Infections with Brachyspira hyodysenteriae, the etiological agent of swine dysentery, result in major economic losses in the pig industry worldwide.
More...Infections with Brachyspira hyodysenteriae, the etiological agent of swine dysentery, result in major economic losses in the pig industry worldwide. Even though microbial differentiation of various Brachyspira species can be obtained via PCR, no quick diagnostics for antimicrobial susceptibility testing are in place to date, which is mainly due to its time-consuming (4-7 days) anaerobic growth requirements. Veterinarians often rely on a clinical diagnosis for initiating antimicrobial treatment. These empirical treatments are not always effective, which may be due to high levels of acquired resistance in B. hyodysenteriae field isolates. By using long-read only whole genome sequencing and a custom-trained Bonito basecalling model, 81 complete B. hyodysenteriae genomes with median Q51 scores and 99% completeness were obtained from 86 field strains. This allowed to assess the predictive potential of genetic markers in relation to the observed acquired resistance phenotypes as obtained via agar dilution susceptibility testing. Multi-drug resistance was observed in 88% or 46% of the tested strains based on epidemiological cut-off and clinical breakpoint values, respectively. The predictive power of genetic hallmarks (genes and/or gene mutations) for antimicrobial susceptibility testing was promising. Sensitivity and specificity for tiamulin (tva(A) & 50SL2N148S - 99%/67%), valnemulin (tva(A) - 97%/92%), lincomycin (23SA2153T/G & lnuC - 94%/100%), tylvalosin (23SA2153T/G - 99%/93%), and doxycycline (16SG1026C - 93%/87%) were determined. Exploiting these genotypic features in sequencing-based workflows will speed up swine dysentery diagnostics in veterinary medicine and tailor proper antimicrobial use.
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