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Vilela FP, Felice AG, Seribelli AA, Rodrigues DP, Soares SC, Allard MW, Falcão JP. Comparative genomics reveals high genetic similarity among strains of Salmonella enterica serovar Infantis isolated from multiple sources in Brazil. PeerJ 2024; 12:e17306. [PMID: 38784399 PMCID: PMC11114117 DOI: 10.7717/peerj.17306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 04/04/2024] [Indexed: 05/25/2024] Open
Abstract
Background Salmonella enterica serovar Infantis (Salmonella Infantis) is a zoonotic, ubiquitous and foodborne pathogen of worldwide distribution. Despite Brazil's relevance as a major meat exporter, few studies were conducted to characterize strains of this serovar by genomic analyses in this country. Therefore, this study aimed to assess the diversity of 80 Salmonella Infantis strains isolated from veterinary, food and human sources in Brazil between 2013 and 2018 by comparative genomic analyses. Additional genomes of non-Brazilian countries (n = 18) were included for comparison purposes in some analyses. Methods Analyses of whole-genome multi-locus sequence typing (wgMLST), using PGAdb-builder, and of fragmented genomes, using Gegenees, were conducted to compare the 80 Brazilian strains to the 18 non-Brazilian genomes. Pangenome analyses and calculations were performed for all Salmonella Infantis genomes analyzed. The presence of prophages was determined using PHASTER for the 80 Brazilian strains. The genome plasticity using BLAST Ring Image Generator (BRIG) and gene synteny using Mauve were evaluated for 20 selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Unique orthologous protein clusters were searched in ten selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Results wgMLST and Gegenees showed a high genomic similarity among some Brazilian Salmonella Infantis genomes, and also the correlation of some clusters with non-Brazilian genomes. Gegenees also showed an overall similarity >91% among all Salmonella Infantis genomes. Pangenome calculations revealed an open pangenome for all Salmonella Infantis subsets analyzed and a high gene content in the core genomes. Fifteen types of prophages were detected among 97.5% of the Brazilian strains. BRIG and Mauve demonstrated a high structural similarity among the Brazilian and non-Brazilian isolates. Unique orthologous protein clusters related to biological processes, molecular functions, and cellular components were detected among Brazilian and non-Brazilian genomes. Conclusion The results presented using different genomic approaches emphasized the significant genomic similarity among Brazilian Salmonella Infantis genomes analyzed, suggesting wide distribution of closely related genotypes among diverse sources in Brazil. The data generated contributed to novel information regarding the genomic diversity of Brazilian and non-Brazilian Salmonella Infantis in comparison. The different genetically related subtypes of Salmonella Infantis from Brazil can either occur exclusively within the country, or also in other countries, suggesting that some exportation of the Brazilian genotypes may have already occurred.
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Affiliation(s)
- Felipe P. Vilela
- School of Pharmaceutical Sciences of Ribeirão Preto, Department of Clinical Analyses, Toxicology and Food Science, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Andrei G. Felice
- Institute of Biological and Natural Sciences, Department of Microbiology, Immunology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Amanda A. Seribelli
- Medical School of Ribeirão Preto, Department of Cellular and Molecular Biology, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Dália P. Rodrigues
- Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Siomar C. Soares
- Institute of Biological and Natural Sciences, Department of Microbiology, Immunology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America
| | - Juliana P. Falcão
- School of Pharmaceutical Sciences of Ribeirão Preto, Department of Clinical Analyses, Toxicology and Food Science, Universidade de São Paulo, Ribeirão Preto, São Paulo, 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: 0] [Impact Index Per Article: 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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Awosile B, Rahman MK, Levent G, Botero Y, Ajulo S, Ojasanya R, Williams RB, Loneragan GH. Comparing individual antimicrobial resistant and multi-drug resistant Salmonella enterica across serotypes, sampling sources, sampling periods, and food animal types in the United States (2014-2018). Prev Vet Med 2023; 219:106008. [PMID: 37651892 DOI: 10.1016/j.prevetmed.2023.106008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023]
Abstract
This study aimed to compare the antimicrobial-resistant Salmonella enterica profiles from three sampling sources cecal contents, HACCP (during processing), and retail meat using phenotypic antibiotic susceptibility and serotype data gathered from 2014 and 2018. Antimicrobial resistance data for 29 major Salmonella serotypes from three sampling sources and associated food animal types (cattle, swine, chicken, and turkey) were obtained from the database of the United States National Antimicrobial Resistance Monitoring System. Using multivariable logistic regression models, we compared individual and multi-drug resistance (MDR) in Salmonella enterica between the three sampling sources, food animal types, sampling period, and Salmonella serotypes. Across the three sources and throughout the sampling period, the recovery of antimicrobial-resistant Salmonella enterica - including MDR, MDR-AmpC, and ACSSuT - among food animal types were dependent on the sampling period and, in some cases, sampling sources and period for the selected antimicrobials. The predicted probability of antimicrobial resistance was greater in Salmonella serotypes from turkey compared to other food animal types, conditional on sampling sources. Ceftriaxone-resistant (OR=0.83, 95% CI: 0.69-0.99), and Sulfisoxazole-resistant (OR=0.84, 95% CI: 0.72-0.98) Salmonella serotypes were less likely to be recovered from the Hazard Analysis and Critical Control Point (HACCP) sources than with the cecal sources. Except for Salmonella serotypes Dublin and Newport, most of the Salmonella serotypes were less likely to be resistant to the selected antimicrobials, or found as MDR, compared to serotype Typhimurium. This study offers an integrated view on the predicted probability of MDR Salmonella serotypes, as well as insights into which serotypes are persistent, emerging or declining across sampling sources and food animal types in the United States.
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Affiliation(s)
- Babafela Awosile
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA.
| | - Md Kaisar Rahman
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA
| | - Gizem Levent
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA
| | - Yesica Botero
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA
| | - Samuel Ajulo
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA
| | - Rasaq Ojasanya
- Ontario Veterinary College, Department of Population Medicine, Guelph, Ontario, Canada
| | - Ryan B Williams
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA
| | - Guy H Loneragan
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA
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