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Vilela FP, Rodrigues DDP, Allard MW, Falcão JP. CRISPR and CRISPR-MVLST reveal conserved spacer distribution and high similarity among Salmonella enterica serovar Infantis genomes from Brazil and other countries. Mol Genet Genomics 2024; 299:61. [PMID: 38806731 DOI: 10.1007/s00438-024-02147-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/24/2024] [Indexed: 05/30/2024]
Abstract
Salmonella enterica serovar Infantis (S. Infantis) is a globally distributed non-typhoid serovar infecting humans and food-producing animals. Considering the zoonotic potential and public health importance of this serovar, strategies to characterizing, monitor and control this pathogen are of great importance. This study aimed to determine the genetic relatedness of 80 Brazilian S. Infantis genomes in comparison to 40 non-Brazilian genomes from 14 countries using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-Multi-Locus Virulence Sequence Typing (CRISPR-MVLST). CRISPR spacers were searched using CRISPR-Cas++ and fimH and sseL alleles using BLAST and MEGA X. Results were analyzed using BioNumerics 7.6 in order to obtain similarity dendrograms. A total of 23 CRISPR1 and 11 CRISPR2 alleles formed by 37 and 26 types of spacers, respectively, were detected. MVLST revealed the presence of five fimH and three sseL alleles. CRISPR's similarity dendrogram showed 32 strain subtypes, with an overall similarity ≥ 78.6. The CRISPR-MVLST similarity dendrogram showed 37 subtypes, with an overall similarity ≥ 79.2. In conclusion, S. Infantis strains isolated from diverse sources in Brazil and other countries presented a high genetic similarity according to CRISPR and CRISPR-MVLST, regardless of their source, year, and/or place of isolation. These results suggest that both methods might be useful for molecular typing S. Infantis strains using WGS data.
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Affiliation(s)
- Felipe Pinheiro Vilela
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, s/n. Bloco S - Sala 41, Ribeirão Preto, SP, 14040-903, Brazil
| | | | - Marc William Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, s/n. Bloco S - Sala 41, Ribeirão Preto, SP, 14040-903, Brazil.
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Mattock J, Chattaway MA, Hartman H, Dallman TJ, Smith AM, Keddy K, Petrovska L, Manners EJ, Duze ST, Smouse S, Tau N, Timme R, Baker DJ, Mather AE, Wain J, Langridge GC. A One Health Perspective on Salmonella enterica Serovar Infantis, an Emerging Human Multidrug-Resistant Pathogen. Emerg Infect Dis 2024; 30:701-710. [PMID: 38526070 PMCID: PMC10977846 DOI: 10.3201/eid3004.231031] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
Salmonella enterica serovar Infantis presents an ever-increasing threat to public health because of its spread throughout many countries and association with high levels of antimicrobial resistance (AMR). We analyzed whole-genome sequences of 5,284 Salmonella Infantis strains from 74 countries, isolated during 1989-2020 from a wide variety of human, animal, and food sources, to compare genetic phylogeny, AMR determinants, and plasmid presence. The global Salmonella Infantis population structure diverged into 3 clusters: a North American cluster, a European cluster, and a global cluster. The levels of AMR varied by Salmonella Infantis cluster and by isolation source; 73% of poultry isolates were multidrug resistant, compared with 35% of human isolates. This finding correlated with the presence of the pESI megaplasmid; 71% of poultry isolates contained pESI, compared with 32% of human isolates. This study provides key information for public health teams engaged in reducing the spread of this pathogen.
