Carbapenem resistant Enterobacteriaceae (CRE) pose an urgent risk to global human health. The dissemination of carbapenem resistance plasmids amongst human pathogens and the emergence CRE that are non-susceptible to all commercially available antibiotics threaten to return us to the pre-antibiotic era. As a result the rapid assembly and characterisation of bacterial genomes to identify critical resistance elements is of great clinical importance.
To date, obtaining complete genome sequences from second generation sequencing (SGS) data has been challenging. Although they generate more sequence, assembly using short read data can result in numerous gaps, missing data and incomplete reference sequences. However, the Pacific Biosciences Single Molecule Real-time (SMRT) sequencing platform provides an alternative approach for reconstructing complete genomes.
Here we determined the complete genome of a pandrug-resistant Klebsiella pneumoniae isolate, representing the first complete genome sequence of CRE resistant to all commercially available antibiotics. Using SMRT sequencing the precise location of acquired antibiotic resistance elements, including mobile elements carrying genes for the OXA-181 carbapenemase, were defined. Remarkably, our analysis showed that the ISEcp1-blaOXA-181 mobile element conferring resistance to carbapenem antibiotics is itself responsible for driving resistance to the last-resort antibiotic, colistin by insertional inactivation of the mgrB regulatory gene.
These findings provide the first description of pandrug-resistant CRE at the genomic level, and reveal the critical role of mobile resistance elements in accelerating the emergence of resistance to other last resort antibiotics. Furthermore, our experience with this isolate and five other CRE clinical isolates show that the SMRT platform readily produces high-quality, finished plasmid sequences that can discriminate plasmid diversity, and are indispensable for defining the genetic structure and position of complex resistance loci.