Cryptococcus neoformans and Other Opportunistic Cryptococcus Species in Pigeon Dropping in Saudi Arabia: Identification and Characterization by DNA Sequencing
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SUBMITTER: Sirag B
PROVIDER: S-EPMC8544600 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Bird fecal matter is considered a potential source of pathogenic microbes such as yeast species that contaminate the environment. Therefore, it needs to be scrutinized to assess potential environmental health risks. The aim of this study was to investigate the diversity of the yeasts in pigeon fecal droppings, their antifungal susceptibility patterns, and virulence factors. We used culturing techniques to detect the yeasts in pigeon fecal droppings. The isolates were then characterized based on colony morphologies, microscopic examinations, and biochemical reactions. The molecular identification of all yeast isolates was performed by sequencing of the amplified ITS gene. Genes encoding virulence factors CAP1, CAP59, and PLB were also detected. Antifungal susceptibility patterns were examined by the disk diffusion method. A total of 46 yeast-like isolates were recovered, and they belonged to nine different genera, namely, Cryptococcus, Saccharomyces, Rhodotorula, Candida, Meyerozyma, Cyberlindnera, Rhodosporidium, Millerozyma, and Lodderomyces. The prevalence of two genera Cryptococcus and Rhodotorula was high. None of the yeast isolates exhibited any resistance to the antifungal drugs tested; however, all pathogenic Cryptococcus species were positive for virulence determinants like urease activity, growth at 37°C, melanin production, the PLB and CAP genes. This is the first report on the molecular diversity of yeast species, particularly, Cryptococcus species and their virulence attributes in pigeon fecal droppings in Saudi Arabia.Bird fecal matter is considered a potential source of pathogenic microbes such as yeast species that contaminate the environment. Therefore, it needs to be scrutinized to assess potential environmental health risks. The aim of this study was to investigate the diversity of the yeasts in pigeon fecal droppings, their antifungal susceptibility patterns, and virulence factors. We used culturing techniques to detect the yeasts in pigeon fecal droppings. The isolates were then characterized based on colony morphologies, microscopic examinations, and biochemical reactions. The molecular identification of all yeast isolates was performed by sequencing of the amplified ITS gene. Genes encoding virulence factors CAP1, CAP59, and PLB were also detected. Antifungal susceptibility patterns were examined by the disk diffusion method. A total of 46 yeast-like isolates were recovered, and they belonged to nine different genera, namely, Cryptococcus, Saccharomyces, Rhodotorula, Candida, Meyerozyma, Cyberlindnera, Rhodosporidium, Millerozyma, and Lodderomyces. The prevalence of two genera Cryptococcus and Rhodotorula was high. None of the yeast isolates exhibited any resistance to the antifungal drugs tested; however, all pathogenic Cryptococcus species were positive for virulence determinants like urease activity, growth at 37°C, melanin production, the PLB and CAP genes. This is the first report on the molecular diversity of yeast species, particularly, Cryptococcus species and their virulence attributes in pigeon fecal droppings in Saudi Arabia.
| S-EPMC7260702 | biostudies-literature
Project description:Duckweeds, or Lemnaceae, are widespread aquatic plants. Morphology-based identification of duckweed species is difficult because of their structural complexity. Hence, molecular tools provide significant advantages for characterizing and selecting species or clones for sustainable commercial use. In this study, we collected and characterized ten duckweed isolates from nine different regions in Saudi Arabia (SA). Based on the morphological characterization and phylogenetic analysis of intergenic spacer sequences of chloroplast DNA using six barcoding markers, the clones were classified into three genera, represented by seven species: Lemna gibba L., Lemna minor L., Lemna japonica Landolt, Lemna aequinoctialis Welw., Lemna perpusilla Torr., Spirodela polyryiza (L.) Schleid., and Landoltia punctate G. Mey. Lemna gibba was revealed to be a distinct dominant duckweed species in many regions of SA. Five barcoding markers showed that L. gibba, L. minor, and L. punctata were the most widely distributed species in the country. However, L. punctata, L. perpusilla, and S. polyryiza were the dominant species in the Al-Qassim, Madinah-1, and Madinah-2 regions, respectively. Moreover, the morphological traits revealed variations for these clones, relative to other studied duckweed clones. According to the results obtained in this study, three out of six plastid markers (trnH-psbA, matK, and atpF-atpH) helped to identify the dominant duckweed species in Saudi Arabia. Further evaluation based on adaptability, molecular genetic studies, and functional genomics is needed for these species to be used at the commercial level in Saudi Arabia.
