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.

FIG. 1.

Molecular characterization of strains. From right to left: (i) a dendrogram showing the estimated relationships of the 36 strains based on a whole-genome DNA microarray with a scale indicating the Pearson correlation coefficient for each node (0, totally unrelated; 1, identical); (ii) a listing of strains (MSA, Musser S. aureus; red, MRSA strains); (iii) MLEE lineage and ET for each strain; (iv) spa and coa lineages, types, and profiles for each strain (note that coa lineages 7A and 7B can be considered separate lineages [lineages I] or together as one lineage [lineages II]); (v) PFGE patterns and types (λ, molecular weight standard of lambda DNA concatemers from New England BioLabs). NA, strain was not available. The dendrogram was adapted from reference with permission of the publisher.

FIG. 2.

DNA sequences for the 38 spa repeats identified to date in S. aureus. Individual repeat codes are shown on the right. Sequences are organized and displayed as eight colored codons, and codons in the same column with the same color represent the same three nucleotides. Asterisks indicate repeats that have been redefined, and crosses indicate new repeats found since those previously reported (30).