title: Discriminatory Indices of Typing Methods for Epidemiologic Analysis of Contemporary Staphylococcus aureus Strains.
abstract: Historically, a number of typing methods have been evaluated for Staphylococcus aureus strain characterization. The emergence of contemporary strains of community-associated S. aureus, and the ensuing epidemic with a predominant strain type (USA300), necessitates re-evaluation of the discriminatory power of these typing methods for discerning molecular epidemiology and transmission dynamics, essential to investigations of hospital and community outbreaks. We compared the discriminatory index of 5 typing methods for contemporary S. aureus strain characterization. Children presenting to St. Louis Children's Hospital and community pediatric practices in St. Louis, Missouri (MO), with community-associated S. aureus infections were enrolled. Repetitive sequence-based PCR (repPCR), pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), staphylococcal protein A (spa), and staphylococcal cassette chromosome (SCC) mec typing were performed on 200 S. aureus isolates. The discriminatory index of each method was calculated using the standard formula for this metric, where a value of 1 is highly discriminatory and a value of 0 is not discriminatory. Overall, we identified 26 distinct strain types by repPCR, 17 strain types by PFGE, 30 strain types by MLST, 68 strain types by spa typing, and 5 strain types by SCCmec typing. RepPCR had the highest discriminatory index (D) of all methods (D = 0.88), followed by spa typing (D = 0.87), MLST (D = 0.84), PFGE (D = 0.76), and SCCmec typing (D = 0.60). The method with the highest D among MRSA isolates was repPCR (D = 0.64) followed by spa typing (D = 0.45) and MLST (D = 0.44). The method with the highest D among MSSA isolates was spa typing (D = 0.98), followed by MLST (D = 0.93), repPCR (D = 0.92), and PFGE (D = 0.89). Among isolates designated USA300 by PFGE, repPCR was most discriminatory, with 10 distinct strain types identified (D = 0.63). We identified 45 MRSA isolates which were classified as identical by PFGE, MLST, spa typing, and SCCmec typing (USA300, ST8, t008, SCCmec IV, respectively); within this collection, there were 5 distinct strain types identified by repPCR. The typing methods yielded comparable discriminatory power for S. aureus characterization overall; when discriminating among USA300 isolates, repPCR retained the highest discriminatory power. This property is advantageous for investigations conducted in the era of contemporary S. aureus infections.
authors.affiliation: From the Department of Pediatrics (MR, PGH, TW, C-ADB, SAF); Department of Pediatrics, McDonnell Genome Institute (TW, HG, ES, GMW); Department of Pathology and Immunology at Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MI 63110 (C-ADB); Department of Medicine at Emory University School of Medicine, 201 Dowman Dr., Atlanta, GA 30322 (SWS, EC); Southern Illinois University School of Medicine, 801 North Rutledge St., Springfield, IL 62702 (MR); and Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032 (ES, GMW).
authors.forename: Marcela
authors.initials: M
authors.lastname: Rodriguez
authors.forename: Patrick G
authors.initials: PG
authors.lastname: Hogan
authors.forename: Sarah W
authors.initials: SW
authors.lastname: Satola
authors.forename: Emily
authors.initials: E
authors.lastname: Crispell
authors.forename: Todd
authors.initials: T
authors.lastname: Wylie
authors.forename: Hongyu
authors.initials: H
authors.lastname: Gao
authors.forename: Erica
authors.initials: E
authors.lastname: Sodergren
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.forename: Carey-Ann D
authors.initials: CD
authors.lastname: Burnham
authors.forename: Stephanie A
authors.initials: SA
authors.lastname: Fritz
mesh_terms: D055624:Methicillin-Resistant Staphylococcus aureus; D058885:Multilocus Sequence Typing; D016133:Polymerase Chain Reaction