Table 2.
The top 15 candidate markers ranked according to the contribution of each marker to the support vector machine classifier for each drug based on the best performing combination of data types
| Drug | Data type | PA14/CARD gene_id | PA14/CARD gene_acc | Prokka/Roary gene_id | SNP position |
|---|---|---|---|---|---|
| TOB (GPA_EXPR) | GPA | A7J11_00271 | qacEdelta1 | emrE | |
| GPA | A7J11_02078 | sul1 | folP_2_indel | ||
| GPA | PA14_04410 | ptsP | ptsP | ||
| GPA | group_282 | ||||
| GPA | PA14_20840 | group_14073 | |||
| GPA | group_20477 | ||||
| EXPR | PA14_15450 | traJ | |||
| GPA | PA14_15100 | mepM_1 | |||
| GPA | A7J11_02078 | sul1 | folP_2 | ||
| GPA | group_8948 | ||||
| GPA | group_51714 | ||||
| EXPR | PA14_38410 | amrB | |||
| GPA | PA14_18565 | alg8 | alg8 | ||
| GPA | group_3462 | ||||
| GPA | group_17749 | ||||
| MEM (GPA_EXPR) | GPA | group_596_indel/oprD_1 | |||
| GPA | PA14_51880 | oprD | oprD_4_indel | ||
| EXPR | PA14_46070 | gbuA | |||
| EXPR | PA14_05550 | oprM | |||
| GPA | group_3638 | ||||
| EXPR | PA14_51880 | oprD | |||
| GPA | group_6217/pknK_1 | ||||
| EXPR | PA14_05540 | mexB | |||
| EXPR | PA14_07630 | ||||
| EXPR | PA14_63090 | lldD | |||
| GPA | PA14_11960 | yabI_indel | |||
| EXPR | PA14_70940 | betA | |||
| GPA | group_6280 | ||||
| GPA | group_15876 | ||||
| GPA | group_10960 | ||||
| CIP (SNPs) | SNP | PA14_23260 | gyrA | 2015001 | |
| SNP | PA14_65605 | parC | 5845617 | ||
| SNP | PA14_55600 | 4947631 | |||
| SNP | PA14_56040 | 5004892 | |||
| SNP | PA14_30960 | traG | 2690138 | ||
| SNP | PA14_31010 | 2694327 | |||
| SNP | PA14_29390 | 2545634 | |||
| SNP | PA14_41560 | nasA | 3710561 | ||
| SNP | PA14_18260 | fruK | 1567193 | ||
| SNP | PA14_30910 | trbE | 2685860 | ||
| SNP | PA14_30960 | traG | 2689741 | ||
| SNP | PA14_59210 | 5274257 | |||
| SNP | PA14_44640 | 3974007 | |||
| SNP | PA14_41110 | 3665768 | |||
| SNP | PA14_15460 | merA | 1310089 | ||
| CAZ (GPA_EXPR) | EXPR | PA14_10790 | ampC | ||
| GPA | A7J11_02078 | sul1 | folP_2 | ||
| GPA | group_8955 | ||||
| EXPR | PA14_48900 | ||||
| GPA | PA14_00810 | group_13626 | |||
| EXPR | PA14_15770 | ||||
| GPA | group_3462 | ||||
| GPA | PA14_33690 | pvdE | yojI | ||
| GPA | group_23010 | ||||
| GPA | petE_indel | ||||
| EXPR | PA14_31240 | ||||
| EXPR | PA14_53500 | ||||
| GPA | group_5517 | ||||
| GPA | PA14_22650 | group_14516_indel | |||
| GPA | group_63043 |
For gene presence/absence (GPA) markers, we provide the gene id and accession based on PA14 reference genome gene family member or based on the Comprehensive Antibiotic Resistance Database (CARD) (Jia et al, 2017). Otherwise, we include the gene name or id of each marker as generated by the bacterial genome annotation tool Prokka (Seemann, 2014) and protein family clustering software Roary (Page et al, 2015). Expression markers are based on the PA14 genome, too. For short nucleotide polymorphisms (SNPs), we report the genome position in the reference PA14 genome.