Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch.
Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch.
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DOI：
10.1093/cid/ciab784
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发表时间：
2021-12-01
期刊：
影响因子：
--
通讯作者：
NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance
中科院分区：
文献类型：
--
作者：
Argimón S;David S;Underwood A;Abrudan M;Wheeler NE;Kekre M;Abudahab K;Yeats CA;Goater R;Taylor B;Harste H;Muddyman D;Feil EJ;Brisse S;Holt K;Donado-Godoy P;Ravikumar KL;Okeke IN;Carlos C;Aanensen DM;NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance
克雷伯氏菌，包括著名的肺炎克雷伯菌，越来越多地与抗菌素耐药性(AMR)有关。基于基因组的监测可以为旨在控制AMR的干预措施提供信息。然而，它的广泛实施需要工具来简化生物信息分析和公共卫生报告。我们开发了网络应用程序Pathgenwatch，它实现了针对克雷伯氏菌物种的分析，用于整合和可视化基因组和流行病学数据。我们用16537个公共克雷伯氏菌基因组填充了Pathgenwatch，以实现用户基因组的情景化。我们用来自4个低收入和中等收入国家(LMIC)的1636个基因组展示了它的特征，这些基因组参加了AMR上的NIHR全球卫生研究单位(GHRU)。通过病原学观察，我们发现Ghru基因组主要由少数流行的肺炎克雷伯菌耐药克隆所控制。然而，它们的分布存在差异(例如，ST258/512在哥伦比亚占主导地位，ST231在印度，ST307在尼日利亚，ST147在菲律宾)。包括公共基因组在内的系统发育分析使人们能够追溯监测其传播情况。特别是，我们识别了医院暴发，检测到了来自国外的引入，并发现了与耐药性和毒力基因相关的克隆性扩张。对肺炎克雷伯菌代表疫苗候选的O-抗原和衣壳基因座的分析表明，3O型(O1-O3型)占总基因组的88.9%，而衣壳类型的多样性更大。病原体观察为克雷伯氏菌基因组的实时分析提供了一个免费、可访问的平台，以帮助在地方、国家和全球层面进行监测。我们改进了Ghru参与国基因组的代表性，进一步促进了正在进行的监测。
Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting. We developed the web application Pathogenwatch, which implements analytics tailored to Klebsiella species for integration and visualization of genomic and epidemiological data. We populated Pathogenwatch with 16 537 public Klebsiella genomes to enable contextualization of user genomes. We demonstrated its features with 1636 genomes from 4 low- and middle-income countries (LMICs) participating in the NIHR Global Health Research Unit (GHRU) on AMR. Using Pathogenwatch, we found that GHRU genomes were dominated by a small number of epidemic drug-resistant clones of K. pneumoniae. However, differences in their distribution were observed (eg, ST258/512 dominated in Colombia, ST231 in India, ST307 in Nigeria, ST147 in the Philippines). Phylogenetic analyses including public genomes for contextualization enabled retrospective monitoring of their spread. In particular, we identified hospital outbreaks, detected introductions from abroad, and uncovered clonal expansions associated with resistance and virulence genes. Assessment of loci encoding O-antigens and capsule in K. pneumoniae, which represent possible vaccine candidates, showed that 3 O-types (O1–O3) represented 88.9% of all genomes, whereas capsule types were much more diverse. Pathogenwatch provides a free, accessible platform for real-time analysis of Klebsiella genomes to aid surveillance at local, national, and global levels. We have improved representation of genomes from GHRU participant countries, further facilitating ongoing surveillance.
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影响因子：
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作者：
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通讯作者：
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影响因子：
16.6
作者：
Argimón S;Yeats CA;Goater RJ;Abudahab K;Taylor B;Underwood A;Sánchez-Busó L;Wong VK;Dyson ZA;Nair S;Park SE;Marks F;Page AJ;Keane JA;Baker S;Holt KE;Dougan G;Aanensen DM
通讯作者：
Aanensen DM