应用全基因组测序对引起人类临床感染的弯曲菌进行分子特征分析：爱尔兰的毒力、抗菌药物耐药性和系统发生。
Molecular characterization of Campylobacter causing human clinical infection using whole-genome sequencing: Virulence, antimicrobial resistance and phylogeny in Ireland.
机构信息
Public Health Laboratory, Dublin-Health Service Executive, Dublin, Ireland.
European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control, Stockholm, Sweden.
出版信息
PLoS One. 2019 Jul 10;14(7):e0219088. doi: 10.1371/journal.pone.0219088. eCollection 2019.
OBJECTIVES
We characterized clinical isolates of Campylobacter using whole-genome sequencing (WGS) for detection of virulence genes, antimicrobial resistance markers and phylogenetic analysis in order to increase the knowledge on the molecular epidemiology of Campylobacter in Ireland, where there are significant gaps due to the widespread in the use of culture independent methods for the diagnosis of campylobacteriosis.
METHODS
WGS was applied to 122 Campylobacter human isolates collected over a 10-years period, from diarrhoeal stool samples submitted for routine enteric screening.
RESULTS
Genes associated with cytotoxin production such as cdtA, cdtB and cdtC were found in 88%, 89% and 89% isolates, respectively; adherence, colonization and invasion genes such as cadF, dnaJ, racR, iam, virB11 and ciaB were found in 99%, 99%, 98%, 99%, 1% and 80% isolates, respectively. Genetic markers associated with resistance to quinolones (C257T in gyrA), beta-lactams (blaoxa-61) and tetracycline (tet(O)) were present in 43%, 71% and 25% isolates, respectively. The cmeABC operon was present in 94% of isolates. No macrolide or aminoglycoside resistance markers were detected. Phylogenetic analysis showed that 112 isolates were assigned to 29 sequence types grouped into 17 clonal complexes. Four clusters previously unidentified were detected. These results shown the similarity of Irish data compared to what has been described globally.
CONCLUSIONS
WGS has shown a high discriminatory power for cluster detection, demonstrating that its integration in routine laboratory surveillance could improve the detection and management of outbreaks. In addition we were able to demonstrate that virulence genes in clinical Campylobacter infections in Ireland were similar to those known previously. High prevalence of quinolone resistance markers has been found, which has implications for antimicrobial stewardship.
目的
我们通过全基因组测序（WGS）对弯曲杆菌临床分离株进行特征分析，以检测毒力基因、抗生素耐药标记物和系统发育分析，从而增加对爱尔兰弯曲杆菌分子流行病学的了解，由于广泛使用非培养方法诊断弯曲杆菌病，爱尔兰在这方面存在重大空白。
方法
对 122 株来自腹泻粪便样本的人类弯曲杆菌临床分离株进行了为期 10 年的 WGS 分析，这些样本是为常规肠道筛查而提交的。
结果
分别在 88%、89%和 89%的分离株中发现了与细胞毒素产生相关的基因 cdtA、cdtB 和 cdtC；在 99%、99%、98%、99%、1%和 80%的分离株中发现了与黏附、定植和侵袭相关的基因 cadF、dnaJ、racR、iam、virB11 和 ciaB；在 43%、71%和 25%的分离株中发现了与喹诺酮类（gyrA 中的 C257T）、β-内酰胺类（blaoxa-61）和四环素类（tet(O))）耐药相关的遗传标记；cmeABC 操纵子存在于 94%的分离株中。未检测到大环内酯类或氨基糖苷类耐药标记物。系统发育分析显示，112 株分离株被分配到 29 个序列类型，分为 17 个克隆复合体。检测到 4 个以前未识别的聚类。这些结果表明爱尔兰的数据与全球已描述的数据相似。
结论
WGS 对聚类检测显示出很高的分辨力，表明将其整合到常规实验室监测中可以提高暴发的检测和管理。此外，我们能够证明爱尔兰弯曲杆菌临床感染中的毒力基因与以前已知的相似。发现了高比例的喹诺酮耐药标记物，这对抗菌药物管理具有重要意义。
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