ABSTRACT. Pneumocystis carinii (P. carinii) is an opportunistic fungal pathogen commonly found in many mammalian host species, but rarely in goats. A 3-year-old, female, Tokara-native-goat (Capra hircus domesticus) died of apparent malnutrition caused by multibacillary paratuberculosis. While inflammatory response was slightly observed in the respiratory organs, P. carinii trophozoites and cysts were immunohistochemically observed in the pulmonary alveoli of the infected animal. P. carinii specific DNA was amplified from the formalin fixed and paraffin embedded lung samples. Molecular phylogenetic analyses of the mitochondrial large subunit ribosomal RNA region of P. carinii revealed genetic divergence from previously described P. carinii isolates from other mammalian host species. This is the first description of concurrent infection with P. carinii and the Mycobacterium avium subspecies paratuberculosis in a domestic goat. Pneumocystis carinii(P. carinii) is an opportunistic fungal pathogen that can cause severe and sometimes fatal pneumonia in immunosuppressed hosts. It affects a variety of mammalian host species including humans, monkeys, rats, mice, ferrets, sloths, dogs, cats, sheeps, marmosets and voles [1]. In goats, P. carinii infection is very rare with only a few clinical cases reported thus far [9,15]. The basic biology and genomic signature of goat-derived P. carinii have not yet been verified.Mycobacterium avium, subspecies paratuberculosis (MAP), is the causative bacterial agent of 'paratuberculosis' (or 'Johne's disease') in ruminant species. The resulting infection will either be cleared by the host or develop into subclinical and in some cases clinical disease. Classical clinical signs of paratuberculosis in cattle are chronic, profuse and watery diarrhea coupled with chronic emaciation, despite adequate food intake [16]. In goats, the signs are less specific, and weight loss is the only obvious sign [16]. In Japan, paratuberculosis in goats occurs sporadically, and, despite nationwide eradication strategies, new cases of paratuberculosis are often identified. The purpose of the current report is to describe the histopathological and molecular features of P. carinii infection in a MAP infected goat.A 3-year-old female Tokara-native-goat (Capra hircus domesticus) with a 6-month history of systemic hair loss, intermittent 'muddy' diarrhea and marked emaciation died and was submitted to the Ishikari Livestock Hygiene Service Center for postmortem examination. The necropsy revealed that the cecal mucosa was dark red in color and heavily thickened. The jejunum, ileum and colon had a similar hue. There were annular thickenings of the wall or scattered, firm elevations on the mucosal surface of the jejunum and ileum, with smaller nodules sparsely distributed on the mucosal surface in the colon. The jejunal, ileal, cecal, colic and mesenteric lymph nodes were highly enlarged, and scattered small white foci were observed on section. Cultures of rectal feces and mesenteric lymph nodes were performed as d...

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