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Dechêne-Tempier M, de Boisséson C, Lucas P, Bougeard S, Libante V, Marois-Créhan C, Payot S. Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France. Microb Genom 2024; 10:001224. [PMID: 38536216 PMCID: PMC10995628 DOI: 10.1099/mgen.0.001224] [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: 11/16/2023] [Accepted: 03/08/2024] [Indexed: 04/07/2024] Open
Abstract
Streptococcus suis is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes (n=217) was found in the genomes. Apart from the frequently reported erm(B) and tet(O) genes, more recently described AMR genes were identified [vga(F)/sprA, vat(D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.
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Affiliation(s)
- Manon Dechêne-Tempier
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, BP53 22440 Ploufragan, France
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | - Claire de Boisséson
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, BP53 22440 Ploufragan, France
| | - Pierrick Lucas
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Génétique Virale et Biosécurité, BP53 22440 Ploufragan, France
| | - Stéphanie Bougeard
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Épidémiologie, santé et bien-être, BP53 22440 Ploufragan, France
| | | | - Corinne Marois-Créhan
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, BP53 22440 Ploufragan, France
| | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
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Liu Z, Xu Q, Liang P, Peng Z, Yao H, Zheng H, Wu Z. The characteristics of population structure and antimicrobial resistance of Streptococcus suis serotype 8, a non-negligible pathotype. Transbound Emerg Dis 2022; 69:e2495-e2505. [PMID: 35560732 DOI: 10.1111/tbed.14592] [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: 03/22/2022] [Revised: 04/23/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022]
Abstract
Streptococcus suis, the leading causative agent of swine streptococcosis, is considered as a severe zoonotic and foodborne pathogen for humans. Characteristics of population structure and pathogenicity of S. suis vary significantly by serotypes. As one of the main pathogenic serotypes causing clinical disease in pigs, very little is known about the pathogenicity, population structure, and antimicrobial resistance of S. suis serotype 8 (SS8). In this study, the genome of 26 SS8 strains isolated from healthy and diseased pigs was sequenced. Together with 38 sequences from NCBI, we found that SS8 population was clustered into 12 sequence types (ST) and 4 minimum core genome (MCG) groups, linked to the geographical distribution. Noteworthily, 10 strains belonged to MCG group 1 which was defined to possess the capacity to cause global outbreaks in our previous study. We found that 75% (9/12) of representative SS8 strains were virulent in mice and zebrafish, including all ST1241 strains. No virulence indicators were identified from 67 putative virulence-associated genes mainly identified among pathogenic serotype 2 strains. Instead, we found that the genotype of some of these genes was correlated to their evolution. All 26 isolates were classified as multidrug-resistant strains by antimicrobial susceptibility testing. The high carrying rate of tetO and ermB, mainly disseminated by integrative mobilizable elements, contributed to the prevalent resistance phenotypes to macrolides, lincosamides and tetracyclines. These findings indicated that the pathogenic potential of SS8 cannot be ignored and provided valuable information for SS8 surveillance.
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Affiliation(s)
- Zhaoying Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
| | - Qiuhua Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
| | - Pujun Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Zeren Peng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
| | - Huochun Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Zongfu Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
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3
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Lemaire C, Le Gallou B, Lanotte P, Mereghetti L, Pastuszka A. Distribution, Diversity and Roles of CRISPR-Cas Systems in Human and Animal Pathogenic Streptococci. Front Microbiol 2022; 13:828031. [PMID: 35173702 PMCID: PMC8841824 DOI: 10.3389/fmicb.2022.828031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/10/2022] [Indexed: 12/26/2022] Open
Abstract
Streptococci form a wide group of bacteria and are involved in both human and animal pathologies. Among pathogenic isolates, differences have been highlighted especially concerning their adaptation and virulence profiles. CRISPR-Cas systems have been identified in bacteria and many streptococci harbor one or more systems, particularly subtypes I-C, II-A, and III-A. Since the demonstration that CRISPR-Cas act as an adaptive immune system in Streptococcus thermophilus, a lactic bacteria, the diversity and role of CRISPR-Cas were extended to many germs and functions were enlarged. Among those, the genome editing tool based on the properties of Cas endonucleases is used worldwide, and the recent attribution of the Nobel Prize illustrates the importance of this tool in the scientific world. Another application is CRISPR loci analysis, which allows to easily characterize isolates in order to understand the interactions of bacteria with their environment and visualize species evolution. In this review, we focused on the distribution, diversity and roles of CRISPR-Cas systems in the main pathogenic streptococci.
