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A number of studies have suggested using comparisons between DNA sequences ofclosely related bacterial isolates to estimate the relative rate ofrecombination to mutation for that bacterial species. We consider such anapproach which uses single-locus variants: pairs of isolates whose DNA differat a single gene locus. One way of deriving point estimates for the relativerate of recombination to mutation from such data is to use composite likelihoodmethods. We extend recent work in this area so as to be able to constructconfidence intervals for our estimates, without needing to resort tocomputationally-intensive bootstrap procedures, and to develop a test forwhether the relative rate varies across loci. Both our test and method forconstructing confidence intervals are obtained by modeling the dependencestructure in the data, and then applying asymptotic theory regarding thedistribution of estimators obtained using a composite likelihood. We appliedthese methods to multi-locus sequence typing (MLST) data from eight bacteria,finding strong evidence for considerable rate variation in three of these:Bacillus cereus, Enterococcus faecium and Klebsiella pneumoniae.

Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods