Application of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure

Outbreak investigation of foodborne salmonellosis is hindered when the food source is contaminated by multiple strains of , creating difficulties matching an incriminated organism recovered from patients with the specific strain in the suspect food. An outbreak of the rare Adjame was caused by multi...

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Published inFrontiers in microbiology Vol. 14; p. 1086198
Main Authors Gao, Ruimin, Duceppe, Marc-Olivier, Chattaway, Marie Anne, Goodridge, Lawrence, Ogunremi, Dele
Format Journal Article
LanguageEnglish
Published Switzerland Frontiers Media SA 03.03.2023
Frontiers Media S.A
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Summary:Outbreak investigation of foodborne salmonellosis is hindered when the food source is contaminated by multiple strains of , creating difficulties matching an incriminated organism recovered from patients with the specific strain in the suspect food. An outbreak of the rare 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 should enable a more precise strain characterization and aid the investigation of foodborne salmonellosis. We have carried out genomic analysis of Adjame strains recovered during the course of a recent outbreak and compared them with other strains of the organism (  = 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. The PST analysis of the Adjame isolates showed a high degree of strain heterogeneity. We observed small clusters made up of 2-6 isolates (  = 27) and singletons (  = 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. Mutations in the core and accessory genomes of 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.
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USDOE Office of Electricity (OE), Advanced Grid Research & Development. Power Systems Engineering Research
Present addresses: Ruimin Gao, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, Winnipeg, Man., Canada
Reviewed by: Eswarappa Pradeep Bulagonda, Sri Sathya Sai Institute of Higher Learning, India; Mansura Sherif Mulani, Savitribai Phule Pune University, India
Edited by: Swapnil Prakash Doijad, University Hospital Giessen and Marburg, Germany
This article was submitted to Evolutionary and Genomic Microbiology, a section of the journal Frontiers in Microbiology
ISSN:1664-302X
1664-302X
DOI:10.3389/fmicb.2023.1086198