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Abstract
Salmonella enterica remains an important foodborne pathogen in all regions of the world, with Typhimurium as one of the most frequent serotypes causing foodborne disease. However, the past two decades have seen a rapid worldwide emergence of a new Salmonella serotype, namely monophasic variant of S. Typhimurium, whose antigenic formula is 1,4,[5],12:i:-. It has become one of the 2-5 most common Salmonella serotypes responsible for animal and human infections in different regions. The global epidemic of monophasic S. 1,4,[5],12:i:- has mainly been characterized by an increase in multidrug-resistant S. 1,4,[5],12:i:- isolated in Europe since 1997. The unexpected link to swine has escalated monophasic S. Typhimurium infections to the status of a global public health emergency. The large-scale application of whole genome sequencing (WGS) in the last 10 years has revealed the phylogenetic associations of the bacterium and its antimicrobial resistance (AMR) genes. Local and global transmission reconstructed by WGS have shown that different clones have emerged following multiple independent events worldwide, and have elucidated the role of this zoonotic pathogen in the spread of AMR. This article discusses our current knowledge of the global ecology, epidemiology, transmission, bacterial adaptation, and evolution of this emerging Salmonella serotype.
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Affiliation(s)
- Honghu Sun
- 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.,Chengdu Institute for Food and Drug Control, Chengdu, China
| | - Yuping Wan
- Chengdu Institute for Food and Drug Control, Chengdu, China
| | - Pengcheng Du
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 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
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2
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Arai N, Sekizuka T, Tamamura Y, Kusumoto M, Hinenoya A, Yamasaki S, Iwata T, Watanabe-Yanai A, Kuroda M, Akiba M. Salmonella Genomic Island 3 Is an Integrative and Conjugative Element and Contributes to Copper and Arsenic Tolerance of Salmonella enterica. Antimicrob Agents Chemother 2019; 63:e00429-19. [PMID: 31209002 DOI: 10.1128/AAC.00429-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/07/2019] [Indexed: 01/26/2023] Open
Abstract
Salmonella genomic island 3 (SGI3) was first described as a chromosomal island in Salmonella 4,[5],12:i:-, a monophasic variant of Salmonella enterica subsp. enterica serovar Typhimurium. The SGI3 DNA sequence detected from Salmonella 4,[5],12:i:- isolated in Japan was identical to that of a previously reported one across entire length of 81 kb. SGI3 consists of 86 open reading frames, including a copper homeostasis and silver resistance island (CHASRI) and an arsenic tolerance operon, in addition to genes related to conjugative transfer and DNA replication or partitioning, suggesting that the island is a mobile genetic element. We successfully selected transconjugants that acquired SGI3 after filter-mating experiments using the S. enterica serovars Typhimurium, Heidelberg, Hadar, Newport, Cerro, and Thompson as recipients. Southern blot analysis using I-CeuI-digested genomic DNA demonstrated that SGI3 was integrated into a chromosomal fragment of the transconjugants. PCR and sequencing analysis demonstrated that SGI3 was inserted into the 3' end of the tRNA genes pheV or pheR The length of the target site was 52 or 55 bp, and a 55-bp attI sequence indicating generation of the circular form of SGI3 was also detected. The transconjugants had a higher MIC against CuSO4 compared to the recipient strains under anaerobic conditions. Tolerance was defined by the cus gene cluster in the CHASRI. The transconjugants also had distinctly higher MICs against Na2HAsO4 compared to recipient strains under aerobic conditions. These findings clearly demonstrate that SGI3 is an integrative and conjugative element and contributes to the copper and arsenic tolerance of S. enterica.
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Gosling RJ, Mueller-Doblies D, Martelli F, Nunez-Garcia J, Kell N, Rabie A, Wales AD, Davies RH. Observations on the distribution and persistence of monophasic Salmonella Typhimurium on infected pig and cattle farms. Vet Microbiol 2018; 227:90-96. [PMID: 30473358 DOI: 10.1016/j.vetmic.2018.10.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/26/2018] [Accepted: 10/31/2018] [Indexed: 11/24/2022]
Abstract
Following a rapid rise in cases of monophasic Salmonella Typhimurium DT193 (mST) in humans and pigs since 2007 a detailed study of the prevalence and persistence of mST on pig and cattle farms in Great Britain (GB) was undertaken. Thirteen commercial pig farms and twelve cattle farms, identified as mST-positive from surveillance data, were intensively sampled over a three year period. Five indoor and eight outdoor pig farms and four beef and eight dairy farms were included. Individual and pooled faecal samples were collected from each epidemiological group and environmental samples throughout each farm and the antimicrobial resistance profile determined for a selection of mST-positive isolates. Indoor pig farms had a higher mST prevalence than outdoor pig farms, and across both cattle and pig farms the juvenile animals had a higher mST prevalence than the adult animals. Overall, mST prevalence decreased with time across all pig farms, from 25% to less than 15% of environmental samples and 22% to 15% of pooled faecal samples; only one organic outdoor breeding farm was Salmonella-negative at the end of the study. Across the cattle farms no mST was detected by the end of the study, apart from one persistent farm. Clearance time of mST was between seven and twenty-five months. Farms were selected based on having the antimicrobial resistance profile ampicillin, streptomycin, sulphonamides and tetracycline (A, S, SU, T), although resistance to trimethoprim-potentiated sulphamethoxazole was also identified on five pig farms sampled. This study provided a detailed insight into the distribution and persistence of mST on individual pig and cattle farms in GB. It has identified variation in mST shedding of individual animals, and the data can be applied to the wider livestock industry when considering the distribution of mST once identified on an individual farm.
