with Salmonella may excrete large amounts of Salmonella, increasing the risk of spread of this pathogen in the food chain. Identifying Salmonella high shedder pigs is therefore required to mitigate this risk. We analyzed immune-associated markers and composition of the gut microbiota in specific-pathogen-free pigs presenting different shedding levels after an oral infection with Salmonella. Immune response was studied through total blood cell counts, production of anti-Salmonella antibodies and cytokines, and gene expression quantification. Total Salmonella shedding for each pig was estimated and hierarchical clustering was used to cluster pigs into high, intermediate, and low shedders. Gut microbiota compositions were assessed using 16S rRNA microbial community profiling. Comparisons were made between control and inoculated pigs, then between high and low shedders pigs. Prior to infection, high shedders had similar immunological profiles compared to low shedders. As soon as 1 day postinoculation (dpi), significant differences on the cytokine production level and on the expression level of several host genes related to a proinflammatory response were observed between high and low shedders. Infection with Salmonella induced an early and profound remodeling of the immune response in all pigs, but the intensity of the response was stronger in high shedders. In contrast, low shedders seroconverted earlier than high shedders. Just after induction of the proinflammatory response (at 2 dpi), some taxa of the fecal microbiota were specific to the shedding phenotypes. This was related to the enrichment of several functional pathways related to anaerobic respiration in high shedders. In conclusion, our data show that the immune response to Salmonella modifies the fecal microbiota and subsequently could be responsible for shedding phenotypes. Influencing the gut microbiota and reducing intestinal inflammation could be a strategy for preventing Salmonella high shedding in livestock. IMPORTANCE Salmonellosis remains the most frequent human foodborne zoonosis after campylobacteriosis and pork meat is considered one of the major sources of human foodborne infections. At the farm, host heterogeneity in pig infection is problematic. High Salmonella shedders contribute more significantly to the spread of this foodborne pathogen in the food chain. The identification of predictive biomarkers for high shedders could help to control Salmonella in pigs. The purpose of the present study was to investigate why some pigs become super shedders and others low shedders. We thus investigated the differences in the fecal microbial composition and the immune response in orally infected pigs presenting different Salmonella shedding patterns. Our data show that the proinflammatory response induced by S. Typhimurium at 1 dpi could be responsible for the modification of the fecal microbiota composition and functions observed mainly at 2 and 3 dpi and to the low and super shedder phenotypes.
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15
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Plumb ID, Brown AC, Stokes EK, Chen JC, Carleton H, Tolar B, Sundararaman P, Saupe A, Payne DC, Shah HJ, Folster JP, Friedman CR. Increased Multidrug-Resistant Salmonella enterica I Serotype 4,[5],12:i:- Infections Associated with Pork, United States, 2009-2018. Emerg Infect Dis 2023; 29. [PMID: 36692335 PMCID: PMC9881761 DOI: 10.3201/eid2902.220950] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Reports of Salmonella enterica I serotype 4,[5],12:i:- infections resistant to ampicillin, streptomycin, sulphamethoxazole, and tetracycline (ASSuT) have been increasing. We analyzed data from 5 national surveillance systems to describe the epidemiology, resistance traits, and genetics of infections with this Salmonella strain in the United States. We found ASSuT-resistant Salmonella 4,[5],12:i:- increased from 1.1% of Salmonella infections during 2009-2013 to 2.6% during 2014-2018; the proportion of Salmonella 4,[5],12:i:- isolates without this resistance pattern declined from 3.1% to 2.4% during the same timeframe. Among isolates sequenced during 2015-2018, a total of 69% were in the same phylogenetic clade. Within that clade, 77% of isolates had genetic determinants of ASSuT resistance, and 16% had genetic determinants of decreased susceptibility to ciprofloxacin, ceftriaxone, or azithromycin. Among outbreaks related to the multidrug-resistant clade, 63% were associated with pork consumption or contact with swine. Preventing Salmonella 4,[5],12:i:- carriage in swine would likely avert human infections with this strain.
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Salmonella enterica prevalence, serotype diversity, antimicrobial resistance and control in the European pork production chain. Trends Food Sci Technol 2023. [DOI: 10.1016/j.tifs.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Arnold K, Lim S, Rakler T, Rovira A, Satuchne C, Yechezkel E, Wiseman A, Pima Y, Yakunin E, Rokney A, Elnekave E. Using genetic markers for detection and subtyping of the emerging Salmonella enterica subspecies enterica serotype Muenchen. Poult Sci 2022; 101:102181. [PMID: 36215738 PMCID: PMC9554807 DOI: 10.1016/j.psj.2022.102181] [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: 06/24/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
Non-typhoidal Salmonella (NTS) poses a global threat to public health. Poultry, one of the main reservoirs of NTS, is usually not clinically affected by most NTS, yet the economic losses to the poultry industry due to control and mitigation efforts, and due to negative publicity can be tremendous. NTS strains are routinely characterized into serotypes in a time-consuming, labor-intensive multistep process that requires skilled personnel. Moreover, the discriminatory power of serotyping is limited compared to other subtyping methods. Whole-genome sequence data enable the identification of genetic variation within serotypes. However, sequencing is often limited by available resources, and analyzing and interpreting the genetic data may be time-consuming. Source tracing during epidemiological outbreak investigations requires rapid and efficient characterization of strains to control pathogen spread. Here we designed a multiplex polymerase chain reaction (PCR) assay for the detection of genetic variants of Salmonella Muenchen, a serotype that has emerged in Israel in the last 3 yr in both clinical human cases and different hosts. Test sensitivity of 99.21% and specificity of 94 to 100% were determined using in-silico PCR with a dataset of 18,282 NTS assemblies from 37 NTS serotypes. Similarly, test sensitivity of 100% and specificity of 96.2 to 100% were determined in-vitro with 120 NTS isolates of 52 serotypes. Moreover, the test enabled differentiation between the common sequence types of serotype Muenchen using both approaches. As opposed to traditional serotyping and other subtyping methods, the designed test allows for rapid and cost-efficient detection of the emerging S. Muenchen serotype and its variants in a single step. Future development of similar assays for other dominant serotypes may help reduce the time and cost required for detection and initial characterization of dominant NTS strains. Overall, these tests will be beneficial to both public health and for reducing of the economic losses to the poultry industry due to NTS infections.
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Zhao W, Li X, Shi X, Li K, Shi B, Sun J, Zhao C, Wang J. Whole Genome Sequencing, Antibiotic Resistance, and Epidemiology Features of Nontyphoidal Salmonella Isolated From Diarrheic Children: Evidence From North China. Front Microbiol 2022; 13:882647. [PMID: 35651495 PMCID: PMC9150820 DOI: 10.3389/fmicb.2022.882647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Nontyphoidal Salmonella (NTS) in children remains a growing burden on public health and often causes children to be hospitalized with diarrheic symptoms. In this work, 260 strains of human Salmonella isolated from Jilin, China were characterized by serotypes and antimicrobial resistance using whole genome sequencing (WGS). The most prevalent serotype was Salmonella enteritidis (47.3%), followed by S. I 4,[5],12:i:- (33.1%), and Salmonella Typhimurium (7.3%). Furthermore, the consistency between resistance phenotype and genotype was confirmed. Similarly, strains harbored blaTEM−1B and tetA genes were detected, which verified the level of resistant phenotype in β-lactams and tetracyclines. The presence of a single mutation in parC, gyrA, and qnrS1 genes corresponding to quinolones was also observed. In our work, multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) were found to have a high resolution to molecular traceability, and the combination of both was conducive to practical application in an actual situation. Taking all of this into account, we suggested that the comprehensive surveillance of Salmonella infection in children should be carried out to monitor antimicrobial-resistant trends from various sources and to alert on outbreaks of foodborne diseases to protect public health.
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Affiliation(s)
- Wei Zhao
- Jilin Center for Disease Prevention and Control, Changchun, China
| | - Xin Li
- School of Public Health, Jilin University, Changchun, China
| | - Xuening Shi
- School of Public Health, Jilin University, Changchun, China
| | - Kewei Li
- Jilin Center for Disease Prevention and Control, Changchun, China
| | - Ben Shi
- Jilin Center for Disease Prevention and Control, Changchun, China
| | - Jingyu Sun
- Jilin Center for Disease Prevention and Control, Changchun, China
| | - Chao Zhao
- School of Public Health, Jilin University, Changchun, China
| | - Juan Wang
- School of Public Health, Jilin University, Changchun, China
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Long L, You L, Wang D, Wang M, Wang J, Bai G, Li J, Wei X, Li S. Highly prevalent MDR, frequently carrying virulence genes and antimicrobial resistance genes in Salmonella enterica serovar 4,[5],12:i:- isolates from Guizhou Province, China. PLoS One 2022; 17:e0266443. [PMID: 35588421 PMCID: PMC9119451 DOI: 10.1371/journal.pone.0266443] [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: 02/17/2022] [Accepted: 04/05/2022] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serovar 4,[5],12:i:-, a monophasic variant of Salmonella Typhimurium lacking the phase 2 flagellin, is one of the common serotypes causing Salmonellosis worldwide. However, information on Salmonella serovar 4,[5],12:i:- from Guizhou Province has lacked so far. This study aimed to investigate the antimicrobial resistance, the presence of antimicrobial resistance genes and virulence genes, and characterize the MLST genotypes of Salmonella serovar 4,[5],12:i:- isolates from Guizhou province, China. We collected 363 non-typhoid Salmonella (NTS) isolates of Guizhou from 2013 to 2018. Biochemical identification, serogroups testing, and specific multiplex polymerase chain reaction (mPCR) assay were conducted to identify Salmonella 4,[5],12:i:- isolates. Isolates were determined the antimicrobial resistance by the micro broth dilution method, detected the presence of antimicrobial resistance genes and virulence genes by PCR, and examined the molecular genotyping by Multilocus sequence typing (MLST). Eighty-seven Salmonella 4,[5],12:i:- isolates were detected, accounting for 23.9% (87/363) of the total NTS isolates. All Salmonella 4,[5],12:i:- isolates showed highly resistant to sulfaoxazole (93.1%), streptomycin (90.8%), ampicillin (88.5%), tetracycline (86.2%) and doxycycline (86.2%). A high proportion (94.2%) of multi-drug resistance (MDR) isolates were found. Most (83.9%) Salmonella 4,[5],12:i:- isolates carried four antimicrobial resistance genes, especially blaTEM-1, strA-strB, sul2, and tetB genes. Salmonella 4,[5],12:i:- isolates showed a high rate of invA, sseL, mgtC, siiE, sopB, gipA, gtgB, sspH1, and sspH2 (72.4%~98.9%). On the contrary, none of the isolates were detected the spvC and pefA genes. MLST analysis revealed three sequence types (STs), and ST34 (97.7%) was the dominant sequence type. This study is the first report of Salmonella 4,[5],12:i:- in humans from Guizhou province, China. The data might be useful for rational antimicrobial usage against Salmonella 4,[5],12:i:- infections, risk management, and public health strategies in Guizhou.