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Affiliation(s)
- Coralie Lemaire
- Université de Tours, INRAE, Infectiologie et Santé Publique, BRMF, Tours, France
- Service de Bactériologie-Virologie, Centre Hospitalier Régional Universitaire de Tours, Tours, France
| | - Brice Le Gallou
- Université de Tours, INRAE, Infectiologie et Santé Publique, BRMF, Tours, France
- Service de Bactériologie-Virologie, Centre Hospitalier Régional Universitaire de Tours, Tours, France
| | - Philippe Lanotte
- Université de Tours, INRAE, Infectiologie et Santé Publique, BRMF, Tours, France
- Service de Bactériologie-Virologie, Centre Hospitalier Régional Universitaire de Tours, Tours, France
- *Correspondence: Philippe Lanotte,
| | - Laurent Mereghetti
- Université de Tours, INRAE, Infectiologie et Santé Publique, BRMF, Tours, France
- Service de Bactériologie-Virologie, Centre Hospitalier Régional Universitaire de Tours, Tours, France
| | - Adeline Pastuszka
- Université de Tours, INRAE, Infectiologie et Santé Publique, BRMF, Tours, France
- Service de Bactériologie-Virologie, Centre Hospitalier Régional Universitaire de Tours, Tours, France
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4
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Kerdsin A, Hatrongjit R, Wongsurawat T, Jenjaroenpun P, Chopjitt P, Boueroy P, Fittipaldi N, Zheng H, Gottschalk M. Genomic Characterization of Streptococcus suis Serotype 24 Clonal Complex 221/234 From Human Patients. Front Microbiol 2022; 12:812436. [PMID: 35003043 PMCID: PMC8733411 DOI: 10.3389/fmicb.2021.812436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/06/2021] [Indexed: 12/26/2022] Open
Abstract
Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. Although S. suis serotype 2 is prevalent among patient and swine infections, other serotypes are occasionally detected in humans. Of these, serotype 24 clonal complex (CC) 221/234 are recognized as emerging clones of human infection. Genomic exploration of three S. suis serotype 24 CC221/234 strains revealed antimicrobial resistance genes, pathotyping, virulence-associated gene (VAG) profiles, minimum core genome (MCG) typing, and comparison of the genomes. Based on these analyzes, all three serotype 24 strains were MCG7-3 and should be classified in the intermediate/weakly virulent (I/WV) group. All selected serotype 24 strains were susceptible to several antibiotics including β-lactam, fluoroquinolone, and chloramphenicol. Resistance to tetracycline, macrolide, and clindamycin was observed and attributed to the genes tet(O) and erm(B). Genomic comparison revealed the strains S12X, LSS66, LS0L, LS0E, 92–4,172, and IMT40201 that had phylogenetic affinity with serotype 24 CC221/234. Analysis of 80 virulence-associated genes (VAG) showed that all three serotype 24 strains lacked 24 genes consisting of adhesin P, epf, hyl, ihk, irr, mrp, nadR, neuB, NisK/R, ofs, permease (SSU0835), rgg, revS, salK/R, sao, sly, spyM3_0908, srtBCD, srtF, srtG, SSU05_0473, virA, virB4, and virD4. Eleven specific sequences were identified in the 3 serotype 24 genomes that differed from the genomes of the representative strains of epidemic (E; SC84), highly virulent (HV; P1/7), I/WV (89–1,591), and avirulent (T15 and 05HAS68).
