TABLE 7.
Concordance between broth microdilution susceptibility and WGS of 48 Mannheimia haemolytica isolates
| Genotype (+ or −)/broth microdilution susceptibility (S, I, or R)b | No. isolates (%) | Error type a | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Antimicrobial | Occasion | −/S | +/S | −/I | +/I | −/R | +/R | P‐value | Concordant | Discordant | Very major | Major | Minor |
| FLOR | Arrival | 26 | 0 | 0 | 0 | 0 | 0 | 1 | 26 (100%) | 0 | 0 | 0 | 0 |
| Revacc | 7 | 0 | 6 | 0 | 1 | 8 | .03 | 15 (68.2%) | 7 (31.8%) | 1 (4.5%) | 0 | 6 (27.3%) | |
| CEF | Arrival | 26 | 0 | 0 | 0 | 0 | 0 | 1 | 26 (100%) | 0 | 0 | 0 | 0 |
| Revacc | 22 | 0 | 0 | 0 | 0 | 0 | 1 | 22 (100%) | 0 | 0 | 0 | 0 | |
| PEN | Arrival | 11 | 0 | 13 | 0 | 2 | 0 | 0 | 11 (42.3%) | 15 (57.7%) | 2 (7.7%) | 0 | 13 (50%) |
| Revacc | 0 | 0 | 0 | 3 | 0 | 19 | .2 | 19 (86.4%) | 3 (13.6%) | 0 | 0 | 3 (13.6%) | |
| OXY | Arrival | 25 | 0 | 0 | 0 | 0 | 1 | 1 | 26 (100%) | 0 | 0 | 0 | 0 |
| Revacc | 0 | 0 | 0 | 0 | 0 | 22 | 1 | 22 (100%) | 0 | 0 | 0 | 0 | |
| ENR | Arrival | 26 | 0 | 0 | 0 | 0 | 0 | 1 | 26 (100%) | 0 | 0 | 0 | 0 |
| Revacc | 0 | 0 | 0 | 0 | 0 | 22 | 1 | 22 (100%) | 0 | 0 | 0 | 0 | |
| DANO | Arrival | 26 | 0 | 0 | 0 | 0 | 0 | 1 | 26 (100%) | 0 | 0 | 0 | 0 |
| Revacc | 0 | 0 | 0 | 0 | 0 | 22 | 1 | 22 (100%) | 0 | 0 | 0 | 0 | |
| TIL | Arrival | 22 | 0 | 3 | 0 | 1 | 0 | .5 | 22 (84.6%) | 4 (15.4%) | 1 (3.8%) | 0 | 3 (11.5%) |
| Revacc | 0 | 0 | 0 | 0 | 0 | 22 | 1 | 22 (100%) | 0 | 0 | 0 | 0 | |
| TUL | Arrival | 26 | 0 | 0 | 0 | 0 | 0 | 1 | 26 (100%) | 0 | 0 | 0 | 0 |
| Revacc | 0 | 0 | 0 | 1 | 0 | 21 | 1 | 21 (95.5%) | 1 (4.5%) | 0 | 0 | 1 (4.5%) | |
Notes: Concordance for arrival isolates assessed out of 26 isolates, concordance for revaccination isolates assessed out of 22 isolates. Susceptibility interpretation indicated as susceptible (S), intermediate (I), and resistant (R).
Abbreviations: CEF, ceftiofur; ENR, enrofloxacin; FLOR, florfenicol; GAM, gamithromycin; TIL, tilmicosin; TUL, tulathromycin.
Very major = negative for resistance gene but classified as resistant by broth microdilution; Major = positive for resistance gene but classified as susceptible by broth microdilution; Minor = classified as intermediate by broth microdilution.
Phenotype (S or R or I)/genotype (−) = Any susceptibility phenotype and negative for all macrolide resistance genes or phenotype (S or R or I)/genotype (+) = Any susceptibility phenotype and positive for any one macrolide resistance gene.