Campylobacter jejuni is a leading cause of enteric bacterial illness in the United States. Traditional molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST), provided limited resolution to adequately identify C. jejuni outbreaks and separate out sporadic isolates during outbreak investigations. Whole-genome sequencing (WGS) has emerged as a powerful tool for C. jejuni outbreak detection. In this investigation, 45 human and 11 puppy isolates obtained during a 2016–2018 outbreak linked to pet store puppies were sequenced. Core genome multilocus sequence typing (cgMLST) and high-quality single nucleotide polymorphism (hqSNP) analysis of the sequence data separated the isolates into the same two clades containing minor within-clade differences; however, cgMLST analysis does not require selection of an appropriate reference genome, making the method preferable to hqSNP analysis for Campylobacter surveillance and cluster detection. The isolates were classified as sequence type 2109 (ST2109)—a rarely seen MLST sequence type. PFGE was performed on 38 human and 10 puppy isolates; PFGE patterns did not reliably predict clustering by cgMLST analysis. Genetic detection of antimicrobial resistance determinants predicted that all outbreak-associated isolates would be resistant to six drug classes. Traditional antimicrobial susceptibility testing (AST) confirmed a high correlation between genotypic and phenotypic antimicrobial resistance determinations. WGS analysis linked C. jejuni isolates in humans and pet store puppies even when canine exposure information was unknown, aiding the epidemiological investigation during the outbreak. WGS data were also used to quickly identify the highly drug-resistant profile of these outbreak-associated C. jejuni isolates.

中文翻译：

---

与宠物店幼犬相关的广泛耐药空肠弯曲菌感染的大规模多州爆发中使用的分子分型和抗菌素耐药性检测方法的比较。


空肠弯曲菌是美国肠道细菌性疾病的主要原因。传统的分子分型方法，例如脉冲场凝胶电泳 (PFGE) 和 7 基因多位点序列分型 (MLST)，其分辨率有限，无法充分识别空肠弯曲菌疫情并在疫情调查期间分离出零星分离株。全基因组测序 (WGS) 已成为检测空肠弯曲菌爆发的强大工具。在这项调查中，对 2016 年至 2018 年爆发期间与宠物店小狗有关的 45 份人类和 11 份小狗分离株进行了测序。核心基因组多位点序列分型 (cgMLST) 和序列数据的高质量单核苷酸多态性 (hqSNP) 分析将分离株分为相同的两个进化枝，且进化枝内差异较小；然而，cgMLST 分析不需要选择适当的参考基因组，因此该方法比 hqSNP 分析更适合弯曲杆菌监测和聚类检测。这些分离株被分类为序列类型 2109 (ST2109)——一种罕见的 MLST 序列类型。对 38 个人类和 10 个小狗分离株进行了 PFGE； PFGE 模式无法通过 cgMLST 分析可靠地预测聚类。抗菌素耐药性决定因素的基因检测预测，所有与疫情相关的分离株将对六种药物具有耐药性。传统的抗菌药物敏感性测试（AST）证实了基因型和表型抗菌药物耐药性测定之间的高度相关性。即使在犬类暴露信息未知的情况下，全基因组测序分析也将人类和宠物店小狗中的空肠弯曲菌分离株联系起来，有助于疫情爆发期间的流行病学调查。 全基因组测序数据还用于快速识别这些与疫情相关的空肠弯曲菌分离株的高度耐药性。