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Affiliation(s)
| | - Marie Anne Chattaway
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Hassan Hartman
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | | | - Anthony M. Smith
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Karen Keddy
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | | | | | - Sanelisiwe T. Duze
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Shannon Smouse
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Nomsa Tau
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Ruth Timme
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Dave J. Baker
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Alison E. Mather
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - John Wain
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Gemma C. Langridge
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
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Vázquez X, Fernández J, Rodríguez-Lozano J, Calvo J, Rodicio R, Rodicio MR. Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the blaCTX-M-65 Gene with or without fosA3 in pESI-like Plasmids. Antibiotics (Basel) 2022; 11:786. [PMID: 35740192 PMCID: PMC9219668 DOI: 10.3390/antibiotics11060786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 02/04/2023] Open
Abstract
Salmonella enterica serovar Infantis (S. Infantis) is a broiler-associated pathogen which ranks in the fourth position as a cause of human salmonellosis in the European Union. Here, we report a comparative genomic analysis of two clinical S. Infantis isolates recovered in Spain from children who just returned from Peru. The isolates were selected on the basis of resistance to cefotaxime, one of the antibiotics of choice for treatment of S. enterica infections. Antimicrobial susceptibility testing demonstrated that they were resistant to eight classes of antimicrobial agents: penicillins, cephalosporins, phenicols, aminoglycosides, tetracyclines, inhibitors of folate synthesis, (fluoro)quinolones and nitrofurans, and one of them was also resistant to fosfomycin. As shown by whole-genome sequence analysis, each isolate carried a pESI-like megaplasmid of ca. 300 kb harboring multiple resistance genes [blaCTX-M-65, aph(4)-Ia, aac(3)-IVa, aph(3')-Ia, floR, dfrA14, sul1, tet(A), aadA1 ± fosA3], as well as genes for resistance to heavy metals and disinfectants (mer, ars and qacEΔ1). These genes were distributed in two complex regions, separated by DNA belonging to the plasmid backbone, and associated with a wealth of transposable elements. The two isolates had a D87Y amino acid substitution in the GyrA protein, and truncated variants of the nitroreductase genes nfsA and nsfB, accounting for chromosomally encoded resistances to nalidixic acid and nitrofurantoin, respectively. The two S. Infantis isolates were assigned to sequence type ST32 by in silico multilocus sequence typing (MLST). Phylogenetic analysis revealed that they were closely related, differing only by 12 SNPs, although they were recovered from different children two years apart. They were also genetically similar to blaCTX-M-65-positive ± fosA3 isolates obtained from humans and along the poultry production chain in the USA, South America, as well as from humans in several European countries, usually associated with a travel history to America. However, this is the first time that the S. Infantis blaCTX-M-65 ± fosA3 MDR clone has been reported in Spain.
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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; (J.F.); (R.R.)
| | - Javier Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (J.F.); (R.R.)
- 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, 20029 Madrid, Spain
| | - Jesús Rodríguez-Lozano
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla (IDIVAL), 39008 Santander, Spain; (J.R.-L.); (J.C.)
| | - Jorge Calvo
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla (IDIVAL), 39008 Santander, Spain; (J.R.-L.); (J.C.)
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rosaura Rodicio
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (J.F.); (R.R.)
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo (UO), 33006 Oviedo, Spain
| | - M. 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; (J.F.); (R.R.)
