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

Abstract

Brachyspira hyodysenteriae is the principal cause of swine dysentery, a disease that threatens economic productivity of pigs in many countries as it can spread readily within and between farms, and only a small number of antimicrobials are authorized for treatment of pigs. In this study, we performed whole-genome sequencing (WGS) of 81 B. hyodysenteriae archived at the Animal and Plant Health Agency (APHA) from diagnostic submissions and herd monitoring in England and Wales between 2004 and 2015. The resulting genome sequences were analyzed alongside 34 genomes we previously published. Multi-locus sequence typing (MLST) showed a diverse population with 32 sequence types (STs) among the 115 APHA isolates, 25 of them identified only in England; while also confirming that the dominant European clonal complexes, CC8 and CC52, were common in the United Kingdom. A core-genome SNP tree typically clustered the isolates by ST, with isolates from some STs detected only within a specific region in England, although others were more widespread, suggesting transmission between different regions. Also, some STs were more conserved in their core genome than others, despite these isolates being from different holdings, regions and years. Minimum inhibitory concentrations to commonly used antimicrobials (Tiamulin, Valnemulin, Doxycycline, Lincomycin, Tylosin, Tylvalosin) were determined for 82 of the genome-sequenced isolates; genomic analysis revealed mutations generally correlated well with the corresponding resistance phenotype. There was a major swine dysentery intervention program in 2009–2010, and antimicrobial survival curves showed a significant reduction in sensitivity to tiamulin and valnemulin in isolates collected in and after 2010, compared to earlier isolates. This correlated with a significant increase in post-2009 isolates harboring the pleuromutilin resistance gene tva(A), which if present, may facilitate higher levels of resistance. The reduction in susceptibility of Brachyspira from diagnostic submissions to pleuromutilins, emphasizes the need for prudent treatment, control and eradication strategies.

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

“…3A, the tva(A) gene is widely distributed among the B. hyodysenteriae population. Its presence showed sensitivity and specificity (Sn/Sp) of 94.4%/61.8% and 99.1%/84.6%, respectively, for tiamulin (38), Germany (13), Sweden (15), Spain (23,39), the UK (1,11), Italy (41), Poland (40), Brazil (42), and Switzerland (26). Belgian strains from 2010 to 2015 (24) and 2018 to 2020 (this study) are indicated with dashed and solid black lines, respectively.…”

“…This work was initiated because an increased number of PCR-positive B. hyodysenteriae cases were seen at Animal Health Care Flanders since 2015 (12.6% to 20.4% in 2018). While standard antimicrobial susceptibility testing for widely used antimicrobials, such as pleuromutilins (tiamulin and valnemulin), macrolides (tylvalosin), lincosamides (lincomycin), and tetracyclines (doxycycline), was performed using the agar microdilution method, 81 complete and high-quality genomes From inside to outside, circles represent the presence and nucleotide identity of the lnuC gene, lincomycin-associated 23S rRNA gene mutation (G484A), phenotypic resistance profiles of lincomycin and tylvalosin, and genetic markers in the 23S rRNA gene (A2153T/G and A2154G) (1,48).…”

“…As described by Vyt and Hommez and by Pringle et al, MICs of all tested antimicrobial compounds should be in quality control ranges for this strain (55,56). Evaluation of resistance was based on most recently published ECOFFs and CBs, respectively, as summarized by Stubberfield et al (1): tiamulin, >0.25 and >2 mg mL 21 ; valnemulin, >0.125 mg mL 21 ; lincomycin, >1 and >16 mg mL 21 ; tylvalosin, >1 and >16 mg mL 21 ; and doxycycline, >0.5 and >4 mg mL 21 . In addition, MIC 50 s and MIC 90 s were determined as the MICs that inhibited the growth of 50% and 90% of all tested isolates, respectively.…”

“… Brachyspira hyodysenteriae is the major etiological agent of swine dysentery (SD) in pigs ( 1 ). However, in recent years, Brachyspira hampsonii and B. suanatina have also been linked to SD ( 2 , 3 ).…”

“…For example, a point mutation in the 16S rRNA gene (G1058C [ Escherichia coli numbering]) has been linked to tetracycline resistance, and multiple mutations in the fifth domain of the 23S rRNA gene (peptidyl transferase loop; A2058G/T, T2528C, and G2535A/C) and 50S ribosmal protein L3 (RPLC) protein (N148S) have been shown to result in acquired resistance to macrolide, pleuromutilin, and lincosamide antibiotics in B. hyodysenteriae ( 23 ). Also, the tva (A) and transposon-linked lnu (C) genes have been identified as genetic factors in pleuromutilin and lincomycin resistance, respectively ( 1 , 11 , 24 , 25 ).…”