AUTHOR=Cabarcas Felipe , Galvan-Diaz Ana Luz , Arias-Agudelo Laura M. , García-Montoya Gisela María , Daza Juan M. , Alzate Juan F. 

TITLE=Cryptosporidium hominis Phylogenomic Analysis Reveals Separate Lineages With Continental Segregation

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.740940

DOI=10.3389/fgene.2021.740940

ISSN=1664-8021

ABSTRACT=<p><italic>Cryptosporidium</italic> is a leading cause of waterborne outbreaks globally, and <italic>Cryptosporidium hominis</italic> and <italic>C. parvum</italic> are the principal cause of human cryptosporidiosis on the planet. Thanks to the advances in Next-Generation Sequencing (NGS) sequencing and bioinformatic software development, more than 100 genomes have been generated in the last decade using a metagenomic-like strategy. This procedure involves the parasite oocyst enrichment from stool samples of infected individuals, NGS sequencing, metagenomic assembly, parasite genome computational filtering, and comparative genomic analysis. Following this approach, genomes of infected individuals of all continents have been generated, although with striking different quality results. In this study, we performed a thorough comparison, in terms of assembly quality and purity, of 100+ <italic>de novo</italic> assembled genomes of <italic>C. hominis</italic>. Remarkably, after quality genome filtering, a comprehensive phylogenomic analysis allowed us to discover that <italic>C. hominis</italic> encompasses two lineages with continental segregation. These lineages were named based on the observed continental distribution bias as <italic>C. hominis</italic> Euro-American (EA) and the <italic>C. hominis</italic> Afro-Asian (AA) lineages.</p>