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Affiliation(s)
- Li Long
- Laboratory of Bacterial Disease, Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, People’s Republic of China
| | - Lv You
- Laboratory of Bacterial Disease, Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, People’s Republic of China
| | - Dan Wang
- Institute of Communicable Disease Control and Prevention, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, People’s Republic of China
| | - Ming Wang
- Laboratory of Bacterial Disease, Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, People’s Republic of China
| | - Junhua Wang
- School of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
| | - Guihuan Bai
- School of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
| | - Jianhua Li
- Tongren City Center for Disease Control and Prevention, Tongren, People’s Republic of China
| | - Xiaoyu Wei
- Laboratory of Bacterial Disease, Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, People’s Republic of China
- * E-mail: (XW); (SL)
| | - Shijun Li
- Laboratory of Bacterial Disease, Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, People’s Republic of China
- * E-mail: (XW); (SL)
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20
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Trachsel JM, Bearson BL, Brunelle BW, Bearson SMD. Relationship and distribution of Salmonella enterica serovar I 4,[5],12:i:- strain sequences in the NCBI Pathogen Detection database. BMC Genomics 2022; 23:268. [PMID: 35387579 PMCID: PMC8985322 DOI: 10.1186/s12864-022-08458-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/10/2022] [Indexed: 11/14/2022] Open
Abstract
Background Of the > 2600 Salmonella serovars, Salmonella enterica serovar I 4,[5],12:i:- (serovar I 4,[5],12:i:-) has emerged as one of the most common causes of human salmonellosis and the most frequent multidrug-resistant (MDR; resistance to ≥3 antimicrobial classes) nontyphoidal Salmonella serovar in the U.S. Serovar I 4,[5],12:i:- isolates have been described globally with resistance to ampicillin, streptomycin, sulfisoxazole, and tetracycline (R-type ASSuT) and an integrative and conjugative element with multi-metal tolerance named Salmonella Genomic Island 4 (SGI-4). Results We analyzed 13,612 serovar I 4,[5],12:i:- strain sequences available in the NCBI Pathogen Detection database to determine global distribution, animal sources, presence of SGI-4, occurrence of R-type ASSuT, frequency of antimicrobial resistance (AMR), and potential transmission clusters. Genome sequences for serovar I 4,[5],12:i:- strains represented 30 countries from 5 continents (North America, Europe, Asia, Oceania, and South America), but sequences from the United States (59%) and the United Kingdom (28%) were dominant. The metal tolerance island SGI-4 and the R-type ASSuT were present in 71 and 55% of serovar I 4,[5],12:i:- strain sequences, respectively. Sixty-five percent of strain sequences were MDR which correlates to serovar I 4,[5],12:i:- being the most frequent MDR serovar. The distribution of serovar I 4,[5],12:i:- strain sequences in the NCBI Pathogen Detection database suggests that swine-associated strain sequences were the most frequent food-animal source and were significantly more likely to contain the metal tolerance island SGI-4 and genes for MDR compared to all other animal-associated isolate sequences. Conclusions Our study illustrates how analysis of genomic sequences from the NCBI Pathogen Detection database can be utilized to identify the prevalence of genetic features such as antimicrobial resistance, metal tolerance, and virulence genes that may be responsible for the successful emergence of bacterial foodborne pathogens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08458-z.
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Affiliation(s)
- Julian M Trachsel
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA. .,Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, USA.
| | - Bradley L Bearson
- Agroecosystems Management Research Unit, National Laboratory for Agriculture and the Environment, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA.
| | - Brian W Brunelle
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA.,Present address: Arbor Biosciences, Ann Arbor, MI, USA
| | - Shawn M D Bearson
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA
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21
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Harrison OL, Rensing S, Jones CK, Trinetta V. Salmonella enterica 4,[5],12:i:-, an Emerging Threat for the Swine Feed and Pork Production Industry. J Food Prot 2022; 85:660-663. [PMID: 34936694 DOI: 10.4315/jfp-21-400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Salmonella continues to be a significant cause of foodborne illnesses in human medicine. The Centers for Disease Control and Prevention reported Salmonella as the second leading cause of foodborne illness in the United States and the leading cause of both hospitalizations and deaths. Salmonella enterica 4,[5],12:i:- (STM) is a monophasic variant of Salmonella Typhimurium, and it is an emerging threat to both human and animal health. STM was first identified in the 1980s from poultry products and has become increasingly prevalent in meat products including pork. STM has also been identified in swine farms as well as in feed manufacturing environments and feed itself. Similar pulse-field gel electrophoresis profiles have been observed between human clinical cases and the STM samples originating from swine feed. These related profiles suggest a link between ingestion of contaminated feed by swine and the source of foodborne illness in human. The objective of this article was to better understand the history of STM and the possible pathway from swine feed to table. Continued research is necessary to better understand how STM can enter both the feed supply chain and the pork production chain to avoid contamination of pork products destined for human consumption. HIGHLIGHTS
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Affiliation(s)
- Olivia L Harrison
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Susan Rensing
- Department of Gender, Women, and Sexuality Studies, Kansas State University, Manhattan, Kansas 66506, USA
| | - Cassandra K Jones
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Valentina Trinetta
- Food Science Institute, Kansas State University, Manhattan, Kansas 66506, USA
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22
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Holohan N, Wallat M, Hai Yen Luu T, Clark E, Truong DTQ, Xuan SD, Vu HTK, Van Truong D, Tran Huy H, Nguyen-Viet H, Unger F, Thi Thanh Dang S, Stabler RA. Analysis of Antimicrobial Resistance in Non-typhoidal Salmonella Collected From Pork Retail Outlets and Slaughterhouses in Vietnam Using Whole Genome Sequencing. Front Vet Sci 2022; 9:816279. [PMID: 35425826 PMCID: PMC9002014 DOI: 10.3389/fvets.2022.816279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/09/2022] [Indexed: 12/03/2022] Open
Abstract
Non-typhoidal salmonella (TS) remains a significant health burden worldwide. In Vietnam, pork accounts for 70% of the total meat consumed, and contamination with Salmonella is high. High levels of antimicrobial resistance (AMR) have emerged among porcine NTS and of particular concern is the emergence of colistin resistance, a “last defense” antibioic against multi-drug resistant (MDR) Gram-negative pathogens. This study aimed to investigate the antibiotic susceptibility of 69 NTS isolates collected from the pork retail outlets and slaughterhouses in Vietnam during 2014 a nd 2018/19. Phenotypic testing and whole genome sequencing was used to assess the serotype and AMR gene profiles of the 69 NTS isolates. Seventeen different serotypes were identified, of which S. enterica subsp enterica serotype Typhimurium was the most common followed by S. ser. Rissen, S. ser. London, S. ser. Anatum, and S. ser. Derby. Phenotype AMR was common with 41 (59.4%) isolates deemed MDR. MDR strains were most common in slaughterhouses (83%) and supermarkets (75%) and lowest in traditional markets (38%) and convenience stores (40%). Colistin resistance was identified in 18 strains (15 resistant, three intermediate) with mcr-1 identified in seven isolates (S. ser. Meleagridis, S. Rissen, S. Derby) and mcr-3 in two isolates (S. Typhimurium). This includes the first mcr positive S. Meleagridis to our knowledge. Surprisingly, boutique stores had high levels (60%) of MDR isolates including 5/20 isolates with mcr-1. This study demonstrates that pork from modern retail stores classed as supermarkets or boutique (with pork claiming to be high quality, traceable, environmentally friendly marketed toward higher income consumers) still contained NTS with high levels of AMR.
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Affiliation(s)
- Niamh Holohan
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Maximilian Wallat
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Thi Hai Yen Luu
- Department of Bacteriology, National Institute of Veterinary Research (NIVR), Hanoi, Vietnam
| | - Eleanor Clark
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Duong Thi Quy Truong
- Department of Bacteriology, National Institute of Veterinary Research (NIVR), Hanoi, Vietnam
| | - Sinh Dang Xuan
- International Livestock Research Institute, Regional Office for East and Southeast Asia, Hanoi, Vietnam
| | - Hue Thi Kim Vu
- Department of Veterinary Hygiene, National Institute of Veterinary Research (NIVR), Hanoi, Vietnam
| | - Dung Van Truong
- Department of Veterinary Hygiene, National Institute of Veterinary Research (NIVR), Hanoi, Vietnam
| | - Hoang Tran Huy
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Hung Nguyen-Viet
- International Livestock Research Institute, Regional Office for East and Southeast Asia, Hanoi, Vietnam
| | - Fred Unger
- International Livestock Research Institute, Regional Office for East and Southeast Asia, Hanoi, Vietnam
| | - Son Thi Thanh Dang
- Department of Veterinary Hygiene, National Institute of Veterinary Research (NIVR), Hanoi, Vietnam
| | - Richard A. Stabler
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
- *Correspondence: Richard A. Stabler
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Vázquez X, Forcelledo L, Balboa-Palomino S, Fernández J, Rodicio MR. Nosocomial Pneumonia Caused in an Immunocompetent Patient by the Emergent Monophasic ST34 Variant of Salmonella enterica Serovar Typhimurium: Treatment-Associated Selection of Fluoroquinolone and Piperacillin/Tazobactam Resistance. Antibiotics (Basel) 2022; 11:antibiotics11030303. [PMID: 35326766 PMCID: PMC8944838 DOI: 10.3390/antibiotics11030303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023] Open
Abstract
The present report describes an uncommon case of nosocomial pneumonia caused by Salmonellaenterica in an immunocompetent patient. The patient was admitted to ICU of a tertiary hospital due to low level of consciousness, aphasia and seizure episodes. Four days after hospitalization, he developed nosocomial pneumonia, which evolved into septic shock. Gram-negative bacilli were recovered from blood, tracheal aspirate and fecal samples of the patient. The isolates, which were identified as Salmonella enterica, proved to be resistant to ciprofloxacin, amoxicillin/clavulanic acid and piperacillin/tazobactam. Four months before, the same bacterial species was recovered from feces and blood cultures of the patient, admitted to the nephrology ward of the same hospital with diagnosis of gastroenteritis and acute renal failure. However, at that time, the isolates were susceptible to the above-mentioned antibiotics. Genome sequencing revealed that all isolates were closely related and belonged to the emergent ST34 monophasic variant of S. enterica serovar Typhimurium. Since the patient has received therapy with fluoroquinolones and amoxicillin/clavulanic acid, these results support treatment-associated selection of the acquired resistances. In conclusion, this case represents a paradigm of selective pressure leading to in vivo development of resistance to highly relevant antibiotics, including the piperacillin/tazobactam combination used for empirical management of severe infections at ICU.
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Affiliation(s)
- Xenia Vázquez
- Área de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo (UO), 33006 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (L.F.); (J.F.)
| | - Lorena Forcelledo
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (L.F.); (J.F.)
