Abstract
Nontyphoidal Salmonella (NTS) is a common pathogen in food-producing animals and a public health concern worldwide. Various NTS serovars may be present in apparently healthy animals. This could result in carcass contamination during the slaughter process leading to human exposure. While most genomic research has focused on Salmonella pathogenesis, little is known on the factors associated with subclinical infections and environmental persistence. We report here the widespread distribution of typhoidal toxin genes (i. e. the cdtB islet, hlyE, taiA), among NTS strains from a beef slaughter operation (n = 39) and from epidemiologically unconnected ground beef (n = 20). These genes were present in 76% of the strains, regardless of serovar, isolation source or geographical location. Moreover, strains that predominated in the slaughterhouse carry plasmid-borne type IV secretion systems (T4SS), which have been linked to persistent infections in numerous pathogens. Population genomics supports clonal dissemination of NTS along the food production chain, highlighting its role as reservoir of genetic variability in the environment. Overall, the study provides a thorough characterization of serovar diversity and genomic features of beef-associated NTS in Mexico. Furthermore, it reveals how common genetic factors could partially explain the emergence and persistence of certain NTS serovars in the beef industry.
Highlights
Nontyphoidal salmonellosis is one of the leading causes of foodborne illness around the world[1]
To gain insights into the potential health risks and lifestyle dynamics allowing S. enterica serovars from bovine reservoirs to colonize humans, we focused on functional traits that may be revealed after comparative genomics analyses
Divergence was only observed in strains of subsp. diarizonae and the S. enterica subsp. enterica serovar Mbandaka strain, isolated from a pond in the United States
Summary
Nontyphoidal salmonellosis is one of the leading causes of foodborne illness around the world[1]. There is limited information on why certain Salmonella strains colonize the intestines of livestock without causing apparent illness in the host, creating a reservoir for human diseases[4]. We set up a long-term surveillance experimental scheme to conduct comparative genomics of bovine-associated Salmonella strains isolated from non-clinical sources along the beef production continuum in Mexico. Our collection includes strains from multiple serovars and distant geographical regions within Mexico We assessed their genetic diversity and conducted comparative genomics of virulence factors, stress response genes and plasmids, with the finding that most strains carry a conserved repertoire of virulence and stress response genes. This study provides evidence of clonal dissemination of NTS along the food production chain, highlighting the significance of isolates colonizing apparently healthy animals, as reservoirs of genetic variability in the environment. Further research is needed to test whether the observed differences affect host adaptation and/or pathogen fitness under intensive beef cattle production settings
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