Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health

Abstract

Klebsiella pneumoniae is now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. K. pneumoniae is ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure of K. pneumoniae, so it is difficult to recognize or understand the emergence of clinically important clones within this highly genetically diverse species. Here we present a detailed genomic framework for K. pneumoniae based on whole-genome sequencing of more than 300 human and animal isolates spanning four continents. Our data provide genome-wide support for the splitting of K. pneumoniae into three distinct species, KpI (K. pneumoniae), KpII (K. quasipneumoniae), and KpIII (K. variicola). Further, for K. pneumoniae (KpI), the entity most frequently associated with human infection, we show the existence of >150 deeply branching lineages including numerous multidrug-resistant or hypervirulent clones. We show K. pneumoniae has a large accessory genome approaching 30,000 protein-coding genes, including a number of virulence functions that are significantly associated with invasive community-acquired disease in humans. In our dataset, antimicrobial resistance genes were common among human carriage isolates and hospital-acquired infections, which generally lacked the genes associated with invasive disease. The convergence of virulence and resistance genes potentially could lead to the emergence of untreatable invasive K. pneumoniae infections; our data provide the whole-genome framework against which to track the emergence of such threats.

Keywords: Klebsiella pneumoniae; antimicrobial resistance; genomics; population structure; virulence.

Fig. 1.

The phylogroups and pangenome of K. pneumoniae. (A) Split network of 328 K. pneumoniae genomes with phylogroups highlighted. (B) Pangenome accumulation curves. (C) PCA analysis based on the presence of common (5–95% prevalence) accessory genes.

Fig. 2.

Population structure of the K. pneumoniae KpI phylogroup. (A) Phylogeny of core gene SNPs. Branch colors indicate bootstrap support according to the legend provided in the figure. Black leaves indicate bovine isolates. Lineages with more than one genome are highlighted in alternating colors and labeled by sequence type. Rh, rhinoscleromatis. (B) Rarefaction curves show the accumulation of KpI lineages in each country, labeled with Simpson’s diversity index (1-D) on a scale of 0–1 (0 = no diversity, i.e., all isolates are in same lineage; 1 = total diversity, i.e., every isolate is in a different lineage).

Fig. 3.

Virulence genes in human K. pneumoniae KpI isolates. (A) Frequency of gene clusters among KpI isolated from different human sources. Invasive, isolated from a normally sterile site; noninvasive, associated with infections and isolated from respiratory, urinary tract, or wound infections in the absence of bacteremia; carriage, isolated in the absence of symptoms. OR, odds ratio for association between the presence of the gene cluster and invasive infection vs. others; P values were calculated using Fisher’s exact test. (B) Number of KpI in each sample group, colored to indicate the total number of siderophore gene clusters in each isolate. Community-acquired, isolated ≤48 h after hospital admission; hospital-acquired, isolated >48 h after admission.

Fig. 4.

AMR genes in KpI isolates. (A) Number of acquired AMR genes per isolate. (B) Frequency of individual AMR genes in human isolates by hospital status (black) or by infection status (blue). (C) Number of acquired AMR genes per isolate for different classes of human-associated isolates. P values were calculated using the Wilcoxon test. For boxplots, numbers indicate average numbers within each group.