title: Harnessing the genome: development of a hierarchical typing scheme for meticillin-resistant Staphylococcus aureus.
abstract: A major barrier to using genome sequencing in medical microbiology is the ability to interpret the data. New schemes that provide information about the importance of sequence variation in both clinical and public health settings are required. Meticillin-resistant Staphylococcus aureus (MRSA) is an important nosocomial pathogen that is being observed with increasing frequency in community settings. Better tools are needed to improve our understanding of its transmissibility and micro-epidemiology in order to develop effective interventions. Using DNA microarray technology we identified a set of 20 binary targets whose presence or absence could be determined by PCR, producing a PCR binary typing scheme (PCR-BT). This was combined with multi-locus sequence type-based, sequence nucleotide polymorphism typing to form a hierarchical typing scheme. When applied to a set of epidemiologically unrelated isolates, a high degree of concordance was observed with PFGE (98.8 %). The scheme was able to detect the presence or absence of an outbreak strain in eight out of nine outbreak investigations, demonstrating epidemiological concordance. PCR-BT was better than PFGE at distinguishing between outbreak strains, particularly where epidemic MRSA-15 was involved. The method developed here is a rapid, digital typing scheme for S. aureus for use in both micro- and macro-epidemiological investigations that has the advantage of being suitable for use in routine diagnostic laboratories. The targets are defined and therefore the types can be defined by any platform capable of detecting the sequences used, including whole genome sequencing.
authors.affiliation: Department of Infectious Disease and Immunity, Imperial College, London, UK.|Department of Microbiology, Imperial College Healthcare NHS Trust, London, UK.
authors.forename: Madeline J
authors.initials: MJ
authors.lastname: Stone
authors.affiliation: Laboratory of Gastrointestinal Pathogens, Microbiology Services Division, Health Protection Agency, Colindale, London, UK.
authors.forename: John
authors.initials: J
authors.lastname: Wain
authors.affiliation: Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK.
authors.forename: Alasdair
authors.initials: A
authors.lastname: Ivens
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Theresa
authors.initials: T
authors.lastname: Feltwell
authors.affiliation: Laboratory of Healthcare Associated Infection, Microbiology Services Division, Health Protection Agency, Colindale, London, UK.
authors.forename: Angela M
authors.initials: AM
authors.lastname: Kearns
authors.affiliation: Department of Infectious Disease and Immunity, Imperial College, London, UK.|Department of Microbiology, Imperial College Healthcare NHS Trust, London, UK.
authors.forename: Kathleen B
authors.initials: KB
authors.lastname: Bamford
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D015373:Bacterial Typing Techniques / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D008712:Methicillin / Q000494:pharmacology; D016106:Methicillin Resistance / Q000235:genetics*; D055624:Methicillin-Resistant Staphylococcus aureus / Q000235:genetics*; D058885:Multilocus Sequence Typing / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results
chemical_list: D000900:Anti-Bacterial Agents; D008712:Methicillin