Genome Sequencing and Comparative Genomic Analysis of Multidrug-Resistant Klebsiella pneumoniae in a Neurological Intensive Care Unit

Abstract

Background: Klebsiella pneumoniae is an important cause of nosocomial infections and community-acquired pneumonia. However, the evolutionary convergence of multidrug resistance (MDR) and virulence factors undoubtedly increases the risk of infection and lethality of K. pneumoniae, especially in intensive care units. How to effectively prevent and correctly treat K. pneumoniae infections has become a significant challenge for healthcare professionals. Objective: To assess multidrug-resistant Klebsiella pneumoniae (MDR-KP) resistance patterns in a Neurological ICU (NICU) and guide infection control strategies. Methods: A total of 156 non-repetitive K. pneumoniae isolates from the NICU underwent strain identification and antimicrobial susceptibility testing. Six MDR-KP isolates were selected for whole genome sequencing (WGS) using high-throughput sequencing technologies, followed by comparative genomics and phylogenetic analysis. Results: Antimicrobial susceptibility testing revealed that the 6 MDR-KP strains exhibited a resistance rate of 59% to 21 commonly used antibiotics, with seven antibiotics showing a resistance rate of 100%. The sequencing results provided basic genomic information such as genome size and GC content for the 6 MDR-KP strains. Six different sequence (ST)-capsular locus (KL) types were identified: ST11-KL47, ST11-KL64, ST23-KL1, ST25-KL2, ST412-KL57, and ST753-KL3. All strains carried multiple resistance genes and virulence factors. Among them (No. P14, P97) are carbapenem-resistant K. pneumoniae (CRKP) strains, which should attract our sufficient attention. Phylogenetic analysis showed that P116 was more closely related to the reference strain KP20, and P14 had the highest affinity to P97. Conclusion: NICU K. pneumoniae could colonise patients and the ward air environment for a long time, suggesting that there may be a similar evolutionary or direct transmission relationship between strains. The ST11-KL47 and ST11-KL64 phenotypes were the dominant clone types of CRKP in China, suggesting that the ST11-type MDR-KP should be the focus of infection prevention and control in our hospital. Comparative genomics revealed homology and genetic variability of NICU K. pneumoniae.