The combined results of fragment-size analysis at all 3 markers were used to create a multilocus fragment type for subtypes within C. parvum and C. hominis as described elsewhere (25, 26 ).
with software for fragment analysis.
Subtypes were identified by using a multilocus fragment-size analysis approach to target 3 microsatellite markers (ML1, ML2, and gp60 [synonymous with gp15]) as previously described (25 ).
Multilocus sequence analysis and MLST gene fragments were repeatedly inspected when getting the whole genome nucleotide sequences of strains (see below).
Previous phylogenetic studies of L. reuteri used amplified-fragment length polymorphism and multilocus sequence analysis (MLSA) to study more than 100 strains, and these identified host origin as one basis for intraspecies diversity (Oh et al. 2010), with lineage-specific genomic differences reflecting the niche characteristics in the GI tract of respective hosts (Frese et al. 2011).
Multiple genetic methods have been developed to identify different strains of C. burnetii, including restriction fragment length polymorphism (RFLP) [ 18], multilocus variability analysis (MLVA) [ 19, 20], and multispacer sequence typing (MST) [ 21].
However, genetic variations are known to occur within M. mycoides subsp. mycoides SC as evidenced by restriction fragment length polymorphism [3,4], by IS 1296 and IS 1634 fingerprinting [5 7], and by multilocus sequence analysis [8].
Multilocus sequence analysis of Borrelia bissettii strains from North America reveals a new Borrelia species, Borrelia kurtenbachii.
DNA sequencing methods, including whole genome sequencing and multilocus sequence analysis (MLSA), likewise have proved useful in the identification of bacteria.
Phylogenies based on mating type genes could discriminate between the species analysed and are in concordance with the results obtained with the more conventional multilocus phylogenetic analysis approach.
