Worldwide transmission of ST11-KL64 carbapenem-resistant Klebsiella pneumoniae: an analysis of publicly available genomes

ST11-KL64 is an internationally distributed lineage of carbapenem-resistant Klebsiella pneumoniae and is the most common type in China. The international and interprovincial (in China) transmission of ST11-KL64 CRKP remains to be elucidated. We used both static clusters defined based on a fixed cutoff of & LE;21 pairwise single-nucleotide polymorphisms and dynamic groups defined by modeling the likelihood to be linked by a transmission threshold to investigate the transmission of ST11-KL64 strains based on genome sequences mining. We analyzed all publicly available genomes (n = 730) of ST11-KL64 strains, almost all of which had known carbapenemase genes with KPC-2 being dominant. We identified 4 clusters of international transmission and 14 clusters of interprovincial transmission across China of ST11-KL64 strains. We found that dynamic grouping could provide further resolution for determining clonal relatedness in addition to the widely adopted static clustering and therefore increases the confidence for inferring transmission.IMPORTANCECarbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious challenge for clinical management and is prone to spread in and between healthcare settings. ST11-KL64 is the dominant CRKP type in China with a worldwide distribution. Here, we used two different methods, the widely used clustering based on a fixed single-nucleotide polymorphism (SNP) cutoff and the recently developed grouping by modeling transmission likelihood, to mine all 730 publicly available ST11-KL64 genomes. We identified international transmission of several strains and interprovincial transmission in China of a few, which warrants further investigations to uncover the mechanisms for their spread. We found that static clustering based on & LE;21 fixed SNPs is sensitive to detect transmission and dynamic grouping has higher resolutions to provide complementary information. We suggest the use of the two methods in combination for analyzing transmission of bacterial strains. Our findings highlight the need of coordinated actions at both international and interprovincial levels for tackling multi-drug resistant organisms. Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious challenge for clinical management and is prone to spread in and between healthcare settings. ST11-KL64 is the dominant CRKP type in China with a worldwide distribution. Here, we used two different methods, the widely used clustering based on a fixed single-nucleotide polymorphism (SNP) cutoff and the recently developed grouping by modeling transmission likelihood, to mine all 730 publicly available ST11-KL64 genomes. We identified international transmission of several strains and interprovincial transmission in China of a few, which warrants further investigations to uncover the mechanisms for their spread. We found that static clustering based on & LE;21 fixed SNPs is sensitive to detect transmission and dynamic grouping has higher resolutions to provide complementary information. We suggest the use of the two methods in combination for analyzing transmission of bacterial strains. Our findings highlight the need of coordinated actions at both international and interprovincial levels for tackling multi-drug resistant organisms.

Automated summary

This study investigated the transmission of ST11-KL64 strains based on genome sequencing and identified international and interprovincial transmission of these strains in China. The use of dynamic grouping in addition to static clustering provided higher resolution and increased confidence in determining transmission. These findings highlight the importance of coordinated actions to tackle multi-drug resistant organisms.