Within-patient and global evolutionary dynamics of Klebsiella pneumoniae ST17

Abstract

Klebsiella pneumoniae sequence type (ST) 17 is a global problem clone that causes multidrug-resistant (MDR) hospital infections worldwide. In 2008-2009, an outbreak of MDR ST17 occurred at a neonatal intensive care unit (NICU) in Stavanger, Norway. Fifty-seven children were colonized. We observed intestinal persistence of ST17 in all of the children for up to two years after hospital discharge. Here, we investigated the within-host evolution of ST17 in 45 of those children during long-term colonization and compared the outbreak with 254 global strains. Ninety-two outbreak-related isolates were whole-genome sequenced. They had capsule locus KL25, O locus O5 and carried yersiniabactin. During within-host colonization ST17 remained stable with few single nucleotide polymorphisms, no acquisition of antimicrobial resistance (AMR) or virulence determinants, and persistent carriage of a bla _CTX-M-15-encoding IncFII(K) IncFIB(K) plasmid (pKp2177_1). The global collection included ST17 from 1993 to 2020 from 34 countries, that were from human infection (41.3%), colonization (39.3%) and respiratory specimens (7.3%), from animals (9.3%), and from the environment (2.7%). We estimate that ST17 emerged mid-to-late 19th century (1859, 95 % HPD 1763-1939) and diversified through recombinations of the K and O loci to form several sublineages, with various AMR genes, virulence loci and plasmids. There was limited evidence of persistence of AMR genes in any of these lineages. A globally disseminated sublineage with KL25/O5 accounted for 52.7 % of the genomes. It included a monophyletic subclade that emerged in the mid-1980s, which comprised the Stavanger NICU outbreak and 10 genomes from three other countries, which all carried pKp2177_1. The plasmid was also observed in a KL155/OL101 subclade from the 2000s. Three clonal expansions of ST17 were identified; all were healthcare-associated and carried either yersiniabactin and/or pKp2177_1. To conclude, ST17 is globally disseminated and associated with opportunistic hospital-acquired infections. It contributes to the burden of global MDR infections, but many diverse lineages persist without acquired AMR. We hypothesize that non-human sources and human colonization may play a crucial role for severe infections in vulnerable patients, such as preterm neonates.

Keywords: Klebsiella pneumoniae; ST17; colonization; global dynamics; in vivo evolution; infection.

Fig. 1.

Phylogeny of 92 Klebsiella pneumoniae ST17 outbreak isolates and their gene content. (a) Midpoint-rooted maximum likelihood phylogeny of the 45 NICU (orange tip) and 45 follow-up (purple) isolates from colonization and the BSI isolate (red) against the outbreak index isolate Kp2177 (green). (b) Presence (colour) or absence (white) of AMR genes as listed in the columns (blocks are coloured by drug class). (c) Presence (colour) or absence of the Kp2177 plasmids and (d) of acquired plasmid replicon markers.

Fig. 2.

Geographical distribution of Klebsiella pneumoniae ST17 genomes, their K and O loci, and reports of ST17. (a) World map highlighting countries of collection for ST17 genomes that were available for download (coloured by region as in Fig. 3) and countries with isolates reported but not included in the global dataset (coloured dark grey). The pie charts show the distribution of K and O loci per region (n, number of genomes), highlighting loci with ≥10 genomes. (b) Number of ST17 genomes by collection year (bars, coloured by KL/OL) and cumulative number (red line, secondary axis), and cumulative number of reports of ST17 in PubMed abstracts or titles (black line, secondary axis) as of November 2021.

Fig. 3.

Global phylogeny of 300 Klebsiella pneumoniae ST17 genomes. (a) Maximum likelihood tree with tips coloured by region of collection. Additionally, the Stavanger NICU outbreak genomes are coloured red and other genomes from Norway green. The three clonal expansions that were observed in ST17 are labelled. (b) Sample type and loci as indicated in the column names. The most prevalent loci are indicated in the inset legend. (c) Presence (colour) or absence (white) of genes encoding resistance to the listed antimicrobial resistance drug classes (blocks are coloured by drug class). Lighter colour in the ESBL column indicates bla _CTX-M-15. (d) Presence (colour) or absence (white) of the Kp2177 plasmids. Several plasmid replicon markers were present across ST17; these are shown in Fig. S4. More details about the metadata and genotypes are available for interactive viewing at https://microreact.org/project/kpst17. *, acquired genes and mutations.

Fig. 4.

Recombinations and K/O loci diversity. (a) Recombination counts per base calculated over non-overlapping windows of 1000 base pairs. There is a peak in the recombination count, which surrounds the K and O loci. The red arrow indicates the gene galF, which is the 5’-most K locus gene. (b) Combinations of K and O loci found among the 300 genomes. Bubbles indicate the number of genomes and are coloured by the K/O combinations as in Figs 2 and 3.