Antimicrobial resistant bacteria are one of the foremost threats to public health, particularly among hospital patients, who are disproportionately affected by multidrug-resistant organisms (MDROs), with corresponding high levels of morbidity and mortality. Whilst diagnostic microbiology laboratories can usually detect MDROs in patient samples, current microbiological methods have insufficient resolution to detect transmission and identify potential outbreaks, leading to delays in implementation of appropriate infection control measures. As whole genome sequencing becomes more feasible, we trialled the use of genomics for detection of MDRO transmission in hospitals in Melbourne, Australia.
A 15 month prospective multicentre study spanning four hospital networks was conducted. Hospital inpatients with MRSA, vanA VRE, ESBL K. pneumoniae, and ESBL+ciprofloxacin resistant E. coli from clinical or screening cultures were eligible; samples were sequenced at the central reference laboratory (Illumina NextSeq), and clinical data was collected contemporaneously. Multilocus sequence typing, antimicrobial resistance gene detection, and phylogenetic analyses were performed. Interim reporting sessions with participating hospitals were conducted to educate on genomics, communicate results, evaluate clinical utility, and identify any changes made to infection control measures arising from genomics results.
Putative transmission events associated with all organisms and numerous sequence types were detected both within and between hospital networks, although relative numbers of MDROs varied. Hospitals used the detailed transmission data provided by genomics for focused outbreak investigations, to implement targeted infection prevention and control measures. Genomic evidence of transmission was useful for advocating for enhanced infection control resources.
Genomics can provide high-resolution discrimination between bacterial sequences and, in combination for high-quality epidemiologic data, can inform hospital infection prevention and control. This is integral to limiting the spread of MDROs in hospital. ‘Ruling-out’ isolates from potential outbreaks also saved infection control resources. Future challenges include improving turnaround times, streamlining transmission analyses, and developing creative ways to communicate genomic data to clinicians and hospitals.