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Emerging challenges of whole-genome-sequencing-powered epidemiological surveillance of globally distributed clonal groups of bacterial infections, giving Acinetobacter baumannii ST195 as an example.
International Journal of Medical Microbiology ( IF 4.1 ) Pub Date : 2019-08-19 , DOI: 10.1016/j.ijmm.2019.151339
Huiqiong Jia 1 , Yan Chen 2 , Jianfeng Wang 3 , Xinyou Xie 1 , Zhi Ruan 1
Affiliation  

Whole-genome sequencing (WGS) has revolutionized the genotyping of bacterial pathogens and is expected to become the new gold standard for tracing the transmissions of bacterial infectious diseases for public health purposes. However, it is still unexpectedly demanding to employ WGS for global epidemiological surveillance because of the high degree of similarity between the genomes of intercontinental isolates. The aim of this study was to utilize genomically derived bioinformatics analysis to identify globally distributed A. baumannii ST195 lineage and differentiation outbreaks to address this issue. The genomic sequences and their related epidemiological metadata of 2850 A. baumannii isolates were recruited from NCBI Genbank database. Assignment into sequence type (Oxford scheme) and lineage (global clone 2/CC92) were performed. A total of 91 ST195 A. baumannii isolates were subsequently classified to perform the bacterial source tracking analysis by implementing both core genome MLST (cgMLST) and core genome SNP (cgSNP) strategy that were integrated in our recently updated BacWGSTdb 2.0 server. Antibiotic resistance genes were identified using the ResFinder database. The ST195 A. baumannii isolates distributed widely in eight countries and harboured multiple antimicrobial resistance genes simultaneously. In most cases, the bacterial isolates recovered from geographically distant sources may present less genomic sequence similarity, i.e., the phylogenetic relationship between these ST195 isolates worldwide was roughly congruent with their country of isolation. However, a few isolates collected from distant geographic regions were revealed to possess smaller genetic distances (less than 8 loci or 20 SNPs) than the threshold without an observable epidemiological link. Our study highlights the emerging challenges entailed in the WGS-powered epidemiological surveillance of globally distributed clonal groups. Standardization is urgently required before WGS can be routinely applied to infectious diseases outbreak investigations.



中文翻译:

全基因组测序技术对全球分布的细菌感染无性系进行流行病学监测的新挑战,以鲍曼不动杆菌ST195为例。

全基因组测序(WGS)彻底改变了细菌病原体的基因分型,有望成为追踪细菌传染病传播以达到公共卫生目的的新金标准。但是,由于洲际分离株基因组之间的高度相似性,仍然意外地要求将WGS用于全球流行病学监测。这项研究的目的是利用基因组学上的生物信息学分析来确定全球分布的鲍曼不动杆菌ST195谱系和分化爆发,以解决这一问题。2850鲍曼不动杆菌的基因组序列及其相关流行病学元数据从NCBI Genbank数据库中招募了分离株。进行了序列类型(牛津方案)和谱系(全局克隆2 / CC92)的分配。随后,通过实施整合在我们最近更新的BacWGSTdb 2.0服务器中的核心基因组MLST(cgMLST)和核心基因组SNP(cgSNP)策略,总共对91个ST195鲍曼不动杆菌进行了分类,以进行细菌来源跟踪分析。使用ResFinder数据库鉴定抗生素抗性基因。ST195鲍曼不动杆菌分离株广泛分布于八个国家,并同时具有多个抗菌素耐药基因。在大多数情况下,从地理位置遥远的来源中分离出的细菌分离株可能呈现出较少的基因组序列相似性,即,全世界这些ST195分离株之间的系统发生关系与其分离国家大致相符。但是,从远处地理区域收集到的一些分离株被发现具有比阈值更小的遗传距离(小于8个基因座或20个SNP),而没有可观察到的流行病学联系。我们的研究突出了由WGS驱动的全球分布的克隆群体的流行病学监测带来的新挑战。在将WGS常规应用于传染病暴发调查之前,迫切需要标准化。

更新日期:2019-08-19
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