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Application of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure
INTRODUCTION: Outbreak investigation of foodborne salmonellosis is hindered when the food source is contaminated by multiple strains of Salmonella, creating difficulties matching an incriminated organism recovered from patients with the specific strain in the suspect food. An outbreak of the rare Sa...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10020630/ https://www.ncbi.nlm.nih.gov/pubmed/36937281 http://dx.doi.org/10.3389/fmicb.2023.1086198 |
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author | Gao, Ruimin Duceppe, Marc-Olivier Chattaway, Marie Anne Goodridge, Lawrence Ogunremi, Dele |
author_facet | Gao, Ruimin Duceppe, Marc-Olivier Chattaway, Marie Anne Goodridge, Lawrence Ogunremi, Dele |
author_sort | Gao, Ruimin |
collection | PubMed |
description | INTRODUCTION: Outbreak investigation of foodborne salmonellosis is hindered when the food source is contaminated by multiple strains of Salmonella, creating difficulties matching an incriminated organism recovered from patients with the specific strain in the suspect food. An outbreak of the rare Salmonella Adjame was caused by multiple strains of the organism as revealed by single-nucleotide polymorphism (SNP) variation. The use of highly discriminatory prophage analysis to characterize strains of Salmonella should enable a more precise strain characterization and aid the investigation of foodborne salmonellosis. METHODS: We have carried out genomic analysis of S. Adjame strains recovered during the course of a recent outbreak and compared them with other strains of the organism (n = 38 strains), using SNPs to evaluate strain differences present in the core genome, and prophage sequence typing (PST) to evaluate the accessory genome. Phylogenetic analyses were performed using both total prophage content and conserved prophages. RESULTS: The PST analysis of the S. Adjame isolates showed a high degree of strain heterogeneity. We observed small clusters made up of 2-6 isolates (n = 27) and singletons (n = 11) in stark contrast with the three clusters observed by SNP analysis. In total, we detected 24 prophages of which only four were highly prevalent, namely: Entero_p88 (36/38 strains), Salmon_SEN34 (35/38 strains), Burkho_phiE255 (33/38 strains) and Edward_GF (28/38 strains). Despite the marked strain diversity seen with prophage analysis, the distribution of the four most common prophages matched the clustering observed using core genome. DISCUSSION: Mutations in the core and accessory genomes of S. Adjame have shed light on the evolutionary relationships among the Adjame strains and demonstrated a convergence of the variations observed in both fractions of the genome. We conclude that core and accessory genomes analyses should be adopted in foodborne bacteria outbreak investigations to provide a more accurate strain description and facilitate reliable matching of isolates from patients and incriminated food sources. The outcomes should translate to a better understanding of the microbial population structure and an 46 improved source attribution in foodborne illnesses. |
format | Online Article Text |
id | pubmed-10020630 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-100206302023-03-18 Application of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure Gao, Ruimin Duceppe, Marc-Olivier Chattaway, Marie Anne Goodridge, Lawrence Ogunremi, Dele Front Microbiol Microbiology INTRODUCTION: Outbreak investigation of foodborne salmonellosis is hindered when the food source is contaminated by multiple strains of Salmonella, creating difficulties matching an incriminated organism recovered from patients with the specific strain in the suspect food. An outbreak of the rare Salmonella Adjame was caused by multiple strains of the organism as revealed by single-nucleotide polymorphism (SNP) variation. The use of highly discriminatory prophage analysis to characterize strains of Salmonella should enable a more precise strain characterization and aid the investigation of foodborne salmonellosis. METHODS: We have carried out genomic analysis of S. Adjame strains recovered during the course of a recent outbreak and compared them with other strains of the organism (n = 38 strains), using SNPs to evaluate strain differences present in the core genome, and prophage sequence typing (PST) to evaluate the accessory genome. Phylogenetic analyses were performed using both total prophage content and conserved prophages. RESULTS: The PST analysis of the S. Adjame isolates showed a high degree of strain heterogeneity. We observed small clusters made up of 2-6 isolates (n = 27) and singletons (n = 11) in stark contrast with the three clusters observed by SNP analysis. In total, we detected 24 prophages of which only four were highly prevalent, namely: Entero_p88 (36/38 strains), Salmon_SEN34 (35/38 strains), Burkho_phiE255 (33/38 strains) and Edward_GF (28/38 strains). Despite the marked strain diversity seen with prophage analysis, the distribution of the four most common prophages matched the clustering observed using core genome. DISCUSSION: Mutations in the core and accessory genomes of S. Adjame have shed light on the evolutionary relationships among the Adjame strains and demonstrated a convergence of the variations observed in both fractions of the genome. We conclude that core and accessory genomes analyses should be adopted in foodborne bacteria outbreak investigations to provide a more accurate strain description and facilitate reliable matching of isolates from patients and incriminated food sources. The outcomes should translate to a better understanding of the microbial population structure and an 46 improved source attribution in foodborne illnesses. Frontiers Media S.A. 2023-03-03 /pmc/articles/PMC10020630/ /pubmed/36937281 http://dx.doi.org/10.3389/fmicb.2023.1086198 Text en Copyright © 2023 Gao, Duceppe, Chattaway, Goodridge and Ogunremi. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Gao, Ruimin Duceppe, Marc-Olivier Chattaway, Marie Anne Goodridge, Lawrence Ogunremi, Dele Application of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure |
title | Application of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure |
title_full | Application of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure |
title_fullStr | Application of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure |
title_full_unstemmed | Application of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure |
title_short | Application of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure |
title_sort | application of prophage sequence analysis to investigate a disease outbreak involving salmonella adjame, a rare serovar and implications for the population structure |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10020630/ https://www.ncbi.nlm.nih.gov/pubmed/36937281 http://dx.doi.org/10.3389/fmicb.2023.1086198 |
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