Comparative Genome Hybridisation of Streptococcus mutans strains

Objectives: To compare the gene content of a selection of S. mutans strains with the reference strain UA159.

Methods: Genomic DNA of 9 strains of S. mutans was fractionated by sonication, labelled with Cy3 or Cy5 and mixed with UA159 DNA labelled with the alternate dye. The mixed DNAs were used to probe a microarray consisting of oligonucleotides representing 1948 ORFs of S. mutans UA159, generously provided through the NIDCR Oral Microbe Microarray Initiative. The arrays were scanned and analysed to identify ORFs to which the test strain probe failed to hybridise, and hence were concluded to be deletions from the test strain or insertions acquired by UA159.

Results: A total of 385 (c. 20%) of the UA159 ORFs were found to be absent from one or more of the test strains. 81 of these were absent from only a single strain but others were absent from between 2 and 9 strains, suggesting a possible common origin. Deletions frequently affected blocks of adjacent ORFs and represented deletions previously experimentally detected by PCR, predicted genomic islands and IS elements as well as novel ORFs.

Conclusion: Certain regions of the S. mutans chromosome are subject to insertion/deletion events. Approximately half appear to involve foreign DNA acquired by horizontal transmission. These, and other genes that are affected, may help explain the phenotypic and genotypic variation within S. mutans.