Genomic landscape and phylogenetic reconstruction of Chinese monophasic Salmonella enterica serovar 1,4,[5],12:i:- : Focus on fljAB locus variation and microevolutionary dynamics.

Abstract

Salmonella enterica serovar Typhimurium monophasic variant 1,4,[5],12:i:- has emerged as a major cause of non-typhoidal salmonellosis worldwide, including in China. However, comprehensive investigations into the evolutionary trajectory, genomic features, and genetic variation of this pathogen remain limited. Therefore, this study performed whole-genome sequencing and detailed characterization of confirmed S. 1,4,[5],12:i:- isolates obtained from food sources and human clinical specimens in China during 2011-2019, aiming to elucidate their evolutionary and genomic background. Bayesian phylodynamic analysis of core SNP data identified two major S. 1,4,[5],12:i:- lineages circulating in China, each associated with distinct profiles of antimicrobial resistance genes and characteristic deletions and insertions in the phase 2 flagellin locus. Genomic analysis revealed fourteen distinct deletion patterns affecting the fljAB operon region, all linked to phase 2 flagellar antigen loss. The dominant S. 1,4,[5],12:i:- strains in China harbor a characteristic deletion spanning from nucleotide 374 of STM2745 to hin, with the intervening region replaced by a novel 28,661 bp resistance module (RR3.1). This module carries blaTEM-1, strA-strB, sul2, and tet(B), and differs from the previously reported RR3 solely by an additional partial IS26 copy upstream of the ΔtnpR-blaTEM-1 segment. Our results demonstrate that Chinese S. 1,4,[5],12:i:- strains represent multiple independent lineages. The disruption of phase 2 flagellin-associated genomic regions, resulting in monophasic phenotypes, has evolved progressively through the accumulation of mobile resistance elements.