Molecular genetic basis of ribotyping.
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.
Bouchet
Valérie
V
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, Boston, MA 02118, USA.
Huot
Heather
H
Goldstein
Richard
R
D015373:Bacterial Typing Techniques; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D004275:DNA, Ribosomal / Q000032:analysis* / Q000235:genetics; D020459:Genes, rRNA; D008967:Molecular Biology; D016133:Polymerase Chain Reaction / Q000379:methods; D012150:Polymorphism, Restriction Fragment Length; D021521:Ribotyping / Q000379:methods*; D012407:rRNA Operon
D004269:DNA, Bacterial; D004275:DNA, Ribosomal