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Alba P, Leekitcharoenphon P, Carfora V, Amoruso R, Cordaro G, Di Matteo P, Ianzano A, Iurescia M, Diaconu EL, Study Group EEAN, Pedersen SK, Guerra B, Hendriksen RS, Franco A, Battisti A. Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid. Microb Genom 2020; 6. [PMID: 32271142 PMCID: PMC7371121 DOI: 10.1099/mgen.0.000365] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Salmonella Infantis is one of the five serovars most frequently causing human salmonellosis in Europe, mainly associated with poultry. A clone harbouring a conjugative plasmid of emerging S. Infantis (pESI)-like megaplasmid, carrying multidrug resistant (MDR) and extended-spectrum beta-lactamases (ESBL) genes, has spread in the Italian broiler chicken industry also causing human illness. This work is aimed at elucidating the molecular epidemiology of S. Infantis and pESI-like in Europe using whole-genome sequencing and bioinformatics analysis, and to investigate the genetic relatedness of S. Infantis clones and pESI-like from animals, meat, feed and humans provided by institutions of nine European countries. Two genotyping approaches were used: chromosome or plasmid SNP-based analysis and the minimum spanning tree (MST) algorithm based on core-genome multilocus sequence typing (cgMLST). The European S. Infantis population appeared heterogeneous, with different genetic clusters defined at core-genome level. However, pESI-like variants present in 64.1 % of the isolates were more genetically homogeneous and capable of infecting different clonal lineages in most of the countries. Two different pESI-like with ESBL genes (n=82) were observed: blaCTX-M-1-positive in European isolates and blaCTX-M-65-positive in American isolates (study outgroup). Both variants had toxin-antitoxin systems, resistance genes towards tetracyclines, trimethoprim, sulphonamides and aminoglycosides, heavy metals (merA) and disinfectants (qacEΔ). Worryingly, 66 % of the total isolates studied presented different gyrA chromosomal point mutations associated with (fluoro)quinolone resistance (MIC range 0.125–0.5 mg/L), while 18 % displayed transferable macrolide resistance mediated by mph, mef and erm(B) genes. Proper intervention strategies are needed to prevent further dissemination/transmission of MDR S. Infantis and pESI-like along the food chain in Europe.
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Affiliation(s)
- Patricia Alba
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Pimlapas Leekitcharoenphon
- European Union Reference Laboratory for Antimicrobial-Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Virginia Carfora
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Roberta Amoruso
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Gessica Cordaro
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Paola Di Matteo
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Angela Ianzano
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Manuela Iurescia
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Elena L Diaconu
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | | | - Susanne K Pedersen
- European Union Reference Laboratory for Antimicrobial-Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Rene S Hendriksen
- European Union Reference Laboratory for Antimicrobial-Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alessia Franco
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Antonio Battisti
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
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Nagy T, Szmolka A, Wilk T, Kiss J, Szabó M, Pászti J, Nagy B, Olasz F. Comparative Genome Analysis of Hungarian and Global Strains of Salmonella Infantis. Front Microbiol 2020; 11:539. [PMID: 32318036 PMCID: PMC7147451 DOI: 10.3389/fmicb.2020.00539] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/12/2020] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION The emergence and spread of new strains of zoonotic bacteria, such as multidrug resistant (MDR) Salmonella Infantis, represent a growing health risk for humans in and outside Europe due to foodborne infections of poultry meat origin. OBJECTIVES In order to understand genome relations of S. Infantis strains from Hungary and from different geographic regions, we performed a comprehensive genome analysis of nine Hungarian and 67 globally selected strains of S. Infantis and 26 Salmonella strains representing 13 non-Infantis serovars. RESULTS Analyses of whole-, and accessory genomes, showed that almost all S. Infantis strains were separated from the non-Infantis serovars. S. Infantis strains from Hungary formed subclusters based on their time of isolation. In whole genome sequence analysis, the Swiss strains of S. Infantis were closely related to each other and clustered together with subclusters of strains from Hungary, Japan, Italy, United States, and Israel. The accessory genome analysis revealed that the Swiss strains were distinct from most of the strains investigated, including the Hungarian ones. Analysis of the cloud genes offered the most detailed insight into the genetic distance and relationship of S. Infantis strains confirming that the Swiss and Hungarian strains belonged to different lineages. As expected, core genome analysis provided the least discriminatory power for analysis of S. Infantis. Genomic sequences of nine strains from Brazil, Israel, Mexico, Nigeria, and Senegal (deposited as S. Infantis) proved to be outliers from the S. Infantis clade. They were predicted to be Salmonella Rissen, Salmonella Ouakarm, Salmonella Kentucky, Salmonella Thompson, and Salmonella enterica subsp. diarizonae. CONCLUSION Accessory genome of S. Infantis showed the highest diversity suggesting a faster evolution than that of the whole genomes contributing to the emergence of multiple genetic variants of S. Infantis worldwide. Accordingly, in spite of the comprehensive analysis of several genomic characteristics, no epidemiologic links between these S. Infantis strains from different countries could be established. It is also concluded that several strains originally designated as S. Infantis need in databanks reclassification.
