Genomic analysis of carbapenemase-producing Enterobacteriaceae in Queensland reveals widespread transmission of bla IMP-4 on an IncHI2 plasmid

Abstract

Carbapenemase-producing <i>Enterobacteriaceae</i> (CPE) are an increasingly common cause of healthcare-associated infections and may occasionally be identified in patients without extensive healthcare exposure. <i>bla</i>_IMP-4 is the most frequently detected carbapenemase gene in <i>Enterobacteriaceae</i> within Australia, but little is known about the mechanisms behind its persistence. Here we used whole genome sequencing (WGS) to investigate the molecular epidemiology of <i>bla</i>_IMP-4 in Queensland, Australia. In total, 107 CPE were collected between 2014 and 2017 and sent for WGS on an Illumina NextSeq500. Resistance genes and plasmid types were detected using a combination of read mapping and nucleotide comparison of <i>de novo</i> assemblies. Six isolates were additionally sequenced using Oxford Nanopore MinION to generate long-reads and fully characterize the context of the <i>bla</i>_IMP-4 gene. Of 107 CPE, 93 carried the <i>bla</i>_IMP-4 gene; 74/107 also carried an IncHI2 plasmid, suggesting carriage of the <i>bla</i>_IMP-4 gene on an IncHI2 plasmid. Comparison of these isolates to a previously characterized IncHI2 plasmid pMS7884A (isolated from an <i>Enterobacter hormaechei</i> strain in Brisbane) suggested that all isolates carried a similar plasmid. Five of six representative isolates sequenced using Nanopore long-read technology carried IncHI2 plasmids harbouring the <i>bla</i>_IMP-4 gene. While the vast majority of isolates represented <i>E. hormaechei</i>, several other species were also found to carry the IncHI2 plasmid, including <i>Klebsiella</i> species, <i>Escherichia coli</i> and <i>Citrobacter</i> species. Several clonal groups of <i>E. hormaechei</i> were also identified, suggesting that persistence of <i>bla</i>_IMP-4 is driven by both presence on a common plasmid and clonal spread of certain <i>E. hormaechei</i> lineages.