A multidrug-resistant Salmonella enterica Typhimurium DT104 complex lineage circulating among humans and cattle in the United States lost the ability to produce pertussis-like toxin ArtAB

Salmonella enterica subspecies enterica serotype Typhimurium definitive type 104 (DT104) can infect both humans and animals and is often multidrug-resistant (MDR). Previous studies have indicated that, unlike most S. Typhimurium, the overwhelming majority of DT104 strains produce pertussis-like toxin ArtAB via prophage-encoded genes artAB. However, DT104 that lack artAB have been described on occasion. Here, we identify a MDR DT104 complex lineage circulating among humans and cattle in the United States, which lacks artAB (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 harbor artAB on prophage Gifsy-1 (n = 177), members of the U.S. artAB-negative major clade lack Gifsy-1, as well as anti-inflammatory effector gogB. 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 lost artAB, Gifsy-1, and gogB circa 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, sporadic artAB, Gifsy-1, and/or gogB loss 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 raw P-value > 0.05); thus, future research is needed to elucidate the roles that artAB, gogB, and Gifsy-1 play in DT104 virulence in humans and animals. Impact Statement Multi-drug resistant (MDR) Salmonella enterica serotype 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-encoded artAB. 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 digestion in 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 Summary Supplementary Data is available under DOI 10.5281/zenodo.7688792, with URL https://doi.org/10.5281/zenodo.7688792.