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Molecular Genetic Basis of Ribotyping

Valérie Bouchet,^1,2 Heather Huot,^1, and Richard Goldstein^1*

Section of Molecular Genetics, Division of Pediatric Infectious Diseases, The Maxwell Finland Laboratory for Infectious Diseases, Boston University School of Medicine, Boston Medical Center, BioSquare-III, 670 Albany Street, Boston, Massachusetts 02118,¹ Department of Environmental Health, Boston University School of Public Health, 715 Albany Street, Talbot Building, Boston, Massachusetts 02118²

Summary: Nearly 2,000 ribotyping-based studies exist, ranging from epidemiology to phylogeny and taxonomy. None precisely reveals the molecular genetic basis, with many incorrectly attributing detected polymorphisms to rRNA gene sequences. Based on in silico genomics, we demonstrate that ribotype polymorphisms result from sequence variability in neutral housekeeping genes flanking rRNA operons, with rRNA gene sequences serving solely as conserved, flank-linked tags. We also reveal that from such an informatics perspective, it is readily feasible a priori to design an interpretable ribotyping scheme for a genomically sequenced microbial species, and we discuss limitations to the basic restriction fragment length polymorphism-based method as well as alternate PCR ribotyping-based schemes.

Supplemental material for this article may be found at http://cmr.asm.org/.

Present address: Institute for Genome Sciences, University of Maryland Baltimore, School of Medicine, HSF-II, Room S-445, 20 Penn St., Baltimore, MD 21201.