Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei.
Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei.
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DOI：
10.1038/s41467-021-22700-4
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发表时间：
2021-05-11
影响因子：
16.6
通讯作者：
Holt KE
中科院分区：
文献类型：
--
作者：
Hawkey J;Paranagama K;Baker KS;Bengtsson RJ;Weill FX;Thomson NR;Baker S;Cerdeira L;Iqbal Z;Hunt M;Ingle DJ;Dallman TJ;Jenkins C;Williamson DA;Holt KE
宋内志贺氏菌是高收入国家最常见的志贺氏菌病病原体，并在低收入和中等收入国家造成重大疾病负担。抗菌素耐药性在所有环境中都越来越普遍。全基因组测序 (WGS) 越来越多地用于宋内链球菌疫情调查和监测，但研究和实验室之间的数据比较具有挑战性。在这里，我们提出了 S. sonnei 的基因组框架和基因分型方案，以从 WGS 数据中有效识别基因型和抗性决定因素。该方案在软件包 Mykrobe 中实施，并在数千个基因组上进行了测试。应用这种方法对三个国家的公共卫生实验室测序的超过 4,000 个宋内沙门氏菌分离株进行分析，确定了几种与环丙沙星耐药性和阿奇霉素耐药性增加相关的常见基因型，证实了高耐药性宋内沙门氏菌克隆的洲际传播，并证明基因组框架有助于监测耐药克隆的传播，包括最近出现的耐药克隆在当地和全球范围内的传播。全基因组测序越来越多地用于宋内志贺氏菌疫情调查和监测，但尚无全球分类标准。在这里，作者开发并验证了使用开源软件实现的基因组框架，并使用监测数据演示了其应用。
Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for S. sonnei to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse >4,000 S. sonnei isolates sequenced in public health labs in three countries identified several common genotypes associated with increased rates of ciprofloxacin resistance and azithromycin resistance, confirming intercontinental spread of highly-resistant S. sonnei clones and demonstrating the genomic framework can facilitate monitoring the spread of resistant clones, including those that have recently emerged, at local and global scales. Whole genome sequencing is increasingly being adopted for Shigella sonnei outbreak investigation and surveillance, but there is no global classification standard. Here, the authors develop and validate a genomic framework implemented using open-source software, and demonstrate its application using surveillance data.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
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作者：
Ingle, Danielle J.;Easton, Marion;Williamson, Deborah A.
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通讯作者：
Dallman, Timothy J.
影响因子：
4.9
作者：
Campos-Madueno, Edgar, I;Bernasconi, Odette J.;Endimiani, Andrea
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