Table 2.
Predicted resistance of human and pig ear treat Salmonella isolates.
| Serotype | Clinical isolates screened for resistancea n = 135 n (%) | Resistance determinants present; No. with resistance mechanism/No. of isolates of that serotype with resistance information (%), Antimicrobial resistance predicted by mechanism | No. MDRb isolates n (%) | No. clinically important resistantc isolates n (%) | Pig ear treat isolates screened for resistance n = 135 n (%) | Resistance determinants present; No. with resistance mechanism/No. of isolates of that serotype with resistance information (%), Antimicrobial resistance predicted by mechanism | No. MDRb isolates n (%) | No. clinically important resistantc isolates n (%) |
|---|---|---|---|---|---|---|---|---|
| I 4,[5],12:i:- | 62 (46%) |
aac(3)-IId: 62/62 (100%), gentamicin aadA2: 62/62 (100%), streptomycin aph(3″)-Ib & aph(6)-Id: 61/62 (98%), streptomycin aph(3′)-IIa: 4/62 (6%), kanamycin aph(6)-Ic: 4/62 (6%), streptomycin blaTEM-1B: 61/62 (98%), ampicillin dfrA12: 55/62 (89%), trimethoprimd floR: 5/62 (8%), chloramphenicol gyrA(83): 62/62 (100%), nalidixic acid, ciprofloxacine mef(C): 1/62 (2%), azithromycin mph(G): 1/62 (2%), azithromycin sul2: 56/62 (90%), sulfisoxazole tet(A): 2/62 (3%), tetracycline tet(B): 61/62 (98%), tetracycline |
61/62 (98%) | 62/62 (100%) | 4 (3%) |
aac(3)-IId: 4/4 (100%), gentamicin aadA2: 4/4 (100%), streptomycin aph(3″)-Ib & aph(6)-Id: 4/4 (100%), streptomycin aph(3′)-IIa: 2/4 (50%), kanamycin aph(6)-Ic: 2/4 (50%), streptomycin blaTEM-1B: 4/4 (100%), ampicillin dfrA12: 2/4 (50%), trimethoprimd floR: 2/4 (50%), chloramphenicol gyrA(83): 4/4 (100%), nalidixic acid, ciprofloxacine mef(C): 0/4 (0%), azithromycin mph(G): 0/4 (0%), azithromycin sul2: 2/4 (50%), sulfisoxazole tet(A): 0/4 (0%), tetracycline tet(B): 4/4 (100%), tetracycline |
4/4 (100%) | 4/4 (100%) |
| Infantis | 39 (29%) |
blaTEM-1B: 39/39 (100%), ampicillin dfrA8: 36/39 (92%), trimethoprim floR: 39/39 (100%), chloramphenicol qnrB19: 0/39 (0%), ciprofloxacinf tet(A): 39/39 (93%), tetracycline No determinants detected: 0/39 (0%) |
39/39 (100%) | 39/39 (100%) | 47 (35%) |
blaTEM-1B: 40/47 (85%), ampicillin dfrA8: 41/47 (87%), trimethoprim floR: 41/47 (87%), chloramphenicol qnrB19: 3/47 (6%), ciprofloxacinf tet(A): 41/47 (87%), tetracycline No determinants detected: 6/47 (13%) |
41/47 (87%) | 40/47 (85%) |
| London | 21 (16%) |
aac(3)-IIa: 3/21 (14%), gentamicin aadA1: 3/21 (14%), streptomycin aph(3″)-Ib & aph(6)-Id: 3/21 (14%), streptomycin blaTEM-1B: 3/21 (14%), ampicillin dfrA1: 3/21 (14%), trimethoprim floR: 2/21 (10%), chloramphenicol qnrB19: 18/21 (86%), ciprofloxacinf qnrE1: 3/21 (14%), ciprofloxacinf sul1: 3/21 (14%), sulfisoxazole tet(A): 3/21 (14%), tetracycline |
3/21 (14%) | 21/21 (100%) | 28 (21%) |
aac(3)-IIa: 4/28 (14%), gentamicin aadA1: 4/28 (14%), streptomycin aph(3″)-Ib & aph(6)-Id: 4/28 (14%), streptomycin blaTEM-1B: 4/28 (14%), ampicillin dfrA1: 4/28 (14%), trimethoprim floR: 3/28 (11%), chloramphenicol qnrB19: 24/28 (86%), ciprofloxacinf qnrE1: 4/28 (14%), ciprofloxacinf sul1: 4/28 (14%), sulfisoxazole tet(A): 4/28 (14%), tetracycline |
4/28 (14%) | 28/28 (100%) |
| Newport | 10 (7%) |
qnrB19: 1/10 (10%), ciprofloxacinf No determinants detected: 9/10 (93%) |
0/10 (0%) | 1/10 (10%) | 20 (15%) |
qnrB19: 1/20 (5%), ciprofloxacinf No determinants detected: 19/20 (93%) |
0/20 (0%) | 1/20 (5%) |
| Rissen | 1 (<1%) | No determinants detected: 1/1 (100%) | 0/1 (0%) | 0/1 (0%) | 1 (<1%) | No determinants detected: 1/1 (100%) | 0/1 (0%) | 0/1 (0%) |
