A major problem confronting physicians, nurses, and other hospital personnel is transmission of pathogens among inpatients or between medical personnel and inpatients (in either direction).  A crucial component in efforts to control such infectious outbreaks in hospital wards is determining whether particular cases are linked by instances of person-to-person transmission.  Standard methods of analysis involve epidemiological data, determinations of antibiotic sensitivities, and evaluation (multilocus sequence typing or MLST) of alleles at a limited number (<1%) of bacterial loci.  A recent paper by Harris et al. in Lancet Infect Dis. (2012) offers results that support the use of whole-genome sequencing (WGS), which covers >95% of loci, of infectious isolates from individuals that might reasonably be thought to be part of an outbreak.  In this particular study, focused on infection by methicillin-resistant Staphylococcus aureus (MRSA), both inpatients and outpatients were likely involved.

There are several interesting aspects to this study that began when, in 2011, the authors identified three simultaneous cases of MRSA carriage in the special care baby unit (SCBU) at the Cambridge University Hospitals National Health Service Foundation Trust.  The hospital infection-control specialists identified thirteen other SCBU patients with at least one positive screen for MRSA.  Nevertheless, using conventional approaches to analysis of the putative outbreak, the team was unable to confirm an outbreak stretching over the relevant time period.   Application of whole-genome sequencing to MRSA isolates permitted the identification of a plausible network of infection transmission events corresponding to an outbreak.

There were several key findings associated with the whole-genome sequencing data.  First, a new sequence type (ST) of MRSA, ST2371, was identified.  ST2371 is related to ST22, a strain of MRSA known to be involved in approximately 80% of hospital-associated MRSA infections in the United Kingdom.  However, ST2371 appears to have acquired genes encoding an exotoxin, Panton-Valentine leucocidin (PVL), which were not found in ST22.

Second, using the analysis based on whole-genome sequencing the authors were able to demonstrate that transmission events occurred from infants in the SCBU to their mothers, among mothers in a post-natal hospital unit, and from mothers to their partners in the outside community.  The result of applying WGS as part of a prospective longitudinal surveillance program in the SCBU was that a new MRSA infection, after a deep clean of the SCBU and an absence of new SCBU MRSA cases over more than two months, was inferred to be part of the outbreak.  The authors therefore screened SCBU staff members for MRSA, and one member of the staff, out of 154, was found to be positive for MRSA.  WGS confirmed that the staff member carried the outbreak MRSA, ST2371.  These results suggested to the infection-control team that this staff member reintroduced the outbreak-associated strain to at least one patient in the SCBU.

One aspect of the of evidence that the authors used to suggest that the member of the SCBU staff infected one or more infants and not the reverse is that multiple isolates of the staff member were subjected to WGS and were shown to possess significant genetic differences.  The authors reasoned that this diversity in a single host, the staff member, implicated a relatively long history of infection.  Furthermore, some of the colonies from the staff member seemed most closely related (phyogenetically) to the MRSA isolate of the last SCBU outbreak patient and other colonies were most closely related to MRSA isolates from SCBU patients infected early in the outbreak.   Nevertheless, it cannot be ruled out that the vector of transmission was from SCBU patient(s) to staff member instead of the other way around (Kupferschmidt, 2012).  Unfortunately, only single MRSA isolates from SCBU patients were sequenced.

Irrespective of the direction of transmission between SCBU patients and staff member, it may be the first time that substantial genetic diversity of a bacterial pathogen within a single host has been definitively documented by WGS.  This possibility, if widespread, raises troubling questions.  For example, if substantial bacterial pathogen genetic diversity can evolve within individual patients, it could be the case that a series of transmission events involvimg different variants within a single host, would be difficult to trace back to a single source with certainty if only one isolate per patient is subjected to genetic profiling, even by WGS, as has been typical.

In conclusion, investigation of the small-scale evolution of a bacterial pathogen (i.e., molecular phylogenetic analysis) using WGS can provide clinically relevant, even invaluable, information.  Harris et al. used results from WGS to connect MRSA infections that otherwise might not have been associated with one another and to effectively intervene in an ongoing outbreak.


Harris SR, Cartwright EJ, Török ME, Holden MT, Brown NM, Ogilvy-Stuart AL, Ellington MJ, Quail MA, Bentley SD, Parkhill J, Peacock SJ. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis. 2012 Nov 9. doi:pii: S1473-3099(12)70268-2. 10.1016/S1473-3099(12)70268-2. [Epub ahead of print] PubMed PMID: 23158674.

Kupferschmidt K. Infectious diseases. Genome study helps contain MRSA outbreak–and breeds new questions. Science. 2012 Nov 23;338(6110):1019. doi: 10.1126/science.338.6110.1019. PubMed PMID: 23180838.