- Servicio de Medicina Intensiva, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain;
| | - Salvador Balboa-Palomino
- Servicio de Medicina Intensiva, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain;
| | - Javier Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (L.F.); (J.F.)
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain
- Research & Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, 33003 Oviedo, Spain
- Centro de Investigación Biomédica en Red-Enfermedades Respiratorias, 28029 Madrid, Spain
| | - María Rosario Rodicio
- Área de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo (UO), 33006 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (L.F.); (J.F.)
- Correspondence: ; Tel.: +34-985103562
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Xiao X, Bai L, Wang S, Liu L, Qu X, Zhang J, Xiao Y, Tang B, Li Y, Yang H, Wang W. Chlorine Tolerance and Cross-Resistance to Antibiotics in Poultry-Associated Salmonella Isolates in China. Front Microbiol 2022; 12:833743. [PMID: 35185838 PMCID: PMC8854976 DOI: 10.3389/fmicb.2021.833743] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 12/28/2021] [Indexed: 01/10/2023] Open
Abstract
Chlorine disinfectants have been widely used in the poultry supply chain but this exposure can also result in the development of bacterial tolerance to chlorine and this is often linked to antibiotic cross-resistance. The objectives of this study were to investigate sodium hypochlorite (NaClO) tolerance of Salmonella isolated from poultry supply chains and evaluate cross-resistance. We collected 172 Salmonella isolates from poultry farms, slaughter houses and retail markets in China during 2019–2020. We found that S. Enteritidis, S. Kentucky, and S. Typhimurium constituted > 80% of our Salmonella isolates. Overall, 68% of Salmonella isolates were resistant to > 3 antibiotics and S. Kentucky displayed a significantly (p > 0.05) higher frequency (93.2%) of multidrug resistance than the other serovars. Tolerance to chlorine at MIC > 256 mg/L was detected in 93.6% of isolates (161/172) and tolerant isolates displayed higher decimal reduction times (D value) and less ultrastructural damage than did the suspectable strains under chlorine stress. Spearman analysis indicated significant positive correlations between chlorine tolerance (evaluated by the OD method) and antibiotic resistance (p < 0.05) to ceftiofur, tetracycline, ciprofloxacin and florfenicol and this was most likely due to efflux pump over-expression. The most frequently detected chlorine resistance gene was qacEΔ1 (83.1%, n = 143) and we found a positive correlation between its presence and MIC levels (r = 0.66, p < 0.0001). Besides, we found weak correlations between chlorine-tolerance and antibiotic resistance genes. Our study indicated that chlorine disinfectants most likely played an important role in the emergence of chlorine tolerance and spread of antibiotic resistance and therefore does not completely control the risk of food-borne disease. The issue of disinfectant resistance should be examined in more detail at the level of the poultry production chain.
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Affiliation(s)
- Xingning Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ministry of Agriculture (MOA) Laboratory of Quality and Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Li Bai
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People’s Republic of China, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Sheng Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ministry of Agriculture (MOA) Laboratory of Quality and Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Lisha Liu
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People’s Republic of China, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Xiaoyun Qu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jianmin Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ministry of Agriculture (MOA) Laboratory of Quality and Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ministry of Agriculture (MOA) Laboratory of Quality and Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR, United States
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ministry of Agriculture (MOA) Laboratory of Quality and Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Hua Yang,
| | - Wen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ministry of Agriculture (MOA) Laboratory of Quality and Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Wen Wang,
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Vázquez X, García V, Fernández J, Bances M, de Toro M, Ladero V, Rodicio R, Rodicio MR. Colistin Resistance in Monophasic Isolates of Salmonella enterica ST34 Collected From Meat-Derived Products in Spain, With or Without CMY-2 Co-production. Front Microbiol 2022; 12:735364. [PMID: 35069462 PMCID: PMC8770973 DOI: 10.3389/fmicb.2021.735364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/17/2021] [Indexed: 12/02/2022] Open
Abstract
Colistin is a last-resort antibiotic in fighting severe infections caused by multidrug resistant Gram negative pathogens in hospitals. Zoonotic bacteria acquire colistin resistance in animal reservoirs and mediate its spread along the food chain. This is the case of non-typhoid serovars of Salmonella enterica. Colistin-resistant S. enterica in foods represents a threat to human health. Here, we assessed the prevalence of colistin-resistance in food-borne isolates of S. enterica (2014–2019; Asturias, Spain), and established the genetic basis and transferability of this resistance. Five out of 231 isolates tested (2.2%) were resistant to colistin. Four of them, belonging to the European monophasic ST34 clone of S. Typhimurium, were characterized in the present study. They were collected from pork or pork and beef meat-derived products, either in 2015 (three isolates) or 2019 (one isolate). Molecular typing with XbaI-PFGE and plasmid profiling revealed distinct patterns for each isolate, even though two of the 2015 isolates derived from the same sample. The MICs of colistin ranged from 8 to 16 mg/L. All isolates carried the mcr-1.1 gene located on conjugative plasmids of the incompatibility groups IncX4 (2015 isolates) or IncHI2 (2019 isolate). Apart from colistin resistance, the four isolates carried chromosomal genes conferring resistance to ampicillin, streptomycin, sulfonamides and tetracycline [blaTEM–1, strA-strB, sul2, and tet(B)] and heavy metals, including copper and silver (silESRCFBAGP and pcoGE1ABCDRSE2), arsenic (arsRSD2A2BCA1D1) ± mercury (merEDACPTR), which are characteristically associated with the European ST34 monophasic clone. The 2019 isolate was also resistant to other antibiotics, comprising third generation cephalosporins and cephamycins. The latter phenotype was conferred by the blaCMY–2 gene located on an IncI1-I(α)-ST2 plasmid. Results in the present study identified meat-derived products as a reservoir of a highly successful clone harboring transferable plasmids which confer resistance to colistin and other clinically important antibiotics. An important reduction in the number of food-borne S. enterica detected during the period of the study, together with the low frequency of colistin resistance, underlines the success of One Health initiatives, such as those implemented at the UE, to control zoonotic bacteria along the food chain and to halt the spread of antimicrobial resistance.
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Affiliation(s)
- Xenia Vázquez
- Área de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain.,Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Javier Fernández
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
| | - Margarita Bances
- Laboratorio de Salud Pública (LSP), Consejería de Sanidad del Principado de Asturias, Oviedo, Spain
| | - María de Toro
- Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | - Víctor Ladero
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain.,Grupo de Microbiología Molecular, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Rosaura Rodicio
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - M Rosario Rodicio
- Área de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain.,Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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26
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Fernandes SA, Tavechio AT, Ghilardi ÂCR, Almeida EAD, Silva JMLD, Camargo CH, Tiba-Casas MR. Salmonella enterica serotypes from human and nonhuman sources in Sao Paulo State, Brazil, 2004-2020. Rev Inst Med Trop Sao Paulo 2022; 64:e66. [PMID: 36197427 PMCID: PMC9528755 DOI: 10.1590/s1678-9946202264066] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/21/2022] Open
Abstract
Salmonellosis ranks among the most frequently reported zoonosis worldwide and is often associated with foodborne outbreaks. Since the 1950s, the distribution of Salmonella serotypes in Sao Paulo State, Brazil, has been documented and periodically reported. In this study, we updated the data on the distribution of Salmonella serotypes received in our reference laboratory, isolated from human infections and nonhuman sources, from 2004 to 2020. In that period, a total of 9,014 Salmonella isolates were analyzed, of which 3,553 (39.4%) were recovered from human samples, mainly of stool (65%) and blood (25.6%), and 5,461 (60.6%) were isolated from nonhuman origins, such as animals (47.2%), food (27.7%) and animal environments (18.6%). In human isolates, a total of 104 serotypes were identified and the most frequent ones were Enteritidis, Typhimurium, S . I. 4,[5],12:i:-, Dublin and Typhi. A consistent reduction of the Enteritidis proportion was observed over the years. Among the 156 serotypes identified in isolates with nonhuman origins, Enteritidis, Mbandaka, Typhimurium, Agona and Anatum were ranked as the top five Salmonella serotypes; in more recent years, S . Heidelberg has increased in frequency. Although with different proportions, the top 10 prevalent serotypes were identified in both human and nonhuman origins, underscoring the role of animals, food products and environment as reservoirs of Salmonella with potential to cause human salmonellosis.
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27
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Kuus K, Kramarenko T, Sõgel J, Mäesaar M, Fredriksson-Ahomaa M, Roasto M. Prevalence and Serotype Diversity of Salmonella enterica in the Estonian Meat Production Chain in 2016-2020. Pathogens 2021; 10:pathogens10121622. [PMID: 34959577 PMCID: PMC8708786 DOI: 10.3390/pathogens10121622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Salmonella enterica represents a considerable public concern worldwide, with farm animals often recognised as an important reservoir. This study gives an overview of the prevalence and serotype diversity of Salmonella over a 5-year period in the meat production chain in Estonia. Data on human salmonellosis over the same period are provided. Methods: Salmonella surveillance data from 2016 to 2020 were analysed. Results: The prevalence of Salmonella at the farm level was 27.7%, 3.3% and 0.1% for fattening pigs, cattle and poultry, respectively. S. Derby was the most prevalent serotype at the farm level for fattening pigs and S. Dublin for cattle. The top three serotypes isolated at the slaughterhouse and meat cutting levels were S. Derby, monophasic S. Typhimurium and S. Typhimurium with proportions of 64.7%, 9.4% and 7.0%, respectively. These serotypes were the top five most common Salmonella serotypes responsible for human infections in Estonia. S. Enteritidis is the main cause (46.9%) of human salmonellosis cases in Estonia, but in recent years, Enteritidis has not been detected at the slaughterhouse or meat cutting level. Conclusion: In recent years, monophasic S. Typhimurium has become epidemiologically more important in Estonia, with the second-highest cause in human cases and third-highest among the most prevalent serotypes of Salmonella enterica in the meat chain.
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Affiliation(s)
- Kaisa Kuus
- Chair of Food Hygiene and Veterinary Public Health, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 56-3, 51006 Tartu, Estonia; (K.K.); (M.M.)
| | - Toomas Kramarenko
- Veterinary and Food Laboratory, Fr. R. Kreutzwaldi 30, 51006 Tartu, Estonia;
| | - Jelena Sõgel
- Agriculture and Food Board, Väike-Paala 3, 11415 Tallinn, Estonia;
| | - Mihkel Mäesaar
- Chair of Food Hygiene and Veterinary Public Health, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 56-3, 51006 Tartu, Estonia; (K.K.); (M.M.)
| | - Maria Fredriksson-Ahomaa
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, P.O. Box 66, 00014 Helsinki, Finland;
| | - Mati Roasto
- Chair of Food Hygiene and Veterinary Public Health, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 56-3, 51006 Tartu, Estonia; (K.K.); (M.M.)