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Affiliation(s)
- Tibor Nagy
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Ama Szmolka
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Budapest, Hungary
| | - Tímea Wilk
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - János Kiss
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Mónika Szabó
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Judit Pászti
- National Center for Epidemiology, Budapest, Hungary
| | - Béla Nagy
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Budapest, Hungary
| | - Ferenc Olasz
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
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Aoki Y, Watanabe Y, Kitazawa K, Ando N, Hirai S, Yokoyama E. Emergence of Salmonella enterica subsp. enterica serovar Chester in a rural area of Japan. J Vet Med Sci 2020; 82:580-584. [PMID: 32188802 PMCID: PMC7273606 DOI: 10.1292/jvms.20-0033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In Japan, only one outbreak of Salmonella enterica subsp. enterica serovar Chester (S. Chester) has been confirmed in 1999. We performed a single-center retrospective case review of S. Chester infections that occurred in a rural area of Japan in 2016 (n=8). Case 5 and 6 occurred in twin infants who had contact with a pet dog. The dog's stool culture was positive for S. Chester. Pulsed-field gel electrophoresis and cluster analysis of S. Chester strains revealed that all the isolates appeared to be derived from the same genetic clone. Emergence of Salmonella infection can be overlooked if cases are not reported to health authorities; therefore, core hospitals should play a role to alert the occurrence of public health issue.
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Affiliation(s)
- Yoshihiro Aoki
- Department of Pediatrics, Asahi General Hospital, 1326 I, Asahi, Chiba 289-2511, Japan.,Department of Emergency and Critical Care Medicine, Aizawa Hospital, 2-5-1 Honjo, Matsumoto, Nagano 390-8510, Japan
| | - Yudai Watanabe
- Department of Clinical Laboratory, Asahi General Hospital, 1326 I, Asahi, Chiba 289-2511, Japan
| | - Katsuhiko Kitazawa
- Department of Pediatrics, Asahi General Hospital, 1326 I, Asahi, Chiba 289-2511, Japan
| | - Naoshi Ando
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba 260-8715, Japan
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba 260-8715, Japan
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba 260-8715, Japan
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7
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Bogomazova AN, Gordeeva VD, Krylova EV, Soltynskaya IV, Davydova EE, Ivanova OE, Komarov AA. Mega-plasmid found worldwide confers multiple antimicrobial resistance in Salmonella Infantis of broiler origin in Russia. Int J Food Microbiol 2019; 319:108497. [PMID: 31927155 DOI: 10.1016/j.ijfoodmicro.2019.108497] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/08/2019] [Accepted: 12/20/2019] [Indexed: 01/06/2023]
Abstract
Plasmids which are the mobile part of the bacterial genome can acquire and carry over genes conferring antimicrobial resistance, thus contributing to rapid adaptation of bacterial community to human-defined environment. In 2014, Israeli scientists have reported a large conjugative mega-plasmid pESI (plasmid for emerging S. Infantis) that provides multiple drug resistance (MDR) of Salmonella Infantis isolated from broilers. Later, very similar pESI-like plasmids have been found in Salmonella isolated from poultry in the United States, Italy, Switzerland, Hungary, and Japan. Here we report detection of pESI-like plasmids in Salmonella Infantis isolated from chicken food products in Russia. Whole genome sequencing of three MDR isolates revealed pESI-like plasmids in all three cases. These plasmids have such typical pESI features as a locus for siderophore yersiniabactin, a cluster of IncI1 conjugative genes, a cluster of type IV pilus genes, and three toxin-antitoxin modules. The pESI-like plasmids carry from two to five resistance genes in each isolate. In total, we observed six antimicrobial resistance genes associated with pESI-like plasmids (aadA1, blaCTX-M-14, dfrA14, sul1, tetA/tetR, tetM). Besides plasmid genes of antimicrobial resistance, all three MDR isolates of S. Infantis harbor a mutation in chromosomal gene gyrA (p.S83Y or p.D87Y) that is associated with resistance to fluoroquinolones. In addition, we performed a comparative bioinformatics meta-analysis of 25 pESI-like plasmids hosted by S. Infantis from the USA, Europe, Latin America, Israel, and Japan. This analysis identified a 173 kB sequence that is common for all pESI-like plasmids and carries virulence operons and toxin-antitoxin modules.
