Temporal analysis of Mesomycoplasma ovipneumoniae strain composition from domestic sheep reveals complex dynamics within nasal swabs

ABSTRACT Mesomycoplasma ovipneumoniae is a respiratory pathogen commonly found in domestic sheep that represents a significant challenge to bighorn sheep conservation. Contemporary strain-typing strategies do not discriminate between single- and multi-strain infections, where multi-strain infections are suggested to result in more severe clinical disease. Herein, strain-typing markers were adapted to deep amplicon sequencing to quantify and determine the relative ratios of M. ovipneumoniae strains from nasal swabs. Sampling was performed on three domestic breeds within a single flock and geographic location over the course of 1 year, during different management stages. The resultant amplicon sequence variants (ASVs) revealed high genetic variation; however, the time course did not discern changes in the percentage of disparate ASVs within the flock. Individuals tended to have multi-genotype (MG) detections that later predominated with single-genotype (SG) detections during the February sampling; specifically, within the Targhee breed. Swabs were commonly comprised of a major ASV with one or multiple minor ASVs. Analysis of ASV transitions between samplings revealed that the Targhee breed had a season-based effect, while Suffolk was most stable over time. Despite being limited to a small number of animals and breeds, this study reveals the dynamic nature of M. ovipneumoniae genotypes isolated via nasal swabs collected from domestic sheep. While the genotypic composition of shed bacteria is likely multifactorial, these data suggest a potential effect of breed and season. Additional studies are required to determine the effect of multi-strain infections and rapid change in shed strains on domestic sheep production and potential spillover into wildlife. IMPORTANCE Mesomycoplasma ovipneumoniae is an important pathogen of the ovine respiratory complex, which results in pneumonia within domestic sheep. Strain typing of this bacterium has historically involved PCR amplification of a small number of housekeeping genes with subsequent Sanger sequencing. While informative, this method leaves a knowledge gap with respect to multi-strain infections. Within this study, strain typing was modernized by adapting typical multi-locus strain typing to a next-generation sequencing technology via deep amplicon sequencing on the Illumina platform. Using this updated methodology resulted in the uncovering of dynamic shifts in the genetic makeup of M. ovipneumoniae shed from the nasal passages of domestic sheep within the studied flock. Additionally, it was discerned that the multi-strain infection dynamics were affected by both breed and seasonality.