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Affiliation(s)
- Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Rujirat Hatrongjit
- Department of General Sciences, Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Nahuel Fittipaldi
- Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Quebec, QC, Canada
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Marcelo Gottschalk
- Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Quebec, QC, Canada
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5
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Dechêne-Tempier M, Marois-Créhan C, Libante V, Jouy E, Leblond-Bourget N, Payot S. Update on the Mechanisms of Antibiotic Resistance and the Mobile Resistome in the Emerging Zoonotic Pathogen Streptococcus suis. Microorganisms 2021; 9:microorganisms9081765. [PMID: 34442843 PMCID: PMC8401462 DOI: 10.3390/microorganisms9081765] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
Streptococcus suis is a zoonotic pathogen causing important economic losses in swine production. The most commonly used antibiotics in swine industry are tetracyclines, beta-lactams, and macrolides. Resistance to these antibiotics has already been observed worldwide (reaching high rates for macrolides and tetracyclines) as well as resistance to aminoglycosides, fluoroquinolones, amphenicols, and glycopeptides. Most of the resistance mechanisms are encoded by antibiotic resistance genes, and a large part are carried by mobile genetic elements (MGEs) that can be transferred through horizontal gene transfer. This review provides an update of the resistance genes, their combination in multidrug isolates, and their localization on MGEs in S. suis. It also includes an overview of the contribution of biofilm to antimicrobial resistance in this bacterial species. The identification of resistance genes and study of their localization in S. suis as well as the environmental factors that can modulate their dissemination appear essential in order to decipher the role of this bacterium as a reservoir of antibiotic genes for other species.
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Affiliation(s)
- Manon Dechêne-Tempier
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, F-22440 Ploufragan, France; (M.D.-T.); (C.M.-C.); (E.J.)
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (V.L.); (N.L.-B.)
| | - Corinne Marois-Créhan
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, F-22440 Ploufragan, France; (M.D.-T.); (C.M.-C.); (E.J.)
| | - Virginie Libante
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (V.L.); (N.L.-B.)
| | - Eric Jouy
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, F-22440 Ploufragan, France; (M.D.-T.); (C.M.-C.); (E.J.)
| | | | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (V.L.); (N.L.-B.)
- Correspondence:
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6
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Zhu Y, Dong W, Ma J, Zhang Y, Zhong X, Pan Z, Liu G, Wu Z, Yao H. Comparative genetic analyses provide clues about capsule switching in Streptococcus suis 2 strains with different virulence levels and genetic backgrounds. Microbiol Res 2021; 250:126814. [PMID: 34256310 DOI: 10.1016/j.micres.2021.126814] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/22/2021] [Accepted: 07/04/2021] [Indexed: 12/19/2022]
Abstract
Streptococcus suis (S. suis) is a major bacterial pathogen in the swine industry and an emerging zoonotic agent. S. suis produces an important extracellular component, capsular polysaccharide (CPS), based on which dozens of serotypes have been identified. Through virulence genotyping, we revealed the relatedness between subpopulations of S. suis serotype 2 (SS2), S. suis serotype 3 (SS3) and S. suis serotype 7 (SS7) strains despite their serotype differences. Multilocus sequence typing (MLST) was used to characterize the whole S. suis population and revealed capsule switching between S. suis strains. Importantly, capsule switching occurred in the SS2, SS3 and SS7 strains belonging to CC28 and CC29, which are phylogenetically distinct from the main CC1 SS2 lineage. To further explore capsule switching in S. suis, comparative genomic analyses were performed using available complete S. suis genomes. Phylogenetic analyses suggested that the SS2 strains could be divided into two clades (1 and 2), and those classified into clade 2 colocalized with SS3 and SS7 strains, in accordance with the above virulence genotyping and MLST analyses. Clade 2 SS2 strains presented high genetic similarity to SS3 and SS7 and shared common competence and defensive elements with them but were significantly different from Clade 1 SS2 strains. Notably, although the cps loci shared by Clade 1 and 2 SS2 strains were almost identical, a specific region of the cps locus of strain NSUI002 (Clade 2 SS2) could be found in the SS3 cps locus but not in the Clade 1 SS2 strain. These data indicated that the SS2 strains in CC28 and CC29 might have acquired the cps locus through capsule switching, which could explain the distinct genetic lineages within the SS2 population.
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Affiliation(s)
- Yinchu Zhu
- Institute of Animal Husbandry and Veterinary Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing, 210095, China
| | - Wenyang Dong
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing, 210095, China; Beijing Advanced Innovation Center for Genomics (ICG) & Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Jiale Ma
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing, 210095, China
| | - Yue Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing, 210095, China; College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaojun Zhong
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing, 210095, China
| | - Zihao Pan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing, 210095, China
| | - Guangjin Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing, 210095, China
| | - Zongfu Wu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing, 210095, China
| | - Huochun Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing, 210095, China.
