AUTHOR=Sirag Bashir , Khidir El-Shiekh , Dumyati Mohammed , Sindi Basam , Alsinnari Mahir , Faidah Hani , Ahmed Abdalla 

TITLE=Cryptococcus neoformans and Other Opportunistic Cryptococcus Species in Pigeon Dropping in Saudi Arabia: Identification and Characterization by DNA Sequencing

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.726203

DOI=10.3389/fmicb.2021.726203

ISSN=1664-302X

ABSTRACT=<p>The prevalent variants of <italic>Cryptococcus neoformans</italic>, and other <italic>Cryptococcus species</italic> in pigeon excreta in Western Region of Saudi Arabia were studied. Ninety pigeon dropping samples were plated directly on Niger seed agar, and suspected colonies were sequenced using Illumina MiSeq. Species identification was determined using sequence read mapping to reference genomes of the two <italic>C. neoformans</italic> variants. In addition, sequence reads were identified using the KmerFinder tool. internal transcribed spacer 2 in the rDNA was also used for fungal barcoding of none of the <italic>C. neoformans</italic> species using two fungal identification databases. Phylogeny was studied using CSI Phylogeny (Center for Genomic Epidemiology, Denmark). The <italic>C. neoformans</italic> var. <italic>grubii</italic> mitochondrion and chromosome 1 reference sequences (accession numbers <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="NC_004336.1" xmlns:xlink="http://www.w3.org/1999/xlink">NC_004336.1</ext-link> and <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="CP022321.1" xmlns:xlink="http://www.w3.org/1999/xlink">CP022321.1</ext-link>, respectively) were used for sequence comparison and variant calling. Fifteen <italic>Cryptococcus</italic> isolates were isolated, 11 were identified as <italic>C. neoformans</italic> var. <italic>grubii</italic>, and 4 were found to be other opportunistic <italic>Cryptococcus</italic> species. Phylogeny analysis of <italic>C. neoformans</italic> var. <italic>grubii</italic> isolates showed a high degree of similarity between the <italic>C. neoformans</italic> isolates especially at the mitochondrial genome level. This study supports the fact that pathogenic and opportunistic <italic>Cryptococcus</italic> species are prevalent in domestic bird excreta which is an easy source of infection in the susceptible population.</p>