Dissemination of a single ST11 clone of OXA-48-producing Klebsiella pneumoniae within a large polyclonal hospital outbreak determined by genomic sequencing

Abstract

The population structure of a set of OXA-48-producing Klebsiella pneumoniae isolates belonging to sequence type 11 (ST11 Kp-OXA) and obtained from two hospitals in Madrid in the period from 2012 to 2015 was studied by genome sequencing. Overall, 97 ST11 Kp-OXA isolates were sequenced and their population structure and demography were studied by Bayesian phylodynamic analysis using core-genome SNVs. In total, 92 isolates were from Hospital La Paz, 57 of them from two selected units. The remaining five isolates were from different units of Hospital Doce de Octubre. Altogether, 96 out of the 97 ST11 Kp-OXA isolates could be ascribed to a single lineage that evolved into three sublineages. Demographic inference showed an expansion of the ST11 Kp-OXA in the first half of 2013 in agreement with the registered incidences. Dated phylogeny showed transmission clusters within hospital wards, between wards and between hospitals. The ST11 Kp-OXA outbreak in Hospital La Paz was largely due to the expansion of a single clone that was transmitted between different units and to Hospital Doce de Octubre. This clone diverged into three sub-lineages and spread out following a mixed mode of neutral core-genome evolution with some features of antibiotic selection, frequent large deletions and plasmid loss and gain events.

Keywords: OXA-48; OXA-48-producing Klebsiella pneumoniae; ST11; carbapenemases; genomic analysis; hospital outbreak; phylodynamics.

Fig. 1.

Bayesian inference of the demographic history of our population of ST11 Kp-OXA during the study period. Demography was reconstructed with the Beast 2.6.3 package using a relaxed lognormal clock model and a coalescent bayesian skyline prior. Calculated and drawn with Tracer v1.7.1. (a) Bayesian skyline plot of the effective population size. (b) Number of lineages over time. In both panels, the graphs show the medians and 95 % HPD intervals.

Fig. 2.

Dated phylogenetic tree of the 96 ST11 Kp-OXA isolates constructed using Bayesian inference with Beast 2.6.3. Trees were summarized as maximum clade credibility tree using TreeAnnotator v1.8.4 and then visualized with FigTree v1.4.4. The three major lineages are indicated. Highlighted: green, Vascular Surgery ward of HULP; magenta, Nephrology ward of HULP; orange, H12O. Not highlighted: isolates obtained from 18 different wards at HULP. Isolate names have been shortened for clarity.