Whole-Genome Sequencing of Brachyspira hyodysenteriae Isolates From England and Wales Reveals Similarities to European Isolates and Mutations Associated With Reduced Sensitivity to Antimicrobials

Molecular characterization of antimicrobial resistance in Brachyspira species isolated from UK chickens: Identification of novel variants of pleuromutilin and beta-lactam resistance genes

Brachyspira species are Gram negative, anaerobic bacteria that colonise the gut of many animals, including poultry. In poultry, Brachyspira species can be commensal (B. innocens, B. murdochii, 'B. pulli') or pathogenic (B. pilosicoli, B. intermedia, B. alvinipulli or rarely B. hyodysenteriae), the latter causing avian intestinal spirochaetosis (AIS). Antimicrobial therapy options for treatment is limited, frequently involving administration of the pleuromutilin, tiamulin, in water. In this study 38 Brachyspira isolates from chickens in the UK, representing both commensal and pathogenic species, were whole genome sequenced to identify antimicrobial resistance (AMR) mechanisms and the minimum inhibitory concentration (MIC) to a number of antimicrobials was also determined. We identified several new variants of blaOXA in B. pilosicoli and B. pulli isolates, and variations in tva which led to two new tva variants in B.murdochii and B.pulli. A number of isolates also harboured mutations known to encode AMR in the 16S and 23S rRNA genes. The percentage of isolates that were genotypically multi-drug resistance (MDR) was 16%, with the most common resistance profile being: tetracycline, pleuromutilin and beta-lactam, which were found in three 'B. pulli' and one B. pilosicoli. There was good correlation with the genotype and the corresponding antibiotic MIC phenotypes: pleuromutilins (tiamulin and valnemulin), macrolides (tylosin and tylvalosin), lincomycin and doxycycline. The occurrence of resistance determinants identified in this study in pathogenic Brachyspira, especially those which were MDR, is likely to impact treatment of AIS and clearance of infections on farm.

Antimicrobial susceptibility of U.S. porcine Brachyspira isolates and genetic diversity of B. hyodysenteriae by multilocus sequence typing

Swine dysentery, caused by Brachyspira hyodysenteriae and the newly recognized Brachyspira hampsonii in grower-finisher pigs, is a substantial economic burden in many swine-rearing countries. Antimicrobial therapy is the only commercially available measure to control and prevent Brachyspira-related colitis. However, data on antimicrobial susceptibility trends and genetic diversity of Brachyspira species from North America is limited. We evaluated the antimicrobial susceptibility profiles of U.S. Brachyspira isolates recovered between 2013 and 2022 to tiamulin, tylvalosin, lincomycin, doxycycline, bacitracin, and tylosin. In addition, we performed multilocus sequence typing (MLST) on 64 B. hyodysenteriae isolates. Overall, no distinct alterations in the susceptibility patterns over time were observed among Brachyspira species. However, resistance to the commonly used antimicrobials was seen sporadically with a higher resistance frequency to tylosin compared to other tested drugs. B. hampsonii was more susceptible to the tested drugs than B. hyodysenteriae and B. pilosicoli. MLST revealed 16 different sequence types (STs) among the 64 B. hyodysenteriae isolates tested, of which 5 STs were previously known, whereas 11 were novel. Most isolates belonged to the known STs: ST93 (n = 32) and ST107 (n = 13). Our findings indicate an overall low prevalence of resistance to clinically important antimicrobials other than tylosin and bacitracin, and high genetic diversity among the clinical Brachyspira isolates from pigs in the United States during the past decade. Further molecular, epidemiologic, and surveillance studies are needed to better understand the infection dynamics of Brachyspira on swine farms and to help develop effective control measures.

Predictive Power of Long-Read Whole-Genome Sequencing for Rapid Diagnostics of Multidrug-Resistant Brachyspira hyodysenteriae Strains

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, which is mainly due to the time-consuming (4 to 7 days) anaerobic growth requirements of these organisms. Veterinarians often rely on a clinical diagnosis for initiating antimicrobial treatment. These 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 base-calling model, 81 complete B. hyodysenteriae genomes with median Q51 scores and 99% completeness were obtained from 86 field strains. 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. Multidrug resistance was observed in 77% and 21% of the tested strains based on epidemiological cutoff 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) and 50SL3^N148S, 99% and 67%], valnemulin [tva(A), 97% and 92%), lincomycin (23S^A2153T/G and lnuC, 94% and 100%), tylvalosin (23S^A2153T/G, 99% and 93%), and doxycycline (16S^G1026C, 93% and 87%) were determined. 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. IMPORTANCE Diagnostics for swine dysentery rely on the identification of Brachyspira species using molecular techniques. Nevertheless, no quick diagnostic tools are available for antimicrobial susceptibility testing due to extended growth requirements (7 to 14 days). 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, their potential implementation should be validated extensively. This mainly implies assessing sequencing accuracy and the predictive power of genetic hallmarks in relation to their observed (multi)resistance phenotypes.