Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.
Institute of Medical Technology, Peking University Health Science Center, Beijing, China.
Commun Biol. 2024 Aug 23;7(1):1038. doi: 10.1038/s42003-024-06720-6.
Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain feature identification in CMg samples and CRKP traceability. A database targeting high-prevalence horizontal gene transfer in CRKP strains and a ST11-only database for distinguishing two sub-lineages in China were created. To make the database user-friendly, facilitate immediate downstream strain feature identification from raw Nanopore metagenomic data, and avoid the need for phylogenetic analysis from scratch, we developed data analysis methods. The methods included pre-performed phylogenetic analysis, gene-isolate-cluster index and multilevel pan-genome database and reduced storage space by 10-fold and random-access memory by 52-fold compared with normal methods. PathoTracker can provide accurate and fast strain-level analysis for CMg data after 1 h Nanopore sequencing, allowing early warning of outbreaks. A user-friendly page ( http://PathoTracker.pku.edu.cn/ ) was developed to facilitate online analysis, including strain-level feature, species identifications and phylogenetic analyses. PathoTracker proposed in this study will aid in the downstream analysis of CMg.
临床宏基因组学（CMg）纳米孔测序有助于传染病诊断。在中国，ST11-KL64 和 ST11-KL47 碳青霉烯类耐药肺炎克雷伯菌（CRKP）亚系广泛流行。我们提出了 PathoTracker，这是一个专门为 CMg 样本中菌株特征识别和 CRKP 溯源而编制的数据库和排列方法。创建了一个针对 CRKP 菌株中高流行水平基因转移的数据库和一个仅针对 ST11 的数据库，用于区分中国的两个亚系。为了使用户友好，方便从原始纳米孔宏基因组数据中立即进行下游菌株特征识别，并避免从头进行系统发育分析，我们开发了数据分析方法。这些方法包括预先进行的系统发育分析、基因-分离物-聚类索引和多层次泛基因组数据库，与常规方法相比，存储空间减少了 10 倍，随机存取存储器减少了 52 倍。PathoTracker 可以在 1 小时的纳米孔测序后为 CMg 数据提供准确快速的菌株水平分析，从而实现疫情的早期预警。开发了一个用户友好的页面（http://PathoTracker.pku.edu.cn/），用于在线分析，包括菌株特征、物种鉴定和系统发育分析。本研究中提出的 PathoTracker 将有助于 CMg 的下游分析。