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Affiliation(s)
- Alexandra N Bogomazova
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia.
| | - Veronika D Gordeeva
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia
| | - Ekaterina V Krylova
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia
| | - Irina V Soltynskaya
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia
| | - Ekaterina E Davydova
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia
| | - Olga E Ivanova
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia
| | - Alexander A Komarov
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia
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8
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Gymoese P, Kiil K, Torpdahl M, Østerlund MT, Sørensen G, Olsen JE, Nielsen EM, Litrup E. WGS based study of the population structure of Salmonella enterica serovar Infantis. BMC Genomics 2019; 20:870. [PMID: 31730461 PMCID: PMC6858691 DOI: 10.1186/s12864-019-6260-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella Infantis (S. Infantis) is one of the most frequent Salmonella serovars isolated from human cases of salmonellosis and the most detected serovar from animal and food sources in Europe. The serovar is commonly associated with poultry and there is increasing concern over multidrug resistant clones spreading worldwide, as the dominating clones are characterized by presence of large plasmids carrying multiple resistance genes. Increasing the knowledge of the S. Infantis population and evolution is important for understanding and preventing further spread. In this study, we analysed a collection of strains representing different decades, sources and geographic locations. We analysed the population structure and the accessory genome, in particular we identified prophages with a view to understand the role of prophages in relation to the evolution of this serovar. RESULTS We sequenced a global collection of 100 S. Infantis strains. A core-genome SNP analysis separated five strains in e-Burst Group (eBG) 297 with a long branch. The remaining strains, all in eBG31, were divided into three lineages that were estimated to have separated approximately 150 years ago. One lineage contained the vast majority of strains. In five of six clusters, no obvious correlation with source or geographical locations was seen. However, one cluster contained mostly strains from human and avian sources, indicating a clone with preference for these sources. The majority of strains within this cluster harboured a pESI-like plasmid with multiple resistance genes. Another lineage contained three genetic clusters with more rarely isolated strains of mainly animal origin, possibly less sampled or less infectious clones. Conserved prophages were identified in all strains, likely representing bacteriophages which integrated into the chromosome of a common ancestor to S. Infantis. We also saw that some prophages were specific to clusters and were probably introduced when the clusters were formed. CONCLUSIONS This study analysed a global S. Infantis population and described its genetic structure. We hypothesize that the population has evolved in three separate lineages, with one more successfully emerging lineage. We furthermore detected conserved prophages present in the entire population and cluster specific prophages, which probably shaped the population structure.
