Infection by the invasive parasite Myxobolus cerebralis (causing whirling disease in salmonids) is strongly influenced by a stream's physico-chemical characteristics, which might affect host pathology. We examined whether environmental variables of a M. cerebralis-positive tributary to Yellowstone Lake, Yellowstone National Park, U.S.A., correlated with the histopathology of naturally infected native cutthroat trout Oncorhynchus clarkii bouvieri. Host inflammatory response and cranial cartilage lesions were the main correlates with whirling behavior. Canonical correlation analyses showed that the prevalence of trout with severe lesions in the cranial and jaw cartilages was highest in stream sites with a combination of high temperature and low specific conductivity. Our results reveal that environmental components can affect when and where a pathogen resides within the host, and manifestation of disease. Recognition of the synergism among environmental and histopathology factors most conducive to whirling disease will increase our prediction and detection abilities for M. cerebralis in salmonid hosts.

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