Table 3.
Correlation and discrepancies between genotype and phenotype of Campylobacter spp. resistance profile using AMR FinderPlus
| Antibiotic class | Antibiotic tested | #Isolates tested | #Isolates resistant | Resistance determinant | Correlation between pheno- and genotype | Reason for discrepancy† |
|---|---|---|---|---|---|---|
| Aminoglycosides | GEN | 494 | 114 | aph(2’’)-li1, aph(2’’)-If, bifunctional aac(6’)-Ie/aph(2’’)-Ia | 99.1% (113/114) | isolate with yet unknown resistance determinant (MIC > 16 mg/L; GEN-R; n = 1), |
| STR | 494 | 143 | aadE1-3, aadE-Cc, RpsL_K43R, RpsL_K88R | 78.1% (114/146) | aadE3 gene not found (missing in database (WP_057035408.1); STR-R; n = 29), partial aadE1 genes (STR-R; n = 2), isolate slightly resistant (MIC = 8 mg/L), but harboring none of the known resistance determinants (n = 1) | |
| KAN | 157 | 139 | aph(2’’)-If, bifunctional aac(6’)-Ie/aph(2’’)-Ia, aph(3’)-IIIa | 100% (139/139) | n.a. | |
| SPC | 139 | 118 | aad9 | 30.5% (36/118) | partial genes found due to frame-shift within poly-C tract (SPC-R; n = 82) | |
| β-Lactams | AMP | 139 | 134 | blaOXA−61 and − 184 family genes | 98.5% (132/134) | Isolate susceptible (MIC = 16 mg/L), but harboring blaOXA−193 (n = 1); isolate slightly resistant (MIC = 32 mg/L), but harboring no blaOXA gene (n = 1) |
| (Fluoro-) Quinolones | CIP | 494 | 442 | GyrA_T86I, GyrA_T86V | 100% (442/442) | n.a. |
| NAL | 494 | 432 | GyrA_T86I, GyrA_T86V | 97.7% (432/442) | CIP-R/NAL-S phenotype, yet unknown mechanism (n = 10) | |
| Lincosamides | LCM | 44 | 35 | lnu(C), 23S_A2075G, erm(B) | 88.6% (31/35) | isolates slightly resistant (MIC = 16 mg/L), but harboring none of the known resistance determinants (n = 4) |
| Macrolides | ERY | 494 | 115 | 23S_A2075G, erm(B) | 100% (115/115) | n.a. |
| 50S_L22_A103V | 20% (31/155) | point mutation not associated with resistance to erythromycin; 20% correlation due to additional presence of either 23_A2075G or erm(B) | ||||
| Nourseothricin | NTC | 98 | 56** | sat4 | 100% (56/56) | n.a. |
| Phenicols | CHL | 130 | 93 | catA9, catA13, fexA, optrA | 100% (94/94) | n.a. |
| FLO | 53 | 29 | fexA, optrA | 62.1% (18/29) | isolates slightly resistant (MIC = 8–16 mg/L) in absence of known phenicol resistance determinants (n = 11) | |
| Tetracyclines | TET | 494 | 412 | tet(O), tet(O/32/O), tet(W), tet(O/M/O), tet(L) | 84.6% (351*/415) | partial (mosaic-) tet(O) genes found (TET-R; n = 54), (mosaic-) tet(O) genes not found, but phenotypic resistance expressed (under coverage threshold; TET-R; n = 8), tet(W) with two point mutations (G511A/G1736A leading to D171N/G579D; TET-S; n = 2) |
AMP, ampicillin; CHL, chloramphenicol; CIP, ciprofloxacin; ERY, erythromycin; FLO, florfenicol; GEN, gentamicin; KAN, kanamycin; LCM, lincomycin; NAL, nalidixic acid; NTC, nourseothricin; SPC, spectinomycin; STR, streptomycin; TET, tetracycline; n.a., not applicable (100% correlation); * tet(O/32/O) found as tet(O) with reduced identity (93.4%; missing in database; TET-R; n = 41) not depicted here, since pheno- and genotype were consistent with only incorrect nomenclature; **Considering a cut-off value of > 4 mg/L as resistant; †Based on the prediction of resistance determinants obtained via the BakCharak pipeline (comprises the AMRFinderPlus tool and its corresponding database version 2023-08-08.2)