A rapid multi-loci gene analysis system was developed that achieved high sensitivity, was reproducible, and provided three-tier sequence-specific interrogation of DNA targets.
Our MC procedure is based on a two-region multi-locus gene-drop.
While there are multiple causes for missing some well-known genetic risk factors or disease heritability (including e.g., rare variants not genotyped in a GWAS study), a frequently cited reason is that most common diseases have complex mechanisms, involving multi-locus gene-gene and gene-environment interactions [ 5, 28- 31].
This indicates that phylogenetic classification of genus Brucella based on marker genes, for instance multi locus sequence typing [ 22], show a surprising similarity to the organism's total gene content.
A detailed analysis of the ibeA sequences revealed the phylogeny of this gene to be consistent with that obtained by Multi Locus Sequence Typing of the strains.
However, recent MLSA (multi locus sequence analyses) analyses showed that this strain, which does not possess the albicidin biosynthesis gene cluster, is close to X. albilineans but belongs to a separate phylogenetic clade (I. Pieretti, unpublished data).
Isolates were classified in clonal groups based upon sequence analysis of conserved house-keeping genes and comparison of the results with the data on the Neisseria Multi Locus Sequence Typing website (http://pubmlst.org/neisseria/) [ 44].
Multi locus sequence typing (MLST) based phylogenetic analysis was performed for Xcaw12879 and other Xanthomonas spp. using nine housekeeping genes (uvrD, secA, carA, recA, groEL, dnaK, atpD, gyrB, and infB) that are highly conserved in bacteria.
For other gene loci, prototype sequences needed for the design of MLST were obtained from the genomes of L. interrogans serovar Lai (NC_004342 and NC_004343) and L. interrogans serovar Copenhageni (NC_005823 and NC_005824) The multi locus sequences of all the 271 isolates obtained as a part of this study are available in full under supporting information (Table S2).
Isolates of S. suis were serotyped and characterized by multi locus sequence typing (MLST) and pulse field gel electrophoresis (PFGE).
MLST: Multi locus sequence typing; ST: Sequence type.
