Genetic diversity of Cryptosporidium isolates from young children and livestock in eastern Ethiopia

Cryptosporidiosis is a leading cause of morbidity and mortality due to diarrhoea during early childhood in low-income countries, including Ethiopia. Human <i>Cryptosporidium</i> infections can be anthroponotically or zoonotically transmitted. This study assesses the diversity and frequency of <i>Cryptosporidium</i> species and genotypes circulating in children and young livestock in eastern Ethiopia, with the aim of tracing the sources of infection. <i>Cryptosporidium</i> isolates from young children (<i>n</i> = 152), calves (<i>n</i> = 8), lambs (<i>n</i> = 4), goat kids (<i>n</i> = 4), and camels (<i>n</i> = 11) were subjected to PCR targeting the SSU rRNA and <i>gp60</i> loci. Species and subtypes were determined by Sanger sequencing. Two <i>Cryptosporidium</i> species were found in children: <i>C. hominis</i> (75.3%, 67/89) and <i>C. parvum</i> (24.7%, 22/89). Three <i>gp60</i> subtype families, Ia (30.0%, 9/30), Ib (10.0%, 3/30), and Id (60.0%, 18/30), were identified within <i>C. hominis</i> whereas <i>gp60</i> subtype families IIe (55.6%, 10/18) and IIc (44.4%, 8/18) were identified within <i>C. parvum</i>. The predominant subtypes were <i>C. hominis</i> IdA15 and <i>C. parvum</i> IIeA10G1. Among livestock, <i>C</i> <i>. ubiquitum</i> was found in two camels and a goat kid, <i>C. xiaoi</i> in a lamb and goat kid, and <i>C. ryanae</i> in a calf. We did not identify any <i>C. parvum</i> among the animal samples. The goat isolate of <i>C. xiaoi</i> was characterised as subtype XXIIIg. Human cryptosporidiosis cases in eastern Ethiopia are primarily caused by anthroponotically transmitted <i>Cryptosporidium</i> species and subtypes, whereas zoonotic transmission events seem infrequent.