Investigating within-host population diversity of Cryptosporidium parvum using BlooMine.

ABSTRACT: Investigating multiplicity-of-infection (MOI) in pathogen populations is central to understanding within-host evolutionary dynamics. In Cryptosporidium parvum, MOI may play a pivotal role in diversification due to the parasite's sexually recombinogenic life cycle, which occurs entirely within a single host. Subtyping of C. parvum typically relies on variation at short tandem repeat (STR) loci - such as that found in the 60kDa surface glycoprotein gene, Gp60 - but accurate profiling of these regions from next-generation sequencing (NGS) data remains technically challenging. Here, we apply BlooMine, an alignment-free, Bloom filter based tool that isolates STR containing reads via a novel pseudo-alignment strategy robust to structural and sequence variation. Using this approach, we analyse th

SUBMITTER: Morris AV 

PROVIDER: S-EPMC12636221 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature