Emerging challenges of whole-genome-sequencing-powered epidemiological surveillance of globally distributed clonal groups of bacterial infections, giving Acinetobacter baumannii ST195 as an example
Emerging challenges of whole-genome-sequencing-powered epidemiological surveillance of globally distributed clonal groups of bacterial infections, giving Acinetobacter baumannii ST195 as an example
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以鲍曼不动杆菌 ST195 为例，对全球分布的细菌感染克隆群进行全基因组测序的流行病学监测面临的新挑战。
DOI：
10.1016/j.ijmm.2019.151339
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发表时间：
2019-11-01
影响因子：
4.1
通讯作者：
Ruan, Zhi
中科院分区：
文献类型：
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作者：
Jia, Huiqiong;Chen, Yan;Ruan, Zhi
全基因组测序（WGS）彻底改变了细菌病原体的基因分型，并有望成为追踪细菌传染病传播的新黄金标准，用于公共卫生目的。然而，由于洲际分离株基因组之间的高度相似性，使用WGS进行全球流行病学监测的要求仍然出乎意料。本研究的目的是利用基因组衍生的生物信息学分析，以确定全球分布的A。鲍曼不动杆菌ST 195谱系和分化爆发来解决这个问题。2850 A.从NCBI Genbank数据库招募鲍曼不动杆菌分离株。进行序列类型（Oxford方案）和谱系（全局克隆2/CC 92）的分配。共91架ST 195 A。随后对鲍曼不动杆菌分离株进行分类，以通过实施核心基因组MLST（cgMLST）和核心基因组SNP（cgSNP）策略来进行细菌来源追踪分析，所述策略被整合到我们最近更新的BacWGSTdb 2.0服务器中。抗生素耐药基因的鉴定使用Resistance数据库。ST195 A.鲍曼不动杆菌广泛分布于8个国家，同时携带多种抗菌药物耐药基因。在大多数情况下，从地理上遥远的来源回收的细菌分离株可能存在较少的基因组序列相似性，即，世界范围内这些ST 195分离株之间的系统发育关系与它们的分离国家大致一致。然而，从遥远的地理区域收集的一些分离株被发现具有小于阈值的遗传距离（小于8个位点或20个SNP），没有可观察到的流行病学联系。我们的研究强调了全球分布的克隆群体的WGS动力流行病学监测所带来的新挑战。在WGS可以常规应用于传染病爆发调查之前，迫切需要标准化。
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.