Prevalence and Distribution Characteristics of blaKPC-2 and blaNDM-1 Genes in Klebsiella pneumoniae

Abstract

Background: Carbapenem-resistant Klebsiella pneumoniae infections have caused major concern and posed a global threat to public health. As bla_KPC-2 and bla_NDM-1 genes are the most widely reported carbapenem resistant genes in K. pneumonia, it is crucial to study the prevalence and geographical distribution of these two genes for further understanding of their transmission mode and mechanism.

Purpose: Here, we investigated the prevalence and distribution of bla_KPC-2 and bla_NDM-1 genes in carbapenem-resistant K. pneumoniae strains from a tertiary hospital and from 1579 genomes available in the NCBI database, and further analyzed the possible core structure of bla_KPC-2 or bla_NDM-1 genes among global genome data.

Materials and methods: K. pneumoniae strains from a tertiary hospital in China during 2013-2018 were collected and their antimicrobial susceptibility testing for 28 antibiotics was determined. Whole-genome sequencing of carbapenem-resistant K. pneumoniae strains was used to investigate the genetic characterization. The phylogenetic relationships of these strains were investigated through pan-genome analysis. The epidemiology and distribution of bla_KPC-2 and bla_NDM-1 genes in K. pneumoniae based on 1579 global genomes and carbapenem-resistant K. pneumoniae strains from hospital were analyzed using bioinformatics. The possible core structure carrying bla_KPC-2 or bla_NDM-1 genes was investigated among global data.

Results: A total of 19 carbapenem-resistant K. pneumoniae were isolated in a tertiary hospital. All isolates had a multi-resistant pattern and eight kinds of resistance genes. The phylogenetic analysis showed all isolates in the hospital were dominated by two lineages composed of ST11 and ST25, respectively. ST11 and ST25 were the major ST type carrying bla_KPC-2 and bla_NDM-1 genes, respectively. Among 1579 global genomes data, 147 known ST types (1195 genomes) have been identified, while ST258 (23.6%) and ST11 (22.1%) were the globally prevalent clones among the known ST types. Genetic environment analysis showed that the ISKpn7-dnaA/ISKpn27 -bla_KPC-2-ISkpn6 and bla_NDM-1-ble-trpf-nagA may be the core structure in the horizontal transfer of bla_KPC-2 and bla_NDM-1 , respectively. In addition, DNA transferase (hin) may be involved in the horizontal transfer or the expression of bla_NDM-1 .

Conclusion: There was clonal transmission of carbapenem-resistant K. pneumoniae in the tertiary hospital in China. The prevalence and distribution of bla_KPC-2 and bla_NDM-1 varied by countries and were driven by different transposons carrying the core structure. This study shed light on the genetic environment of bla_KPC-2 and bla_NDM-1 and offered basic information about the mechanism of carbapenem-resistant K. pneumoniae dissemination.

Keywords: *blaNDM-1; Klebsiella pneumoniae; bioinformatics; blaKPC-2.

Figure 1

Results of phylogenetic trees; Bayesian classification, MIC test, and ARGs identification of 19 samples from ICU rooms. Sampling time, lineages of hierBAPS, presence/absence of bla_KPC-2 and bla_NDM-1 are annotated as colored bars next to the isolate number. (A) Phylogenetic trees of high abundance species from core genome alignments. Maximum likelihood phylogenetic trees from core genome alignments; Tree branches are colored by MLST types. (B) Results of MIC test; class of antibiotics and resistance strength are annotated as colored bars next to the main heatmap. (C) Results of ARGs identification; presence/absence of ARGs are annotated as colored bars next to the main heatmap.

Figure 2

Distribution of K. pneumoniae and carbapenem resistance genes (CRGs) (bla_KPC-2 and bla_NDM-1); Types of CRGs are annotated by different colors. All STs are based on the Pubmlst MLST scheme. (A) Distribution of carbapenem resistance genes of CRGs in K. pneumoniae genomes from NCBI in the ST type with large abundance or with bla_KPC-2 or bla_NDM-1 for display. (B) Geographical distribution of CRGs in K. pneumoniae genomes from NCBI (only countries with ≥1 CRG-containing genome are shown). Countries are shown on the y-axis and the numbers on the x-axis indicate the number of CRGs. (C) Distribution of carbapenem resistance genes of CRGs in K. pneumoniae genomes from Shunde hospital.

Figure 3

Geographic distribution and MLST typing results of K. pneumoniae samples in different countries and regions of genomic samples from NCBI and Shunde hospital; The color shades on the map represent the number of samples. The pie chart link with black line to China on the main map represents the MLST typing results of samples from Shunde hospital. The pie chart next to the main map represents MLST typing results of 13 countries.

Figure 4

bla_KPC-2 and bla_NDM-1 gene environment and comparison of some representative samples; BLAST similarity values and the types of different CDS are annotated by different colors next to the main chart (A) Gene environment of bla_KPC-2 (B) Gene environment of bla_NDM-1.