Whole Genome Sequence Analysis of the First Australian OXA-48-Producing Outbreak-Associated Klebsiella pneumoniae Isolates: The Resistome and In Vivo Evolution

Abstract

Whole genome sequencing was used to characterize the resistome of intensive care unit (ICU) outbreak-associated carbapenem-resistant K. pneumoniae isolates. Importantly, and of particular concern, the carbapenem-hydrolyzing β-lactamase gene bla OXA-48 and the extended-spectrum β-lactamase gene bla CTX-M-14, were identified on a single broad host-range conjugative plasmid. This represents the first report of bla OXA-48 in Australia and highlights the importance of resistance gene surveillance, as such plasmids can silently spread amongst enterobacterial populations and have the potential to drastically limit treatment options. Furthermore, the in vivo evolution of these isolates was also examined after 18 months of intra-abdominal carriage in a patient that transited through the ICU during the outbreak period. Reflecting the clonality of K. pneumoniae, only 11 single nucleotide polymorphisms (SNPs) were accumulated during this time-period and many of these were associated with genes involved in tolerance/resistance to antibiotics, metals or organic solvents, and transcriptional regulation. Collectively, these SNPs are likely to be associated with changes in virulence (at least to some extent) that have refined the in vivo colonization capacity of the original outbreak isolate.

Dominance of IMP-4-Producing Enterobacter cloacae among Carbapenemase-Producing Enterobacteriaceae in Australia

“…In addition, we reveal three novel STs of K. pneumoniae. There are very scarce data on STs of K. pneumoniae in Australia apart from STs of imported carbapenemase-producing K. pneumoniae isolates (6,7).…”

First Report of an OXA-48-Producing Multidrug-Resistant Proteus mirabilis Strain from Gaza, Palestine

“…1). A BLAST search against all completely sequenced bla OXA-48 -harboring plasmids in GenBank (http://www.ncbi.nlm.nih.gov/GenBank/) indicated that pOXA48-PM is closely related to other bla OXA-48 -harboring IncL/M plasmids, including pOXA-48 (14), pKPoxa-48N1 (15), and pJEG011 (16) (Fig. 1).…”

“…1). It displayed the highest query coverage (97%) and overall nucleotide identity (99%) to pJEG011, a bla OXA-48 -harboring IncL/M plasmid from a K. pneumoniae ST101 strain (Kp002) isolated in Australia (16).…”

IS 1R -Mediated Plasticity of IncL/M Plasmids Leads to the Insertion of bla OXA-48 into the Escherichia coli Chromosome

“…(5). Their emergence is mediated by the rapid spread of strains containing broad-host-range conjugative IncL/M plasmids (6)(7)(8) harboring bla OXA-48 located within the Tn1999-type composite transposon (6,(9)(10)(11). The plasmid implicated in the diffusion of bla OXA-48 was a widespread 62-kb IncL/M plasmid (6).…”

“…The plasmid implicated in the diffusion of bla OXA-48 was a widespread 62-kb IncL/M plasmid (6). Derivatives have also been reported (7,8). However, bla OXA-48 was observed in E. coli chromosomes, including in a strong killer strain (12).…”