Methicillin-resistant Staphylococcus aureus (MRSA) persistently plagues hospitals worldwide. Until now, hospital (or healthcare) MRSA (HA-MRSA) was of a different lineage from MRSA found in the community. Since HA-MRSA could not survive in a non-hospital setting, this made things rather convenient. Testing for HA-MRSA was routine and the isolates, in particular one called ST22, could easily be detected.
NGS in the News
However, community-associated MRSAs (CA-MRSA) have started replacing the hospital-based varieties, calling for sequencing that can precisely determine the lineage and sources of MRSA outbreaks. One such MRSA outbreak, at a National Health Service Foundation Trust hospital in Cambridge, was identified and halted by new, next-generation sequencing techniques. It even made the BBC News in the UK. In a paper in the Lancet, Sharon Peacock of the University of Cambridge outlines her team’s efforts (the Sanger Institute also was involved) to sequence the MRSA behind the outbreak, and halt its progress.
This is where NGS comes in
The NHS Rosie Hospital in Cambridge manages around 6,000 baby deliveries each year. All infants in its special care baby unit are screened for MRSA when admitted, and every week whilst in the unit. It was this routine screening that picked up MRSA in 12 infants:
- Bacteria was cultured from swabs and plated on selective media.
- Antimicrobial susceptibility was tested against an array of antibiotics.
- Sequencing libraries were prepared from each MRSA isolate, and amplified.
- Whole genome sequencing was performed using the Illumina MiSeq sequencer.
- Sequencing pointed to a new sequence type, called ST2371, which differed from the benchmark ST22 isolate by one point mutation.
Defeating the outbreak
The sequencing results showed that the MRSAs in the 12 infants were closely related and part of the same outbreak. After two months, however, another case appeared, and analysis showed it was part of the same MRSA strain. This lapse indicated a carrier in the hospital. After tests on staff showed one asymptomatic carrier, all staff were treated, and the outbreak came to an end.
Not the first time though…
While not the first time an outbreak was identified and controlled using NGS, the incident in Cambridge highlights the growing use of NGS techniques in clinical settings, as the cost of sequencing drops (bacterial sequences here cost £50 pounds per organism) and results arrive in hours. In August, the U.S. National Institutes of Health Clinical Center in Maryland used a Roche 454 sequencer from the conveniently located National Human Genome Research Institute to identify a strain of Klebsiella pneumoniae that, it turned out, was being passed through the hospital by living in sink drains.
You can watch the BBC News report here.