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PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak

Shuyi Wang1,2, Shijun Sun1, Qi Wang1

  • 1Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.

Communications Biology
|August 23, 2024
PubMed

Insights

PathoTracker enhances infectious disease diagnosis using clinical metagenomics. This tool rapidly identifies Carbapenem-resistant Klebsiella pneumoniae sub-lineages from Nanopore sequencing data for outbreak detection.

Area of Science:

  • Genomics
  • Infectious Diseases
  • Bioinformatics

Background:

  • Clinical metagenomics (CMg) using Nanopore sequencing offers potential for rapid infectious disease diagnosis.
  • Sub-lineages ST11-KL64 and ST11-KL47 of Carbapenem-resistant Klebsiella pneumoniae (CRKP) are prevalent in China.
  • Accurate and efficient strain identification is crucial for managing CRKP outbreaks.

Purpose of the Study:

  • To develop PathoTracker, a specialized database and method for strain feature identification in CMg samples.
  • To enable rapid traceability of CRKP strains, particularly the prevalent ST11 sub-lineages in China.
  • To provide a user-friendly tool for immediate downstream analysis of Nanopore metagenomic data.

Main Methods:

  • Creation of a targeted database for high-prevalence horizontal gene transfer in CRKP.
  • Development of a ST11-specific database for distinguishing Chinese sub-lineages.
  • Implementation of pre-performed phylogenetic analysis, gene-isolate-cluster indexing, and a multilevel pan-genome database.
  • Optimization of data analysis methods to reduce storage and random-access memory requirements.

Main Results:

  • PathoTracker significantly reduces storage (10-fold) and RAM (52-fold) compared to conventional methods.
  • The tool provides accurate and fast strain-level analysis of CMg data within 1 hour of Nanopore sequencing.
  • A user-friendly online platform (http://PathoTracker.pku.edu.cn/) was established for analysis.

Conclusions:

  • PathoTracker facilitates early warning of infectious disease outbreaks through rapid strain identification.
  • The developed methods and database aid in the downstream analysis of clinical metagenomic data.
  • PathoTracker improves the efficiency and accessibility of CRKP strain traceability and analysis.

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