- Correspondence: ; Tel.: +372-731-3433
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28
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Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases. Microbiol Spectr 2021; 9:e0049521. [PMID: 34704804 PMCID: PMC8549754 DOI: 10.1128/spectrum.00495-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The number of bacterial genomes deposited each year in public databases is growing exponentially. However, efforts to use these genomes to track trends in antimicrobial resistance (AMR) have been limited thus far. We used 22,102 genomes from public databases to track AMR trends in nontyphoidal Salmonella in food animals in the United States. In 2018, genomes deposited in public databases carried genes conferring resistance, on average, to 2.08 antimicrobial classes in poultry, 1.74 in bovines, and 1.28 in swine. This represents a decline in AMR of over 70% compared to the levels in 2000 in bovines and swine, and an increase of 13% for poultry. Trends in resistance inferred from genomic data showed good agreement with U.S. phenotypic surveillance data (weighted mean absolute difference ± standard deviation, 5.86% ± 8.11%). In 2018, resistance to 3rd-generation cephalosporins in bovines, swine, and poultry decreased to 9.97% on average, whereas in quinolones and 4th-generation cephalosporins, resistance increased to 12.53% and 3.87%, respectively. This was concomitant with a decrease of blaCMY-2 but an increase in blaCTX-M-65 and gyrA D87Y (encoding a change of D to Y at position 87). Core genome single-nucleotide polymorphism (SNP) phylogenies show that resistance to these antimicrobial classes was predominantly associated with Salmonella enterica serovar Infantis and, to a lesser extent, S. enterica serovar Typhimurium and its monophasic variant I 4,[5],12:i:−, whereas quinolone resistance was also associated with S. enterica serovar Dublin. Between 2000 and 2018, trends in serovar prevalence showed a composition shift where S. Typhimurium decreased while S. Infantis increased. Our findings illustrate the growing potential of using genomes in public databases to track AMR in regions where sequencing capacities are currently expanding. IMPORTANCE Next-generation sequencing has led to an exponential increase in the number of genomes deposited in public repositories. This growing volume of information presents opportunities to track the prevalence of genes conferring antimicrobial resistance (AMR), a growing threat to the health of humans and animals. Using 22,102 public genomes, we estimated that the prevalence of multidrug resistance (MDR) in the United States decreased in nontyphoidal Salmonella isolates recovered from bovines and swine between 2000 and 2018, whereas it increased in poultry. These trends are consistent with those detected by national surveillance systems that monitor resistance using phenotypic testing. However, using genomes, we identified that genes conferring resistance to critically important antimicrobials were associated with specific MDR serovars that could be the focus for future interventions. Our analysis illustrates the growing potential of public repositories to monitor AMR trends and shows that similar efforts could soon be carried out in other regions where genomic surveillance is increasing.
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29
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Bearson SMD. Salmonella in Swine: Prevalence, Multidrug Resistance, and Vaccination Strategies. Annu Rev Anim Biosci 2021; 10:373-393. [PMID: 34699256 DOI: 10.1146/annurev-animal-013120-043304] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An estimated 1.3 million Salmonella infections and 420 deaths occur annually in the United States, with an estimated economic burden of $3.7 billion. More than 50% of US swine operations test positive for Salmonella according to the National Animal Health Monitoring System, and 20% of Salmonella from swine are multidrug resistant (resistant to ≥3 antimicrobial classes) as reported by the National Antimicrobial Resistance Monitoring System. This review on Salmonella in swine addresses the current status of these topics by discussing antimicrobial resistance and metal tolerance in Salmonella and the contribution of horizontal gene transfer. A major challenge in controlling Salmonella is that Salmonella is a foodborne pathogen in humans but is often a commensal in food animals and thereby establishes an asymptomatic reservoir state in such animals, including swine. As food animal production systems continue to expand and antimicrobial usage becomes more limited, the need for Salmonella interventions has intensified. A promising mitigation strategy is vaccination against Salmonella in swine to limit animal, environmental, and food contamination. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Shawn M D Bearson
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Center, US Department of Agriculture, Ames, Iowa, USA;
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30
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Schwan CL, Lomonaco S, Bastos LM, Cook PW, Maher J, Trinetta V, Bhullar M, Phebus RK, Gragg S, Kastner J, Vipham JL. Genotypic and Phenotypic Characterization of Antimicrobial Resistance Profiles in Non-typhoidal Salmonella enterica Strains Isolated From Cambodian Informal Markets. Front Microbiol 2021; 12:711472. [PMID: 34603240 PMCID: PMC8481621 DOI: 10.3389/fmicb.2021.711472] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/26/2021] [Indexed: 12/03/2022] Open
Abstract
Non-typhoidal Salmonella enterica is a pathogen of global importance, particularly in low and middle-income countries (LMICs). The presence of antimicrobial resistant (AMR) strains in market environments poses a serious health threat to consumers. In this study we identified and characterized the genotypic and phenotypic AMR profiles of 81 environmental S. enterica strains isolated from samples from informal markets in Cambodia in 2018–2019. AMR genotypes were retrieved from the NCBI Pathogen Detection website (https://www.ncbi.nlm.nih.gov/pathogens/) and using ResFinder (https://cge.cbs.dtu.dk/services/) Salmonella pathogenicity islands (SPIs) were identified with SPIFinder (https://cge.cbs.dtu.dk/services/). Susceptibility testing was performed by broth microdilution according to the Clinical and Laboratory Standards Institute (CLSI) standard guidelines M100-S22 using the National Antimicrobial Resistance Monitoring System (NARMS) Sensititre Gram Negative plate. A total of 17 unique AMR genes were detected in 53% (43/81) of the isolates, including those encoding tetracycline, beta-lactam, sulfonamide, quinolone, aminoglycoside, phenicol, and trimethoprim resistance. A total of 10 SPIs (SPI-1, 3–5, 8, 9, 12–14, and centisome 63 [C63PI]) were detected in 59 isolates. C63PI, an iron transport system in SPI-1, was observed in 56% of the isolates (n = 46). SPI-1, SPI-4, and SPI-9 were present in 13, 2, and 5% of the isolates, respectively. The most common phenotypic resistances were observed to tetracycline (47%; n = 38), ampicillin (37%; n = 30), streptomycin (20%; n = 16), chloramphenicol (17%; n = 14), and trimethoprim-sulfamethoxazole (16%; n = 13). This study contributes to understanding the AMR genes present in S. enterica isolates from informal markets in Cambodia, as well as support domestic epidemiological investigations of multidrug resistance (MDR) profiles.
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Affiliation(s)
- Carla L Schwan
- Department of Animal Sciences and Industry, Food Science Institute, Kansas State University, Manhattan, KS, United States
| | - Sara Lomonaco
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Leonardo M Bastos
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Peter W Cook
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Joshua Maher
- Department of Animal Sciences and Industry, Food Science Institute, Kansas State University, Manhattan, KS, United States
| | - Valentina Trinetta
- Department of Animal Sciences and Industry, Food Science Institute, Kansas State University, Manhattan, KS, United States
| | - Manreet Bhullar
- Department of Horticulture and Natural Resources, Kansas State University, Olathe, KS, United States
| | - Randall K Phebus
- Department of Animal Sciences and Industry, Food Science Institute, Kansas State University, Manhattan, KS, United States
| | - Sara Gragg
- Department of Animal Sciences and Industry, Food Science Institute, Kansas State University, Manhattan, KS, United States
| | - Justin Kastner
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, United States
| | - Jessie L Vipham
- Department of Animal Sciences and Industry, Food Science Institute, Kansas State University, Manhattan, KS, United States
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31
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Win AT, Supa-amornkul S, Orsi RH, Carey JH, Wolfgang WJ, Chaturongakul S. Sequence Analyses and Phenotypic Characterization Revealed Multidrug Resistant Gene Insertions in the Genomic Region Encompassing Phase 2 Flagellin Encoding fljAB Genes in Monophasic Variant Salmonella enterica Serovar 4,5,12:i:- Isolates From Various Sources in Thailand. Front Microbiol 2021; 12:720604. [PMID: 34675896 PMCID: PMC8524439 DOI: 10.3389/fmicb.2021.720604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica serovar 4,5,12:i:- (S. 4,5,12:i:-), a monophasic variant of Salmonella Typhimurium (STm) lacking the phase 2 flagellin encoding genes fljAB, has become increasingly prevalent worldwide. The increasing trends in multidrug resistant (MDR) S. 4,5,12:i:- prevalence also pose an important global health threat. Though many reports have characterized phenotypic and genotypic drug resistance of this serovar, few studies have characterized antimicrobial resistance of this serovar in Thailand. In this study, 108 S. 4,5,12:i:- isolates from various sources in Thailand and four international S. 4,5,12:i:- isolates were screened using polymerase chain reaction (PCR) to detect the presence of five target regions which are associated with antimicrobial resistant (AMR) genes, in the genomic region that contained fljAB genes in STm. We determined AMR phenotypes of all isolates by Kirby-Bauer disk diffusion method. Whole genome sequencing (WGS) was performed on 53 representative isolates (based on differences in the pulsed filed gel electrophoresis profiles, the sources of isolate, and the PCR and AMR patterns) to characterize the genetic basis of AMR phenotype and to identify the location of AMR determinants. Based on PCR screening, nine PCR profiles showing distinct deletion patterns of the five target regions have been observed. Approximately 76% of isolates (or 85 of 112 isolates), all of which were Thai isolates, contained five target regions inserted between STM2759 and iroB gene. A total of 21 phenotypic AMR patterns were identified with the predominant AmpST resistant phenotype [i.e., 84% (or 94 of 112) tested positive for resistance to ampicillin, streptomycin, and tetracycline], and 89% (or 100 of 112) were found to be MDR (defined here as resistant to at least three classes of tested antimicrobials). Using WGS data, a total of 24 genotypic AMR determinants belonging to seven different antimicrobial groups were found. AMR determinants (i.e., blaTEM - 1 , strB-A, sul2, and tetB, conferring resistance to ampicillin, streptomycin, sulfonamides, and tetracycline, respectively) were found to be inserted in a region typically occupied by the phase 2 flagellin encoding genes in STm. These resistant genes were flanked by a number of insertion sequences (IS), and co-localized with mercury tolerance genes. Our findings identify AMR genes, possibly associated with multiple IS26 copies, in the genetic region between STM2759 and iroB genes replacing phase 2 flagellin encoding fljAB genes in Thai S. 4,5,12:i:- isolates.
