A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs

Abstract

Background: Members of the Klebsiella pneumoniae species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC are common in non-human niches, but the clinical relevance of these populations is disputed.

Methods: In this study, we analysed 3255 whole-genome sequenced isolates from human, animal and marine sources collected in Norway between 2001 and 2020. We used population genomics in a One Health context to assess the diversity of strains, genes and other clinically relevant genetic features within and between sources. We further explored niche-enriched traits using genome-wide association studies and investigated evidence of spillover and connectivity across the KpSC populations from the three niches.

Results: We found that the KpSC populations in different niches were distinct but overlapping. Overall, there was high genetic diversity both between and within sources, with nearly half (49%) of the genes in the accessory genome overlapping the ecological niches. Further, several sublineages (SLs) including SL17, SL35, SL37, SL45, SL107 and SL3010 were common across sources. There were few niche-enriched traits, except for aerobactin-encoding plasmids and the bacteriocin colicin a, which were associated with KpSC from animal sources. Human infection isolates showed the greatest connectivity with each other, followed by isolates from human carriage, pigs, and bivalves. Nearly 5% of human infection isolates had close relatives (≤22 substitutions) amongst animal and marine isolates, despite temporally and geographically distant sampling of these sources. There were limited but notable recent spillover events, including the movement of plasmids encoding the virulence locus iuc3 between pigs and humans.

Conclusions: Our large One Health genomic study highlights that human-to-human transmission of KpSC is more common than transmission between ecological niches. Still, spillover of clinically relevant strains and genetic features between human and non-human sources does occur and should not be overlooked. Infection prevention measures are essential to limit transmission within human clinical settings and reduce infections. However, preventing transmission that leads to colonisation, e.g. from direct contact with animals or via the food chain, could also play an important role in reducing the KpSC disease burden.

Keywords: Klebsiella pneumoniae species complex; AMR; Ecology; GWAS; Genomics; One Health; Transmission; Zoonotic transmission.

Fig. 1

Key characteristics of the 3255 Klebsiella pneumoniae species complex (KpSC) isolates. A Distribution of genomes by source, with bars coloured by niche (inset legend), and shaded to indicate sequencing type (lighter for short-read only, darker for short- and long-read). Note that the x-axis is broken due to the large number of genomes from human infections. B KpSC species (inset legend) distribution by source. C Summary of clinically relevant features, showing the presence (bubble) of antimicrobial resistance determinants, virulence determinants, heavy metal- and thermoresistance operons/genes, and plasmid replicon markers across the sources. In B and C, the bubble size corresponds to the percentage of isolates with these features, with the number of isolates shown beside each bubble. Abbreviations: AMR Antimicrobial resistance, MDR multidrug resistance

Fig. 2

Heavy metal- and thermoresistance by niche. The proportion of genomes in the human, animal and marine niches that carried heavy metal resistance operons and thermoresistance genes. Statistical comparisons were performed with Chi-squared tests. Significance levels are indicated in the plot as follows: * P < 0.05, ** P < 0.01, *** P < 0.001, ns P ≥ 0.05

Fig. 3

Comparison of the pangenome across niches. A Overall counts of core and accessory genes, in total and by niche. A panstripe analysis indicated no significant differences in gene gain or loss rates across the niches, but the human niche had a higher rate of rare genes observed at the tips of the phylogeny (tip; P < 0.001 when compared with animal genomes, and P < 0.05 compared with marine genomes), which could be driven by a combination of an increased number of highly mobile or singleton genes present in the human niche in addition to technical variation of the annotation algorithm. B Euler diagram showing presence and overlap of the 44,614 unique genes in the pangenome across the niches. C Pairwise Jaccard distances of accessory genes within each source. D Between-source pairwise Jaccard distances of accessory genes. For each source, the Jaccard distance of each genome was compared with the distance in human infection genomes to compare diversity between sources. In C and D, black points indicate median values

Fig. 4

Niche-associated genetic features identified through genome-wide association studies (GWAS). A A heatmap showing the presence of significantly associated genetic features (rows), among the 2456 Klebsiella pneumoniae genomes from humans and animals (columns), coloured by niche (inset legend). All features were positively associated with the animal niche. B Proportions of genomes with genetic features by niche and C source. The total number of K. pneumoniae genomes per niche and source are indicated on top of the columns. D Annotation of genetic features. See Additional file 2: Table S6 and Additional file 3: Fig. S11 for more detail. Genes annotated with more than one name are separated by a semicolon, unitigs found in multiple genes are separated by a slash

Fig. 5

Strain-sharing within and between ecological niches and sources. A Venn-diagram showing the distribution of 857 sublineages (SLs) across human, animal and marine niches. In total, 107 SLs were present in ≥ 2 niches. B Distribution of pairwise single nucleotide polymorphism (SNP) distances, grouped by genome-pairs within the same niche (orange) and between niches (purple), showing distances up to 1000 SNPs. C Connections between sources. The proportion of human infection genomes (y-axis) that were connected to one of the other sources, by the number of pairwise SNPs (x-axis). D Strain-sharing links (clusters of genomes sharing ≤ 22 SNPs) between source pairs, as indicated on the x- and y-axes. The yellow shading highlights within-source clusters, and the purple highlights the cross-niche clusters