Outbreak of Diarrhea Caused by a Novel Cryptosporidium hominis Subtype During British Military Training in Kenya

Abstract

Background We report clinical, epidemiological and laboratory features of a large diarrhoea outbreak caused by a novel Cryptosporidium hominis subtype during British military training in Kenya between February - April 2022. Methods Data were collated from diarrhoea cases and faecal samples were analysed on site using multiplex PCR BioFire® FilmArray®. Water was tested using Colilert kits (IDEXX, UK). DNA was extracted from faeces for molecular characterisation of Cryptosporidium A135, Lib13, ssu rRNA and gp60 genes. Results 172/1200 (14.3%) personnel at risk developed diarrhoea over 69 days. 106 primary faecal samples were tested and 63/106 ([59.4%] 95% CI 0.49-0.69) were positive for Cryptosporidium spp. Thirty-eight had Cryptosporidium spp. alone and 25 had Cryptosporidium spp. with ≥1 other pathogen. A further 27/106 ([25.5%] 95% CI 0.18-0.35%) had non-Cryptosporidium pathogens only and 16/106 ([15.1%] 95% CI 0.09-0.23) were negative. C. hominis was detected in 58/63 (92.1%) Cryptosporidium spp. positive primary samples but the others were not genotypable. Twenty-seven C. hominis specimens were subtypable; one was gp60 subtype IeA11G3T3 and 26 were an unusual subtype ImA13G1 (GenBank accession OP699729), supporting epidemiological evidence suggesting a point source outbreak from contaminated swimming water. Diarrhoea persisted for a mean (SD) 7.6 (4.6) days in Cryptosporidium spp. cases compared to 2.3 (0.9) days in non-Cryptosporidium cases (p = 0.001). Conclusions Real-time multiplex-PCR faecal testing was vital in managing this large cryptosporidiosis outbreak. The aetiology of a rare C. hominis gp60 subtype emphasises the need for more genotypic surveillance to identify widening host and geographic ranges of novel C. hominis subtypes.