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Affiliation(s)
- Aye Thida Win
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sirirak Supa-amornkul
- Mahidol International Dental School, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Renato H. Orsi
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Jaclyn H. Carey
- Bacteriology Laboratory, New York State Department of Health, Wadsworth Center, Albany, NY, United States
| | - William J. Wolfgang
- Bacteriology Laboratory, New York State Department of Health, Wadsworth Center, Albany, NY, United States
| | - Soraya Chaturongakul
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Microbial Genomics (CENMIG), Faculty of Science, Mahidol University, Bangkok, Thailand
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32
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Ingle DJ, Ambrose RL, Baines SL, Duchene S, Gonçalves da Silva A, Lee DYJ, Jones M, Valcanis M, Taiaroa G, Ballard SA, Kirk MD, Howden BP, Pearson JS, Williamson DA. Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia. Nat Commun 2021; 12:4786. [PMID: 34373455 PMCID: PMC8352879 DOI: 10.1038/s41467-021-25073-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emerged as a global cause of multidrug resistant salmonellosis. We used Bayesian phylodynamics, genomic epidemiology, and phenotypic characterization to describe the emergence and evolution of Salmonella 4,[5],12:i:- in Australia. We show that the interruption of the genetic region surrounding the phase II flagellin, FljB, causing a monophasic phenotype, represents a stepwise evolutionary event through the accumulation of mobile resistance elements with minimal impairment to bacterial fitness. We identify three lineages with different population dynamics and discrete antimicrobial resistance profiles emerged, likely reflecting differential antimicrobial selection pressures. Two lineages are associated with travel to South-East Asia and the third lineage is endemic to Australia. Moreover antimicrobial-resistant Salmonella 4,[5],12:i- lineages efficiently infected and survived in host phagocytes and epithelial cells without eliciting significant cellular cytotoxicity, suggesting a suppression of host immune response that may facilitate the persistence of Salmonella 4,[5],12:i:-.
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Affiliation(s)
- Danielle J Ingle
- Research School of Population Health, Australian National University, Canberra, ACT, Australia.
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Rebecca L Ambrose
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Darren Y J Lee
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Miriam Jones
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Martyn D Kirk
- Research School of Population Health, Australian National University, Canberra, ACT, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jaclyn S Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia.
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33
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Zheng D, Ma K, Du J, Zhou Y, Wu G, Qiao X, Wang Y, Ni Y, Fu J, Huo X. Characterization of Human Origin Salmonella Serovar 1,4,[5],12:i:- in Eastern China, 2014 to 2018. Foodborne Pathog Dis 2021; 18:790-797. [PMID: 34287022 DOI: 10.1089/fpd.2021.0008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The prevalence of Salmonella serovar 1,4,[5],12:i:- among diarrhea patients has increased considerably in many countries around the world, including China. However, the characterization of this serovar of human origin has been less reported from China. We characterized 76 isolates of Salmonella 1,4,[5],12:i:- gained from diarrhea patients from 2014 to 2018 in the Jiangsu Province of eastern China. These isolates fell into a single-sequence type (ST34) determined by multilocus sequence typing (MLST), and into 44 pulsed-field gel electrophoresis band patterns, with 1 pattern (JSSMM015) comprising 12 isolates (15.9%). By means of PCR-based assays, the seven prophage located virulence genes were detected in our Salmonella 1,4,[5],12:i:- isolates with a high rate of gipA, gtgB, sspH1, sspH2, sodC1, and gtgE (93.4-97.4%), and with a moderate rate of sopE (42.1%). In contrast, none of the five plasmid-borne virulence genes (spvC, pefA, mig5, rck, and srgA) was identified. We tested the isolates' susceptibility to 18 antibiotics of 9 categories using the VITEK 2 system. A high proportion (89.5%) of the isolates were multidrug resistant (MDR) strains with full resistance to cefazolin, cefotetan, amikacin, gentamycin, and tobramycin, followed by resistance to ampicillin (88.2%) and ampicillin/sulbactam (80.3%). The resistance to piperacillin/tazobactam, ceftazidime, cefepime, and levofloxacin was scarce (2.6-9.2%). Notably, an isolate from 2018 was resistant to carbapenems. blaTEM-1B and aac(6')-Ib-cr were the most common drug resistance genes presented in cephalosporin- and fluoroquinolone-resistant strains. All Salmonella 1,4,[5],12:i:- isolates were capable of forming biofilm, with 13.2% of them having strong ability. However, no association was indicated between the scale of biofilm formation ability and MDR. Our results indicate that the combination of these characteristics may together provide a selective and competitive advantage to those Salmonella 1,4,[5],12:i:- isolates, contributing to their increasing prevalence observed worldwide.
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Affiliation(s)
- Dongyu Zheng
- Department of Food Safety and Assessment, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.,Key laboratory of enteric pathogenic microorganisms of National Health Commission, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Kai Ma
- Department of Food Safety and Assessment, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.,Key laboratory of enteric pathogenic microorganisms of National Health Commission, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jialu Du
- Department of Food Safety and Assessment, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.,Key laboratory of enteric pathogenic microorganisms of National Health Commission, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yijing Zhou
- Department of Food Safety and Assessment, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Gaolin Wu
- Department of Food Safety and Assessment, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xin Qiao
- Department of Food Safety and Assessment, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.,Key laboratory of enteric pathogenic microorganisms of National Health Commission, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yanmei Wang
- Department of Food Safety and Assessment, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.,Key laboratory of enteric pathogenic microorganisms of National Health Commission, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yunlong Ni
- Department of Food Safety and Assessment, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.,Key laboratory of enteric pathogenic microorganisms of National Health Commission, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Junjie Fu
- Nanjing Medical University, School of Public Health, Nanjing, China
| | - Xiang Huo
- Department of Food Safety and Assessment, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
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Analysis of 56,348 Genomes Identifies the Relationship between Antibiotic and Metal Resistance and the Spread of Multidrug-Resistant Non-Typhoidal Salmonella. Microorganisms 2021; 9:microorganisms9071468. [PMID: 34361911 PMCID: PMC8306355 DOI: 10.3390/microorganisms9071468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 01/14/2023] Open
Abstract
Salmonella enterica is common foodborne pathogen that generates both enteric and systemic infections in hosts. Antibiotic resistance is common is certain serovars of the pathogen and of great concern to public health. Recent reports have documented the co-occurrence of metal resistance with antibiotic resistance in one serovar of S. enterica. Therefore, we sought to identify possible co-occurrence in a large genomic dataset. Genome assemblies of 56,348 strains of S. enterica comprising 20 major serovars were downloaded from NCBI. The downloaded assemblies were quality controlled and in silico serotyped to ensure consistency and avoid improper annotation from public databases. Metal and antibiotic resistance genes were identified in the genomes as well as plasmid replicons. Co-occurrent genes were identified by constructing a co-occurrence matrix and grouping said matrix using k-means clustering. Three groups of co-occurrent genes were identified using k-means clustering. Group 1 was comprised of the pco and sil operons that confer resistance to copper and silver, respectively. Group 1 was distributed across four serovars. Group 2 contained the majority of the genes and little to no co-occurrence was observed. Metal and antibiotic co-occurrence was identified in group 3 that contained genes conferring resistance to: arsenic, mercury, beta-lactams, sulfonamides, and tetracyclines. Group 3 genes were also associated with an IncQ1 class plasmid replicon. Metal and antibiotic co-occurrence from group 3 genes is mostly isolated to one clade of S. enterica I 4,[5],12:i:-.
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35
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Medalla F, Gu W, Friedman CR, Judd M, Folster J, Griffin PM, Hoekstra RM. Increased Incidence of Antimicrobial-Resistant Nontyphoidal Salmonella Infections, United States, 2004-2016. Emerg Infect Dis 2021; 27:1662-1672. [PMID: 34013877 PMCID: PMC8153855 DOI: 10.3201/eid2706.204486] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Salmonella is a major cause of foodborne illness in the United States, and antimicrobial-resistant strains pose a serious threat to public health. We used Bayesian hierarchical models of culture-confirmed infections during 2004-2016 from 2 Centers for Disease Control and Prevention surveillance systems to estimate changes in the national incidence of resistant nontyphoidal Salmonella infections. Extrapolating to the United States population and accounting for unreported infections, we estimated a 40% increase in the annual incidence of infections with clinically important resistance (resistance to ampicillin or ceftriaxone or nonsusceptibility to ciprofloxacin) during 2015-2016 (≈222,000 infections) compared with 2004-2008 (≈159,000 infections). Changes in the incidence of resistance varied by serotype. Serotypes I 4,[5],12:i:- and Enteritidis were responsible for two thirds of the increased incidence of clinically important resistance during 2015-2016. Ciprofloxacin-nonsusceptible infections accounted for more than half of the increase. These estimates can help in setting targets and priorities for prevention.
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36
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Arai N, Sekizuka T, Tamamura-Andoh Y, Barco L, Hinenoya A, Yamasaki S, Iwata T, Watanabe-Yanai A, Kuroda M, Akiba M, Kusumoto M. Identification of a Recently Dominant Sublineage in Salmonella 4,[5],12:i:- Sequence Type 34 Isolated From Food Animals in Japan. Front Microbiol 2021; 12:690947. [PMID: 34276624 PMCID: PMC8281233 DOI: 10.3389/fmicb.2021.690947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/09/2021] [Indexed: 12/03/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Typhimurium sequence type 34 (ST34) and its monophasic variant (Salmonella 4,[5],12:i:-) are among the most frequently isolated clones from both humans and animals worldwide. Our previous study demonstrated that Salmonella Typhimurium/4,[5],12:i:- strains isolated in Japan could be classified into nine clades and that clade 9 consisted of ST34 strains. In Japan, ST34/clade 9 was first found in the 1990s and has become predominant among food animals in recent years. In the present study, we analyzed the whole genome-based phylogenetic relationships and temporal information of 214 Salmonella Typhimurium/4,[5],12:i:- ST34/clade 9 strains isolated from 1998 to 2017 in Japan. The 214 strains were classified into two sublineages: the newly identified clade 9–2 diverged from clade 9 in the early 2000s and has predominated in recent years. Clonally expanding subclades in clades 9–1 or 9–2 lacked Gifsy-1 or HP1 prophages, respectively, and some strains in these subclades acquired plasmids encoding antimicrobial resistance genes. Additional genome reduction around the fljB gene encoding the phase 2-H antigen was generated by an IS26-mediated deletion adjacent to the transposon in clade 9–2. Although most of the clade 9 strains were isolated from cattle in Japan, the clonally expanding subclades in clade 9–2 (i.e., all and 24% strains of subclades 9–2a and 9–2b, respectively) were isolated from swine. The spread of clade 9 in recent years among food animals in Japan was responsible for the emergence of multiple host-adapted sublineages involving the clonally expanding subclades generated by mobile genetic element-mediated microevolution.
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Affiliation(s)
- Nobuo Arai
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukino Tamamura-Andoh
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Lisa Barco
- Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Padua, Italy
| | - Atsushi Hinenoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Shinji Yamasaki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Taketoshi Iwata
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Ayako Watanabe-Yanai
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masato Akiba
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Masahiro Kusumoto
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
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Elnekave E, Hong SL, Lim S, Boxrud D, Rovira A, Mather AE, Perez A, Alvarez J. Transmission of Multidrug-Resistant Salmonella enterica Subspecies enterica 4,[5],12:i:- Sequence Type 34 between Europe and the United States. Emerg Infect Dis 2021; 26:3034-3038. [PMID: 33219795 PMCID: PMC7706949 DOI: 10.3201/eid2612.200336] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Multidrug-resistant Salmonellaenterica subspecies enterica 4,[5],12:i:- sequence type 34 represents a worldwide public health risk. To determine its origin in the United States, we reconstructed a time-scaled phylogeny with a discrete trait geospatial model. The clone in the United States was introduced from Europe on multiple occasions in the early 2000s.
