Difei Academic丨WGS explores the resistance mechanism of multi-drug-resistant Klebsiella pneumoniae

Introduction

In September 2023, the respiratory department team of Xuzhou First People's Hospital cooperated with Difei Medical toBMC Microbiology(IF=4.2)The magazine publishes research papers.This article performed whole-genome sequencing (WGS) on 18 clinical multidrug-resistant (MDR-Kp) strains of Klebsiella pneumoniae, analyzed their resistance genes and resistance mechanisms, and evaluated the relationship between this study strain and strains in public databases through phylogenetic analysis. sequence homology between.As a co-author, Diffei Medical participated in the data analysis and article writing of this study.

Research Background

Klebsiella pneumoniae is a Gram-negative bacterium belonging to the Enterobacteriaceae family. Common clinical manifestations of its infection include pneumonia, urinary tract infection, bloodstream infection, and wound infection.Although Klebsiella pneumoniae is generally considered an opportunistic pathogen in hospital-acquired infections and infections in immunocompromised hosts, highly virulent and multidrug-resistant (MDR) strains have emerged.

Data from the China Bacterial Resistance Monitoring Network (CHINET) show that,During 2005-2021, the resistance rate of Klebsiella pneumoniae to carbapenem antibacterial drugs such as imipenem and meropenem increased eightfold (3.0%~23.8%).From 2008 to 2016, the isolation rate of multidrug-resistant (MDR) strains also increased sharply from 0.3% to 3.5%.And the data shows that there are significant geographical differences in the drug resistance of Klebsiella pneumoniae in China, with the isolation rate in East China being significantly higher than other regions.Considering the clinical importance of Klebsiella pneumoniae infection and its high prevalence in East China,A deeper understanding of the mechanisms by which these emerging MDR strains acquire antibiotic resistance and the differences between strains is critical for optimal disease management.

Research methods

This study collected clinical samples from 18 patients, including sputum, urine and blood, to isolate and culture Klebsiella pneumoniae. The strain samples were analyzed using WGS sequencing for resistance genes, and antimicrobial susceptibility testing (AST) was performed in the hospital. ).The sequences of 87 common K. pneumoniae strains were downloaded from the BV-BRC database, and SNP site analysis was performed together with the WGS data of 18 samples in this study to construct a phylogenetic tree.

Research result

Antimicrobial susceptibility of clinical MDR-Kp strains

All MDR-Kp strains were tested for antimicrobial susceptibility to 40 antibiotics by AST,We observed that clinical isolates were highly resistant to β-lactam antibiotics, and all 18 lung culture isolates were resistant to aztreonam and ciprofloxacin (Table 1).At the same time, only one tested strain (1/10, 10%) was resistant to the cephalosporin antibiotics ceftazidime/avibactam, while all tested strains were sensitive to tigecycline and polymyxin B.

Table 1 Drug susceptibility test results

WGSDeciphering the resistance genes of MDR-Kp

Among the 42 potential drug resistance genes detected by whole-genome sequencing, we found that 25 of them (43.9%) were related to known drug resistance mechanisms and could be assessed by traditional drug susceptibility methods.The drug resistance genes KPC-2 and parC had the highest detection rates (14/18, 77.8%), followed by rmtB and sul2 (12/18, 66.7%).Evaluating the performance of WGS in detecting known resistance mechanisms of MDR-Kp strains, it was found that for β-lactam drugs, the sensitivity and accuracy of WGS in identifying penicillin-resistant strains were 100%, but it was not effective in predicting the resistance of Klebsiella pneumoniae to In terms of sensitivity to cephalothin and cefuroxime, the detection performance of WGS decreased by 40% (Table 2).For other commonly used antibiotics, WGS performed moderately, with an accuracy of 77.8% to 100%.

Table 2 Performance of WGS in identifying resistance mechanisms of MDR-Kp strains

Exploring the genetic variation of MDR-Kp strains across temporal and spatial scales

Using multilocus sequence typing (MLST) testing to analyze the diversity and complexity of MDR-Kp strains, a total of four sequence types (STs) were identified, of which ST11 was the predominant type (Fig. 1).This finding is consistent with other findings,It is shown that ST11 is the main cause of Klebsiella pneumoniae infection in China.

Phylogenetic analysis was performed based on single nucleotide polymorphisms (SNPs) to compare the genetic similarities and evolutionary relationships between the 18 MDR-Kp isolates in the study and 87 strains previously discovered in China. .It was found that half of the strains clustered together with strains from Hunan and Shanghai in cluster A, and 6 strains (33.3%) formed different groups in cluster B. The analysis results did not show any spatial or temporal differences in the distribution patterns of these strains.

Figure 1 Comparison of MDR-Kp strains on spatial and temporal scales

in conclusion

WGSIt is of great clinical significance to identify potential antimicrobial resistance genes in MDR-Kp strains, and the comprehensive genomic information revealed by WGS has great potential to guide clinical treatment decisions, monitor drug-resistant bacteria, and further understand bacterial resistance mechanisms.

references:

Yang J, Zhang K, Ding C, Wang S, Wu W, Liu X. Exploring multidrug-resistant Klebsiella pneumoniae antimicrobial resistance mechanisms through whole genome sequencing analysis. BMC Microbiol. 2023 Sep 2;23(1):245. doi: 10.1186 /s12866-023-02974-y. PMID: 37660028; PMCID: PMC10474722.

Compiler: Xue Leng Reviewer: Jia, Zen-Master Typesetting: Lin