Genomics Revealed Novel Chromosomal Integration of Antimicrobial Resistance Cluster (B), 2, , )-Ib, and -Id in Typhimurium.

Antimicrobial-resistant has posed a huge threat to food safety and public health, and tetracycline is the commonly used antibiotic for treating salmonellosis. In this study, eight Typhimurium isolates from diarrhea patients ( = 7) and clam ( = 1) exhibited high-level tetracycline resistance (minimum inhibitory concentration = 128 μg/mL), and these isolates were further resistant to ampicillin and sulfonamides, formatting the R-type ASuT (ampicillin, sulfonamides, and tetracycline). Then, these eight isolates were sequenced using PacBio platform, revealing the presence of tetracycline resistance gene (B), along with sulfonamide-resistance gene 2, extended-spectrum-β-lactamase gene , and aminoglycoside resistance genes -Ib and -Id on the chromosome, which was associated with R-type ASuT. Four types (A, B1, B2, and C) of genetic arrangement for chromosomally encoding (B) were found, inserted into BA operon. Type C (BA operon-(B)-2---Ib--Id-ACDEPTR) was the most common type and was accompanied by various insertion sequences (ISs) (IS, IS, and IS) and recombinases. Pairwise sequence alignment showed that type C arrangement likely resulted from stepwise acquisitions and rearrangements facilitated by the actions of ISs, followed by integration into the chromosome by prophages. Phylogenomic analysis showed that all eight Typhimurium isolates from China in this study, along with a human-borne Typhimurium isolate (DA34821) from Germany and a foodborne Typhimurium isolate (CFSA629) from China, clustered into a single clade, sharing ≤67 SNPs, which suggested that clone spread occurred. These findings underline the emergence of R-type ASuT in Typhimurium, which is attributed to the presence of an antimicrobial resistance gene cluster ((B), 2, , -Ib, and -Id) encoded on the chromosome.