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38
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Lee S, Park N, Yun S, Hur E, Song J, Lee H, Kim Y, Ryu S. Presence of plasmid-mediated quinolone resistance (PMQR) genes in non-typhoidal Salmonella strains with reduced susceptibility to fluoroquinolones isolated from human salmonellosis in Gyeonggi-do, South Korea from 2016 to 2019. Gut Pathog 2021; 13:35. [PMID: 34074336 PMCID: PMC8167944 DOI: 10.1186/s13099-021-00431-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
Non-typhoidal salmonellosis remains a pressing public health problem worldwide. Quinolones, particularly fluoroquinolones, are widely used to treat various infections, including non-typhoidal salmonellosis, which can be a serious illness. The emergence of fluoroquinolone-resistant Salmonella has resulted in treatment failure and high mortality rates. In this study, we estimated the presence of plasmid-mediated quinolone resistance (PMQR) genes in Salmonella enterica isolated from human salmonellosis patients in South Korea from 2016 to 2019. We evaluated the association of these genes with fluoroquinolone susceptibility. Antimicrobial susceptibility tests for Salmonella isolates were performed using the Vitek II system, and the minimum inhibitory concentrations (MIC) of ciprofloxacin and levofloxacin were determined using the E-test method. Plasmid-mediated quinolone resistance (PMQR) genes were detected by PCR amplification and quinolone resistance-determining regions (QRDRs) of the gyrA and parC genes were analyzed following Sanger sequencing of the PCR products. Thirty-four Salmonella strains with reduced susceptibility to fluoroquinolones (ciprofloxacin MIC ≥ 0.125 µg/mL and levofloxacin MIC ≥ 0.25 µg/mL) were selected from 208 human clinical Salmonella isolates. Among them, 22 Salmonella strains harbored one PMQR gene (qnrA, qnrB, or qnrS), and three Salmonella strains carried two PMQR genes (qnrS and aac(6′)-Ib-cr or qnrA and qnrB). qnrS was the most common PMQR gene. Serotyping revealed that Salmonella 4,[5]12:i:- (32.4%, 11/34) and Salmonella Typhimurium (29.4%, 10/34) were the two most predominant serovars, and Multi-locus sequence typing (MLST) showed that ST19 and ST34 were the most frequent sequence types. In conclusion, qnr gene-positive Salmonella 4,[5],12:i:- and Salmonella Typhimurium were the main serovars responsible for reduced susceptibility to fluoroquinolones. Therefore, our findings suggest that PMQR-positive Salmonella strains, which can be isolated from various samples including human, food, and the environment, should be carefully monitored.
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Affiliation(s)
- Sohyun Lee
- Gyeonggi-do Research Institute of Health & Environment, Suwon, 16381, South Korea
| | - Nanjoo Park
- Gyeonggi-do Research Institute of Health & Environment, Suwon, 16381, South Korea.,Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, South Korea
| | - Sujung Yun
- Gyeonggi-do Research Institute of Health & Environment, Suwon, 16381, South Korea
| | - Eunseon Hur
- Gyeonggi-do Research Institute of Health & Environment, Suwon, 16381, South Korea
| | - Jiwon Song
- Gyeonggi-do Research Institute of Health & Environment, Suwon, 16381, South Korea
| | - Hanna Lee
- Gyeonggi-do Research Institute of Health & Environment, Suwon, 16381, South Korea
| | - Yongsug Kim
- Gyeonggi-do Research Institute of Health & Environment, Suwon, 16381, South Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, South Korea.
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39
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Cadel-Six S, Cherchame E, Douarre PE, Tang Y, Felten A, Barbet P, Litrup E, Banerji S, Simon S, Pasquali F, Gourmelon M, Mensah N, Borowiak M, Mistou MY, Petrovska L. The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Salmonella Typhimurium Circulating in Europe. Front Microbiol 2021; 12:651124. [PMID: 34093465 PMCID: PMC8175864 DOI: 10.3389/fmicb.2021.651124] [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: 01/08/2021] [Accepted: 04/16/2021] [Indexed: 01/23/2023] Open
Abstract
The European epidemic monophasic variant of Salmonella enterica serovar Typhimurium (S. 1,4,[5],12:i:-) characterized by the multi locus sequence type ST34 and the antimicrobial resistance ASSuT profile has become one of the most common serovars in Europe (EU) and the United States (US). In this study, we reconstructed the time-scaled phylogeny and evolution of this Salmonella in Europe. The epidemic S. 1,4,[5],12:i:- ST34 emerged in the 1980s by an acquisition of the Salmonella Genomic Island (SGI)-4 at the 3' end of the phenylalanine phe tRNA locus conferring resistance to copper and arsenic toxicity. Subsequent integration of the Tn21 transposon into the fljAB locus gave resistance to mercury toxicity and several classes of antibiotics used in food-producing animals (ASSuT profile). The second step of the evolution occurred in the 1990s, with the integration of mTmV and mTmV-like prophages carrying the perC and/or sopE genes involved in the ability to reduce nitrates in intestinal contents and facilitate the disruption of the junctions of the host intestinal epithelial cells. Heavy metals are largely used as food supplements or pesticide for cultivation of seeds intended for animal feed so the expansion of the epidemic S. 1,4,[5],12:i:- ST34 was strongly related to the multiple-heavy metal resistance acquired by transposons, integrative and conjugative elements and facilitated by the escape until 2011 from the regulatory actions applied in the control of S. Typhimurium in Europe. The genomic plasticity of the epidemic S. 1,4,[5],12:i:- was demonstrated in our study by the analysis of the plasmidome. We were able to identify plasmids harboring genes mediating resistance to phenicols, colistin, and fluoroquinolone and also describe for the first time in six of the analyzed genomes the presence of two plasmids (pERR1744967-1 and pERR2174855-2) previously described only in strains of enterotoxigenic Escherichia coli and E. fergusonii.
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Affiliation(s)
- Sabrina Cadel-Six
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | - Emeline Cherchame
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | | | - Yue Tang
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Arnaud Felten
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | - Pauline Barbet
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | - Eva Litrup
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sangeeta Banerji
- Robert Koch-Institute, Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Sandra Simon
- Robert Koch-Institute, Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Federique Pasquali
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Michèle Gourmelon
- Ifremer, RBE, SGMM, Health, Environment and Microbiology Laboratory, Plouzané, France
| | - Nana Mensah
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Michel-Yves Mistou
- Université Paris-Saclay, INRAE, Centre International de Ressource Microbienne (CIRM) MaIAGE, Jouy-en-Josas, France
| | - Liljana Petrovska
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
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40
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Clark CG, Kearney AK, Tschetter L, Robertson J, Pollari F, Parker S, Arya G, Ziebell K, Johnson R, Nash J, Nadon C. Population structure, case clusters, and genetic lesions associated with Canadian Salmonella 4,[5],12:i:- isolates. PLoS One 2021; 16:e0249079. [PMID: 33822792 PMCID: PMC8049487 DOI: 10.1371/journal.pone.0249079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 03/10/2021] [Indexed: 11/28/2022] Open
Abstract
Monophasic Salmonella 4,[5]:12:i:- are a major public health problem because they are one of the top five Salmonella serotypes isolated from clinical cases globally and because they can carry resistance to multiple antibiotics. A total of 811 Salmonella 4,[5]:12:i:- and S. Typhimurium whole genome sequences (WGS) were generated. The various genetic lesions causing the Salmonella 4,[5]:12:i:- genotype were identified and assessed with regards to their distribution in the population of 811 Salmonella 4,[5]:12:i:- and S. Typhimurium isolates, their geographical and temporal distribution, and their association with non-human sources. Several clades were identified in the population structure, and the largest two were associated almost exclusively with a short prophage insertion and insertion of a mobile element carrying loci encoding antibiotic and mercury resistance. IS26-mediated deletions and fljB point mutants appeared to spread clonally. 'Inconsistent' Salmonella 4,[5]:12:i:- isolates associated with specific, single amino acid changes in fljA and hin were found in a single clade composed of water, shellfish, and avian isolates. Inclusion of isolates from different case clusters identified previously by PFGE validated some of the clusters and invalidated others. Some wgMLST clusters of clinical isolates composed of very closely related isolates contained an isolate(s) with a different genetic lesion, suggesting continuing mobility of the implicated element responsible. Such cases may need to be left out of epidemiological investigations until sufficient numbers of isolates are included that statistical significance of association with sources is not impaired. Non-human sources were frequently found in or near clinical case clusters. Prospective surveillance and WGS of non-human sources and retrospective analysis by WGS of isolates from existing culture collections provides data critical for epidemiological investigations of food- and waterborne outbreaks.
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Affiliation(s)
- Clifford G. Clark
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Ashley K. Kearney
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Lorelee Tschetter
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - James Robertson
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Frank Pollari
- FoodNet Canada, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Stephen Parker
- FoodNet Canada, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Gitanjali Arya
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kim Ziebell
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Roger Johnson
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - John Nash
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Celine Nadon
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Mandilara G, Sideroglou T, Chrysostomou A, Rentifis I, Papadopoulos T, Polemis M, Tzani M, Tryfinopoulou K, Mellou K. The Rising Burden of Salmonellosis Caused by Monophasic Salmonella Typhimurium (1,4,[5],12:i:-) in Greece and New Food Vehicles. Antibiotics (Basel) 2021; 10:antibiotics10020185. [PMID: 33668483 PMCID: PMC7917691 DOI: 10.3390/antibiotics10020185] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 02/10/2021] [Indexed: 12/20/2022] Open
Abstract
Monophasic Salmonella typhimurium is of increasing importance worldwide. Here we present the available data regarding monophasic S. typhimurium from 2007 to 2019 in Greece, in order to assess its public health impact. Surveillance data, data on antimicrobial resistance, molecular typing by pulsed-field gel electrophoresis (PFGE), and results of the investigation of monophasic S. typhimurium outbreaks were analyzed. Overall, 403 cases were identified; 329 (81.6%) sporadic and 74 (18.4%) related to two community outbreaks in 2017. A total of 305 isolates from sporadic cases tested for antimicrobial resistance revealed resistance to ampicillin, streptomycin, sulphamethoxazole, and tetracycline (41.3%). Some 23.3% were further resistant to trimethoprim and 5.2% were also resistant to chloramphenicol. Outbreak 1 in 2017 with 37 identified cases was attributed to the consumption of raw milk from a vending machine and isolates were resistant to ampicillin, streptomycin, sulphamethoxazole, tetracycline, and trimethoprim. Outbreak 2 also with 37 cases was attributed to the consumption of pork and isolates were resistant to the five above mentioned antibiotics plus chloramphenicol. The number of human monophasic S. typhimurium isolates is low; however, since 2009, it has been among the five most frequently identified serotypes in Greece. Investigation of the outbreaks revealed that other vehicles apart from pork may be implicated in the occurrence of outbreaks.