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Affiliation(s)
- Rebecca J Gosling
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK.
| | | | - Francesca Martelli
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | | | - Nick Kell
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Andre Rabie
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Andy D Wales
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Vet School Main Building, Daphne Jackson Road, University of Surrey, Guildford, GU2 7AL, UK
| | - Robert H Davies
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
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Arai N, Sekizuka T, Tamamura Y, Tanaka K, Barco L, Izumiya H, Kusumoto M, Hinenoya A, Yamasaki S, Iwata T, Watanabe A, Kuroda M, Uchida I, Akiba M. Phylogenetic Characterization of Salmonella enterica Serovar Typhimurium and Its Monophasic Variant Isolated from Food Animals in Japan Revealed Replacement of Major Epidemic Clones in the Last 4 Decades. J Clin Microbiol 2018; 56:JCM.01758-17. [PMID: 29491013 DOI: 10.1128/jcm.01758-17/suppl_file/zjm999095924sd2.xlsx] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/17/2018] [Indexed: 05/27/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) and its monophasic variant (Salmonella 4,[5],12:i:-) are the major causes of gastroenteritis in both humans and animals. Pulsed-field gel electrophoresis and multilocus variable-number tandem-repeat analysis have been used widely as subtyping methods for these pathogens in molecular epidemiological analyses, but the results do not precisely reflect phylogenetic information. In this study, we performed a phylogenetic analysis of these serovars using whole-genome sequencing data and identified nine distinct genotypic clades. Then, we established an allele-specific PCR-based genotyping method detecting a clade-specific single nucleotide polymorphism to rapidly identify the clade of each isolate. Among a total of 815 isolates obtained from cattle in Japan between 1977 and 2017, clades 1, 7, and 9 contained 77% of isolates. Obvious replacement of the dominant clone was observed five times in this period, and clade 9, which mostly contains Salmonella 4,[5],12:i:-, is currently dominant. Among 140 isolates obtained from swine in Japan between 1976 and 2017, clades 3 and 9 contained 64% of isolates. Clade 9 is the latest clone as is the case in cattle isolates. Clade 9 is similar to an epidemic clone from Europe, which is characterized by sequence type 34 (ST34), chromosomal Salmonella genomic island 3, and a composite transposon containing antimicrobial resistance genes. The increased prevalence of clade 9 among food animals in Japan might be a part of the pandemic of the European Salmonella 4,[5],12:i:- clone.
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Affiliation(s)
- Nobuo Arai
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukino Tamamura
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Kiyoshi Tanaka
- Hokkaido Research Station, National Institute of Animal Health, Sapporo, Hokkaido, Japan
| | - Lisa Barco
- Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Hidemasa Izumiya
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masahiro Kusumoto
- Kyushu Research Station, National Institute of Animal Health, Kagoshima, Japan
| | - Atsushi Hinenoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Shinji Yamasaki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Taketoshi Iwata
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Ayako Watanabe
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ikuo Uchida
- Unit of Veterinary Bacteriology, Department of Pathology, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Masato Akiba
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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Arai N, Sekizuka T, Tamamura Y, Tanaka K, Barco L, Izumiya H, Kusumoto M, Hinenoya A, Yamasaki S, Iwata T, Watanabe A, Kuroda M, Uchida I, Akiba M. Phylogenetic Characterization of Salmonella enterica Serovar Typhimurium and Its Monophasic Variant Isolated from Food Animals in Japan Revealed Replacement of Major Epidemic Clones in the Last 4 Decades. J Clin Microbiol 2018; 56:e01758-17. [PMID: 29491013 DOI: 10.1128/JCM.01758-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/17/2018] [Indexed: 01/28/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) and its monophasic variant (Salmonella 4,[5],12:i:-) are the major causes of gastroenteritis in both humans and animals. Pulsed-field gel electrophoresis and multilocus variable-number tandem-repeat analysis have been used widely as subtyping methods for these pathogens in molecular epidemiological analyses, but the results do not precisely reflect phylogenetic information. In this study, we performed a phylogenetic analysis of these serovars using whole-genome sequencing data and identified nine distinct genotypic clades. Then, we established an allele-specific PCR-based genotyping method detecting a clade-specific single nucleotide polymorphism to rapidly identify the clade of each isolate. Among a total of 815 isolates obtained from cattle in Japan between 1977 and 2017, clades 1, 7, and 9 contained 77% of isolates. Obvious replacement of the dominant clone was observed five times in this period, and clade 9, which mostly contains Salmonella 4,[5],12:i:-, is currently dominant. Among 140 isolates obtained from swine in Japan between 1976 and 2017, clades 3 and 9 contained 64% of isolates. Clade 9 is the latest clone as is the case in cattle isolates. Clade 9 is similar to an epidemic clone from Europe, which is characterized by sequence type 34 (ST34), chromosomal Salmonella genomic island 3, and a composite transposon containing antimicrobial resistance genes. The increased prevalence of clade 9 among food animals in Japan might be a part of the pandemic of the European Salmonella 4,[5],12:i:- clone.
