Novel Conserved Genotypes Correspond to Antibiotic Resistance Phenotypes of E. coli Clinical Isolates
Figure 6
Linkage analysis of the mutM, ligB, and recG fluoroquinolone resistance associated SNPs.
A) Relative chromosomal location of mutM, radC, ligB, spoT, and recG in E. coli DH10B. B) To determine the linkage frequency, 39 complete E. coli genomes in GenBank and 83 draft genomes from the Broad Institute were analyzed at the positions of variants in mutM, ligB, and recG. Allelic variants in radC and spoT were selected for relative comparison based on their location between the genes of interest. The linkage of each pair of allelic variants was normalized to a range from never linked (−1) to always linked (+1). The sigma (σ) denotes one standard deviation for a normal distribution. Strains with unannotated genes were not included in the analysis. C) The statistical significance of the linkage was calculated using two-by-two contingency tables and Χ2 analysis. With a Bonferroni correction for multiple comparisons, p-values <0.005 are considered significant. The statistical analysis was done using R version 2.12.2.