Subtyping Novel Zoonotic Pathogen Cryptosporidium Chipmunk Genotype I.

Guo Y1, Cebelinski E2, Matusevich C3, Alderisio KA4, Lebbad M5, McEvoy J6, Roellig DM7, Yang C8, Feng Y9, Xiao L10.

Author information

Abstract

Cryptosporidium chipmunk genotype I is an emerging zoonotic pathogen in humans. The lack of subtyping tools makes it impossible to determine the role of zoonotic transmission in epidemiology. To identify potential subtyping markers, we sequenced the genome of a human chipmunk genotype I isolate. Altogether, 9,509,783 bp of assembled sequences in 853 contigs were obtained, with an N50 of 117,886 bp and over 200-fold coverage. Based on the whole genome sequence data, two genetic markers encoding the 60-kDa glycoprotein (gp60) and a mucin protein (ortholog of cgd1_470) were selected for the development of a subtyping tool. The tool was used in characterizing chipmunk genotype I in 25 human specimens from four US states and Sweden, one specimen each from an eastern grey squirrel, a chipmunk and a deer mouse, and 4 water samples from New York. At the gp60 locus, although different subtypes were seen among animals, water and humans, the 15 subtypes identified differed mostly in the number of trinucleotide repeats (TCA, TCG or TCT) in the serine repeat region, with only two single nucleotide polymorphisms in the non-repeat region. Some geographic differences were found in subtype distribution of chipmunk genotype I from humans. In contrast, only two subtypes were found at the mucin locus, which differed from each other in the number of a 30-bp minisatellite repeat. Thus, Cryptosporidium chipmunk genotype I from humans and wildlife are genetically similar and zoonotic transmission could play a potential role in human infections.