| Summary: | The intestinal protozoan parasite <i>Cryptosporidium</i> is an important cause of diarrheal disease worldwide. The aim of this study was to expand the knowledge on the molecular epidemiology of human cryptosporidiosis in Sweden to better understand transmission patterns and potential zoonotic sources. <i>Cryptosporidium</i>-positive fecal samples were collected between January 2013 and December 2014 from 12 regional clinical microbiology laboratories in Sweden. Species and subtype determination was achieved using small subunit ribosomal RNA and 60 kDa glycoprotein gene analysis. Samples were available for 398 patients, of whom 250 (63%) and 138 (35%) had acquired the infection in Sweden and abroad, respectively. Species identification was successful for 95% (379/398) of the samples, revealing 12 species/genotypes: <i>Cryptosporidium parvum</i> (<i>n </i>=<i> </i>299), <i>C. hominis</i> (<i>n </i>=<i> </i>49), <i>C. meleagridis</i> (<i>n </i>=<i> </i>8), <i>C. cuniculus</i> (<i>n </i>=<i> </i>5), <i>Cryptosporidium</i> chipmunk genotype I (<i>n </i>=<i> </i>5), <i>C. felis</i> (<i>n </i>=<i> </i>4), <i>C. erinacei</i> (<i>n </i>=<i> </i>2), <i>C. ubiquitum</i> (<i>n </i>=<i> </i>2), and one each of <i>C. suis</i>, <i>C. viatorum</i>, <i>C. ditrichi</i>, and <i>Cryptosporidium</i> horse genotype. One patient was co-infected with <i>C. parvum</i> and <i>C. hominis</i>. Subtyping was successful for all species/genotypes, except for <i>C. ditrichi</i>, and revealed large diversity, with 29 subtype families (including 4 novel ones: <i>C. parvum</i> IIr, IIs, IIt, and <i>Cryptosporidium</i> horse genotype Vic) and 81 different subtypes. The most common subtype families were IIa (<i>n </i>=<i> </i>164) and IId (<i>n </i>=<i> </i>118) for <i>C. parvum</i> and Ib (<i>n </i>=<i> </i>26) and Ia (<i>n </i>=<i> </i>12) for <i>C. hominis</i>. Infections caused by the zoonotic <i>C. parvum</i> subtype families IIa and IId dominated both in patients infected in Sweden and abroad, while most <i>C. hominis</i> cases were travel-related. Infections caused by non-<i>hominis</i> and non-<i>parvum</i> species were quite common (8%) and equally represented in cases infected in Sweden and abroad.
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