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

Haijian Zhou; Wenbing Liu; Tian Qin; Chen Liu; Hongyu Ren

doi:10.3389/fmicb.2017.00371

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

Front Microbiol. 2017 Mar 8:8:371. doi: 10.3389/fmicb.2017.00371. eCollection 2017.

Authors

Haijian Zhou¹, Wenbing Liu², Tian Qin¹, Chen Liu², Hongyu Ren³

Affiliations

¹ State 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.
² Novogene Bioinformatics Technology Co. Ltd Beijing, China.
³ State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention Beijing, China.

Abstract

At present, the most used methods for Klebsiella pneumoniae subtyping are multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). However, the discriminatory power of MLST could not meet the need for distinguishing outbreak and non-outbreak isolates and the PFGE is time-consuming and labor-intensive. A core genome multilocus sequence typing (cgMLST) scheme for whole-genome sequence-based typing of K. pneumoniae was developed for solving the disadvantages of these traditional molecular subtyping methods. Firstly, we used the complete genome of K. pneumoniae strain HKUOPLC as the reference genome and 907 genomes of K. pneumoniae download from NCBI database as original genome dataset to determine cgMLST target genes. A total of 1,143 genes were retained as cgMLST target genes. Secondly, we used 26 K. pneumoniae strains from a nosocomial infection outbreak to evaluate the cgMLST scheme. cgMLST enabled clustering of outbreak strains with <10 alleles difference and unambiguous separation from unrelated outgroup strains. Moreover, cgMLST revealed that there may be several sub-clones of epidemic ST11 clone. In conclusion, the novel cgMLST scheme not only showed higher discriminatory power compared with PFGE and MLST in outbreak investigations but also showed ability to reveal more population structure characteristics than MLST.

Keywords: Klebsiella pneumoniae; core genome multilocus sequence typing; outbreak investigation; population structure analysis; whole-genome sequence.