A multidrug-resistantSalmonella entericaTyphimurium DT104 complex lineage circulating among humans and cattle in the United States lost the ability to produce pertussis-like toxin ArtAB

AbstractSalmonella entericasubspeciesentericaserotype Typhimurium definitive type 104 (DT104) can infect both humans and animals and is often multidrug-resistant (MDR). Previous studies have indicated that, unlike mostS.Typhimurium, the overwhelming majority of DT104 strains produce pertussis-like toxin ArtAB via prophage-encoded genesartAB. However, DT104 that lackartABhave been described on occasion. Here, we identify a MDR DT104 complex lineage circulating among humans and cattle in the United States, which lacksartAB(i.e., the “U.S.artAB-negative major clade”;n= 42 genomes). Unlike most other bovine- and human-associated DT104 complex strains from the U.S. (n= 230 total genomes), which harborartABon prophage Gifsy-1 (n= 177), members of the U.S.artAB-negative major clade lack Gifsy-1, as well as anti-inflammatory effectorgogB. The U.S.artAB-negative major clade encompasses human- and cattle-associated strains isolated from ≥11 U.S. states over a twenty-year period. The clade was predicted to have lostartAB, Gifsy-1, andgogBcirca 1985-1987 (95% highest posterior density interval 1979.0-1992.1). When compared to DT104 genomes from other world regions (n= 752 total genomes), several additional, sporadicartAB, Gifsy-1, and/orgogBloss events among clades encompassing ≤5 genomes were observed. Using phenotypic assays that simulate conditions encountered during human and/or bovine digestion, members of the U.S.artAB-negative major clade did not differ from closely related Gifsy-1/artAB/gogB-harboring U.S. DT104 complex strains (ANOVA rawP-value > 0.05); thus, future research is needed to elucidate the roles thatartAB,gogB, and Gifsy-1 play in DT104 virulence in humans and animals.Impact StatementMulti-drug resistant (MDR)Salmonella entericaserotype Typhimurium definitive type 104 (DT104) was responsible for a global epidemic among humans and animals throughout the 1990s and continues to circulate worldwide. Previous studies have indicated that the vast majority of DT104 produce pertussis-like toxin ArtAB via prophage-encodedartAB. Here, we identify a DT104 complex lineage that has been circulating among cattle and humans across ≥11 U.S. states for over twenty years, which lacks the ability to produce ArtAB (i.e., the “U.S.artAB-negative major clade”). The common ancestor of all U.S.artAB-negative major clade members lost the ability to produce ArtAB in the 1980s; however, the reason for this loss-of-function event within this well-established pathogen remains unclear. The role that ArtAB plays in DT104 virulence remains elusive, and phenotypic assays conducted here indicate that members of the U.S.artAB-negative major clade do not have a significant advantage or disadvantage relative to closely related, Gifsy-1/artAB/gogB-harboring U.S. DT104 complex strains when exposed to stressors encountered during human and/or bovine digestionin vitro. However, ArtAB heterogeneity within the DT104 complex suggests clade-specific selection for or against maintenance of ArtAB. Thus, future studies querying the virulence characteristics of the U.S.artAB-negative major clade are needed.Data SummarySupplementary Data is available under DOI 10.5281/zenodo.7688792, with URLhttps://doi.org/10.5281/zenodo.7688792.