Table 3.
Resistance genes and virulence factor genes of the pathogen detected by mNGS.
| Gene name | Reads number | Drug resistance categories |
|---|---|---|
| Resistance gene | ||
| AAC(3)-IId | 217 | Aminoglycoside antibiotic |
| CRP | 98 | Fluoroquinolone antibiotic; macrolide antibiotic; penam |
| Escherichia coli acrA | 219 | Cephalosporin; cephamycin; penam |
| Escherichia coli ampC | 186 | Cephalosporin; fluoroquinolone antibiotic; glycylcycline; penam; phenicol antibiotic; rifamycin antibiotic; tetracycline antibiotic; triclosan |
| Escherichia coli ampH | 161 | Cephalosporin; penam |
| Escherichia coli emrE | 20 | Cephalosporin; penam |
| Escherichia coli mdfA | 126 | Macrolide antibiotic |
| H-NS | 112 | Benzalkonium chloride; rhodamine; tetracycline antibiotic |
| acrB | 506 | Cephalosporin; cephamycin; fluoroquinolone antibiotic; macrolide antibiotic; penam; tetracycline antibiotic |
| acrD | 417 | Carbapenem; cephalosporin; cephamycin; monobactam; penam; penem |
| acrE | 218 | Cephalosporin; fluoroquinolone antibiotic; glycylcycline; penam; phenicol antibiotic; rifamycin antibiotic; tetracycline antibiotic; triclosan |
| acrF | 452 | Aminoglycoside antibiotic |
| acrS | 193 | Cephalosporin; cephamycin; fluoroquinolone antibiotic; penam |
| bacA | 170 | Cephalosporin; cephamycin; fluoroquinolone antibiotic; penam |
| baeR | 63 | Cephalosporin; cephamycin; fluoroquinolone antibiotic; glycylcycline; penam; phenicol antibiotic; rifamycin antibiotic; tetracycline antibiotic; triclosan |
| baeS | 33 | Peptide antibiotic |
| cpxA | 252 | Aminocoumarin antibiotic; aminoglycoside antibiotic |
| emrA | 165 | Aminocoumarin antibiotic; aminoglycoside antibiotic |
| emrB | 175 | Aminocoumarin antibiotic; aminoglycoside antibiotic |
| emrK | 223 | Fluoroquinolone antibiotic |
| emrR | 130 | Fluoroquinolone antibiotic |
| emrY | 321 | Tetracycline antibiotic |
| eptA | 138 | Fluoroquinolone antibiotic |
| evgA | 219 | Tetracycline antibiotic |
| evgS | 1,249 | Peptide antibiotic |
| gadW | 316 | Fluoroquinolone antibiotic; macrolide antibiotic; penam; tetracycline antibiotic |
| gadX | 124 | Fluoroquinolone antibiotic; macrolide antibiotic; penam; tetracycline antibiotic |
| kdpE | 45 | Fluoroquinolone antibiotic; macrolide antibiotic; penam |
| marA | 59 | Fluoroquinolone antibiotic; macrolide antibiotic; penam |
| mdtA | 63 | Aminoglycoside antibiotic |
| mdtB | 197 | Carbapenem; cephalosporin; cephamycin; fluoroquinolone antibiotic; glycylcycline; monobactam; penam; penem; phenicol antibiotic; rifamycin antibiotic; tetracycline antibiotic; triclosan |
| mdtC | 145 | Aminocoumarin antibiotic |
| mdtE | 190 | Aminocoumarin antibiotic |
| mdtF | 409 | Aminocoumarin antibiotic |
| mdtG | 151 | Fluoroquinolone antibiotic; macrolide antibiotic; penam |
| mdtH | 126 | Fluoroquinolone antibiotic; macrolide antibiotic; penam |
| mdtN | 49 | Fosfomycin |
| mdtO | 223 | Fluoroquinolone antibiotic |
| mdtP | 211 | Acridine dye; disinfecting agents and intercalating dyes; nucleoside antibiotic |
| msbA | 273 | Acridine dye; disinfecting agents and intercalating dyes; nucleoside antibiotic |
