AUTHOR=Cohn Alexa R. , Orsi Renato H. , Carroll Laura M. , Liao Jingqiu , Wiedmann Martin , Cheng Rachel A. 

TITLE=Salmonella enterica serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1005215

DOI=10.3389/fmicb.2022.1005215

ISSN=1664-302X

ABSTRACT=<p><italic>Salmonella enterica</italic> subsp<italic>. enterica</italic> (<italic>S.</italic>) serovar Cerro is rarely isolated from human clinical cases of salmonellosis but represents the most common serovar isolated from cattle without clinical signs of illness in the United States. In this study, using a large, diverse set of 316 isolates, we utilized genomic methods to further elucidate the evolutionary history of <italic>S.</italic> Cerro and to identify genomic features associated with its apparent virulence attenuation in humans. Phylogenetic analyses showed that within this polyphyletic serovar, 98.4% of isolates (311/316) represent a monophyletic clade within section Typhi and the remaining 1.6% of isolates (5/316) form a monophyletic clade within subspecies <italic>enterica</italic> Clade A1. Of the section Typhi <italic>S.</italic> Cerro isolates, 93.2% of isolates (290/311) clustered into a large clonal clade comprised of predominantly sequence type (ST) 367 cattle and environmental isolates, while the remaining 6.8% of isolates (21/311), primarily from human clinical sources, clustered outside of this clonal clade. A tip-dated phylogeny of <italic>S.</italic> Cerro ST367 identified two major clades (I and II), one of which overwhelmingly consisted of cattle isolates that share a most recent common ancestor that existed <italic>circa</italic> 1975. Gene presence/absence and rarefaction curve analyses suggested that the pangenome of section Typhi <italic>S.</italic> Cerro is open, potentially reflecting the gain/loss of prophage; human isolates contained the most open pangenome, while cattle isolates had the least open pangenome. Hypothetically disrupted coding sequences (HDCs) displayed clade-specific losses of intact <italic>speC</italic> and <italic>sopA</italic> virulence genes within the large clonal <italic>S.</italic> Cerro clade, while loss of intact <italic>vgrG</italic>, <italic>araH</italic>, and <italic>vapC</italic> occurred in all section Typhi <italic>S.</italic> Cerro isolates. Further phenotypic analysis suggested that the presence of a premature stop codon in <italic>speC</italic> does not abolish ornithine decarboxylase activity in <italic>S.</italic> Cerro, likely due to the activity of the second ornithine decarboxylase encoded by <italic>speF</italic>, which remained intact in all isolates. Overall, our study identifies specific genomic features associated with <italic>S.</italic> Cerro’s infrequent isolation from humans and its apparent adaptation to cattle, which has broader implications for informing our understanding of the evolutionary events facilitating host adaptation in <italic>Salmonella</italic>.</p>