spa Typing Method for Discriminating among Staphylococcus aureus Isolates: Implications for Use of a Single Marker To Detect Genetic Micro- and Macrovariation

Abstract

Strain typing of microbial pathogens has two major aims: (i) to index genetic microvariation for use in outbreak investigations and (ii) to index genetic macrovariation for use in phylogenetic and population-based analyses. Until now, there has been no clear indication that one genetic marker can efficiently be used for both purposes. Previously, we had shown that DNA sequence analysis of the protein A gene variable repeat region (spa typing) provides a rapid and accurate method to discriminate Staphylococcus aureus outbreak isolates from those deemed epidemiologically unrelated. Here, using the hypothesis that the genetic macrovariation within a low-level recombinogenic species would accurately be characterized by a single-locus marker, we tested whether spa typing could congruently index the extensive genetic variation detected by a whole-genome DNA microarray in a collection of 36 isolates, which was recovered from 10 countries on four continents over a period of four decades, that is representative of the breadth of diversity within S. aureus. Using spa and coa typing, pulsed-field gel electrophoresis (PFGE), and microarray and multilocus enzyme electrophoresis (MLEE) data in molecular epidemiologic and evolutionary analyses, we determined that S. aureus likely has a primarily clonal population structure and that spa typing can singly index genetic variation with 88% direct concordance with the microarray and can correctly assign isolates to phylogenetic lineages. spa typing performed better than MLEE, PFGE, and coa typing in discriminatory power and in the degree of agreement with the microarray at various phylogenetic depths. This study showed that genetic analysis of the repeat region of protein A comprehensively characterizes both micro-and macrovariation in the primarily clonal population structure of S. aureus.Staphylococcus aureus is the leading cause of nosocomial infections (21) and is responsible for a wide range of human diseases, including endocarditis, food poisoning, toxic shock syndrome, septicemia, skin infections, soft tissue infections, and bone infections, as well as bovine and ovine mastitis. The recent emergence of community-associated methicillin-resistant S. aureus (MRSA) strains (23) and the movement of the vanA operon from Enterococcus faecalis into MRSA, establishing strains with high-level vancomycin resistance (3), further heighten the public health concerns. Thus, understanding and controlling the spread of S. aureus, in both the hospital and community settings, is now of paramount importance.S. aureus is a heterogenous (polymorphic) species (13) that was recently found to have a clonal population structure (11). Therefore, it is believed that S. aureus does not undergo extensive recombination, diversifies largely by nucleotide mutations, and shows a high degree of linkage disequilibrium (nonrandom associations between genetic loci). In order to distinguish strains within a heterogenous species for local epidemiologic or outbreak investigation purposes, a highly discriminating ge...

Comparison of Genetic Backgrounds of Methicillin-Resistant and -Susceptible Staphylococcus aureus Isolates from Portuguese Hospitals and the Community

“…As done previously (14,32), spa types with similar repeat profiles were grouped together as part of a same lineage (spa lineage), which was identified in the present study by capital letters. Multilocus sequence typing (MLST) was performed in representatives of each PFGE type/spa lineage as described previously (6), with the exception that primer arcCF2 (5Ј-CCT TTA TTT GAT TCA CCA GCG-3Ј) (4) was used.…”

Methicillin-resistant Staphylococcus aureus nasal colonization in a level III neonatal intensive care unit: Incidence and risk factors

“…Additionally, spa typing was carried out on representative MRSA isolates. 12 The spa type was determined using Ridom StaphType software (http://www.ridom.de/staphtype/).…”

Phenotypic and molecular characterization of Staphylococcus aureus recovered from different clinical specimens of inpatients at a teaching hospital in Shanghai between 2005 and 2010

“…The polymorphic X region of the spa gene in S. aureus is composed of a variable number of 24 bp repeats (Shopsin et al, 1999) that allow isolates to be distinguished from one another. Amplification and sequencing of the X region were performed as described previously by Koreen et al (2004). The spa typing was assigned by submitting the data to the S. aureus spa type database (http://www.ridom.de/ spaserver).…”