Henneguya species are myxozoans, a suborder of Cnidaria, which can affect the gills and extrarespiratory organs of the African sharptooth catfish, Clarias gariepinus. This research describes natural infection-induced histological alterations caused by the Henneguya species present. The Henneguya species were also identified molecularly using DNA sequenced from infected tissue cysts, and phylogenetically analyzed. Clinical investigations revealed cyst-like nodules on the fish gill filaments and extrarespiratory organs. Within a milky fluid inside the cysts were several Henneguya-like spores. Henneguya sp. infested 27.5% of the fish, with the highest prevalence in the gills compared to the extrarespiratory organs. The Henneguya species parasitized the gill and the dendritic tissues, resulting in histopathological characteristics. The plasmodia's developmental stages resulted in destructive damage which manifested as marked necrosis, which was replaced by a focal aggregation of inflammatory cells. Amplification of the 18S ribosomal DNA from the fish parasites was followed by sequencing, which confirmed their identities as new species Henneguya qenabranchiae n. sp. and Henneguya qenasuprabranchiae n. sp. with 99.53 and 99.64% identities, respectively, to Henneguya sp. 1 HS-2015. The two C. gariepinus myxozoans shared some characteristics based on morphologic and phylogenetic analysis as previously published, where it was proposed that they were a sister lineage to Henneguya species in Egypt, and it is now proposed that they are new species.

A natural parasitic infection with the external ciliate protozoan, Chilodonella hexasticha, was recorded 3 days post‐transportation (PT) in the gills and skin of African catfish (Clarias gariepinus). Infected fish displayed behavioural changes and typical signs of infection. Mortalities started on day 7 PT and stopped on day 13 PT, where cumulative mortality reached 62.2%. The expression of immune‐relevant genes, interleukin‐1β (IL‐1β), major histocompatibility complex class II (MHC‐II) and interleukin‐10 (IL‐10) in the gills, head kidneys and spleen of the Chilodonella‐infected and control uninfected fish were investigated using quantitative real‐time polymerase chain reaction (PCR) on days 7‐, 14‐ and 28 PT. Expression levels of IL‐1β in the gills showed a significant upregulation on day 7 PT but were not significantly different from those of the control fish in the head kidneys and spleen at all time points investigated. Expression levels of MHC‐II were significantly elevated in the gills (days 7‐ and 14 PT), head kidneys (days 7‐, 14‐ and 28 PT) and spleen (days 7‐ and 14 PT), whereas IL‐10 showed a significant upregulation only in the gills on day 14 PT, with no significant changes in all other tissues examined. Additionally, histological studies were conducted to investigate the alterations in the head kidney and spleen tissue structures associated with the immune response to infection and the changes in the expression profiles of the immune‐related genes in these organs. Depletion of the renal and splenic tissues, simultaneously with prominent melanomacrophage infiltration, was observed. Also, the histopathologic changes caused by C. hexasticha in the gills of infected fish involved aggravated tissue damage characterized by hyperplasia, and necrosis of the gill lamellae was recorded.