National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, P. R.China.
Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, P. R.China.
J Antimicrob Chemother. 2022 Oct 28;77(11):2937-2945. doi: 10.1093/jac/dkac243.
To reconstruct the genomic epidemiology and evolution of MDR Salmonella Indiana in China.
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.
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 decrease around 2011, probably due to geographical barriers, antimicrobial selective pressure and MDR, favouring the establishment of this prevalent multiple antibiotic-resistant lineage and local epidemics.
This study revealed that adaptation to antimicrobial pressure was possibly pivotal in the recent evolutionary trajectory for the clonal spread of ST17 Salmonella Indiana in China.
重建中国耐多药肠炎沙门氏菌的基因组流行病学和进化。
从中国的人和家畜中收集了 108 株肠炎沙门氏菌。对所有分离株进行 WGS 和抗菌药物敏感性测试。使用来自本研究和 NCBI 数据库的 WGS 数据进行系统发育关系和进化分析。
几乎所有 108 株肠炎沙门氏菌均表现出 MDR 表型。重要的是，84 株分离株同时具有对环丙沙星和头孢噻肟的耐药性。WGS 分析表明，染色体上的 class 1 整合子和 IncHI2 质粒是导致肠炎沙门氏菌中多种抗生素耐药基因（ARG）[包括 ESBL 和质粒介导的喹诺酮耐药（PMQR）基因]传播的关键载体。108 株肠炎沙门氏菌数据集显示出相对较大的核心基因组，ST17 是主要的 ST。此外，全球 ST17 肠炎沙门氏菌株可分为五个不同的谱系，每个谱系都与特定的地理分布显著相关。基因组分析揭示了中国谱系中存在多种抗生素耐药决定因素和 QRDR 突变，而这些突变在其他全球谱系中几乎不存在。利用分子钟分析，我们假设 ST17 分离株自 1956 年以来就存在，并在 20 世纪 80 年代至 2000 年代经历了一次主要的种群扩张，而遗传多样性在 2011 年左右开始下降，这可能是由于地理障碍、抗菌药物选择压力和 MDR 有利于建立这种流行的多药耐药谱系和局部流行。
本研究表明，适应抗菌压力可能是中国 ST17 肠炎沙门氏菌克隆传播近期进化轨迹的关键。