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Affiliation(s)
- Pernille Gymoese
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Kristoffer Kiil
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Mia Torpdahl
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Mark T. Østerlund
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Gitte Sørensen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, Frederiksberg C, Denmark
| | - Eva M. Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Eva Litrup
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
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9
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Isolation of Salmonella enterica serovar Agona strains and their similarities to strains derived from a clone caused a serovar shift in broilers. J Infect Chemother 2018; 25:71-74. [PMID: 30054228 DOI: 10.1016/j.jiac.2018.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 11/23/2022]
Abstract
Salmonella enterica serovar Agona strains isolated from human cases were compared to strains that were derived from a clone caused a serovar shift in broilers. Pulsed field gel electrophoresis (PFGE) analysis with XbaI or BlnI digestion showed that three of seven strains from human case strains and most of the 81 strains from broilers were clustered in single complex in a minimum spanning tree (MST) reconstructed from the PFGE data. All the strains from human cases and 22 randomly selected strains from broilers were also analyzed by whole genome sequencing (WGS). Analysis of single nucleotide polymorphism (SNP) in the S. Agona core genes showed that four strains from human cases and all the strains from broilers were clustered in a maximum likelihood phylogenetic tree (ML tree) and an MST. These results indicated that the strains derived from the clone caused the serovar shift had already spread to humans. PFGE analysis with XbaI showed that four strains from broilers did not cluster with the other strains in an MST, though all those strains clustered in an ML tree and an MST reconstructed from SNP data. Moreover, three strains from broilers did not cluster in an MST reconstructed from PFGE with BlnI digestion, though those strains clustered in an ML tree and an MST reconstructed from SNP data. Therefore, it was suggested that S. Agona strains derived from a particular clone could not be traced by PFGE analysis but can be investigated by WGS analysis.
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10
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Ford L, Carter GP, Wang Q, Seemann T, Sintchenko V, Glass K, Williamson DA, Howard P, Valcanis M, Castillo CFS, Sait M, Howden BP, Kirk MD. Incorporating Whole-Genome Sequencing into Public Health Surveillance: Lessons from Prospective Sequencing of Salmonella Typhimurium in Australia. Foodborne Pathog Dis 2018; 15:161-167. [PMID: 29336594 DOI: 10.1089/fpd.2017.2352] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In Australia, the incidence of Salmonella Typhimurium has increased dramatically over the past decade. Whole-genome sequencing (WGS) is transforming public health microbiology, but poses challenges for surveillance. To compare WGS-based approaches with conventional typing for Salmonella surveillance, we performed concurrent WGS and multilocus variable-number tandem-repeat analysis (MLVA) of Salmonella Typhimurium isolates from the Australian Capital Territory (ACT) for a period of 5 months. We exchanged data via a central shared virtual machine and performed comparative genomic analyses. Epidemiological evidence was integrated with WGS-derived data to identify related isolates and sources of infection, and we compared WGS data for surveillance with findings from MLVA typing. We found that WGS data combined with epidemiological data linked an additional 9% of isolates to at least one other isolate in the study in contrast to MLVA and epidemiological data, and 19% more isolates than epidemiological data alone. Analysis of risk factors showed that in one WGS-defined cluster, human cases had higher odds of purchasing a single egg brand. While WGS was more sensitive and specific than conventional typing methods, we identified barriers to uptake of genomic surveillance around complexity of reporting of WGS results, timeliness, acceptability, and stability. In conclusion, WGS offers higher resolution of Salmonella Typhimurium laboratory surveillance than existing methods and can provide further evidence on sources of infection in case and outbreak investigations for public health action. However, there are several challenges that need to be addressed for effective implementation of genomic surveillance in Australia.
