Whole genome sequencing can provide clinically relevant data on bacterial transmission within a timescale that can influence infection control and patient management.

Current laboratory techniques often cannot distinguish between methicillin-resistant Staphylococcus aureus (MRSA) isolates, but whole genome sequencing can provide precise information in a fast turnaround time, and could make a clear distinction between MRSA isolates in a way that was not previously possible.

At the Wellcome Trust Sanger Institute (Hinxton, UK) a team of scientists focused on an outbreak in a neonatal intensive care unit that had already ended. They took the samples and sequenced them as if they had been working in real time. They found they could distinguish between strains that were part of the outbreak and strains that were not, and showed that they could have identified the outbreak earlier than current clinical testing, potentially shortening the outbreak. DNA extracted from each MRSA isolate was prepared for sequencing with the use of a Nextera DNA Sample Prep Kit (Epicenter, Madison, WI, USA). Samples were pooled together and then run on an Illumina MiSeq sequencer (San Diego, CA, USA) for paired-end 150-bp sequencing.

The team constructed a list of all the MRSA genes that cause antibiotic resistance. Rapidly identifying drug resistance in MRSA strains will guide healthcare professionals to give each infected patient the most appropriate treatment possible. This also provides a powerful tool for the discovery of new drug resistance mechanisms. The use of whole genome sequencing will ultimately become part of routine health care. This study indicates that whole genome sequencing in real time will be valuable in controlling MRSA and other outbreaks in a hospital setting.

Julian Parkhill, PhD, a lead author from the Wellcome Trust Sanger Institute, said, "Distinguishing between strains is important for infection control management. Quick action is essential to control a suspected outbreak, but it is of equal importance to identify unrelated strains to prevent unnecessary ward closures and other disruptive control measures. Healthcare needs better, more efficient ways of identifying an outbreak and then processing the data."

Geoffrey P. Smith, PhD, a senior director of research at Illumina, added, "As sequencing has become increasingly accurate and comprehensive, it can be used to answer a wide range of questions. Not only could we distinguish different MRSA strains in the hospital, we were also able to rapidly characterize antibiotic resistance and toxin genes present in the clinical isolates." The study was published on June 14, 2012, in the New England Journal of Medicine (NEJM) .

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Wellcome Trust Sanger Institute
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