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Dong X, Chao Y, Zhou Y, Zhou R, Zhang W, Fischetti VA, Wang X, Feng Y, Li J. The global emergence of a novel Streptococcus suis clade associated with human infections. EMBO Mol Med 2021; 13:e13810. [PMID: 34137500 PMCID: PMC8261479 DOI: 10.15252/emmm.202013810] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/17/2022] Open
Abstract
Streptococcus suis, a ubiquitous bacterial colonizer in pigs, has recently extended host range to humans, leading to a global surge of deadly human infections and three large outbreaks since 1998. To better understand the mechanisms for the emergence of cross-species transmission and virulence in human, we have sequenced 366 S. suis human and pig isolates from 2005 to 2016 and performed a large-scale phylogenomic analysis on 1,634 isolates from 14 countries over 36 years. We show the formation of a novel human-associated clade (HAC) diversified from swine S. suis isolates. Phylogeographic analysis identified Europe as the origin of HAC, coinciding with the exportation of European swine breeds between 1960s and 1970s. HAC is composed of three sub-lineages and contains several healthy-pig isolates that display high virulence in experimental infections, suggesting healthy-pig carriers as a potential source for human infection. New HAC-specific genes are identified as promising markers for pathogen detection and surveillance. Our discovery of a human-associated S. suis clade provides insights into the evolution of this emerging human pathogen and extend our understanding of S. suis epidemics worldwide.
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Affiliation(s)
- Xingxing Dong
- Key Laboratory of Environment Correlative DietologyInterdisciplinary Sciences InstituteCollege of Food Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- National R&D Center for Se‐rich Agricultural Products ProcessingHubei Engineering Research Center for Deep Processing of Green Se‐rich Agricultural ProductsSchool of Modern Industry for Selenium Science and EngineeringWuhan Polytechnic UniversityWuhanChina
| | - Yanjie Chao
- The Center for Microbes, Development and Health (CMDH)CAS Key Laboratory of Molecular Virology and ImmunologyInstitut Pasteur of ShanghaiChinese Academy of SciencesShanghaiChina
| | - Yang Zhou
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
| | - Rui Zhou
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
| | - Wei Zhang
- College of Veterinary MedicineNanjing Agricultural UniversityNanjingChina
| | - Vincent A. Fischetti
- Laboratory of Bacterial Pathogenesis and ImmunologyThe Rockefeller UniversityNew YorkNYUSA
| | - Xiaohong Wang
- Key Laboratory of Environment Correlative DietologyInterdisciplinary Sciences InstituteCollege of Food Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ye Feng
- Institute of Translational MedicineSchool of MedicineZhejiang UniversityHangzhouChina
| | - Jinquan Li
- Key Laboratory of Environment Correlative DietologyInterdisciplinary Sciences InstituteCollege of Food Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Laboratory of Bacterial Pathogenesis and ImmunologyThe Rockefeller UniversityNew YorkNYUSA
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8
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Chaiden C, Jaresitthikunchai J, Kerdsin A, Meekhanon N, Roytrakul S, Nuanualsuwan S. Streptococcus suis serotyping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. PLoS One 2021; 16:e0249682. [PMID: 33945547 PMCID: PMC8096114 DOI: 10.1371/journal.pone.0249682] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/22/2021] [Indexed: 01/01/2023] Open
Abstract
Streptococcus suis, particularly S. suis serotype 2 (SS2), is an important zoonotic pathogen causing meningitis in humans worldwide. Although the proper classification of the causative and pathogenic serotype is salutary for the clinical diagnosis, cross-reactions leading to the indistinguishability of serotypes by the current serotyping methods are significant limitations. In the present study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of extracted peptides was developed to improve the classification of serotype of S. suis. The peptide mass fingerprint (PMFs) database of S. suis was generated from the whole-cell peptides of 32 reference strains of S. suis isolates obtained from pigs. Thirty-two human S. suis isolates from clinical cases in Thailand were used to validate this alternative serotyping method in direct comparison to the multiplex (m)PCR approach. All reference strains, representing 32 serotypes of S. suis, exhibited their individual PMFs patterns, thus allowing differentiation from one another. Highly pathogenic SS2 and SS14 were clearly differentiated from the otherwise serologically closely related SS1/2 and SS1, respectively. The developed MALDI-TOF-MS serotyping method correctly classified the serotype in 68.8% (22/32) of the same serotype isolates generated from the PMFs database; while the validity for the clinical human isolates was 62.5% (20/32). The agreement between the MALDI-TOF-MS and mPCR serotyping was moderate with a Kappa score of 0.522, considering that mPCR could correctly serotype up to 75%. The present study demonstrated that PMFs from the developed MALDI-TOF-MS-based method could successfully discriminate the previously indistinguishable highly pathogenic SS2 and SS14 from SS1/2 and SS1, respectively. Moreover, this serotyping method distinguished pathogenic SS6, and so is an alternative approach of choice to rapidly and reliably serotype clinically pathogenic S. suis isolates.
