We report the outcomes of a small survey on the challenging topic of developing links between researchers working in academia and industry that show that, while people in different sectors strongly support such links, barriers remain that obstruct this process. First, we summarise a workshop held at the European Federation of Biotechnology meeting on Microbial Stress Responses (online in 2020) on “Industrial applications of low pH stress on microbial bio-based production”, as an example of an initiative fostering links between pure and applied research. We present work of our COST Action on “Understanding and exploiting the impacts of low pH on micro-organisms”. This mainly implies assessing sequencing accuracy and the predictive power of genetic hallmarks in relation to their observed (multi)resistance phenotypes. Nevertheless, their potential implementation should be validated extensively. To enable practitioners to tailor antimicrobial treatment to specific strains, long-read sequencing-based methods are expected to lead to rapid methods in the future. Nevertheless, no quick diagnostic tools are available for antimicrobial susceptibility testing due to extended growth requirements (7 to 14 days). IMPORTANCE Diagnostics for swine dysentery rely on the identification of Brachyspira species using molecular techniques. The predictive power of these genetic hallmarks is promising for use in sequencing-based workflows to speed up swine dysentery diagnostics in veterinary medicine and determine proper antimicrobial use. Sensitivity and specificity for tiamulin, valnemulin [tva(A), 97% and 92%), lincomycin (23SA2153T/G and lnuC, 94% and 100%), tylvalosin (23SA2153T/G, 99% and 93%), and doxycycline (16SG1026C, 93% and 87%) were determined. The predictive power of genetic hallmarks (genes and/or gene mutations) for antimicrobial susceptibility testing was promising. Multidrug resistance was observed in 77% and 21% of the tested strains based on epidemiological cutoff and clinical breakpoint values, respectively. This allowed the assessment of the predictive potential of genetic markers in relation to the observed acquired resistance phenotypes obtained via agar dilution susceptibility testing. hyodysenteriae genomes with median Q51 scores and 99% completeness were obtained from 86 field strains. By using long-read-only whole-genome sequencing and a custom-trained Bonito base-calling model, 81 complete B. These treatments are not always effective, which may be due to high levels of acquired resistance in B. Veterinarians often rely on a clinical diagnosis for initiating antimicrobial treatment. Even though microbial differentiation of various Brachyspira species can be obtained via PCR, no quick diagnostics for antimicrobial susceptibility testing are in place, which is mainly due to the time-consuming (4 to 7 days) anaerobic growth requirements of these organisms. " Tableau Desktop.Infections with Brachyspira hyodysenteriae, the etiological agent of swine dysentery, result in major economic losses in the pig industry worldwide.
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