Abstract
The prevalent variants of
Cryptococcus neoformans
, and other
Cryptococcus species
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
C. neoformans
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
C. neoformans
species using two fungal identification databases. Phylogeny was studied using CSI Phylogeny (Center for Genomic Epidemiology, Denmark). The
C. neoformans
var.
grubii
mitochondrion and chromosome 1 reference sequences (accession numbers
NC_004336.1
and
CP022321.1
, respectively) were used for sequence comparison and variant calling. Fifteen
Cryptococcus
isolates were isolated, 11 were identified as
C. neoformans
var.
grubii
, and 4 were found to be other opportunistic
Cryptococcus
species. Phylogeny analysis of
C. neoformans
var.
grubii
isolates showed a high degree of similarity between the
C. neoformans
isolates especially at the mitochondrial genome level. This study supports the fact that pathogenic and opportunistic
Cryptococcus
species are prevalent in domestic bird excreta which is an easy source of infection in the susceptible population.