Genomic characteristics and phylogenetic analyses of colonization and infection with carbapenem-resistant
Klebsiella pneumoniae
in multicenter intensive care units: a cohort study
Authors: Wu Yi-Le , Chu Wen-Wen , Hu Xiao-Qian , Lyu Yi-Yu , Tai Jie-Hao , Li Ruo-Jie , Huang Kai , Zhao Xue , Zhang Wen-Hui , Wang Xue-Ping , Yan Xiang , Liu Zhou , Yang Xi-Yao , Zhou Qiang , Yang Min 
Published: February 2025

ABSTRACT

Carbapenem-resistant
Klebsiella pneumoniae
(
CRKp
) poses a major threat to global public health. This study aimed to investigate the genomic characteristics and phylogenetic relatedness of colonization and infection with
CRKp
among intensive care unit (ICU) patients. A total of 61
CRKp
isolates, including 29 non-ICU-acquired and 32 ICU-acquired strains, were collected by active screening and infection culture from 16 ICUs through a multicenter cohort study. Following whole-genome sequencing (WGS), seven sequence types (STs) were identified, with ST11 (60.7%) being the most dominant, followed by ST15 (27.9%). Most strains (93.4%) carried the
bla
KPC-2 gene, while 9.8% and 3.3% of strains carried either the
bla
NDM-1 gene or both genes. A high abundance of virulence genes including
iutA
(55.7%),
rmpA
(18.0%), and
rmpA2
(52.5%) were identified, with
iutA +rmpA2
(37.7%) being the most common combination. The IncHI1B plasmid was identified in all of the 34 strains carrying the detected virulence genes. Furthermore, results from cgMLST analysis revealed 10 clusters with highly homogeneous
CRKp
strains, from which the potential interregional and intrahospital spread of
CRKp
were hypothesized. Here, this study reveals the widespread distribution of
CRKp
as well as locally specific strains in different regions of Anhui Province. The observed high abundance of virulence genes requires additional attention and continued monitoring. Taken together, these findings highlight the need for coordinated efforts between healthcare facilities and networks to aid
CRKp
control strategies and prevent spread. Moreover, we emphasize the importance of WGS in revealing additional insights, thus improving epidemiological studies and transmission control of
CRKp
.

IMPORTANCE

Carbapenem-resistant
K. pneumoniae
(
CRKp
) has spread rapidly to different parts of the world and poses a serious threat to global health. High genetic diversity in
CRKp
can introduce complexities in disease treatment and management. Intensive care unit (ICU) patients are more susceptible to acquire
CRKp
infections. However, most
CRKp
studies have focused on strains isolated from infections, rather than cases of asymptomatic
CRKp
colonization. This study analyzed clinical
CRKp
isolates from ICU patients as well as isolate cases of active colonization screening. Findings reveal the genetic diversity of
CRKp
in different regions of Anhui Province, emphasizing the necessity for a more comprehensive investigation of the genomic characteristics and phylogenetic relatedness of
CRKp
in different regions. Data regarding antimicrobial resistance genes, virulence genes, and genetic relatedness will improve the understanding of the potential risk of
CRKp
to public health and aid guidance for prevention and control of
CRKp
.