Genomic heterogeneity of NAD(P)H dehydrogenase predisposes Cryptosporidium to clofazimine resistance.

The parasite Cryptosporidium is a leading cause of life-threatening diarrhoeal disease, and effective treatment is not available. Clofazimine, an antimicrobial used for treatment of leprosy and tuberculosis, was found to have potent anti-Cryptosporidium activity but it failed in a human trial. This was attributed to poor bioavailability. Here we observed differential clofazimine susceptibility among C. parvum parasite isolates, which we exploit to identify a single genomic locus encoding the type II NADH dehydrogenase (NDH2) in an unbiased genetic cross. Targeted genetic ablation of ndh2 resulted in high-level clofazimine resistance and biochemical studies demonstrated NDH2-mediated electron transfer to clofazimine. Through genomic analyses, we uncovered heterogeneity at the ndh2 locus for C. parvum and C. hominis, and widespread carriage of a conserved attenuated allele across multiple continents. This heterogeneity allows parasites genomically linked through frequent sexual recombination to adjust to changing NDH2 requirements and predisposes Cryptosporidium to evade clofazimine treatment.