The Swiss Centre for Antibiotic Resistance (ANRESIS) has recently noted an increase of extended-spectrum cephalosporin-resistant (ESC-R) Shigella sonnei isolates nationwide (3.8% in 2016 versus 37.5% in 2019). To understand this phenomenon, we analyzed 25 representative isolates (of which 14 were ESC-R) collected in Switzerland during 2016 to 2019. Whole-genome sequencing was achieved using both the Illumina and the Nanopore platforms. Both ESC-R and extended-spectrum cephalosporin-susceptible isolates belonged to sequence type 152 (ST152). The ESC-R isolates carried bla_CTX-M-3 in IncI1-pST57 (n = 5), bla_CTX-M-15 in IncFII (F2:A-:B-) (n = 5), bla_CTX-M-15 in IncI1-pST16, and bla_CTX-M-27, bla_CTX-M-55, or bla_CTX-M-134 in other IncFII plasmids (n = 1 each). Plasmids having the same bla and Inc group exhibited high degrees of genetic identity to each other but also to plasmids previously reported in other Enterobacterales. Core-genome analysis showed that there were 4 main clusters, each of which included strains that differed by <58 single nucleotide variants (SNVs) and that consisted of both bla_CTX-M-positive and bla_CTX-M-negative isolates. Moreover, most isolates belonging to the same cluster shared an identical core-genome sequence type (cgST). For instance, cluster 1 included 4 isolates of cgST113036, of which only 3 harbored the IncI1-pST57 bla_CTX-M-3-positive plasmid. The 25 S. sonnei isolates were also subjected to phylogenetic comparison with deposited international strains. As a result, matching isolates (isolates that had the same cgST and that differed by <8 SNVs) have been reported in the United Kingdom, the United States, France, and the Netherlands. Overall, our results suggest that some common S. sonnei clusters can spread between continents and can be imported into other nations after international trips. Such clusters include, in part, isolates that do not possess bla_ESBL-harboring plasmids, indicating their tendency to acquire them from other Enterobacterales.

中文翻译：

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由于常见质粒和国际克隆的传播，瑞士生产CTX-M的志贺氏菌分离株迅速增加。

瑞士抗生素抗性中心（ANRESIS）最近指出，全国范围内广谱头孢菌素耐药（ESC-R）志贺氏菌分离株有所增加（2016年为3.8％，2019年为37.5％）。为了了解这种现象，我们分析了2016年至2019年在瑞士收集的25个代表性分离株（其中14个为ESC-R）。使用Illumina和Nanopore平台均可实现全基因组测序。ESC-R和广谱头孢菌素敏感性分离株均属于序列类型152（ST152）。ESC-R分离株在IncI1-pST57中带有bla _CTX-M-3（n = 5），在IncFII中带有bla _CTX-M-15（F2：A-：B-）（n = 5），bla _{CTX-M- 15}IncI1-pST16中的bla _CTX和其他IncFII质粒中的bla _CTX-M-27，bla _CTX-M-55或bla _CTX-M-134（每个n = 1）。具有相同bla和Inc基团的质粒彼此显示出高度的遗传同一性，而且与先前在其他肠杆菌中报道的质粒也表现出高度的遗传同一性。核心基因组分析显示，共有4个主要簇，每个簇包括差异小于58个单核苷酸变体（SNV）的菌株，并且由bla _CTX-M阳性和bla _CTX-M组成-阴性分离株。而且，属于同一簇的大多数分离株共享相同的核心基因组序列类型（cgST）。例如，簇1包括4个cgST113036的分离株，其中只有3个带有Incl1-pST57 bla _CTX-M-3阳性质粒。25 s。sonnei分离株也与存放的国际菌株进行了系统发育比较。结果，在英国，美国，法国和荷兰已报告了匹配的分离株（具有相同cgST且差异小于8 SNV的分离株）。总的来说，我们的结果表明一些常见的S. sonnei这些星团可以在各大洲之间传播，并且可以在国际旅行之后被进口到其他国家。这样的簇部分地包括不具有bla _ESBL携带质粒的分离株，表明它们倾向于从其他肠杆菌中获得它们。