Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association

Authors: NGUYEN, SCOTT - UNIVERSITY COLLEGE DUBLIN; Harhay, Dayna; Bono, James - Jim; Smith, Timothy - Tim; FIELDS, PATRICIA - CENTERS FOR DISEASE CONTROL AND PREVENTION (CDC) - UNITED STATES; DINSMORE, BLAKE - CENTERS FOR DISEASE CONTROL AND PREVENTION (CDC) - UNITED STATES; SANTOVINA, MONICA - CENTERS FOR DISEASE CONTROL AND PREVENTION (CDC) - UNITED STATES; Wang, Rong; Bosilevac, Joseph - Mick; Harhay, Gregory

Submitted to: Microbial Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/5/2018
Publication Date: 8/6/2018
Citation: Nguyen, S.V., Harhay, D.M., Bono, J.L., Smith, T.P.L., Fields, P.I., Dinsmore, B.A., Santovina, M., Wang, R., Bosilevac, J.M., Harhay, G.P. 2018. Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association. Microbial Genomics. 4:1-17. https://doi.org/10.1099/mgen.0.000202.
DOI: https://doi.org/10.1099/mgen.0.000202

Interpretive Summary: Salmonella enterica serotype Montevideo has been linked to recent foodborne illness outbreaks resulting from contamination of products such as produce and spices. This serotype can be found in environments associated with cattle production, although salmonellosis outbreaks linked to beef consumption are rare. It is important to evaluate the potential contributions of cattle production practices in outbreaks in order to improve public health and food safety. One approach is to determine if different strains of Montevideo are found in cattle environments versus human disease cases. Here we report closed, high quality genome assemblies of 13 Montevideo strains isolated from 8 human disease cases or from 5 healthy cattle at harvest. Comparative analysis of Montevideo from this study and 72 publicly available genome sequences reveals 4 previously established groups, and that cattle and human strains differentially occupy these groups, suggesting that cattle-associated Montevideo may be less likely sources of foodborne disease. Genome analyses also suggest that differences in various strain characteristics determine which strains are in which group, and provide explanations for the decreased association between bovine isolates and human illnesses.

Technical Abstract: Salmonella enterica serovar Montevideo has been linked to recent foodborne illness outbreaks resulting from contamination of products such as fruits, vegetables, seeds and spices. Studies have shown that Montevideo also is frequently associated with healthy cattle and can be isolated from ground beef, yet human salmonellosis outbreaks of Montevideo associated with ground beef contamination are rare. This disparity fuelled our interest in characterizing the genomic differences between Montevideo strains isolated from healthy cattle and beef products, and those isolated from human patients and outbreak sources. To that end, we sequenced 13 Montevideo strains to completion, producing high-quality genome assemblies of isolates from human patients (n=8) or from healthy cattle at slaughter (n=5). Comparative analysis of sequence data from this study and publicly available sequences (n=72) shows that Montevideo falls into four previously established clades, differentially occupied by cattle and human strains. The results of these analyses reveal differences in metabolic islands, environmental adhesion determinants and virulence factors within each clade, and suggest explanations for the infrequent association between bovine isolates and human illnesses.