Hybrid Sequencing-Based Genomic Analysis of Klebsiella pneumoniae from Urinary Tract Infections Among Inpatients at a Tertiary Hospital in Beijing

Abstract

Background

Urinary tract infection (UTI) associated with Klebsiella pneumoniae poses a serious threat for inpatients. This study aimed to describe the genomic characteristics of K. pneumoniae causing UTI in a tertiary-care hospital in Beijing, China.

Methods

A total of 20 K. pneumoniae strains collected from 2020 to 2021 were performed whole-genome sequencing. The Antibiotic susceptibility of 19 common antimicrobial agents was tested against all strains. The multi-locus sequence types (MLSTs) and serotypes were determined from the WGS data. De novo assemblies were used to identify resistance and virulence genes. The presence and characteristics of the plasmids were detected using hybrid assembly of long and short-read data.

Results

These K. pneumoniae strains were clustered into nine sequence types (STs) and twelve K-serotypes. All the carbapenem-resistant K. pneumoniae (CRKP) strains acquired carbapenemase bla_KPC-2 (n=7). Two CRKP strains exhibited increased resistance to Polymyxin B with MIC ≥ 4 mg/L due to insertion of an IS5-like sequence in the mgrB gene, and they were also involved in a transmission event in Intensive Care Unit. Long-read assemblies identified many plasmids co-carrying multiple replicons. Acquisition of a new IncM2_1 type bla_CTX-M-3 positive plasmid was observed after transfer from ICU to neurovascular surgery by comparing the two strains collected from the same patient.

Conclusion

K. pneumoniae is a significant pathogen responsible for urinary tract infections. The ST11-KL47 strain, prevalent at our hospital, exhibits a combination of high drug resistance and hypervirulence. It is imperative to enhance ongoing genomic surveillance of urinary tract infection-causing pathogens.

Keywords:

• Antimicrobial resistance
• Klebsiella pneumoniae
• urinary tract infections

Data Confidentiality Statement

In this study, patient data confidentiality was stringently upheld. Due to the retrospective nature of the research, the institutional ethics committees of the Third Medical Center, PLA General Hospital (Beijing, China) waived the requirement for informed consent from individual patients. All methods were conducted in compliance with the relevant regulations and guidelines outlined in the Declaration of Helsinki. We have implemented strict protocols to protect patient confidentiality throughout the process, including during the analysis and dissemination of the genomic data obtained from the bacterial isolates causing urinary tract infections in the studied population.

Author Contributions

All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, or in all these areas; took part in drafting, revising or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work.

Disclosure

The authors declare no conflicts of interest in this work.

Additional information

Funding

This work was supported by grants from National Key Research and Development Program of China (Grant No. 2023YFC2604400), the National Science and Technology Major Project (Grant No. 2018ZX10305410) and Chinese National Natural Science Foundation (Grant No. 31900151).