A pilot study of rapid benchtop sequencing ofStaphylococcus aureusandClostridium difficilefor outbreak detection and surveillance
Eyre DW., Golubchik T., Gordon NC., Bowden R., Piazza P., Batty EM., Ip CLC., Wilson DJ., Didelot X., O'Connor L., Lay R., Buck D., Kearns AM., Shaw A., Paul J., Wilcox MH., Donnelly PJ., Peto TEA., Walker AS., Crook DW.
ObjectivesTo investigate the prospects of newly available benchtop sequencers to provide rapid whole-genome data in routine clinical practice. Next-generation sequencing has the potential to resolve uncertainties surrounding the route and timing of person-to-person transmission of healthcare-associated infection, which has been a major impediment to optimal management.DesignThe authors used Illumina MiSeq benchtop sequencing to undertake case studies investigating potential outbreaks of methicillin-resistantStaphylococcus aureus(MRSA) andClostridium difficile.SettingIsolates were obtained from potential outbreaks associated with three UK hospitals.ParticipantsIsolates were sequenced from a cluster of eight MRSA carriers and an associated bacteraemia case in an intensive care unit, another MRSA cluster of six cases and two clusters ofC difficile. Additionally, allC difficileisolates from cases over 6 weeks in a single hospital were rapidly sequenced and compared with local strain sequences obtained in the preceding 3 years.Main outcome measureWhole-genome genetic relatedness of the isolates within each epidemiological cluster.ResultsTwenty-six MRSA and 15 C difficileisolates were successfully sequenced and analysed within 5 days of culture. Both MRSA clusters were identified as outbreaks, with most sequences in each cluster indistinguishable and all within three single nucleotide variants (SNVs). Epidemiologically unrelated isolates of the samespa-type were genetically distinct (≥21 SNVs). In bothC difficileclusters, closely epidemiologically linked cases (in one case sharing the same strain type) were shown to be genetically distinct (≥144 SNVs). A reconstruction applying rapid sequencing inC difficilesurveillance provided early outbreak detection and identified previously undetected probable community transmission.ConclusionsThis benchtop sequencing technology is widely generalisable to human bacterial pathogens. The findings provide several good examples of how rapid and precise sequencing could transform identification of transmission of healthcare-associated infection and therefore improve hospital infection control and patient outcomes in routine clinical practice.