Table 3 Positive selection and antibiotic resistance. (a) Genes. (b) Mutations.
(a) For positive selection, our data give the gene’s p value and prev. study shows whether the gene appeared in other studies. For genes, core indicates whether a gene is a core gene appearing in at least 95% of genomes and ess. indicates essentiality. The column antibiotic resistance lists resistance functions from literature and whether the gene had antibiotic resistance associated mutations in our data (see B). | ||||||
|---|---|---|---|---|---|---|
Gene | Positive selection | Gene | Antibiotic resistance | |||
Our data | Prev. study | Core | Ess | Our data | Antibiotics resistance Function | |
ompC | 1.57 * 10E−32 | Yes | Yes | No | Yes | Membrane permeability |
yegE (yfaL) | 5.87 * 10E−19 | Yes | Yes | No | No | Biofilm formation |
ycgV | 4.47 * 10E−18 | Yes | No | No | No | Biofilm formation |
lsrA | 2.16 * 10E−12 | No | No | No | No | Biofilm formation |
ompA | 1.74 * 10E−6 | Yes | Yes | No | No | Membrane permeability |
hipA | 1.06 * 10E−5 | No | Yes | No | Yes | Bacterial persistence |
ydhQ | 1.06 * 10E−5 | No | Yes | No | No | Biofilm formation |
dgcE | 1.06 * 10E−5 | No | Yes | No | No | Biofilm formation |
(b) Freq. refers to the frequency of non-synonymous mutations in the site. | ||||||
|---|---|---|---|---|---|---|
Gene | Site | Freq | Antibiotic | P value | ||
ompC | A231 | 15 | Ceftazidime | 0.03 | ||
ompC | G309 | 32 | Cefepime | 0.01 | ||
Cephalotin | 0.02 | |||||
hipA | I104 | 38 | Cefotaxime | 0.03 | ||
hipA | K290 | 25 | Cefotaxime | 0.05 | ||
hipA | G431 | 13 | Imipenem | 0.03 | ||
Nalidixic acid | 0.03 | |||||