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Affiliation(s)
- Georgia Mandilara
- National Reference Centre for Salmonella, Faculty of Public Health Policies, School of Public Health, University of West Attica and Athens, 12243 Egaleo, Greece; (G.M.); (I.R.)
| | - Theologia Sideroglou
- Department of Foodborne and Waterborne Diseases, National Public Health Organization, 15123 Athens, Greece; (T.S.); (A.C.)
| | - Anthi Chrysostomou
- Department of Foodborne and Waterborne Diseases, National Public Health Organization, 15123 Athens, Greece; (T.S.); (A.C.)
| | - Iliodoros Rentifis
- National Reference Centre for Salmonella, Faculty of Public Health Policies, School of Public Health, University of West Attica and Athens, 12243 Egaleo, Greece; (G.M.); (I.R.)
| | - Theofilos Papadopoulos
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), 17165 Stockholm, Sweden; (T.P.); (M.T.)
- Department of Epidemiology and Public Health, Sciensano, 1050 Brussels, Belgium
| | - Michalis Polemis
- Central Laboratory of Public Health, National Public Health Organization, Vari, 16672 Attica, Greece; (M.P.); (K.T.)
| | - Myrsini Tzani
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), 17165 Stockholm, Sweden; (T.P.); (M.T.)
| | - Kyriaki Tryfinopoulou
- Central Laboratory of Public Health, National Public Health Organization, Vari, 16672 Attica, Greece; (M.P.); (K.T.)
| | - Kassiani Mellou
- Department of Foodborne and Waterborne Diseases, National Public Health Organization, 15123 Athens, Greece; (T.S.); (A.C.)
- Correspondence:
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42
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Zeng X, Lv S, Qu C, Lan L, Tan D, Li X, Bai L. Serotypes, antibiotic resistance, and molecular characterization of non-typhoidal salmonella isolated from diarrheic patients in Guangxi Zhuang Autonomous Region, China, 2014–2017. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107478] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Cuenca-Arias P, Montaño LA, Villarreal JM, Wiesner M. Molecular and phenotypic characterization of Salmonella Typhimurium monophasic variant (1,4,[5],12:i:-) from Colombian clinical isolates. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2020; 40:722-733. [PMID: 33275350 PMCID: PMC7808771 DOI: 10.7705/biomedica.5417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/29/2020] [Indexed: 12/04/2022]
Abstract
Introduction. The Salmonella Typhimurium monophasic variant (1,4,[5],12:i:-) is currently the most commonly detected variant in Salmonella surveillance programs worldwide. In Colombia, the Salmonella enterica monophasic variant is the fourth most common clinical isolate recovered through the laboratory surveillance of the Grupo de Microbiología from the Instituto Nacional de Salud; however, it is unknown whether these isolates are closely related to the monophasic Typhimurium variant, which circulates globally, and their genetic and phenotypic characteristics have not been reported. Objective. To characterize monophasic Salmonella enterica isolates identified in Colombia from 2015 to 2018 by the Instituto Nacional de Salud. Materials and methods. Two hundred eighty-six clinical isolates of the monophasic Salmonella enterica variant were analyzed by PCR or whole-genome sequencing to confirm whether they corresponded to the Salmonella Typhimurium monophasic variant while the genetic structure of the operon encoding the second flagellar phase was determined in 54 isolates. Motility, growth, and expression of the outer membrane proteins were evaluated in 23 isolates. Results. During the study period in Colombia, 61% (n=174) of Salmonella monophasic isolates belonged to Salmonella Typhimurium serovar monophasic (1,4,[5],12:i-). Of these, 64.8% (n=35/54) were related to the European/Spanish clone and 13% (n=7/54) to the U.S. clone. Two isolates recovered from urine samples showed differences in motility, growth, and the absence of the OmpD porin in M9 minimal medium. Conclusions. Most of the monophasic Salmonella Typhimurium variants that have circulated in Colombia since 2015 lacked the second phase of operon fljAB, which is related to the European/Spanish clone. The results evidenced phenotypic changes in urine samples suggesting bacterial adaptation in the case of these invasive samples.
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Affiliation(s)
- Paloma Cuenca-Arias
- Grupo de Microbiología, Subdirección de Investigación Científica y Tecnológica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., Colombia.
| | - Lucy Angeline Montaño
- Grupo de Microbiología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá, D. C., Colombia.
| | - José Miguel Villarreal
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, D. C., Colombia; Grupo de Investigación en Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá, D. C., Colombia.
| | - Magdalena Wiesner
- Grupo de Microbiología, Subdirección de Investigación Científica y Tecnológica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., Colombia.
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Genomic Serotyping, Clinical Manifestations, and Antimicrobial Resistance of Nontyphoidal Salmonella Gastroenteritis in Hospitalized Children in Ho Chi Minh City, Vietnam. J Clin Microbiol 2020; 58:JCM.01465-20. [PMID: 32907994 PMCID: PMC7685882 DOI: 10.1128/jcm.01465-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/05/2020] [Indexed: 12/18/2022] Open
Abstract
Nontyphoidal Salmonella (NTS) are among the most common etiological agents of diarrheal diseases worldwide and have become the most commonly detected bacterial pathogen in children hospitalized with diarrhea in Vietnam. Aiming to better understand the epidemiology, serovar distribution, antimicrobial resistance (AMR), and clinical manifestation of NTS gastroenteritis in Vietnam, we conducted a clinical genomics investigation of NTS isolated from diarrheal children admitted to one of three tertiary hospitals in Ho Chi Minh City. Nontyphoidal Salmonella (NTS) are among the most common etiological agents of diarrheal diseases worldwide and have become the most commonly detected bacterial pathogen in children hospitalized with diarrhea in Vietnam. Aiming to better understand the epidemiology, serovar distribution, antimicrobial resistance (AMR), and clinical manifestation of NTS gastroenteritis in Vietnam, we conducted a clinical genomics investigation of NTS isolated from diarrheal children admitted to one of three tertiary hospitals in Ho Chi Minh City. Between May 2014 and April 2016, 3,166 children hospitalized with dysentery were recruited into the study; 478 (∼15%) children were found to be infected with NTS by stool culture. Molecular serotyping of the 450 generated genomes identified a diverse collection of serogroups (B, C1, C2 to C3, D1, E1, G, I, K, N, O, and Q); however, Salmonella enterica serovar Typhimurium was the most predominant serovar, accounting for 41.8% (188/450) of NTS isolates. We observed a high prevalence of AMR to first-line treatments recommended by WHO, and more than half (53.8%; 242/450) of NTS isolates were multidrug resistant (MDR; resistant to ≥3 antimicrobial classes). AMR gene detection positively correlated with phenotypic AMR testing, and resistance to empirical antimicrobials was associated with a significantly longer hospitalization (0.91 days; P = 0.04). Our work shows that genome sequencing is a powerful epidemiological tool to characterize the serovar diversity and AMR profiles in NTS. We propose a revaluation of empirical antimicrobials for dysenteric diarrhea and endorse the use of whole-genome sequencing for sustained surveillance of NTS internationally.
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Plasmid-borne colistin resistance gene mcr-1 in a multidrug resistant Salmonella enterica serovar Typhimurium isolate from an infant with acute diarrhea in China. Int J Infect Dis 2020; 103:13-18. [PMID: 33212253 DOI: 10.1016/j.ijid.2020.11.150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/21/2020] [Accepted: 11/09/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Antimicrobial resistance of Salmonella enterica is a major global concern. Recent findings suggest that colistin as a last resort treatment for multidrug-resistant gram-negative bacteria is seriously threatened by the report of plasmid-mediated colistin resistance gene mcr-1 in China. METHODS A total of 827 S. Typhimurium isolates were recovered from 4 cities of China, including Henan, Shanghai, Zhejiang, and Hubei provinces. Subsequently, mcr-1 presence was identified by PCR screening. Antimicrobial susceptibility testing was performed by broth microdilution using a 96-well microtiter plate. Plasmid conjugation transfer experiments were conducted using Escherichia coli J53 as the recipient. RESULTS Only one mcr-1 positive strain from the stool sample of an infant with acute diarrhea was isolated. Apart from colistin, the mcr-1-positive isolate showed co-resistance to the third-generation cephalosporins, ampicillin, nalidixic acid, tetracycline, chloramphenicol, sulfisoxazole, gentamicin, and cefotaxime revealing a multidrug-resistant phenotype. This strain harbored mcr-1 on a 227 kb IncHI2 plasmid, termed pJZ26, which could be transferred to E. coli J53. In addition to mcr-1, pJZ26 coharbored other resistance genes, including aph(4)-Ia, aac(3)-IVa, fosA, floR, sul2, and blaCTX-M-14. Compared with p2474-MCR1 and pHYEC7-IncHI2, pJZ26 contains an additional 4.6 kb fragment harboring the resistance gene tet(A) and its regulator tetR located on TnAs1 transposable element, which could mediate resistance to tetracycline. CONCLUSIONS These findings highlight that the fact the mcr-1-harboring plasmid pJZ26 has a high potential to disseminate the mcr-1 gene and further challenge the clinical treatment.
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Wilson CN, Pulford CV, Akoko J, Perez Sepulveda B, Predeus AV, Bevington J, Duncan P, Hall N, Wigley P, Feasey N, Pinchbeck G, Hinton JCD, Gordon MA, Fèvre EM. Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets. PLoS Negl Trop Dis 2020; 14:e0008796. [PMID: 33232324 PMCID: PMC7748489 DOI: 10.1371/journal.pntd.0008796] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 12/18/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Salmonella is a major cause of foodborne disease globally. Pigs can carry and shed non-typhoidal Salmonella (NTS) asymptomatically, representing a significant reservoir for these pathogens. To investigate Salmonella carriage by African domestic pigs, faecal and mesenteric lymph node samples were taken at slaughter in Nairobi, Busia (Kenya) and Chikwawa (Malawi) between October 2016 and May 2017. Selective culture, antisera testing and whole genome sequencing were performed on samples from 647 pigs; the prevalence of NTS carriage was 12.7% in Busia, 9.1% in Nairobi and 24.6% in Chikwawa. Two isolates of S. Typhimurium ST313 were isolated, but were more closely related to ST313 isolates associated with gastroenteritis in the UK than bloodstream infection in Africa. The discovery of porcine NTS carriage in Kenya and Malawi reveals potential for zoonotic transmission of diarrhoeal strains to humans in these countries, but not for transmission of clades specifically associated with invasive NTS disease in Africa.