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Affiliation(s)
- Chadaporn Chaiden
- Department of Veterinary Public Health, Faculty of Veterinary Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Janthima Jaresitthikunchai
- Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology for Development Agency, Pathum Thani, Thailand
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Nattakan Meekhanon
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology for Development Agency, Pathum Thani, Thailand
| | - Suphachai Nuanualsuwan
- Department of Veterinary Public Health, Faculty of Veterinary Sciences, Chulalongkorn University, Bangkok, Thailand.,Food Risk Hub, Research Unit of Chulalongkorn University, Bangkok, Thailand
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9
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Capsular polysaccharide switching in Streptococcus suis modulates host cell interactions and virulence. Sci Rep 2021; 11:6513. [PMID: 33753801 PMCID: PMC7985379 DOI: 10.1038/s41598-021-85882-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/05/2021] [Indexed: 11/30/2022] Open
Abstract
The capsular polysaccharide (CPS) of Streptococcus suis defines various serotypes based on its composition and structure. Though serotype switching has been suggested to occur between S. suis strains, its impact on pathogenicity and virulence remains unknown. Herein, we experimentally generated S. suis serotype-switched mutants from a serotype 2 strain that express the serotype 3, 4, 7, 8, 9, or 14 CPS. The effects of serotype switching were then investigated with regards to classical properties conferred by presence of the serotype 2 CPS, including adhesion to/invasion of epithelial cells, resistance to phagocytosis by macrophages, killing by whole blood, dendritic cell-derived pro-inflammatory mediator production and virulence using mouse and porcine infection models. Results demonstrated that these properties on host cell interactions were differentially modulated depending on the switched serotypes, although some different mutations other than loci of CPS-related genes were found in each the serotype-switched mutant. Among the serotype-switched mutants, the mutant expressing the serotype 8 CPS was hyper-virulent, whereas mutants expressing the serotype 3 or 4 CPSs had reduced virulence. By contrast, switching to serotype 7, 9, or 14 CPSs had little to no effect. These findings suggest that serotype switching can drastically alter S. suis virulence and host cell interactions.
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Okura M, Maruyama F, Ota A, Tanaka T, Matoba Y, Osawa A, Sadaat SM, Osaki M, Toyoda A, Ogura Y, Hayashi T, Takamatsu D. Genotypic diversity of Streptococcus suis and the S. suis-like bacterium Streptococcus ruminantium in ruminants. Vet Res 2019; 50:94. [PMID: 31727180 PMCID: PMC6854688 DOI: 10.1186/s13567-019-0708-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/25/2019] [Indexed: 11/13/2022] Open
Abstract
Although Streptococcus suis has attracted public attention as a major swine and human pathogen, this bacterium has also been isolated from other animals, including ruminants. However, recent taxonomic studies revealed the existence of other species that were previously identified as S. suis, and some of these isolates were reclassified as the novel species Streptococcus ruminantium. In Japan, biochemically identified S. suis is frequently isolated from diseased ruminants; however, such isolates have not yet been identified accurately, and their aetiological importance in ruminants is unclear. Therefore, to understand the importance of S. suis and S. suis-like bacteria in ruminants, we reclassified S. suis isolates from ruminants according to the updated classification and investigated their genetic diversity. Although both S. suis and S. ruminantium were isolated from healthy and diseased ruminants, most of the isolates from diseased animals were S. ruminantium, implying that S. ruminantium is more likely to be associated with ruminant disease than S. suis. However, the ruminant S. suis and S. ruminantium isolates from diseased animals were classified into diverse genotypes rather than belonging to certain clonal groups. Genome sequence analysis of 20 S. ruminantium isolates provided information about the antibiotic resistance, potential virulence, and serological diversity of this species. We further developed an S. ruminantium-specific PCR assay to aid in the identification of this bacterium. The information obtained and the method established in this study will contribute to the accurate diagnosis of ruminant streptococcal infections.