| S-EPMC8620982 | biostudies-literature
Project description:Sarcocystosis is induced by species of Sarcocystis, which is an intracellular protozoan parasite in the phylum Apicomplexa. The diversity and importance of Sarcocystis species in sheep and goats in Saudi Arabia are poorly understood. In this study, the tongue, esophagus, heart, diaphragm, and skeletal muscles were collected from 230 sheep and 84 goats, and the tissues were examined for the presence of Sarcocystis species by macroscopic examination and light microscopy. Microscopic Sarcocystis species cysts were found in both sheep and goats. Transmission electron microscopy (TEM) revealed S. tenella in sheep and S. capracanis in goats. Sarcocystis species were confirmed for the first time in Saudi Arabian sheep and goats by molecular testing. S. capracanis was most closely related to S. tenella, with the COX1 sequences sharing 91.7% identity. A phylogenetic analysis produced similar results and indicated that the Sarcocystis isolates were within a group of Sarcocystis species in which dogs were the final host. Finally, the Sarcocystis species cysts from sheep and goats could be grouped together, indicating that they were strongly related.
| S-EPMC6562545 | biostudies-literature
Project description:Leishmania major and Leishmania tropica cause cutaneous leishmaniasis in humans and dogs in several parts of the world, with a large number of cases recorded in the Middle East. However, when they occur in sympatry, the role of each species of Leishmania in the epidemiology of cutaneous leishmaniasis (CL) is not clear. To assess the frequency and to identify the species of Leishmania that infect humans and stray dogs in Riyadh and Al-Qaseem (Saudi Arabia), 311 stray dogs and 27 human patients who were suspected for Leishmania infection were examined for CL by a nested polymerase chain reaction (nPCR). Seven (25.9%) out of 27 human patients scored positive for Leishmania spp. (i.e., L. major in five patients from Riyadh and L. tropica in two patients from Al-Qaseem). Out of 311 dogs, five (1.6%) were infected by L. tropica. Data herein presented demonstrate the occurrence of L. tropica in dogs and humans in Saudi Arabia, as well as the occurrence of L. major in humans.
| S-EPMC8599340 | biostudies-literature
Project description:Background and purposeCryptococcus species are pathogenic and non-pathogenic basidiomycete yeasts that are found widely in the environment. Based on phenotypic methods, this genus has many species; however, its taxonomy is presently being re-evaluated by modern techniques. The Cryptococcus species complex includes two sibling taxa of Cryptococcus neoformans and Cryptococcus gattii. We aimed to investigate the possible distribution of Cryptococcus species in pigeon nests and Eucalyptus trees in Ilam, Iran, using molecular techniques.Materials and methodsTwo hundred and seventy-four specimens were collected from pigeon nests and Eucalyptus trees during 2016-2017. All the specimens were sub-cultured on Sabouraud Glucose Agar with chloramphenicol and bird seed agar. For molecular identification, the ITS15.8SITS2 rDNA region was amplified using the first and fourth internal transcribed spacer (ITS1 and ITS4, respectively) primers. The purified products were applied for cycle sequencing reactions in forward direction with ITS1 primer. The obtained results were analyzed with Chromas 2.3.ResultsThirty-three out of 186 cultures (17.7%) and 11 out of 88 cultures (12.5%) were positive among pigeon nest and Eucalyptus tree specimens, respectively. Cryptococcus albidus (17.2%), C. albidus var. kuetzingii (3.4%), C. adeliensis (3.4%), C. uzbekistanensis (3.4%), and C. neoformans var. grubii (3.4%) were isolated from pigeon nests, and Cryptococcusadeliensis (25%) was the only Cryptococcus species isolated from Eucalyptus trees.ConclusionThe presence of pigeons and Eucalyptus trees in the vicinity of some particular places such as rest homes and hospitals should be considered as a risk factor for the immunocompromised population.
