Comparative Sequencing of the Serine-Aspartate Repeat-Encoding Region of the Clumping Factor B Gene (clfB) for Resolution within Clonal Groups of Staphylococcus aureus

摘要

Moleculartechniques such as spa typing and multilocus sequence typinguse DNA sequence data for differentiating Staphylococcusaureus isolates. Although spa typing is capable ofdetecting both genetic micro- and macrovariation, it has lessdiscriminatory power than the more labor-intensive pulsed-field gelelectrophoresis (PFGE) and costly genomic DNA microarray analyses. Thislimitation hinders strain interrogation for newly emerging clones andoutbreak investigations in hospital or community settings where robustclones are endemic. To overcome this constraint, we developed a typingsystem using DNA sequence analysis of the serine-aspartate (SD)repeat-encoding region within the gene encoding thekeratin- and fibrinogen-binding clumping factor B (clfBtyping) and tested whether it is capable of discriminating withinclonal groups. We analyzed 116 S. aureus strains, and therepeat region was present in all isolates, varying in sequence and inlength from 420 to 804 bp. In a sample of 36 well-characterizedgenetically diverse isolates, clfB typing subdivided identicalspa and PFGE clusters which had been discriminated bywhole-genome DNA microarray mapping. The combination of spatyping and clfB typing resulted in a discriminatory power(99.5%) substantially higher than that of spa typing alone andclosely approached that of the whole-genome microarray (100.0%).clfB typing also successfully resolved genetic differencesamong isolates differentiated by PFGE that had been collected overshort periods of time from single hospitals and that belonged to themost prevalent S. aureus clone in the United States.clfB typing demonstrated in vivo, in vitro, and interpatienttransmission stability yet revealed that this locus may berecombinogenic in a primarily clonal population structure. Takentogether, these data show that the SD repeat-encoding region ofclfB is a highly stable marker of microvariation, that inconjunction with spa typing it may serve as a DNAsequence-based alternative to PFGE for investigating geneticallysimilar strains, and that it is useful for analyzing collections ofisolates in both long-term population-based and local epidemiologicstudies.