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Affiliation(s)
- Laura Ford
- 1 National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University , Canberra, Australia .,2 OzFoodNet, Health Protection Service, Population Health Protection and Prevention , ACT Health, Canberra, Australia
| | - Glen P Carter
- 3 Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia
| | - Qinning Wang
- 4 Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West-Institute of Clinical Pathology and Medical Research , Sydney, Australia
| | - Torsten Seemann
- 3 Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia
| | - Vitali Sintchenko
- 4 Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West-Institute of Clinical Pathology and Medical Research , Sydney, Australia .,5 Centre for Infectious Diseases and Microbiology-Public Health, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney , Sydney, Australia
| | - Kathryn Glass
- 1 National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University , Canberra, Australia
| | - Deborah A Williamson
- 3 Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia .,6 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, Australia
| | - Peter Howard
- 4 Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West-Institute of Clinical Pathology and Medical Research , Sydney, Australia
| | - Mary Valcanis
- 6 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, Australia
| | - Cristina Fabiola Sotomayor Castillo
- 4 Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West-Institute of Clinical Pathology and Medical Research , Sydney, Australia .,5 Centre for Infectious Diseases and Microbiology-Public Health, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney , Sydney, Australia .,7 Sydney Medical School-Westmead, The University of Sydney , Sydney, Australia .,8 Instituto de Salud Publica , Facultad de Medicina, Universidad Austral de Chile, Valdivia, Chile
| | - Michelle Sait
- 5 Centre for Infectious Diseases and Microbiology-Public Health, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney , Sydney, Australia
| | - Benjamin P Howden
- 3 Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia .,6 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, Australia .,9 Infectious Diseases Department, Austin Health , Heidelberg, Australia
| | - Martyn D Kirk
- 1 National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University , Canberra, Australia
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11
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Yokoyama E, Hirai S, Ishige T, Murakami S. Single-Nucleotide Polymorphisms in the Whole-Genome Sequence Data of Shiga Toxin-Producing Escherichia coli O157:H7/H- Strains by Cultivation. Curr Microbiol 2017; 74:425-430. [PMID: 28197720 DOI: 10.1007/s00284-017-1208-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/27/2017] [Indexed: 11/30/2022]
Abstract
Nine Shiga toxin-producing Escherichia coli O157:H7/H- (O157) strains were serially cultured three times on LB agar plates. After each sub-culture, five colonies were picked for DNA isolation and whole genome sequence (WGS) analysis. After exclusion of possible recombination-related SNPs, 11, 9, and 34 single-nucleotide polymorphisms (SNPs) were detected in genes in the backbone, O-island, and mobile elements gene categories. This suggested that those SNPs due to cultivation could influence the threshold value set for molecular epidemiological studies of O157. Significant differences were observed by the Kruskal-Wallis test (P < 0.01) when the number of the SNPs in a strain was compared to that in other strains. This indicated that a specific number of strains could be used for setting the threshold value in molecular epidemiological studies. Due to cultivation, the SNPs were also detected in genes in a few core genome or core gene sets, suggesting that those SNPs could affect studies of phylogeny as well as molecular epidemiology. To improve the accuracy of phylogenetic and molecular epidemiological studies, genes in which the SNPs have arisen due to cultivation should be excluded from WGS data.
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Affiliation(s)
- Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, Chiba, 260-8715, Japan.
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, Chiba, 260-8715, Japan
| | - Taichiro Ishige
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
| | - Satoshi Murakami
- Laboratory of Animal Hygiene, Department of Animal Science, Tokyo University of Agriculture, Kanagawa, Japan
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12
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Wang S, Weller D, Falardeau J, Strawn LK, Mardones FO, Adell AD, Moreno Switt AI. Food safety trends: From globalization of whole genome sequencing to application of new tools to prevent foodborne diseases. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.09.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Yamazaki W, Uemura R, Sekiguchi S, Dong JB, Watanabe S, Kirino Y, Mekata H, Nonaka N, Norimine J, Sueyoshi M, Goto Y, Horii Y, Kurogi M, Yoshino S, Misawa N. Campylobacter and Salmonella are prevalent in broiler farms in Kyushu, Japan: results of a 2-year distribution and circulation dynamics audit. J Appl Microbiol 2016; 120:1711-22. [PMID: 27005691 DOI: 10.1111/jam.13141] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/16/2016] [Accepted: 03/16/2016] [Indexed: 12/22/2022]
Abstract
AIM To elucidate the distribution and circulation dynamics of Campylobacter and Salmonella in Japanese chicken broiler flocks. METHODS AND RESULTS A 2-year investigation of the distribution of Campylobacter and Salmonella was conducted in 25 broiler flocks at nine farms in Japan from 2013 to 2014. Campylobacter and Salmonella tested positive in 11 (44·0%) and 24 (96·0%) broiler flocks respectively. One hundred and ninety-five Campylobacter and 184 Salmonella isolates were characterized into 12 Campylobacter (including two novel genotypes) and three Salmonella MLST genotypes. Only Salmonella isolation between caecal and environmental samples were significantly correlated. Further, one litter sample tested positive for Salmonella before new chicks were introduced. The Campylobacter strains rapidly lost culturability within 2-18 days; in contrast, the Salmonella strains survived from 64-211 days in artificially inoculated water samples. CONCLUSION No persistent circulation-mediated Campylobacter contamination was observed. In contrast, circulation of Salmonella in broiler houses was seen, apparently due to the litter excreted from broiler flocks, as well as Salmonella-contaminated water and feed. SIGNIFICANCE AND IMPACT OF THE STUDY This paper provides the distribution, genotypic data and circulation dynamics of Campylobacter and Salmonella as recently observed in Japanese chicken broiler farms.