| Derby | 1 (<1%) | fos7: 1/1 (100%), fosfomycin | 0/1 (0%) | 0/1 (0%) | 3 (2%) |
fos7: 3/3 (100%), fosfomycin tet(A): 1/3 (33%), tetracycline |
0/3 (0%) | 0/3 (0%) |
| Cerro | 1 (<1%) | No determinants detected: 1/1 (100%) | 0/1 (0%) | 0/1 (0%) | 2 (1%) | No determinants detected: 2/2 (100%) | 0/2 (0%) | 0/2 (0%) |
| Agona | N/A | N/A | N/A | N/A | 1 (<1%) | fos7: 1/1 (100%), fosfomycin | 0/1 (0%) | 0/1 (0%) |
| Anatum | N/A | N/A | N/A | N/A | 3 (2%) | No determinants detected: 3/3 (100%) | 0/3 (0%) | 0/3 (0%) |
| Give | N/A | N/A | N/A | N/A | 2 (1%) | No determinants detected: 2/2 (100%) | 0/2 (0%) | 0/2 (0%) |
| Typhimurium | N/A | N/A | N/A | N/A | 4 (<1%) | No determinants detected: 4/4 (100%) | 0/4 (0%) | 0/4 (0%) |
| Senftenberg | N/A | N/A | N/A | N/A | 2 (1%) |
aph(3″)-Ib & aph(6)-Id: 1/2 (50%), streptomycin floR: 1/2 (50%), chloramphenicol qnrB19: 1/2 (50%), ciprofloxacinf sul2: 1/2 (50%), sulfisoxazole tet(A): 1/2 (50%), tetracycline No determinants detected: 1/2 (50%) |
1/2 (50%) | 1/2 (50%) |
| Uganda | N/A | N/A | N/A | N/A | 5 (4%) | No determinants detected: 5/5 (100%) | 0/5 (0%) | 0/5 (0%) |
| Worthington | N/A | N/A | N/A | N/A | 1 (<1%) |
aadA1: 1/1 (100%), streptomycin aph(3″)-Ib & aph(6)-Id: 1/1 (100%), streptomycin blaTEM-1A: 1/1 (100%), ampicillin dfrA1: 1/1 (100%), trimethoprim floR: 1/1 (100%), chloramphenicol qnrB19: 1/1 (100%), ciprofloxacinf sul1: 1/1 (100%), sulfisoxazole sul2: 1/1 (100%), sulfisoxazole tet(A): 1/1 (100%), tetracycline |
1/1 (100%) | 1/1 (100%) |
| Brandenburg | N/A | N/A | N/A | N/A | 1 (<1%) |
aph(3″)-Ib & aph(6)-Id: 1/1 (100%), streptomycin blaTEM-1A: 1/1 (100%), ampicillin gyrA(87): 1/1 (100%), nalidixic acid, ciprofloxacine sul2: 1/1 (100%), sulfisoxazole tet(A): 1/1 (100%), tetracycline |
1/1 (100%) | 1/1 (100%) |
| Livingstone | N/A | N/A | N/A | N/A | 5 (4%) | No determinants detected: 5/5 (100%) | 0/5 (0%) | 0/5 (0%) |
| Panama | N/A | N/A | N/A | N/A | 6 (4%) |
aadA5: 6/6 (100%), streptomycin aph(3″)-Ib & aph(6)-Id: 6/6 (100%), streptomycin dfrA17: 6/6 (100%), trimethoprim floR: 6/6 (100%), chloramphenicol qnrB19: 6/6 (100%), ciprofloxacinf sul2: 6/6 (100%), sulfisoxazole tet(B): 6/6 (100%), tetracycline |
6/6 (100%) | 6/6 (100%) |
Two hundred and seventy isolates (135 human, 135 pig ear treat samples) were screened for resistance determinants via whole genome sequencing with results as shown.
All sequenced clinical isolates have been deposited to the National Center for Biotechnology Information BioProject PRJNA230403.
MDR = Multidrug resistant, which was defined as resistance (or nonsusceptibility, for ciprofloxacin) to ≥3 antimicrobial classes.
Clinically important resistance was defined as resistance (or nonsusceptibility, for ciprofloxacin) to ≥1 antimicrobial recommended for treatment of salmonellosis (i.e., ampicillin, azithromycin, ceftriaxone, ciprofloxacin, or trimethoprim-sulfamethoxazole).
Although the dfrA12 gene was identified by ResFinder, the gene is interrupted, and the product does not appear functional. Therefore, these isolates are not expected to show phenotypic resistance to trimethoprim.
Single chromosomal mutations in the quinolone resistance-determining region (QRDR) of target enzyme genes such as gyrA typically confers resistance to nalidixic acid and intermediate interpretation to ciprofloxacin by phenotypic testing.
Single plasmid-mediated quinolone resistance genes (such as qnr genes) typically confer intermediate susceptibility to ciprofloxacin by phenotypic testing. No isolates harbored more than one quinolone resistance gene.