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Affiliation(s)
- Catherine N. Wilson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- International Livestock Research Institute, Nairobi, Kenya
| | - Caisey V. Pulford
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | - Blanca Perez Sepulveda
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Alexander V. Predeus
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jessica Bevington
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Patricia Duncan
- Ministry of Agriculture, Food Security, Irrigation and Water Development, Malawi Government
| | - Neil Hall
- Earlham Institute, Norwich, United Kingdom
| | - Paul Wigley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nicholas Feasey
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Gina Pinchbeck
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jay C. D. Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Melita A. Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Eric M. Fèvre
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- International Livestock Research Institute, Nairobi, Kenya
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Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States. mSphere 2020; 5:5/5/e00990-20. [PMID: 33115839 PMCID: PMC8534314 DOI: 10.1128/msphere.00990-20] [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] [Indexed: 12/12/2022] Open
Abstract
Fluoroquinolones and cephalosporins are critically important antimicrobial classes for both human and veterinary medicine. We previously found a drastic increase in enrofloxacin resistance in clinical Escherichia coli isolates collected from diseased pigs from the United States over 10 years (2006 to 2016). However, the genetic determinants responsible for this increase have yet to be determined. The aim of the present study was to identify and characterize the genetic basis of resistance against fluoroquinolones (enrofloxacin) and extended-spectrum cephalosporins (ceftiofur) in swine E. coli isolates using whole-genome sequencing (WGS). blaCMY-2 (carried by IncA/C2, IncI1, and IncI2 plasmids), blaCTX-M (carried by IncF, IncHI2, and IncN plasmids), and blaSHV-12 (carried by IncHI2 plasmids) genes were present in 87 (82.1%), 19 (17.9%), and 3 (2.83%) of the 106 ceftiofur-resistant isolates, respectively. Of the 110 enrofloxacin-resistant isolates, 90 (81.8%) had chromosomal mutations in gyrA, gyrB, parA, and parC genes. Plasmid-mediated quinolone resistance genes [qnrB77, qnrB2, qnrS1, qnrS2, and aac-(6)-lb′-cr] borne on ColE, IncQ2, IncN, IncF, and IncHI2 plasmids were present in 24 (21.8%) of the enrofloxacin-resistant isolates. Virulent IncF plasmids present in swine E. coli isolates were highly similar to epidemic plasmids identified globally. High-risk E. coli clones, such as ST744, ST457, ST131, ST69, ST10, ST73, ST410, ST12, ST127, ST167, ST58, ST88, ST617, ST23, etc., were also found in the U.S. swine population. Additionally, the colistin resistance gene (mcr-9) was present in several isolates. This study adds valuable information regarding resistance to critical antimicrobials with implications for both animal and human health. IMPORTANCE Understanding the genetic mechanisms conferring resistance is critical to design informed control and preventive measures, particularly when involving critically important antimicrobial classes such as extended-spectrum cephalosporins and fluoroquinolones. The genetic determinants of extended-spectrum cephalosporin and fluoroquinolone resistance were highly diverse, with multiple plasmids, insertion sequences, and genes playing key roles in mediating resistance in swine Escherichia coli. Plasmids assembled in this study are known to be disseminated globally in both human and animal populations and environmental samples, and E. coli in pigs might be part of a global reservoir of key antimicrobial resistance (AMR) elements. Virulent plasmids found in this study have been shown to confer fitness advantages to pathogenic E. coli strains. The presence of international, high-risk zoonotic clones provides worrisome evidence that resistance in swine isolates may have indirect public health implications, and the swine population as a reservoir for these high-risk clones should be continuously monitored.
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Elnekave E, Hong SL, Lim S, Johnson TJ, Perez A, Alvarez J. Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica: a large-scale analysis of 37 serotypes with a public health impact in the USA. Microb Genom 2020; 6:mgen000425. [PMID: 32845830 PMCID: PMC7643971 DOI: 10.1099/mgen.0.000425] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/03/2020] [Indexed: 01/21/2023] Open
Abstract
Serotyping has traditionally been used for subtyping of non-typhoidal Salmonella (NTS) isolates. However, its discriminatory power is limited, which impairs its use for epidemiological investigations of source attribution. Whole-genome sequencing (WGS) analysis allows more accurate subtyping of strains. However, because of the relative newness and cost of routine WGS, large-scale studies involving NTS WGS are still rare. We aimed to revisit the big picture of subtyping NTS with a public health impact by using traditional serotyping (i.e. reaction between antisera and surface antigens) and comparing the results with those obtained using WGS. For this purpose, we analysed 18 282 sequences of isolates belonging to 37 serotypes with a public health impact that were recovered in the USA between 2006 and 2017 from multiple sources, and were available at the National Center for Biotechnology Information (NCBI). Phylogenetic trees were reconstructed for each serotype using the core genome for the identification of genetic subpopulations. We demonstrated that WGS-based subtyping allows better identification of sources potentially linked with human infection and emerging subpopulations, along with providing information on the risk of dissemination of plasmids and acquired antimicrobial resistance genes (AARGs). In addition, by reconstructing a phylogenetic tree with representative isolates from all serotypes (n=370), we demonstrated genetic variability within and between serotypes, which formed monophyletic, polyphyletic and paraphyletic clades. Moreover, we found (in the entire data set) an increased detection rate for AARGs linked to key antimicrobials (such as quinolones and extended-spectrum cephalosporins) over time. The outputs of this large-scale analysis reveal new insights into the genetic diversity within and between serotypes; the polyphyly and paraphyly of certain serotypes may suggest that the subtyping of NTS to serotypes may not be sufficient. Moreover, the results and the methods presented here, leading to differentiation between genetic subpopulations based on their potential risk to public health, as well as narrowing down the possible sources of these infections, may be used as a baseline for subtyping of future NTS infections and help efforts to mitigate and prevent infections in the USA and globally.
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Affiliation(s)
- Ehud Elnekave
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Israel
| | - Samuel L. Hong
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, University of Leuven, Leuven, Belgium
| | - Seunghyun Lim
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
- Bioinformatics and Computational Biology Program, University of Minnesota, Rochester, Minnesota, USA
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Andres Perez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Julio Alvarez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
- VISAVET Health Surveillance Center, Universidad Complutense, Madrid, Spain
- Department of Animal Health, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
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Clark CG, Landgraff C, Robertson J, Pollari F, Parker S, Nadon C, Gannon VPJ, Johnson R, Nash J. Distribution of heavy metal resistance elements in Canadian Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype. PLoS One 2020; 15:e0236436. [PMID: 32716946 PMCID: PMC7384650 DOI: 10.1371/journal.pone.0236436] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/06/2020] [Indexed: 12/02/2022] Open
Abstract
Salmonella 4,[5],12:i:- are monophasic S. Typhimurium variants incapable of producing the second-phase flagellar antigen. They have emerged since the mid-1990s to become one of the most prevalent Salmonella serotypes causing human disease world-wide. Multiple genetic events associated with different genetic elements can result in the monophasic phenotype. Several jurisdictions have reported the emergence of a Salmonella 4,[5],12:i:- clone with SGI-4 and a genetic element (MREL) encoding a mercury resistance operon and antibiotic resistance loci that disrupts the second phase antigen region near the iroB locus in the Salmonella genome. We have sequenced 810 human and animal Canadian Salmonella 4,[5],12:i:- isolates and determined that isolates with SGI-4 and the mercury resistance element (MREL; also known as RR1&RR2) constitute several global clades containing various proportions of Canadian, US, and European isolates. Detailed analysis of the data provides a clearer picture of how these heavy metal elements interact with bacteria within the Salmonella population to produce the monophasic phenotype. Insertion of the MREL near iroB is associated with several deletions and rearrangements of the adjacent flaAB hin region, which may be useful for defining human case clusters that could represent outbreaks. Plasmids carrying genes encoding silver, copper, mercury, and antimicrobial resistance appear to be derived from IS26 mediated acquisition of these genes from genomes carrying SGI-4 and the MREL. Animal isolates with the mercury and As/Cu/Ag resistance elements are strongly associated with porcine sources in Canada as has been shown previously for other jurisdictions. The data acquired in these investigations, as well as from the extensive literature on the subject, may aid source attribution in outbreaks of the organism and interventions to decrease the prevalence of this clone and reduce its impact on human disease.
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Affiliation(s)
- Clifford G Clark
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chrystal Landgraff
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - James Robertson
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Frank Pollari
- FoodNet Canada, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Stephen Parker
- FoodNet Canada, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Celine Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- PulseNet Canada, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Victor P J Gannon
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Canada
| | - Roger Johnson
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - John Nash
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
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50
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Elbediwi M, Beibei W, Pan H, Jiang Z, Biswas S, Li Y, Yue M. Genomic Characterization of mcr-1-carrying Salmonella enterica Serovar 4,[5],12:i:- ST 34 Clone Isolated From Pigs in China. Front Bioeng Biotechnol 2020; 8:663. [PMID: 32714906 PMCID: PMC7344297 DOI: 10.3389/fbioe.2020.00663] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/28/2020] [Indexed: 12/31/2022] Open
Abstract
Salmonella enterica serovar 4,[5],12:i:-, so-called Typhimurium monophasic variant, has become one of the most frequently isolated serovars both in humans and in animals all over the world. The increasing prevalence of mcr-1-carrying Salmonella poses significant global health concerns. However, the potential role of Salmonella 4,[5],12:i:- in mcr-1 gene migration through the food chain to the human remains obscure. Here, we investigated 337 Salmonella isolates from apparently healthy finishing pigs, which is rarely studied, obtained from pig farms and slaughterhouses in China. The mcr-1 gene was found in four colistin-resistant S. enterica 4,[5],12:i:- isolates. Notably, all four isolates belonged to sequence type 34 (ST34) with multidrug resistance phenotype. Further genomic sequencing and antimicrobial resistance characterization confirmed that mcr was responsible for the colistin resistance, and the conjugation assay demonstrated that three of four isolates carried mcr-1 in IncHI2 plasmid. Importantly, mcr-1 and class-1 integron were found to co-localize in two strains with IncHI2 plasmid. By collecting all the mcr-1-carrying Typhimurium and monophasic variant strains across the food chain (farm animals, animal-origin food, and humans), our phylogenomic analysis of available 66 genomes, including four strains in this study, demonstrated an independent phylogenetic cluster of all eight Chinese swine-originated isolates and one human isolate. Together, this study provides direct evidence for clonal and pork-borne transmission of mcr-1 by Salmonella 4,[5],12:i:- ST34 in China and highlighted a domestication pathway by acquisition of additional antimicrobial resistance determinants in Chinese ST34 isolates.
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Affiliation(s)
- Mohammed Elbediwi
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Wu Beibei
- Zhejiang Province Center for Disease Control and Prevention, Hangzhou, China
| | - Hang Pan
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zenghai Jiang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Silpak Biswas
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yan Li
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Min Yue
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
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