Whole genome sequencing analysis of Salmonella Enteritidis isolated in Chile provides insights about possible transmission between gulls, poultry and humans.

Toro M1, Retamal P2, Ayers S3, Barreto M4, Allard M5, Brown EW5, Gonzalez-Escalona N6.

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Abstract

Salmonella Enteritidis (SE) is a major cause of human Salmonellosis worldwide; however, little is known about the genetic relationships between SE clinical strains and SE from other sources in Chile. We compared the whole genomes of 30 SE isolated in Chile from gulls, domestic eggs (chicken), and from humans to investigate their phylogenetic relationships and establish their relatedness to international strains. Core genome MLST (cgMLST) analysis showed that only 246/4065 shared loci differed among these Chilean strains, separating them into two clusters (I and II), with cluster II further divided into five sub-clusters. One sub-cluster (sub-cluster 2) contained strains from all surveyed sources differing by a minimum of 1 to a maximum of 18 loci (out of 4065 loci) and 1 to18 SNPs, suggesting interspecies transmission of SE in Chile. Moreover, clusters were formed by strains distant geographically, which could imply that gulls might be spreading the pathogen thought the country. Our cgMLST analysis, using other SE genomes available at GenBank, showed that SE outbreak strains from Chile and the USA belong to different lineages, which suggests SE regional markers could exist and could be used for traceback investigations.

IMPORTANCE:

This study highlights the importance of gulls in the spread of Salmonella Enteritidis (SE) in Chile. We revealed a close genetic relationship between some human and gull SE strains (with as few as 2 out of 4065 genes difference), and we also found that gull strains were present in clusters formed by strains isolated from other sources or from further locations. This suggests, altogether with previous published evidence, that gulls might be spreading this pathogen between different regions in Chile, and that some of these strains have been transmitted to humans. Moreover, we discovered that Chilean SE strains clustered separately from most of SE isolated in the world (NCBI database), and therefore, it might be possible to distinguish strains geographical origin based on specific genomic features. This could be useful for trace back investigation of foodborne illnesses in the world.