Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones ofKlebsiella pneumoniae

Abstract

Klebsiella pneumoniae (Kp) has emerged as an important cause of two distinct public health threats: multi-drug resistant (MDR) healthcare--associated infections 1 and community--acquired invasive infections, particularly pyogenic liver abscess 2 . The majority of MDR hospital outbreaks are caused by a subset of Kp clones with a high prevalence of acquired antimicrobial resistance (AMR) genes, while the majority of community--acquired invasive infections are caused by 'hypervirulent' clones that rarely harbour acquired AMR genes but have high prevalence of key virulence loci 3-5 . Worryingly, the last few years have seen increasing reports of convergence of MDR and the key virulence genes within individual Kp strains 6 , but it is not yet clear whether these represent a transient phenomenon or a significant ongoing threat. Here we perform comparative genomic analyses for 28 distinct Kp clones, including 6 hypervirulent and 8 MDR, to better understand their evolutionary histories and the risks of convergence. We show that MDR clones are highly diverse with frequent chromosomal recombination and gene content variability that far exceeds that of the hypervirulent clones. Consequently, we predict a much greater risk of virulence gene acquisition by MDR Kp clones than of resistance gene acquisition by hypervirulent clones. Kp MDR evolution is largely driven through acquisition of AMR genes on diverse mobilisable plasmids 7 which are particularly prevalent among the subset of clones that have become globally disseminated and frequently cause hospital outbreaks 8 ; e.g. clonal group (CG) 258 which is implicated in global spread of the Kp carbapenemases 9 . Kp pathogenicity is driven by a wide array of interacting factors 10-12 that are present in all strains, including the type III fimbriae (mrk) and the surface polysaccharides (capsule and lipopolysaccharide (LPS)) 12,13 which exhibit antigenic variation between strains. The majority of hypervirulent Kp, distinguished clinically as causing invasive infections even outside the hospital setting 14 , are associated with just two 4,15 of the >130 predicted capsular serotypes 16 , K1 and K2, that are considered particularly antiphagocytic and serum resistant 15,17 . Hypervirulent Kp are also associated with high prevalence of several other key virulence factors; the rmpA/rmpA2 genes that upregulate capsule expression to generate hypermucoidy 18,19 ; the colibactin genotoxin that induces eukaryotic cell death and promotes invasion to the blood from the intestines 20,21 ; and the yersiniabactin, aerobactin and salmochelin siderophores that promote survival in the blood by enhancing iron sequestration 11,[22][23][24] . Yersiniabactin synthesis is encoded by the ybt locus, which is usually mobilised by an integrative, conjugative element known as ICEKp. It is present in 40% of the general Kp population and seems to be frequently acquired and lost from MDR clones 25 . Fourteen distinct ybt+ICEKp variants are recognised, one of which also carries the colibactin synthesis locus (c...

Hypervirulent Klebsiella pneumoniae – clinical and molecular perspectives

“…Large genomic analysis of hvKp has identified relatively low diversity of capsule types and overall genome diversity, despite the emergence of CG23 in the late 1800s . Others have speculated that there may be a barrier to horizontal gene transfer amongst hvKp clones which has largely limited acquisition of AR genes . This barrier may include the upregulation of capsule which obfuscates the conjugation machinery and lowers the efficiency of transformation leading to DNA uptake .…”

“…Others have speculated that there may be a barrier to horizontal gene transfer amongst hvKp clones which has largely limited acquisition of AR genes . This barrier may include the upregulation of capsule which obfuscates the conjugation machinery and lowers the efficiency of transformation leading to DNA uptake . In order to predict the spread of MDR in hvKp strains, it is important to understand the ecological or molecular barriers to acquisition of MDR plasmids by hvKp stains.…”

Common and distinctive genomic features of Klebsiella pneumoniae thriving in the natural environment or in clinical settings

“…The antigen types KL64, KL2, KL102, KL15 were detected in CLI and in ENV genomes, although KL64 (12/13) was significantly more frequent in the first (Fisher’s Exact test, p < 0.05). The KL1, reported to be associated to hypervirulent K. pneumoniae 22 – 24 was only detected in CLI genomes mainly of ST23 (5/6). KL2 antigens also associated with hypervirulent strains 22 – 24 were detected in 8 genomes, all ST14 (n = 7) and in ST15 (n = 1).…”

“…The KL1, reported to be associated to hypervirulent K. pneumoniae 22 – 24 was only detected in CLI genomes mainly of ST23 (5/6). KL2 antigens also associated with hypervirulent strains 22 – 24 were detected in 8 genomes, all ST14 (n = 7) and in ST15 (n = 1). In total, 10 O antigens were detected, being O1/O2v1 (55/139), O1/O2v2 (33/139), O4 (14/139) and OL101 (10/139), the most predominant (Supplementary Table 9 ).…”

Exploiting Homoplasy in Genome-Wide Association Studies to Enhance Identification of Antibiotic-Resistance Mutations in Bacterial Genomes

“…However, it remains challenging to reconstruct a global phylogeny for recombinant species such as Streptococcus pneumoniae 68 and Klebsiella pneumoniae . 69 Without a reliable phylogeny, sites located within the recombined regions may tend to look more homoplasic with respect to a global phylogeny based on SNPs across the whole genome, resulting in more false positives. Recent methods for locating chromosomal boundaries where recombination events occur during evolution may allow us to obtain more reliable trees accounting for the recombined regions 70 or to build up separate local trees for the recombined regions based on inferred recombination breakpoints.…”