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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.

frontiers in microbiology

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