Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing Enterobacterales in Victoria, Australia, 2012 to 2016

Abstract

Carbapenemase-producing Enterobacterales (CPE) are being increasingly reported in Australia, and integrated clinical and genomic surveillance is critical to effectively manage this threat. We sought to systematically characterize CPE in Victoria, Australia, from 2012 to 2016. Suspected CPE were referred to the state public health laboratory in Victoria, Australia, from 2012 to 2016 and examined using phenotypic, multiplex PCR and whole-genome sequencing (WGS) methods and compared with epidemiological metadata. Carbapenemase genes were detected in 361 isolates from 291 patients (30.8% of suspected CPE isolates), mostly from urine (42.1%) or screening samples (34.8%). IMP-4 (28.0% of patients), KPC-2 (25.3%), NDM (24.1%), and OXA carbapenemases (22.0%) were most common. Klebsiella pneumoniae (48.8% of patients) and Escherichia coli (26.1%) were the dominant species. Carbapenemase-inactivation method (CIM) testing reliably detected carbapenemase-positive isolates (100% sensitivity, 96.9% specificity), identifying an additional five CPE among 159 PCR-negative isolates (IMI and SME carbapenemases). When epidemiologic investigations were performed, all pairs of patients designated “highly likely” or “possible” local transmission had ≤23 pairwise single-nucleotide polymorphisms (SNPs) by genomic transmission analysis; conversely, all patient pairs designated “highly unlikely” local transmission had ≥26 pairwise SNPs. Using this proposed threshold, possible local transmission was identified involving a further 16 patients for whom epidemiologic data were unavailable. Systematic application of genomics has uncovered the emergence of polyclonal CPE as a significant threat in Australia, providing important insights to inform local public health guidelines and interventions. Using our workflow, pairwise SNP distances between CPE isolates of ≤23 SNPs suggest local transmission.

Genomic interrogation of the burden and transmission of multidrug-resistant pathogens within and across hospital networks

“…Note: carbapenemase-producing Enterobacterales excluded as already covered by existing state-wide genomic surveillance program [5]. …”

“…Clinical and screening isolates of six MDROs were collected from hospital inpatients: vanA vancomycin-resistant Enterococcus faecium ( vanA VRE), methicillin-resistant Staphylococcus aureus , extended-spectrum beta-lactamase (ESBL)-phenotype Escherichia coli and Klebsiella pneumoniae (ESBL-Ec and ESBL-Kp), carbapenem-resistant Acinetobacter baumannii complex (CRAb) and carbapenem-resistant Pseudomonas aeruginosa (CRPa)(Table 2). Carbapenem-resistant Enterobacterales (CPE) were excluded, as these were already collected for a comprehensive state-wide CPE surveillance program [5, 27]. Whilst vanB VRE are dominant in Australia, we elected to focus on vanA VRE as it emerged more recently in Victoria, has a greater level of associated antimicrobial resistance and costs, and could potentially be more amenable to infection control interventions.…”

“…Infections with these pathogens may be acquired in healthcare settings or in the community, and are associated with increased morbidity, mortality, length of hospital stay and healthcare costs [2-4]. Whilst many healthcare systems, including those in Australia, have successfully implemented surveillance programs for low-burden, high-impact pathogens, such as carbapenemase-producing Enterobacteriaceae (CPE)[5-10], these surveillance systems do not always comprehensively address more common MDROs, resulting in incomplete data about some MDROs frequently affecting patients, such as extended-spectrum beta-lactamase-producing E. coli (ESBL-Ec) or methicillin-resistant Staphylococcus aureus (MRSA).…”

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia

“…These data were used to identify clusters of isolates for which the genomes differed by ≤ 100 and ≤ 25 single nucleotide variants (SNVs). Isolates from the same facility and separated by ≤ 25 SNVs can be considered putative nosocomial transmission clusters [67,69,70]; distances ≤ 100 SNVs also imply descent from a recent common ancestor, but are more consistent with community or between-facility transmission, or regional spread between countries [70].…”

Genomic epidemiology of a complex, multi-species plasmid-borne blaKPC carbapenemase outbreak in Enterobacterales in the UK, 2009-2014

“…The authors concluded that there was strong geographic structuring of strains, and that the expansion of a handful of clonal lineages was predominantly responsible for the spread of carbapenemases in K. pneumoniae in Europe, with onward nosocomial transmission. Like bla KPC-3 in EuSCAPE, bla KPC-2 has also been linked with the clonal expansion of ST258 in Australia(26), where 48% of 176 K. pneumoniae isolates sequenced were bla KPC-2 -containing ST258.…”