Study assesses FFPE tissue ISH test for goat paratuberculosis

A new diagnostic study suggests veterinary pathologists may have a stronger postmortem tool for confirming paratuberculosis in goats. In a Journal of Veterinary Diagnostic Investigation article first published May 14, 2026, Cornell-affiliated researchers found that an RNAscope-based chromogenic pan-Mycobacterium in situ hybridization assay detected signal in 19 of 20 archived goat intestinal cases of paratuberculosis, while all 5 negative controls remained negative. (journals.sagepub.com)

The work addresses a familiar bottleneck in Johne’s disease diagnostics. Paratuberculosis, caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a chronic enteric infection of ruminants that can reduce milk production, drive weight loss, and contribute to mortality. Definitive diagnosis has long relied on culture, PCR, histopathology, and acid-fast staining, but each comes with tradeoffs. Culture is slow, often taking 8 to 16 weeks in this goat study’s framing, and standard stains may fail to show organisms when lesions are paucibacillary or tissue quality is poor. (acvp.org)

According to the conference abstract that appears to match the full paper, the investigators reviewed archived intestinal cases and selected 20 for ISH testing, including 11 multibacillary and 9 paucibacillary infections identified on Ziehl-Neelsen stain, plus 5 negative controls that were culture- and PCR-negative for MAP. Ten cases had prior culture results, with 9 positive. Seven had prior MAP PCR, with all 7 positive. Pan-Mycobacterium PCR performed on FFPE tissue was positive in 18 of 20 cases, while the remaining two had been confirmed by culture and PCR. ISH produced hybridization signal in 19 of 20 cases overall and in 8 of 9 paucibacillary cases. The single ISH-negative case had severe autolysis. (acvp.org)

The goat paper also builds on a broader 2026 validation effort from some of the same investigators, who reported that a pan-Mycobacteriaceae RNAscope assay detected mycobacterial signal across a wide range of archived FFPE tissues from multiple animal species and remained negative in tissues infected with other bacteria. In that study, the authors argued the assay could improve specificity over acid-fast stains and immunohistochemistry, which can be limited by false negatives or cross-reactivity. That broader background helps explain why the goat-specific study is noteworthy: it moves the platform from general mycobacterial detection into a specific, clinically relevant caprine use case. (journals.sagepub.com)

Industry reaction was limited, but the findings line up with current expert thinking that paratuberculosis control is still constrained by imperfect diagnostics. A 2025 DISCONTOOLS-based expert review highlighted ongoing gaps in diagnostics, vaccination, and control strategies, while recent reviews of sheep and goat paratuberculosis have emphasized the need to combine postmortem morphology with molecular methods because no single test performs ideally across all stages of disease. Cornell’s own Johne’s testing guidance likewise recommends tissue culture of the ileocecal region or distal ileum and mesenteric lymph nodes alongside histopathology and acid-fast staining for necropsy samples. (pure.qub.ac.uk)

Why it matters: For veterinary professionals, especially diagnosticians and small ruminant veterinarians, this is less about replacing gold-standard methods than about filling a common diagnostic gap. In practice, goat cases may arrive autolyzed, fixed without fresh tissue retained, or with sparse organisms that make Ziehl-Neelsen interpretation difficult. An assay that works on FFPE tissue and appears to retain sensitivity in paucibacillary disease could improve confidence in postmortem diagnosis, support herd-level decision-making, and reduce the number of equivocal pathology reports. That matters because MAP control depends on recognizing infected animals and herds, even though antemortem and postmortem test performance varies by stage of infection. (acvp.org)

There are still important caveats. The study was small, retrospective, and based on archived material, so it does not yet establish how the assay will perform across laboratories, specimen types, or earlier disease stages. It also appears to function as a pan-Mycobacterium assay rather than a MAP-only probe, meaning diagnostic interpretation still depends on lesion pattern, case context, and ancillary confirmation. Even so, the absence of signal in negative controls and the strong performance in paucibacillary cases suggest the method could become a useful adjunct in veterinary pathology workflows. (acvp.org)

What to watch: The next step is likely broader laboratory validation, including prospective comparison with tissue PCR, culture, and routine histopathology in larger goat cohorts and possibly cattle or sheep, as diagnostic labs assess whether the added value justifies adoption in routine Johne’s disease workups. (journals.sagepub.com)