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Affiliation(s)
- W Yamazaki
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - R Uemura
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - S Sekiguchi
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - J-B Dong
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - S Watanabe
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Y Kirino
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - H Mekata
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - N Nonaka
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - J Norimine
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - M Sueyoshi
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Y Goto
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Y Horii
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - M Kurogi
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | - S Yoshino
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | - N Misawa
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
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14
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Yokoyama E, Ando N, Ohta T, Kanada A, Shiwa Y, Ishige T, Murakami K, Kikuchi T, Murakami S. A novel subpopulation of Salmonella enterica serovar Infantis strains isolated from broiler chicken organs other than the gastrointestinal tract. Vet Microbiol 2014; 175:312-8. [PMID: 25542287 DOI: 10.1016/j.vetmic.2014.11.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 11/30/2022]
Abstract
Salmonella enterica subsp. enterica serovar Infantis strains were isolated from broiler chickens from six farms in Japan and the pathogenicity associated with the recently reported 280kbp mega plasmid was examined by possession of the plasmid and histopathology of tissues from these chickens. S. Infantis strains were isolated from 10 of 24 chickens. Phylogenetic, network and Bayesian cluster analyses were used to determine whether these strains were in the previously defined Clusters 1-5. Phylogenetic analysis classified the strains isolated in this study in two groups (Groups A and B). Both groups contained strains from gastrointestional contents, but only Group A also contained strains from spleen, liver, and lymphoid tissues. Histopathology showed suppurative splenitis in a spleen from which Group A strains were isolated. Although network and Bayesian cluster analyses were unable to differentiate Group A and B strains from the previously defined Clusters 1-5, population genetic analysis indicated that Group A was a different population from Cluster 5, indicating that Group A would be a subpopulation of Cluster 5. The irp2 gene, which is in the mega plasmid carried by a pathogenic S. Infantis strain recently isolated in Israel, was found in both Groups A and B strains and in the previously reported Clusters 4 and 5 strains. These results suggested that Group A would be a novel subpopulation of the previously defined Cluster 5, and presence of the mega plasmid may not be related whether S. Infantis strains can infect certain organs.
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Affiliation(s)
- Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba City, Chiba 260-8715, Japan.
| | - Naoshi Ando
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba City, Chiba 260-8715, Japan
| | - Tomohiro Ohta
- Laboratory of Animal Hygiene, Department of Animal Science, Tokyo University of Agriculture, Japan
| | - Akina Kanada
- Laboratory of Animal Hygiene, Department of Animal Science, Tokyo University of Agriculture, Japan
| | - Yuh Shiwa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Japan
| | - Taichiro Ishige
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Japan
| | - Koichi Murakami
- Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Japan
| | - Takashi Kikuchi
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba City, Chiba 260-8715, Japan
| | - Satoshi Murakami
- Laboratory of Animal Hygiene, Department of Animal Science, Tokyo University of Agriculture, Japan
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