| pmrF | 111 | Acridine dye; disinfecting agents and intercalating dyes; nucleoside antibiotic |
| tolC | 348 | Nitroimidazole antibiotic |
| ugd | 221 | Peptide antibiotic |
| yojI | 196 | Aminocoumarin antibiotic; aminoglycoside antibiotic; carbapenem; cephalosporin; cephamycin; fluoroquinolone antibiotic; glycylcycline; macrolide antibiotic; penam; penem; peptide antibiotic; phenicol antibiotic; rifamycin antibiotic; tetracycline antibiotic; triclosan |
| Virulence factor gene | ||
| fimB | 166 | Adherence |
| fimE | 169 | Adherence |
| fimA | 41 | Adherence |
| fimI | 122 | Adherence |
| fimC | 212 | Adherence |
| fimD | 552 | Adherence |
| fimF | 71 | Adherence |
| fimG | 69 | Adherence |
| fimH | 116 | Adherence |
| papB | 69 | Adherence |
| papI | 29 | Adherence |
| papA | 5 | Adherence |
| sat | 1,480 | Effector delivery system |
| chuS | 270 | Nutritional/metabolic factor |
| chuA | 496 | Nutritional/metabolic factor |
| chuT | 212 | Nutritional/metabolic factor |
| chuW | 228 | Nutritional/metabolic factor |
| chuX | 132 | Nutritional/metabolic factor |
| chuY | 105 | Nutritional/metabolic factor |
| chuU | 196 | Nutritional/metabolic factor |
| fepA | 351 | Nutritional/Metabolic factor |
| fepB | 153 | Nutritional/metabolic factor |
| fepC | 131 | Nutritional/metabolic factor |
| fepD | 145 | Nutritional/metabolic factor |
| fepE | 175 | Nutritional/metabolic factor |
| fepG | 97 | Nutritional/metabolic factor |
| entD | 35 | Nutritional/metabolic factor |
| entF | 527 | Nutritional/metabolic factor |
| entC | 195 | Nutritional/metabolic factor |
| entE | 265 | Nutritional/metabolic factor |
| entB | 149 | Nutritional/metabolic factor |
| entA | 92 | Nutritional/metabolic factor |
| iucD | 38 | Nutritional/metabolic factor |
| iucC | 202 | Nutritional/metabolic factor |
| ompA | 209 | Invasion |
| aslA | 245 | Invasion |
| papX | 158 | Adherence |
| yagY/ecpB | 78 | Adherence |
| ykgK/ecpR | 202 | Adherence |
| yagZ/ecpA | 65 | Adherence |
| yagX/ecpC | 224 | Adherence |
| yagW/ecpD | 308 | Adherence |
| yagV/ecpE | 120 | Adherence |
| sfaC | 31 | Adherence |
| chuS | 21 | Nutritional/metabolic factor |
| chuW | 24 | Nutritional/metabolic factor |
| chuY | 9 | Nutritional/metabolic factor |
| ibeB | 306 | Invasion |
| ibeC | 446 | Invasion |
| espL1 | 97 | Effector delivery system |
| sfaX | 22 | Adherence |
| fes | 218 | Nutritional/metabolic factor |
| entS | 156 | Nutritional/metabolic factor |
| chuV | 222 | Nutritional/metabolic factor |
| fdeC | 762 | Adherence |
| cgsG | 106 | Adherence |
| cgsF | 97 | Adherence |
| cgsE | 98 | Adherence |
| cgsD | 176 | Adherence |
| csgB | 142 | Adherence |
| csgA | 69 | Adherence |
| csgC | 70 | Adherence |
| kpsF | 243 | Invasion |
| kpsE | 223 | Invasion |
| kpsD | 314 | Invasion |
| kpsU | 78 | Invasion |
| kpsC | 300 | Invasion |
| kpsS | 253 | Invasion |
| neuE | 893 | Invasion |
| neuC | 636 | Invasion |
| neuA | 762 | Invasion |
| neuB | 578 | Invasion |
| neuD | 319 | Invasion |
| kpsT | 358 | Invasion |
| kpsM | 246 | Invasion |