Generation of Diversity in Streptococcus mutans Genes Demonstrated by MLST

• Published in: PloS one Vol. 5; no. 2; p. e9073
• Main Authors: Do, Thuy, Gilbert, Steven C., Clark, Douglas, Ali, Farida, Fatturi Parolo, Clarissa C., Maltz, Marisa, Russell, Roy R., Holbrook, Peter, Wade, William G., Beighton, David
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 05.02.2010; Public Library of Science (PLoS)
• Subjects: Acetyl-CoA carboxylase; Acetyl-CoA Carboxylase - genetics; Analysis; Antigens; Bacteria; Bacterial genetics; Bacterial Proteins - classification; Bacterial Proteins - genetics; Bacterial Typing Techniques - methods; Biodiversity; Biotin; Biotin carboxylase; Cloning; Confidence intervals; Dental caries; Dental Caries - microbiology; Dentistry; Deoxyribonucleic acid; DNA; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; Genes; Genetic diversity; Genetic Variation; Genomes; Genomics; Genotypes; Geographical distribution; Glucokinase; Glucokinase - genetics; Glucosyltransferase; GTP-binding protein; GTP-Binding Proteins - genetics; Humans; Infectious Diseases/Bacterial Infections; Isoenzymes; Klebsiella pneumoniae; Laboratories; Ligases; Loci; Microbiology; Microbiology/Medical Microbiology; Multiculturalism & pluralism; Mutation; Phylogenetics; Phylogeny; Polymerase Chain Reaction; Population genetics; Protein binding; Protein Subunits - genetics; Proteins; Recombination; Sequence Analysis, DNA; Serotypes; Species diversity; Species Specificity; Strains (organisms); Streptococcus infections; Streptococcus mutans; Streptococcus mutans - classification; Streptococcus mutans - genetics; Superoxide dismutase; Superoxide Dismutase - genetics; Surface protein antigen I/II; Transfer RNA; Transketolase; Transketolase - genetics; Trees; tRNA; Tyrosine-tRNA ligase; Tyrosine-tRNA Ligase - genetics; Virulence; Brazil; United Kingdom > UK; Japan; Iceland
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0009073

Streptococcus mutans, consisting of serotypes c, e, f and k, is an oral aciduric organism associated with the initiation and progression of dental caries. A total of 135 independent Streptococcus mutans strains from caries-free and caries-active subjects isolated from various geographical locations were examined in two versions of an MLST scheme consisting of either 6 housekeeping genes [accC (acetyl-CoA carboxylase biotin carboxylase subunit), gki (glucokinase), lepA (GTP-binding protein), recP (transketolase), sodA (superoxide dismutase), and tyrS (tyrosyl-tRNA synthetase)] or the housekeeping genes supplemented with 2 extracellular putative virulence genes [gtfB (glucosyltransferase B) and spaP (surface protein antigen I/II)] to increase sequence type diversity. The number of alleles found varied between 20 (lepA) and 37 (spaP). Overall, 121 sequence types (STs) were defined using the housekeeping genes alone and 122 with all genes. However pi, nucleotide diversity per site, was low for all loci being in the range 0.019-0.007. The virulence genes exhibited the greatest nucleotide diversity and the recombination/mutation ratio was 0.67 [95% confidence interval 0.3-1.15] compared to 8.3 [95% confidence interval 5.0-14.5] for the 6 concatenated housekeeping genes alone. The ML trees generated for individual MLST loci were significantly incongruent and not significantly different from random trees. Analysis using ClonalFrame indicated that the majority of isolates were singletons and no evidence for a clonal structure or evidence to support serotype c strains as the ancestral S. mutans strain was apparent. There was also no evidence of a geographical distribution of individual isolates or that particular isolate clusters were associated with caries. The overall low sequence diversity suggests that S. mutans is a newly emerged species which has not accumulated large numbers of mutations but those that have occurred have been shuffled as a consequence of intra-species recombination generating genotypes which can be readily distinguished by sequence analysis.