Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

Abstract

SummaryBackgroundThe emergence of meticillin-resistant Staphylococcus aureus (MRSA) that can persist in the community and replace existing hospital-adapted lineages of MRSA means that it is necessary to understand transmission dynamics in terms of hospitals and the community as one entity. We assessed the use of whole-genome sequencing to enhance detection of MRSA transmission between these settings.MethodsWe studied a putative MRSA outbreak on a special care baby unit (SCBU) at a National Health Service Foundation Trust in Cambridge, UK. We used whole-genome sequencing to validate and expand findings from an infection-control team who assessed the outbreak through conventional analysis of epidemiological data and antibiogram profiles. We sequenced isolates from all colonised patients in the SCBU, and sequenced MRSA isolates from patients in the hospital or community with the same antibiotic susceptibility profile as the outbreak strain.FindingsThe hospital infection-control team identified 12 infants colonised with MRSA in a 6 month period in 2011, who were suspected of being linked, but a persistent outbreak could not be confirmed with conventional methods. With whole-genome sequencing, we identified 26 related cases of MRSA carriage, and showed transmission occurred within the SCBU, between mothers on a postnatal ward, and in the community. The outbreak MRSA type was a new sequence type (ST) 2371, which is closely related to ST22, but contains genes encoding Panton-Valentine leucocidin. Whole-genome sequencing data were used to propose and confirm that MRSA carriage by a staff member had allowed the outbreak to persist during periods without known infection on the SCBU and after a deep clean.InterpretationWhole-genome sequencing holds great promise for rapid, accurate, and comprehensive identification of bacterial transmission pathways in hospital and community settings, with concomitant reductions in infections, morbidity, and costs.FundingUK Clinical Research Collaboration Translational Infection Research Initiative, Wellcome Trust, Health Protection Agency, and the National Institute for Health Research Cambridge Biomedical Research Centre.

MLST revisited: the gene-by-gene approach to bacterial genomics

“…A popular method has been to construct phylogenies on the basis of SNPs (single-nucleotide differences among samples) that have been identified either by the mapping of short-read sequence data to a reference genome, or by aligning de novo-assembled sequences to a reference genome 37,40 . This approach has been used successfully to investigate the epidemiology and evolution of a number of single-clone pathogens or members of the same lineage [41][42][43][44][45][46][47][48][49][50][51][52] , but it is limited by its requirement for a reference sequence or whole-genome alignment 40 . The analysis of diverse or highly recombining organisms in this way will prove challenging because the number of total polymorphisms increases as the number of polymorphisms conforming to a clonal model of descent decreases (BOX 1).…”

“…This, in turn, depends on the particular question being addressed, as some questions require more discrimination among specimens than others. To use the clinical setting as an example: very high resolution is necessary for the detection of outbreaks and the investigation of within-patient variation 43 ; lower resolution is required to determine the membership of a particular clonal complex or lineage 61 ; and even lower resolution is sufficient for determining the species causing an infection 37,62,63 . The gene-bygene approach is inherently hierarchical and scalable, as fewer genes can be used for lowerresolution typing, whereas higher levels of resolution can be attained by increasing the number of genes included in the analysis.…”

“…Consequently, staphylococci have been subjected to many molecular epidemiology studies 80 , including WGS analyses [41][42][43][44][45][46]82 . Many areas of the biology and pathology of these organisms have been investigated, including their evolution (particularly the origins of MRSA) in hospitals and communities 83,84 , the spread of clones among animals and humans 85 , the dynamics of colonization and infection 86 , and outbreak detection and control 87 .…”

“…The detection and control of S. aureus outbreaks remains a high priority in health care systems [41][42][43] . The gene-by-gene approach described above can rapidly establish very highresolution relationships among isolates, as demonstrated by an analysis of isolate data from a study that described an MRSA outbreak in a special-care baby unit 43 .…”

“…Furthermore, an allele-based rMLST analysis of 669 S. aureus isolates identified 229 unique rSTs based on 51 rps loci (two para logous loci, rpsN and rpmG, were excluded for the purposes of this analysis) and resolved the isolates into lineages that corresponded to previously described clonal complexes 83,90 , also indicating genealogical relationships among the clonal complexes (FIG. 3b).The detection and control of S. aureus outbreaks remains a high priority in health care systems [41][42][43] . The gene-by-gene approach described above can rapidly establish very highresolution relationships among isolates, as demonstrated by an analysis of isolate data from a study that described an MRSA outbreak in a special-care baby unit 43 .…”