Multidrug resistant monophasic variants of Salmonella Typhimurium from pig production in Thailand

<b>Background:</b> Monophasic <i>Salmonella</i> Typhimurium or <i>S. enterica</i> 1,4,[5],12:i:- is among the top five serotypes reported in Thailand. In this study, nineteen whole-genome sequenced (WGS) monophasic <i>S</i>. Typhimurium from the pig production chain in Chiang Mai and Lamphun province during 2013–2015 were probed for the presence of antimicrobial resistance genes and <i>Salmonella</i> Pathogenicity Islands<i>.</i> Genetic diversity of the strains was also investigated through whole-genome multilocus sequence typing (wgMLST). <b>Results:</b> All 19 isolates carried aminoglycoside and beta-lactam class resistance genes. However, fusidic acid, glycopeptide, nitroimidazole, oxazolidinone, rifampicin associated-resistance genes were not observed. Seven out of 14 known SPIs were detected, including SPI-5, SPI-13 and SPI-14, which were deteced in all isolates. Core (2,978 genes) and pangenomes (5,022 genes) were analysed on a gene-by-gene basis (wgMLST). All isolates were from sequence type (ST-) 34 and clustered similarly in core and pangenome genealogies. The two closest related isolates showed differences in only eighteen loci and likely share a common ancestor. <b>Conclusions:</b> WGS data is can provide higher resolution for epidemiological surveillance and outbreak investigation. Similarities in the isolates we collected suggests either a common source of infection, or persistence though the pork production process. This highlights the importance of surveillance to successfully control <i>Salmonella</i> contamination in the region.

<b>背景：</b>单相鼠伤寒沙门氏菌（*Salmonella* Typhimurium）或肠炎沙门氏菌1,4,[5],12:i:-（*S. enterica* 1,4,[5],12:i:-）是泰国报告的前五大血清型之一。本研究针对2013-2015年间采自清迈府与南奔府生猪产业链的19株经全基因组测序（whole-genome sequenced, WGS）的单相鼠伤寒沙门氏菌，检测其抗菌耐药基因与沙门氏菌致病岛（Salmonella Pathogenicity Islands）的携带情况，并通过全基因组多位点序列分型（whole-genome multilocus sequence typing, wgMLST）分析菌株的遗传多样性。<b>结果：</b>19株分离株均携带氨基糖苷类与β-内酰胺类耐药基因，但未检出夫西地酸、糖肽类、硝基咪唑类、恶唑烷酮类及利福平相关耐药基因。本研究检出14种已知沙门氏菌致病岛中的7种，其中SPI-5、SPI-13与SPI-14在所有分离株中均存在。基于基因逐个分析（wgMLST）的核心基因组（2978个基因）与泛基因组（5022个基因）分析显示，所有分离株均属于序列型34（sequence type 34, ST34），且在核心基因组与泛基因组系统发育谱系中聚类模式相似。亲缘关系最近的两株分离株仅在18个基因座存在差异，推测二者拥有共同祖先。<b>结论：</b>全基因组测序数据可为流行病学监测与暴发调查提供更高分辨率的分析依据。本研究采集的分离株具有较高同源性，提示其可能源自共同感染源，或是在生猪生产流程中持续存在。本研究凸显了开展监测工作对该区域沙门氏菌污染防控的重要意义。