Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing ofKlebsiella pneumoniae.
At present, the most used methods forKlebsiella pneumoniaesubtyping 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 ofK. pneumoniaewas developed for solving the disadvantages of these traditional molecular subtyping methods. Firstly, we used the complete genome ofK. pneumoniaestrain HKUOPLC as the reference genome and 907 genomes ofK. pneumoniaedownload 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 26K. pneumoniaestrains 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.
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.
Haijian
H
Zhou
Novogene Bioinformatics Technology Co. Ltd Beijing, China.
Wenbing
W
Liu
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.
Tian
T
Qin
Novogene Bioinformatics Technology Co. Ltd Beijing, China.
Chen
C
Liu
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.
Hongyu
H
Ren
Klebsiella pneumoniae; core genome multilocus sequence typing; outbreak investigation; population structure analysis; whole-genome sequence