Detection of Neorickettsia risticii in antemortem fecal and postmortem fetal samples, with genomic insights from complete genome sequencing of a strain recovered from an aborted equine fetus.

Neorickettsia risticii (N. risticii) is an obligatory intracellular bacterium that causes Potomac horse fever (PHF), a disease clinically characterized by diarrhea, pyrexia, and laminitis in horses. Although sporadic reports of N. risticii infection have been linked to abortion in mares, a detailed retrospective study, including genomic analysis of the pathogen from an aborted fetus, has not been published. This study examined 546 fecal samples from clinically ill horses (January 1, 2017-December 31, 2024) and 833 colon samples from aborted equine fetuses (September 20, 2018-December 31, 2024). Using real-time PCR, N. risticii was detected in 11.5 % of fecal samples and 1.08 % of fetal colon samples. Positive antemortem cases were detected between May and September, while fetal cases occurred from September to December. The fetuses were 5-8 months of gestational age, all showing microscopic evidence of colitis. A shotgun metagenomic approach was applied directly to an archived fetal colon sample using the MiSeq platform, yielding a complete genome of N. risticii (strain KY18-EqFetus) with 99.72 % nucleotide identity to the N. risticii strain Illinois reference genome. The genome was 879,923 bp with a GC content of 41.3 %, and 2024 variants (including indels and nucleotide polymorphisms) were identified. Notably, three genes coding for small hypothetical proteins present in the reference strain were absent in KY18-EqFetus. This study provides a comprehensive investigation of N. risticii in both antemortem and postmortem equine samples and reports the first complete genome assembly of the pathogen directly from an aborted equine.