Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA.
Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA.
Antimicrob Agents Chemother. 2018 Dec 21;63(1). doi: 10.1128/AAC.01913-18. Print 2019 Jan.
The fluoroquinolone-resistant sequence type 1193 (ST1193) of , from the ST14 clonal complex (STc14) within phylogenetic group B2, has appeared recently as an important cause of extraintestinal disease in humans. Although this emerging lineage has been characterized to some extent using conventional methods, it has not been studied extensively at the genomic level. Here, we used whole-genome sequence analysis to compare 355 ST1193 isolates with 72 isolates from other STs within STc14. Using core genome phylogeny, the ST1193 isolates formed a tightly clustered clade with many genotypic similarities, unlike ST14 isolates. All ST1193 isolates possessed the same set of three chromosomal mutations conferring fluoroquinolone resistance, carried the allele, and were lactose non-fermenting. Analysis revealed an evolutionary progression from K1 to K5 capsular types and acquisition of an F-type virulence plasmid, followed by changes in plasmid structure congruent with genome phylogeny. In contrast, the numerous identified antimicrobial resistance genes were distributed incongruently with the underlying phylogeny, suggesting frequent gain or loss of the corresponding resistance gene cassettes despite retention of the presumed carrier plasmids. Pangenome analysis revealed gains and losses of genetic loci occurring during the transition from ST14 to ST1193 and from the K1 to K5 capsular types. Using time-scaled phylogenetic analysis, we estimated that current ST1193 clades first emerged approximately 25 years ago. Overall, ST1193 appears to be a recently emerged clone in which both stepwise and mosaic evolution have contributed to epidemiologic success.
B2 型进化枝中的 ST14 克隆复合体（STc14）内的 耐氟喹诺酮序列型 1193（ST1193），最近已成为人类肠外疾病的重要病因。尽管已经使用常规方法对这种新兴谱系进行了一定程度的描述，但尚未在基因组水平上进行广泛研究。在这里，我们使用全基因组序列分析比较了 355 株 ST1193 分离株和 72 株来自 STc14 内其他 ST 的分离株。使用核心基因组系统发育，ST1193 分离株形成了一个紧密聚类的分支，与 ST14 分离株有许多相似的基因型，而与 ST14 分离株不同。所有 ST1193 分离株均具有赋予氟喹诺酮耐药性的三个染色体突变体相同的集合，携带 等位基因，并且不发酵乳糖。分析表明，从 K1 到 K5 荚膜型的进化进展以及 F 型毒力质粒的获得，然后是与基因组系统发育一致的质粒结构变化。相比之下，许多鉴定出的抗生素耐药基因与潜在的系统发育不一致，这表明尽管保留了假定的载体质粒，但相应的耐药基因盒经常获得或丢失。泛基因组分析显示，在从 ST14 到 ST1193 的转变过程中以及在从 K1 到 K5 荚膜型的转变过程中，遗传基因座的获得和丧失。使用时间尺度系统发育分析，我们估计当前的 ST1193 分支大约在 25 年前首次出现。总的来说，ST1193 似乎是一个最近出现的克隆，其中逐步进化和镶嵌进化都促成了其流行病学成功。
