Characterization of a CTX-M-15 Producing Klebsiella Pneumoniae Outbreak Strain Assigned to a Novel Sequence Type (1427)

Abstract

Extended-spectrum -lactamase producing Klebsiella pneumoniae have emerged as one of the major nosocomial pathogens. Between July and September 2012, a CTX-M-15 producing K. pneumoniae caused an outbreak in a university hospital in the Netherlands. The outbreak isolates were characterized and assigned to a novel sequence type (ST1427). An epidemiological link between affected patients was supported by patient contact tracing and whole-genome phylogenetic analysis. Intra-strain polymorphism was detected among multiple isolates obtained from different body sites of the index patient, which may relate to antibiotic treatment and/or host adaptation. Environmental contamination caused by the outbreak clone was found in the patient rooms even on medical equipment. The novel clone was not closely related to any known endemic/epidemic clone, but carried a set of a plasmid-borne resistance genes [bla CTX-M-15, bla TEM-1, bla OXA-1, aac(6')-Ib-cr, qnrB1, tetA(A), aac(3)-II]. Analysis of its virulence factors revealed a previously uncharacterized capsular biosynthesis region and two uncharacterized fimbriae gene clusters, and suggested that the new clone was not hypervirulent. To our knowledge, this is the first outbreak report of K. pneumoniae ST1427, and our study could be of help to understand the features of this newly emerging clone.

Keywords: CTX-M-15; Klebsiella pneumoniae; extended-spectrum ß-lactamase; hospital outbreak; polymorphism; sequence type 1427; whole-genome sequencing.

Figure 1

Intra-hospital patient movements during the outbreak period. The white spot shown on the bar represents the sequenced isolate. Patient 5 (P-5) was sampled at home after being discharged from the hospital. Different wards are indicated by different colors.

Figure 2

Core-genome phylogenetic analysis of K. pneumoniae. (A) A maximum likelihood tree was constructed based on alignments of 4.4 Mb genomes which were defined as the core genomes in this study. The tree was rooted at the midpoint. The percentage of the supported bootstrap (>90) is shown. The isolates sequenced in this study are marked by dots colored red (patients involved in the outbreak), purple (environmental isolates), and blue (unrelated patients). The genomes of unmarked isolates were retrieved from GenBank. Sequence types of isolates are indicated between brackets. (B) The inset shows a close-up of the unrooted maximum likelihood phylogenetic tree of outbreak isolates based on 21 reliable SNPs as described in the text. The number of SNPs is indicated on the branches by different colors.

Figure 3

Comparison of the capsular polysaccharide synthesis (cps) region. The cps region (including conserved flanking region) of K. pneumoniae KPNIH29 (GenBank accession number: CP009863) is retrieved from GenBank. The gradients (dark to pale) of the alignment region represent the percentage of sequence identity between samples as defined by BLASTn. GT represents glycosyltransferase.