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Ido N, Lee KI, Iwabuchi K, Izumiya H, Uchida I, Kusumoto M, Iwata T, Ohnishi M, Akiba M. Characteristics of Salmonella enterica serovar 4,[5],12:i:- as a monophasic variant of serovar Typhimurium. PLoS One 2014; 9:e104380. [PMID: 25093666 PMCID: PMC4122451 DOI: 10.1371/journal.pone.0104380] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 07/11/2014] [Indexed: 12/01/2022] Open
Abstract
Salmonella enterica subspecies enterica serovar 4,[5],12:i:- (S. 4,[5]12:i:-) is believed to be a monophasic variant of S. enterica serovar Typhimurium (S. Typhimurium). This study was conducted to corroborate this hypothesis and to identify the molecular and phenotypic characteristics of the S. 4,[5]12:i:- isolates in Japan. A total of 51 S. 4,[5]12:i:- isolates derived from humans, cattle, swine, chickens, birds, meat (pork), and river water in 15 prefectures in Japan between 2000 and 2010 were analyzed. All the S. 4,[5],12:i:- isolates were identified as S. Typhimurium by two different polymerase chain reactions (PCR) for identification of S. Typhimurium. Of the 51 S. 4,[5],12:i:- isolates, 39 (76.5%) harbored a 94-kb virulence plasmid, which is known to be specific for S. Typhimurium. These data suggest that the S. 4,[5],12:i:- isolates are monophasic variants of S. Typhimurium. The flagellar phase variation is induced by three adjacent genes (fljA, fljB, and hin) in the chromosome. The results of PCR mapping of this region and comparative genomic hybridization analysis suggested that the deletion of the fljAB operon and its flanking region was the major genetic basis of the monophasic phenotype of S. 4,[5],12:i:-. The fljAB operon and hin gene were detectable in eight of the S. 4,[5],12:i:- isolates with common amino acid substitutions of A46T in FljA and R140L in Hin. The introduction of these mutations into S. Typhimurium isolates led to the loss of selectability of isolates expressing the phase 2 H antigen. These data suggested that a point mutation was the genetic basis, at least in part, of the S. 4,[5],12:i:- isolates. The results of phenotypic analysis suggested that the S. 4,[5],12:i:- isolates in Japan consist of multiple distinct clones. This is the first detailed characterization of the S. 4,[5],12:i:- isolates derived from various sources across Japan.
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Affiliation(s)
- Noriko Ido
- Iwate Prefecture Central Livestock Hygiene Service Center, Iwate, Japan
| | - Ken-ichi Lee
- Bacterial and Parasitic Disease Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Kaori Iwabuchi
- Research Institute for Environmental Sciences and Public Health of Iwate Prefecture, Iwate, Japan
| | - Hidemasa Izumiya
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ikuo Uchida
- Hokkaido Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, Hokkaido, Japan
| | - Masahiro Kusumoto
- Bacterial and Parasitic Disease Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Taketoshi Iwata
- Bacterial and Parasitic Disease Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Makoto Ohnishi
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masato Akiba
- Bacterial and Parasitic Disease Research Division, 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
- * E-mail:
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Myšková P, Oslanecová L, Drahovská H, Karpíšková R. Clonal distribution of monophasic Salmonella enterica subsp. enterica serotype 4,[5],12:i:- in the Czech Republic. Foodborne Pathog Dis 2014; 11:664-6. [PMID: 24823892 DOI: 10.1089/fpd.2013.1703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract Salmonella 4,[5],12:i:- has become the third most common serotype in Europe, including the Czech Republic. In this study, phenotypic and genotypic methods for a more detailed description of this serotype were used. Analysis of a limited number of isolates revealed that 76% of them belonged to phage type DT193. Also, rare phage types DT208 and U311 were identified. In total, 88.6% of the isolates were resistant to at least four antimicrobial agents. In this study, 24 multilocus variable-number tandem-repeat analysis profiles were detected, and some of them matched with the profiles recently described in Europe.
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Affiliation(s)
- Petra Myšková
- 1 Department of Bacteriology, Veterinary Research Institute , Brno, Czech Republic
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