Phylogenomic analysis of Salmonella Indiana ST17, an emerging MDR clonal group in China

作者：Ruan-Yang Sun, Wen-Ying Guo, Ji-Xing Zhang, Min-Ge Wang, Linlin Wang, Xin-Lei Lian, Bi-Xia Ke, Jian Sun, Changwen Ke, Ya-Hong Liu, Xiao‐Ping Liao, Liang‐Xing Fang · 发表于：Journal of Antimicrobial Chemotherapy · 年份：2022 · DOI：10.1093/jac/dkac243 · 被引用次数：19 · 研究领域：Salmonella and Campylobacter epidemiology、Antibiotic Resistance in Bacteria、Escherichia coli research studies

OBJECTIVES: To reconstruct the genomic epidemiology and evolution of MDR Salmonella Indiana in China. METHODS: A total of 108 Salmonella Indiana strains were collected from humans and livestock in China. All isolates were subjected to WGS and antimicrobial susceptibility testing. Phylogenetic relationships and evolutionary analyses were conducted using WGS data from this study and the NCBI database. RESULTS: Almost all 108 Salmonella Indiana strains displayed the MDR phenotype. Importantly, 84 isolates possessed concurrent resistance to ciprofloxacin and cefotaxime. WGS analysis revealed that class 1 integrons on the chromosome and IncHI2 plasmids were the key vectors responsible for multiple antibiotic resistance gene (ARG) [including ESBL and plasmid-mediated quinolone resistance (PMQR) genes] transmission among Salmonella Indiana. The 108 Salmonella Indiana dataset displayed a relatively large core genome and ST17 was the predominant ST. Moreover, the global ST17 Salmonella Indiana strains could be divided into five distinct lineages, each of which was significantly associated with a geographical distribution. Genomic analysis revealed multiple antimicrobial resistance determinants and QRDR mutations in Chinese lineages, which almost did not occur in other global lineages. Using molecular clock analysis, we hypothesized that ST17 isolates have existed since 1956 and underwent a major population expansion from the 1980s to the 2000s and the genetic diversity started to decr...