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

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.

The phylogenomics of CRISPR-Cas system and revelation of its features in Salmonella

“…Further, HGT and recombination events significantly influence the evolutionary framework of the bacteria. Our study probes into the evolution of Salmonella with respect to CRISPR-Cas system that influences genome evolution 16 and bacterial virulence 13 . We categorized the CRISPR-Cas system into two types, namely, CRISPR1-STM/cas-STM and CRISPR1-STY/cas-STY based on the phylogenetic segregation and differences in the CRISPR1-leader and cas genes features of the strains studied.…”

“…Thus, the acquisition of the spacers could be a primitive event, with different selection pressures operating on different serovars to maintain the spacer composition. One elucidation is, the spacer composition of the system could potentially leverage protection against invading MGE 16 or pathogenic potential possibly through endogenous gene regulation 10,13,42 as implicated elsewhere 10,13,16,42 , thereby resulting in the spacers preservation. This polymorphism of spacers, across serotypes, finds utility in serotyping 43,44 .…”

Whole-Genome-Based Survey for Polyphyletic Serovars of Salmonella enterica subsp. enterica Provides New Insights into Public Health Surveillance

“…Previous studies revealed that certain Salmonella lineages have preferred niche ranges, and explored this aspect of Salmonella biology by source attribution [ 10 , 19 ]. To investigate the possible lineage-specific niche preference in a broad context, the EnteroBase database was acquired for the source niche metadata for 6142 strains carrying the given STs of Montevideo, Bareilly, Saintpaul, and Muenchen (see Table S3 ).…”

“…Montevideo, Bareilly, Saintpaul, and Muenchen caused 1018, 412, 778, and 1216 illnesses in the USA (total = 32,271) in 2016, respectively ( Table 1 ). As one of the top 10 most common serovars, Montevideo is associated with contaminated foods, including black and red peppercorn, tahini, and pistachio [ 19 , 33 , 34 ], and is linked to more than 240 illnesses in 38 states with contaminated Italian-style spiced meats [ 34 , 35 ]. Bareilly, first identified in India in 1928, is known for its wide host range and has been associated with multiple multistate outbreaks, for instance, a widespread foodborne outbreak in the United States associated with scraped tuna imported from India [ 36 ].…”

Complete Genome Sequences of Four Salmonella enterica Strains Associated with Pistachios Assembled Using a Combination of Short- and Long-Read Sequencing

“…The S . Montevideo strains belong to clade I of the four clades previously described for S. Montevideo and to eBurstGroup 39 (eBG 39) (9). The other three clades belong to eBG 40, which contains the majority of the S .…”