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Affiliation(s)
- Masatoshi Okura
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan.
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Atsushi Ota
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Tanaka
- Nairiku Meat Inspection Center, Yamagata Prefectural Government, Yamagata, Japan
| | - Yohei Matoba
- Murayama Public Health Center, Yamagata Prefectural Government, Yamagata, Japan
| | - Aya Osawa
- Matsumoto Livestock Hygiene Service Center, Nagano Prefectural Government, Matsumoto, Japan
| | - Sayed Mushtaq Sadaat
- Ministry of Agriculture, Irrigation and Livestock, Animal Health Directorate, Central Veterinary Diagnostic and Research Laboratory, Kabul, Afghanistan
| | - Makoto Osaki
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan.,Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Daisuke Takamatsu
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan.,United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
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Sun Y, Veseli IA, Vaillancourt K, Frenette M, Grenier D, Pombert JF. The bacteriocin from the prophylactic candidate Streptococcus suis 90-1330 is widely distributed across S. suis isolates and appears encoded in an integrative and conjugative element. PLoS One 2019; 14:e0216002. [PMID: 31039174 PMCID: PMC6490898 DOI: 10.1371/journal.pone.0216002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 04/12/2019] [Indexed: 01/09/2023] Open
Abstract
The Gram-positive α-hemolytic Streptococcus suis is a major pathogen in the swine industry and an emerging zoonotic agent that can cause several systemic issues in both pigs and humans. A total of 35 S. suis serotypes (SS) have been identified and genotyped into > 700 sequence types (ST) by multilocus sequence typing (MLST). Eurasian ST1 isolates are the most virulent of all S. suis SS2 strains while North American ST25 and ST28 strains display moderate to low/no virulence phenotypes, respectively. Notably, S. suis 90–1330 is an avirulent Canadian SS2-ST28 isolate producing a lantibiotic bacteriocin with potential prophylactic applications. To investigate the suitability of this strain for such purposes, we sequenced its complete genome using the Illumina and PacBio platforms. The S. suis 90–1330 bacteriocin was found encoded in a locus cargoed in what appears to be an integrative and conjugative element (ICE). This bacteriocin locus was also found to be widely distributed across several streptococcal species and in a few Staphylococcus aureus strains. Because the locus also confers protection from the bacteriocin, the potential prophylactic benefits of using this strain may prove limited due to the spread of the resistance to its effects. Furthermore, the S. suis 90–1330 genome was found to code for genes involved in blood survival, suggesting that strain may not be a benign as previously thought.
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Affiliation(s)
- Yukun Sun
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Iva A. Veseli
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Katy Vaillancourt
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC, Canada
| | - Michel Frenette
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole, Fonds de Recherche du Québec–Nature et Technologies, Québec, QC, Canada
| | - Daniel Grenier
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole, Fonds de Recherche du Québec–Nature et Technologies, Québec, QC, Canada
| | - Jean-François Pombert
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
- * E-mail:
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Meekhanon N, Kaewmongkol S, Jirawattanapong P, Kaminsonsakul T, Kongsoi S, Chumsing S, Okura M, Ueno Y, Sekizaki T, Takamatsu D. High rate misidentification of biochemically determined Streptococcus isolates from swine clinical specimens. J Vet Med Sci 2019; 81:567-572. [PMID: 30814435 PMCID: PMC6483909 DOI: 10.1292/jvms.18-0678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In this study, 22 bacterial isolates from swine necropsy specimens, which were biochemically identified as Streptococcus suis and other Streptococcus species, were re-examined using species-specific PCR for authentic S. suis and 16S rRNA gene sequencing for the verification of the former judge. Identification of S. suis on the basis of biochemical characteristics showed high false-positive (70.6%) and false-negative (60%) rates. The authentic S. suis showed various capsular polysaccharide synthesis gene types, including type 2 that often isolated from human cases. Five of 22 isolates did not even belong to the genus Streptococcus. These results suggested that the misidentification of the causative pathogen in routine veterinary diagnosis could be a substantial obstacle for the control of emerging infectious diseases.
