Genomic characteristics and phylogenetic analyses of colonization and infection with carbapenem-resistant Klebsiella pneumoniae in multicenter intensive care units: a cohort study.

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 blaKPC-2 gene, while 9.8% and 3.3% of strains carried either the blaNDM-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.