Article Text

A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance
  1. David W Eyre1,2,
  2. Tanya Golubchik2,3,
  3. N Claire Gordon1,2,
  4. Rory Bowden2,3,4,
  5. Paolo Piazza4,
  6. Elizabeth M Batty2,3,
  7. Camilla L C Ip2,3,
  8. Daniel J Wilson1,4,
  9. Xavier Didelot2,3,
  10. Lily O'Connor1,5,
  11. Rochelle Lay5,
  12. David Buck4,
  13. Angela M Kearns6,
  14. Angela Shaw7,
  15. John Paul8,
  16. Mark H Wilcox9,
  17. Peter J Donnelly4,
  18. Tim E A Peto1,2,5,
  19. A Sarah Walker1,2,10,
  20. Derrick W Crook1,2,5
  1. 1Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
  2. 2NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
  3. 3Department of Statistics, University of Oxford, Oxford, UK
  4. 4Wellcome Trust Centre for Human Genetics, Oxford, UK
  5. 5Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Trust, Oxford, UK
  6. 6Staphylococcus Reference Unit, Centre for Infections, Health Protection Agency, London, UK
  7. 7Department of Microbiology, Ashford and St. Peter's Hospitals, NHS Foundation Trust, Surrey, UK
  8. 8Health Protection Agency, Royal Sussex County Hospital, Brighton, UK
  9. 9Department of Microbiology, Leeds General Infirmary Old Medical School, Leeds Teaching Hospitals and University of Leeds, Leeds, UK
  10. 10Medical Research Council, Clinical Trials Unit, London, UK
  1. Correspondence to Dr Derrick W Crook; derrick.crook{at}


Objectives To 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.

Design The authors used Illumina MiSeq benchtop sequencing to undertake case studies investigating potential outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) and Clostridium difficile.

Setting Isolates were obtained from potential outbreaks associated with three UK hospitals.

Participants Isolates 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 of C difficile. Additionally, all C difficile isolates 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 measure Whole-genome genetic relatedness of the isolates within each epidemiological cluster.

Results Twenty-six MRSA and 15 C difficile isolates 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 same spa-type were genetically distinct (≥21 SNVs). In both C difficile clusters, 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 in C difficile surveillance provided early outbreak detection and identified previously undetected probable community transmission.

Conclusions This 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.

This is an open-access article distributed under the terms of the Creative Commons Attribution Non-commercial License, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited, the use is non commercial and is otherwise in compliance with the license. See: and

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  • The following two groups of authors contributed equally to this article: DWE, TG, NCG and RB; and TEAP, ASW and DWC.

  • To cite: Eyre DW, Golubchik T, Gordon NC, et al. A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open 2012;2:e001124. doi:10.1136/bmjopen-2012-001124

  • Contributors All authors were involved in critical review of the manuscript and have seen and approved the final version. Specific contributions as follows: study conception and design: DWC, TEAP, ASW, PJD, RB, MW and JP; sample acquisition: LO, RL, NCG, AK, AS and JP; sample sequencing: PP and DB; sequence data processing pipeline: RB, TG, EMB and CLCI; analysis of epidemiological and sequence data: DWE, TG, NCG, DJW, XD, TEAP, ASW and DWC; drafting the manuscript: DWE, NCG, TG, ASW, TEAP and DWC. The following two groups of authors contributed equally to this article, DWE, TG, NCG and RB; and TEAP, ASW and DWC. All authors had full access to all the study data and take responsibility for the integrity of the data and the accuracy of the data analysis. DWC is the guarantor.

  • Funding This study was supported by the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre and the UKCRC Modernising Medical Microbiology Consortium, the latter funded under the UKCRC Translational Infection Research Initiative supported by Medical Research Council, Biotechnology and Biological Sciences Research Council and the NIHR on behalf of the Department of Health (grant G0800778) and the Wellcome Trust (grant 087646/Z/08/Z). We acknowledge the support of Wellcome Trust core funding (grant 090532/Z/09/Z). TEAP and DWC are NIHR Senior Investigators. DWE is an NIHR Doctoral Research Fellow.

  • Competing interests All authors have completed the Unified Competing Interest form at (available on request from the corresponding author). The institution of DWC and TEAP received per-case funding from Optimer Pharmaceuticals to support fidaxomicin trial patient expenses. DWC and TEAP also received honoraria from Optimer Pharmaceuticals for participation in additional meetings related to investigative planning for fidaxomicin. MHW has received honoraria for consultancy work, financial support to attend meetings and research funding from bioMerieux, Optimer, Novacta, Pfizer, Summit, The Medicines Company, Viropharma and Astellas.

  • Ethics approval Ethical approval for sequencing S aureus and C difficile isolates from routine clinical samples and linkage to patient data without individual patient consent was obtained from Berkshire Ethics Committee (10/H0505/83) and the UK National Information Governance Board (8-05(e)/2010). The Health Protection Agency has Patient Information Advisory Group approval to hold and analyse surveillance data for public health purposes under Section 60 of the Health and Social Care Act 2001.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data sharing statement The sequences reported in this paper have been deposited in the European Nucleotide Archive Sequence Read Archive under study accession number ERP001413 (

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