Table 1. Genera of Gram-positive human urinary tract inhabitants and pathogens detected by culture-dependent and –independent techniques.
“culture negative” means specimens that did not reach the cutoff value, usually 105 CFU/ml urine in a clean catch specimen or 104 CFU/ml for collections by catheter or suprapubic aspiration.
|
Culture-Dependent Clinical Reports |
Culture-Independent Detection in Urinary Tract | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Phylum | Genus | Bladder/ Kidney infection |
Bacteremia & Urosepsis |
Urethritis | Female, culture unknown |
Female, culture positive |
Female culture-negative, nitrite and leukocyte esterase negative or asymptomatic |
Male asymptomatic |
Male symptomatic |
|||
| TUC | CC,TUC | CC | TUC | SPA | urine | urethral swab |
urine | |||||
| Firmicutes | Staphylococcus | 5–20% of CAUTI [47] |
[328] | [53, 55, 56] |
[292, 329] | n/r | [318, 319] | [317, 329] | [317] | [319, 322– 324] |
[323] | [330] |
| Enterococcus | 15–30% of CAUTI [13, 115, 119] |
[328] | [331, 332] | [318] | [316, 333] | [319] | n/r | n/r | [322, 323] |
[323] | [330] | |
| Streptococcus | 1–2% of UTI [180] |
[180] | [334] | [292, 318, 329] |
n/r | [316, 318, 319] |
[317, 329] | [317] | [322– 324] |
[323] | [330] | |
| Aerococcus | [230, 232, 237, 239] |
[233–236, 278] |
n/r | [329, 335] | [317] | [318, 319] | [317] | [317] | [319, 322, 323] |
[323] | n/r | |
| Anaerococcus | n/r | n/r | n/r | [292, 329, 335] |
[333] | [316, 318, 319, 333] |
n/r | [317] | [319, 322– 324] |
[323] | n/r | |
| Peptostreptococcus | [321, 336]* | [337] | n/r | [335] | [333] | [318, 319] | n/r | n/r | [319, 322, 324] |
n/r | n/r | |
| Peptoniphilus | n/r | [338] | n/r | [335] | [333] | [317–319] | n/r | n/r | [319, 322] |
n/r | n/r | |
| Lactobacillus | [321, 339, 340] * |
n/r | n/r | [335] | [333] | [316–319, 333] |
[317, 329] | [317] | [319, 322– 324] |
[323] | [330] | |
| Finegoldia | n/r | n/r | n/r | [335] | [317, 318, 333] |
[319] | n/r | [317] | [319, 322– 324] |
[323] | [330] | |
| Veillonella | [341, 342] | [337, 341] |
n/r | [335] | [317] | n/r | [292, 329] | n/r | [322, 323] |
[324] | n/r | |
| Gemella | [343] | n/r | n/r | n/r | n/r | n/r | n/r | n/r | [319, 322, 323] |
[323] | n/r | |
| Actinobacteria | Corynebacterium | [246–249, 344– 349] |
[350] | [351–353] | [292, 329, 335] |
n/r | [316, 318, 319] |
[317, 329] | [317] | [319, 322, 323] |
[323] | n/r |
| Actinobaculum | [155, 261, 262, 266, 267, 269, 272, 274, 276, 277, 354] |
[270, 275, 278, 355] |
n/r | [335] | [317, 333] | [318, 319] | [292, 317, 329] |
[317] | [322] | n/r | n/r | |
| Gardnerella | [285, 300]* | [293, 300, 303, 356] |
[307–309, 357–359] |
[335] | [333] | [316, 318, 319, 333] |
[317, 322– 324, 329, 360] |
[317] | [319, 322] |
[323] | n/r | |
| Atopobium | n/r | n/r | n/r | [335] | [333] | [317, 319, 333] |
[292, 317, 329] |
[317] | [319, 322, 323, 361] |
[323] | [361] | |
| Actinomyces | [362–366] | [367] | n/r | [335] | n/r | [319] | [292] | n/r | [322] | n/r | n/r | |
| Bifidobacterium | n/r | n/r | n/r | [335] | [333] | n/r | [292, 329] | n/r | n/r | n/r | [330] | |
| Mycoplasma | [368–371] | n/r | [358, 372– 379] |
n/r | n/r | n/r | n/r | n/r | [319, 322, 323] |
[323] | n/r | |
n/r = not reported, CAUTI = community acquired UTI,
*
Questionable clinical significance, CC = clean catch, TUC = transurethral catheter, SPA = suprapubic aspiration.