Hospital transmission of carbapenemase-producing Enterobacterales (CPE) and Salmonella enterica – two outbreaks linked by using whole genome sequencing (WGS)

Dr Andie S. Lee1,2, Elizabeth White3, Jacquelyn Petty3, Dr Rebecca J. Davis1,2, Dr Ken Liu2,4, Dr Alicia G. Beukers1, A/Prof Sebastiaan  van Hal1

1Departments of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia,
2Sydney Medical School, University of Sydney, Sydney, Australia,
3Infection Prevention and Control Department, Royal Prince Alfred Hospital, Sydney, Australia,
4AW Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Sydney, Australia


Carbapenemase-producing Enterobacterales (CPE) outbreaks cause significant morbidity and mortality. Detection of transmission using conventional microbiology is suboptimal as plasmid-encoded CPE resistance genes can move between bacterial species. We aimed to fully characterise a CPE outbreak using whole genome sequencing (WGS).


This study was conducted at Royal Prince Alfred Hospital where isolates of CPE and other organisms associated with healthcare-associated outbreaks routinely undergo WGS. From January 2018, two clusters were recognised: 1) CPE carrying the NDM gene and 2) healthcare-associated Salmonella.  Preliminary information linked these two outbreaks as a single Salmonella isolate had acquired a NDM gene.  WGS was performed and analysed using an in-house pipeline.


WGS confirmed that 4 Klebsiella pneumoniae isolates clustered together consistent with an outbreak. Similarly, three Salmonella isolates were clonal and distinct from community isolates, confirming healthcare-associated acquisition. Plasmid analysis confirmed that the NDM gene in the Salmonella isolate was almost identical to those found in the Klebsiella isolates. A subsequent screening swab collected from the patient harbouring the Salmonella NDM also detected a NDM positive Klebsiella pneumoniae, consistent with plasmid transfer between bacterial species in the same patient. WGS data were used to refine the suspected epidemiological transmission links.


CPE transmission may be missed using traditional microbiological methods. Gene- rather than organism-based surveillance for CPE is recommended. The high discriminatory power of WGS provides further valuable information for outbreak investigations, facilitating targeted and effective interventions.


Dr Andie Lee is an Infectious Diseases Physician and Microbiologist at Royal Prince Alfred Hospital in Sydney. She has a clinical and research interest in multi-resistant organisms and healthcare associated infections. She is also the Clinical Adviser to the Healthcare Associated Infections Program at the Clinical Excellence Commission in NSW.


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