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Affiliation(s)
- Nattakan Meekhanon
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok 10900, Thailand
| | - Sarawan Kaewmongkol
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok 10900, Thailand
| | - Pichai Jirawattanapong
- Department of Farm Resources and Production Medicines, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom 73140, Thailand
| | - Tanyanant Kaminsonsakul
- Kamphaengsaen Veterinary Diagnostic Unit, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom 73140, Thailand
| | - Siriporn Kongsoi
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom 73140, Thailand
| | - Suksan Chumsing
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom 73140, Thailand
| | - Masatoshi Okura
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0856, Japan
| | - Yuichi Ueno
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0856, Japan
| | - Tsutomu Sekizaki
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Daisuke Takamatsu
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0856, Japan.,The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu 501-1193, Japan
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13
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Zhu Y, Dong W, Ma J, Zhang Y, Pan Z, Yao H. Utilization of the ComRS system for the rapid markerless deletion of chromosomal genes in Streptococcus suis. Future Microbiol 2019; 14:207-222. [DOI: 10.2217/fmb-2018-0279] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To develop a markerless gene deletion strategy in Streptococcus suis to solve the problem that several serotypes against electrotransformation of foreign DNA. Materials & methods: Bioinformatics retrieval was performed to identified ComRS systems functioning for natural transformation. A sacB-spc cassette with the upper and lower homologous fragments was amplification by fusion-PCR for spectinomycin-positive and sucrose-negative selection during gene deletion. Results & conclusion: Three phylogenetic clusters of ComR were identified to function for natural transformation by specific recognition to competence pheromone in S. suis. Thus, they were employed to establish gene deletion method. Its efficiency for genetic replacement was dependent on the length of homologs fragment and the concentration of donor DNA. This rapid gene-editing technique may greatly facilitate molecular studies on S. suis.
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Affiliation(s)
- Yinchu Zhu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- Office International Des Epizooties (OIE) Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wenyang Dong
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- Office International Des Epizooties (OIE) Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jiale Ma
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- Office International Des Epizooties (OIE) Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yue Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- Office International Des Epizooties (OIE) Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zihao Pan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- Office International Des Epizooties (OIE) Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Huochun Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- Office International Des Epizooties (OIE) Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
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Tsuchida S, Maruyama F, Ogura Y, Toyoda A, Hayashi T, Okuma M, Ushida K. Genomic Characteristics of Bifidobacterium thermacidophilum Pig Isolates and Wild Boar Isolates Reveal the Unique Presence of a Putative Mobile Genetic Element with tetW for Pig Farm Isolates. Front Microbiol 2017; 8:1540. [PMID: 28861055 PMCID: PMC5561799 DOI: 10.3389/fmicb.2017.01540] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/31/2017] [Indexed: 01/16/2023] Open
Abstract
Genomic analysis was performed on seven strains of Bifidobacterium thermacidophilum, a Sus-associated Bifidobacterium. Three strains from the feces of domestic pigs (Sus scrofa domesticus) and four strains from the rectal feces of free-range Japanese wild boars (S. s. scrofa) were compared. The phylogenetic position of these isolates suggested by genomic analyses were not concordant with that suggested by 16S rRNA sequence. There was biased distribution of genes for virulence, phage, metabolism of aromatic compounds, iron acquisition, cell division, and DNA metabolism. In particular four wild boar isolates harbored fiber-degrading enzymes, such as endoglucanase, while two of the pig isolates obtained from those grown under an intensive feeding practice with routine use of antimicrobials, particularly tetracycline harbored a tetracycline resistance gene, which was further proved functional by disk diffusion test. The tetW gene is associated with a serine recombinase of an apparently non-bifidobacterial origin. The insertion site of the tetW cassette was precisely defined by analyzing the corresponding genomic regions in the other tetracycline-susceptible isolates. The cassette may have been transferred from some other bacteria in the pig gut.
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Affiliation(s)
- Sayaka Tsuchida
- Laboratory of Animal Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto UniversityKyoto, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of GeneticsMishima, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuoka, Japan
| | - Moriya Okuma
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Japan
| | - Kazunari Ushida
- Laboratory of Animal Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
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