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核糖体分型017的全球进化动力学及耐药基因组分析

Global evolutionary dynamics and resistome analysis of ribotype 017.

作者信息

Imwattana Korakrit, Putsathit Papanin, Collins Deirdre A, Leepattarakit Teera, Kiratisin Pattarachai, Riley Thomas V, Knight Daniel R

机构信息

School of Biomedical Sciences, The University of Western Australia, Australia.

Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand.

出版信息

Microb Genom. 2022 Mar;8(3). doi: 10.1099/mgen.0.000792.

Abstract

PCR ribotype (RT) 017 ranks among the most successful strains of in the world. In the past three decades, it has caused outbreaks on four continents, more than other ‘epidemic’ strains, but our understanding of the genomic epidemiology underpinning the spread of RT 017 is limited. Here, we performed high-resolution phylogenomic and Bayesian evolutionary analyses on an updated and more representative dataset of 282 non-clonal RT 017 isolates collected worldwide between 1981 and 2019. These analyses place an estimated time of global dissemination between 1953 and 1983 and identified the acquisition of the -positive transposon Tn as a key factor behind global emergence. This coincided with the introduction of clindamycin, a key inciter of infection, into clinical practice in the 1960s. Based on the genomic data alone, the origin of RT 017 could not be determined; however, geographical data and records of population movement suggest that RT 017 had been moving between Asia and Europe since the Middle Ages and was later transported to North America around 1860 (95 % confidence interval: 1622–1954). A focused epidemiological study of 45 clinical RT 017 genomes from a cluster in a tertiary hospital in Thailand revealed that the population consisted of two groups of multidrug-resistant (MDR) RT 017 and a group of early, non-MDR RT 017. The significant genomic diversity within each MDR group suggests that although they were all isolated from hospitalized patients, there was probably a reservoir of RT 017 in the community that contributed to the spread of this pathogen.

摘要

PCR核糖体分型(RT)017是世界上最成功的菌株之一。在过去三十年中,它在四大洲引发了疫情,比其他“流行”菌株引发的疫情更多,但我们对RT 017传播背后的基因组流行病学的了解有限。在此,我们对1981年至2019年间在全球收集的282株非克隆RT 017分离株的更新且更具代表性的数据集进行了高分辨率系统发育基因组学和贝叶斯进化分析。这些分析估计全球传播时间在1953年至1983年之间,并确定获得阳性转座子Tn是全球出现的关键因素。这与20世纪60年代克林霉素引入临床实践相吻合,克林霉素是感染的关键诱因。仅基于基因组数据,无法确定RT 017的起源;然而,地理数据和人口流动记录表明,RT 017自中世纪以来一直在亚洲和欧洲之间传播,后来在1860年左右(95%置信区间:1622 - 1954)被运往北美。对泰国一家三级医院一个集群中的45个临床RT 017基因组进行的重点流行病学研究表明,该群体由两组多重耐药(MDR)RT 017和一组早期非MDR RT 017组成。每个MDR组内显著的基因组多样性表明,尽管它们都从住院患者中分离出来,但社区中可能存在RT 017的储存库,这有助于这种病原体的传播。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/11bd/9176289/e7326d1c3808/mgen-8-0792-g001.jpg

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