Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

Abstract

BackgroundKlebsiella pneumoniae is a recognised agent of multidrug-resistant (MDR) healthcare-associated infections; however, individual strains vary in their virulence potential due to the presence of mobile accessory genes. In particular, gene clusters encoding the biosynthesis of siderophores aerobactin (iuc) and salmochelin (iro) are associated with invasive disease and are common amongst hypervirulent K. pneumoniae clones that cause severe community-associated infections such as liver abscess and pneumonia. Concerningly, iuc has also been reported in MDR strains in the hospital setting, where it was associated with increased mortality, highlighting the need to understand, detect and track the mobility of these virulence loci in the K. pneumoniae population.MethodsHere, we examined the genetic diversity, distribution and mobilisation of iuc and iro loci amongst 2503 K. pneumoniae genomes using comparative genomics approaches and developed tools for tracking them via genomic surveillance.ResultsIro and iuc were detected at low prevalence (< 10%). Considerable genetic diversity was observed, resolving into five iro and six iuc lineages that show distinct patterns of mobilisation and dissemination in the K. pneumoniae population. The major burden of iuc and iro amongst the genomes analysed was due to two linked lineages (iuc1/iro1 74% and iuc2/iro2 14%), each carried by a distinct non-self-transmissible IncFIBK virulence plasmid type that we designate KpVP-1 and KpVP-2. These dominant types also carry hypermucoidy (rmpA) determinants and include all previously described virulence plasmids of K. pneumoniae. The other iuc and iro lineages were associated with diverse plasmids, including some carrying IncFII conjugative transfer regions and some imported from Escherichia coli; the exceptions were iro3 (mobilised by ICEKp1) and iuc4 (fixed in the chromosome of K. pneumoniae subspecies rhinoscleromatis). Iro/iuc mobile genetic elements (MGEs) appear to be stably maintained at high frequency within known hypervirulent strains (ST23, ST86, etc.) but were also detected at low prevalence in others such as MDR strain ST258.ConclusionsIuc and iro are mobilised in K. pneumoniae via a limited number of MGEs. This study provides a framework for identifying and tracking these important virulence loci, which will be important for genomic surveillance efforts including monitoring for the emergence of hypervirulent MDR K. pneumoniae strains.Electronic supplementary materialThe online version of this article (10.1186/s13073-018-0587-5) contains supplementary material, which is available to authorized users.

Convergence of virulence and multidrug resistance in a single plasmid vector in multidrug-resistant Klebsiella pneumoniae ST15

“…The complete genome sequence resolved seven plasmids (Supplementary data 2), including a novel 346 kbp mosaic hv-MDR plasmid pKp104014_1, which harboured bla CTX-M-15 and seven additional AMR genes (Figure 1). Plasmid pKp104014_1 shares regions of homology with typical KpVP-1-type Kp IncFIB K virulence plasmids 9 , such as pK2044 (40% coverage, including iuc and rmpA2), in addition to regions of homology to IncFII K conjugative AMR plasmids (closest match: 246 kbp plasmid pKp_Goe_579-1, accession CP018313.1, from a ST147 Kp isolated in Germany, 59% coverage). The IncFII K regions include genes for conjugative transfer, suggesting the plasmid may be self-transmissible.…”

K. pneumoniaeST258 genomic variability and bacteriophage susceptibility

“…DNA libraries for whole genome sequencing (WGS) were prepared using the Nextera XT kit and sequencing was performed at the Australian Genome Research Facility (AGRF, Melbourne, Australia). De novo assembly of sequencing reads and simulated reads of NCBI reference genomes were performed as previously described (23), using our WGS analysis workflow based on publicly available tools including SPAdes 3.9.0 (24); Nullarbor 1.20 (25); Kleborate 0.2.0 (26) to confirm identity ( in silico MLST), virulence and antibiotic resistance genotypes. A maximum-likelihood recombination-free phylogenetic tree was computed using RAxML 8.2.4 (27) and Gubbins 2.2.0 (28), using a reference-based core genome alignment as an input.…”

“…The pangenome was determined using Roary version 3.11.0 (29) and used to classify regions of differences across the strain dataset, based on their contiguity and functional categories of the genes encoded. Kleborate 0.2.0 (26) was used to perform capsule typing, O antigen (LPS) serotyping and siderophore typing. Plasmid replicon identification and typing was performed using PlasmidFinder and pMLST implemented in BAP (30).…”

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

“…Fourteen distinct ybt+ICEKp variants are recognised, one of which also carries the colibactin synthesis locus (clb) 25 . In contrast, the salmochelin (iro), aerobactin (iuc) and rmpA/rmpA2 loci are usually co--located on a virulence plasmid 26,27 . These loci are much less common in the Kp population (<10% prevalence each) and until recently were rarely reported among MDR strains 3,5 .…”

“…Alternatively, the key virulence determinants themselves, or other proteins encoded on the virulence plasmid, may play a role. Two variants of the virulence plasmid predominate among hypervirulent clones and share limited homology aside from the iuc, iro and rmpA loci 27 . It seems unlikely that a siderophore system would influence DNA uptake, however it is conceivable that upregulation of capsule expression by rmpA 18,56 may play a role by exacerbating the inhibitory effect of the capsule.…”