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

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.

Search for Cryptococcus neoformans/gattii Complexes and Related Genera (Filobasidium, Holtermanniella, Naganishia, Papiliotrema, Solicoccozyma, Vishniacozyma) spp. Biotope: Two Years Surveillance of Wild Avian Fauna in Southern France

“…Five others, namely, Cryptococcus ovalis , N. chernovii , H. festucosa , F. oeirense , and F. wieringae , were previously isolated from various infected or asymptomatic mammals, such as cats, dogs, or horses, but have not been isolated from any birds [ 40 , 53 , 54 ]. The fourteen remaining species had already been isolated from bird sources but mostly from pigeon droppings [ 55 , 56 , 57 , 58 ] and captive or pet birds [ 59 , 60 , 61 , 62 ]. In fact, very few wild birds have been described as possible sources for RCFC.…”

Exposure of Cryptococcus neoformans to Seven Commonly Used Agricultural Azole Fungicides Induces Resistance to Fluconazole as Well as Cross-Resistance to Voriconazole, Posaconazole, Itraconazole and Isavuconazole

“…Among the aforementioned fungi, the most widespread in human pathology are the yeast from the Cryptococcus neoformans and Cryptococcus gattii species complexes. C. neoformans and C. gattii are environmental yeasts found in bird feces [ 19 , 20 ], some insects [ 21 , 22 ], decaying wood [ 20 , 23 ] and various plants, including cultured grapes [ 24 ]. As such, they are quite likely to be present in crops that are attractive for avian fauna.…”

Asymptomatic pulmonary cryptococcosis presenting with mixed lesions of infiltrative and nodular shadow in an immunocompromised patient

“…It is transmitted by inhalation of C. neoformans spores, which are mainly present in pigeon droppings. 1 PC is known to occur not only in immunocompromised individuals, such as those with AIDS or those receiving immunosuppressive therapy, but also in immunocompetent individuals. 2 While PC in immunocompetent individuals is often asymptomatic, fever and cough are relatively common in immunocompromised individuals.…”

“…Pulmonary cryptococcosis (PC) is a rare lung disease caused by cryptococcal fungi, most notably Cryptococcus neoformans . It is transmitted by inhalation of C. neoformans spores, which are mainly present in pigeon droppings 1. PC is known to occur not only in immunocompromised individuals, such as those with AIDS or those receiving immunosuppressive therapy, but also in immunocompetent individuals 2.…”