Table 2.
Performance of mPCR and concordance of phenotypical and genotypical antimicrobial susceptibility of all tested isolates
| Pathogen/Antimicrobial | Gene target | Susceptible by mPCR [no.] | Resistant by mPCR [no.] | Susceptible by culture [no.] | Resistant by culture [no.] | Sensitivity [%] (95% CI) | Specificity [%] (95% CI) | Concordance [%] (95% CI) | NPV [%] (95% CI) | PPV [%] (95% CI) |
|---|---|---|---|---|---|---|---|---|---|---|
| Coagulase-negative staphylococci | ||||||||||
| Oxacillin (n = 30) | mecA, mecC | 20 | 10 | 7 | 23 | 44 (26–63) | 100 (59–100) | 57 (39–74) | 35 (14–56) | 100 (100) |
| Aminoglycosides (n = 32) | aac(6′)/aph(2″) | 23 | 9 | 13 | 19 | 42 (23–64) | 92 (64–100) | 63 (46–79) | 52 (32–73) | 89 (68–100) |
| Macrolides/lincos-amides (n = 33) | ermA, ermC | 19 | 14 | 14 | 19 | 58 (36–77) | 79 (51–93) | 67 (51–83) | 58 (36–80) | 79 (57–100) |
| Rifampin (n = 28) | rpoB | 28 | 0 | 22 | 6 | 0 (0–46) | 100 (85–100) | 78 (59–91) | 79 (79) | – |
| Staphylococcus aureus | ||||||||||
| Oxacillin (n = 16) | mecA, mecC | 14 | 2 | 14 | 2 | 100 (29–100) | 100 (74–100) | 100 (100) | 100 (100) | 100 (100) |
| Aminoglycosides (n = 16) | aac(6′)/aph(2″) | 16 | 0 | 15 | 1 | 0 (0–98) | 100 (78–100) | – | 94 (94) | 94 (70–100) |
| Macrolides/lincos-amides (n = 16) | ermA, ermC | 14 | 2 | 12 | 4 | 50 (15–85) | 100 (71–100) | 88 (71–100) | 86 (67–100) | 100 (100) |
| Rifampin (n = 15) | rpoB | 13 | 2 | 14 | 1 | 100 (17–100) | 93 (66–100) | 93 (81–100) | 100 (100) | 50 (0–100) |
| Enterococcus spp. | ||||||||||
| Aminoglycosides (high-level) (n = 7) | aac(6′)/aph(2″) | 6 | 1 | 4 | 3 | 33 (6–80) | 100 (45–100) | 71 (38–100) | 67 (29–100) | 100 (100) |
| Vancomycin (n = 10) | vanA, vanB | 10 | 0 | 10 | 0 | – | 100 (69–100) | 100 (69–100) | 100 (100) | – |
| Enterobacteriaceae | ||||||||||
| Aminoglycosides (n = 14) | aacA4 | 10 | 4 | 14 | 0 | – | 71 (42–92) | 71 (42–92) | 100 | 0 |
| Carbapenems (n = 14) | blavim, blaimp, blakpc, blandm, blaoxa-23, blaoxa-24, blaoxa-48, blaoxa-58 | 14 | 0 | 14 | 0 | – | 100 (77–100) | 100 (77–100) | 100 | – |
| Third-generation cephalosporins (n = 14) | ctx-M | 14 | 0 | 14 | 0 | – | 100 (77–100) | 100 (77–100) | 100 | – |
| Fluoroquinolonesa (n = 9) | gyrA83, gyrA87 | 5 | 4 | 6 | 3 | 100 (38–100) | 83 (42–98) | 89 (68–100) | 100 (100) | 75 (33-100) |
| Streptococcus agalactiae | ||||||||||
| Macrolides/lincosamides (n = 10) | ermA, ermC | 10 | 0 | 8 | 2 | 0 (0–84) | 100 (63–100) | 80 (44–97) | 80 (80) | – |
| Cutibacterium spp | ||||||||||
| Rifampin (n = 6) | rpoB | 6 | 0 | 6 | 0 | – | 100 (54–100) | 100 (54–100) | 100 (100) | – |
| Total, median (range) | 46 (36–56) | 95 (90–97) | 80 (75–84) | 80 (74–85) | 79 (68–91) | |||||
Note: Sensitivity and specificity of mPCR considering culture testing (VITEK) as gold standard
aOnly E. coli isolates were tested for fluoroquinolone resistance by mPCR