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Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of

Haijian Zhou1, Wenbing Liu2, Tian Qin1

  • 1State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and PreventionBeijing, China; Collaborative Innovation Centre for Diagnosis and Treatment of Infectious DiseasesHangzhou, China.

Frontiers in Microbiology
|March 25, 2017
PubMed

Insights

A new core genome multilocus sequence typing (cgMLST) method offers superior subtyping for Klebsiella pneumoniae. This advanced technique provides higher discriminatory power than traditional methods for tracking bacterial infections and understanding population structures.

Area of Science:

  • Microbiology
  • Genomics
  • Epidemiology

Background:

  • Traditional Klebsiella pneumoniae subtyping methods like MLST and PFGE have limitations in discriminatory power and efficiency.
  • MLST lacks sufficient resolution for distinguishing outbreak from non-outbreak isolates.
  • PFGE is effective but is labor-intensive and time-consuming.

Purpose of the Study:

  • To develop and evaluate a core genome multilocus sequence typing (cgMLST) scheme for whole-genome sequence-based subtyping of Klebsiella pneumoniae.
  • To overcome the limitations of existing subtyping methods for K. pneumoniae.
  • To enhance the accuracy and efficiency of molecular subtyping for epidemiological investigations.

Main Methods:

  • A cgMLST scheme was developed using a reference genome (K. pneumoniae strain HKUOPLC) and 907 publicly available genomes.
  • 1,143 target genes were identified for the cgMLST scheme.
  • The cgMLST scheme was validated using 26 K. pneumoniae strains from a nosocomial infection outbreak.

Main Results:

  • The developed cgMLST scheme demonstrated high discriminatory power, effectively clustering outbreak strains with fewer than 10 allele differences.
  • cgMLST clearly separated outbreak strains from unrelated strains.
  • The scheme revealed potential sub-clones within the epidemic ST11 clone of K. pneumoniae.

Conclusions:

  • The novel cgMLST scheme offers higher discriminatory power for Klebsiella pneumoniae outbreak investigations compared to PFGE and MLST.
  • cgMLST provides a more detailed understanding of K. pneumoniae population structures than MLST.
  • This whole-genome sequence-based typing method represents a significant advancement in molecular subtyping for K. pneumoniae.
Keywords:
Klebsiella pneumoniaecore genome multilocus sequence typingoutbreak investigationpopulation structure analysiswhole-genome sequence

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