| Summary: | Contagious ovine digital dermatitis (CODD) and footrot (FR), a sub-acute or acute necrotic (decaying) infectious disease involving the hoof and underlying tissues, pose economic challenges to herds in Spain and worldwide. The aetiological agent for FR is <i>Dichelobacter nodosus</i>, while CODD is caused by pathogenic <i>Treponema</i> phylogroups. We detail the findings derived from the analysis by qPCR of 105 pooled samples from 100 ovine and five caprine herds in Spain and Portugal, alongside 15 samples from healthy flocks in order to identify <i>Dichelobacter nodosus</i>, <i>Fusobacterium necrophorum</i>, <i>Treponema</i> spp., and three pathogenic <i>Treponema</i> phylogroups (<i>T. phagedenis</i>, <i>T. medium</i>, and <i>T. pedis</i>). <i>Treponema</i> spp. were detected in all 120 pools, including samples from the 15 healthy flocks where only one positive result for <i>F. necrophorum</i> was recorded. Mixed infections by agents different from <i>Treponema</i> spp. were identified in 68.57% of samples. Positive results for <i>F. necrophorum</i> and/or <i>D. nodosus</i>, were obtained for 91.4% of the pools, whereas the presence of the three pathogenic <i>Treponema</i> phylogroups was rare: each of them appeared in isolation in a single pool, while they were found in 18 pools in combination with other agents. While <i>F. necrophorum</i> was the sole finding in 16.2% of samples from affected herds, <i>D. nodosus</i> (the footrot causative agent) was only detected in 61% of affected farms. An improved qPCR protocol was implemented to determine the serogroups of <i>D. nodosus</i> in the samples and found all of them (except the G serogroup), often in combined infections (35.1%). This report concludes with comprehensive proposals for diagnosing, preventing, and treating hoof ailments, remarking the interest of the information about <i>D. nodosus</i> serogroups in order to improve the efficiency of immunization by choosing appropriate vaccine protocols.
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