| S-EPMC5763894 | biostudies-literature
Project description:BackgroundProtein-O-mannosyltransferases (Pmt's) catalyze the initial step of protein-O-glycosylation, the addition of mannose residues to serine or threonine residues of target proteins.Methodology/principal findingsBased on protein similarities, this highly conserved protein family can be divided into three subfamilies: the Pmt1 sub-family, the Pmt2 sub-family and the Pmt4 sub-family. In contrast to Saccharomyces cerevisiae and Candida albicans, but similar to filamentous fungi, three putative PMT genes (PMT1, PMT2, and PMT4) were identified in the genome of the human fungal pathogen Cryptococcus neoformans. Similar to Schizosaccharomyces pombe and C. albicans, C. neoformans PMT2 is an essential gene. In contrast, the pmt1 and pmt4 single mutants are viable; however, the pmt1/pmt4 deletions are synthetically lethal. Mutation of PMT1 and PMT4 resulted in distinct defects in cell morphology and cell integrity. The pmt1 mutant was more susceptible to SDS medium than wild-type strains and the mutant cells were enlarged. The pmt4 mutant grew poorly on high salt medium and demonstrated abnormal septum formation and defects in cell separation. Interestingly, the pmt1 and pmt4 mutants demonstrated variety-specific differences in the levels of susceptibility to osmotic and cell wall stress. Delayed melanin production in the pmt4 mutant was the only alteration of classical virulence-associated phenotypes. However, the pmt1 and pmt4 mutants showed attenuated virulence in a murine inhalation model of cryptococcosis.Conclusion/significanceThese findings suggest that C. neoformans protein-O-mannosyltransferases play a crucial role in maintaining cell morphology, and that reduced protein-O-glycosylation leads to alterations in stress resistance, cell wall composition, cell integrity, and survival within the host.
| S-EPMC2711527 | biostudies-literature
Project description:Hybridization has resulted in the origin and variation in extant species, and hybrids continue to arise despite pre- and post-zygotic barriers that limit their formation and evolutionary success. One important system that maintains species boundaries in prokaryotes and eukaryotes is the mismatch repair pathway, which blocks recombination between divergent DNA sequences. Previous studies illuminated the role of the mismatch repair component Msh2 in blocking genetic recombination between divergent DNA during meiosis. Loss of Msh2 results in increased interspecific genetic recombination in bacterial and yeast models, and increased viability of progeny derived from yeast hybrid crosses. Hybrid isolates of two pathogenic fungal Cryptococcus species, Cryptococcus neoformans and Cryptococcus deneoformans, are isolated regularly from both clinical and environmental sources. In the present study, we sought to determine if loss of Msh2 would relax the species boundary between C. neoformans and C. deneoformans. We found that crosses between these two species in which both parents lack Msh2 produced hybrid progeny with increased viability and high levels of aneuploidy. Whole-genome sequencing revealed few instances of recombination among hybrid progeny and did not identify increased levels of recombination in progeny derived from parents lacking Msh2. Several hybrid progeny produced structures associated with sexual reproduction when incubated alone on nutrient-rich medium in light, a novel phenotype in Cryptococcus. These findings represent a unique, unexpected case where rendering the mismatch repair system defective did not result in increased meiotic recombination across a species boundary. This suggests that alternative pathways or other mismatch repair components limit meiotic recombination between homeologous DNA and enforce species boundaries in the basidiomycete Cryptococcus species.
| S-EPMC7846113 | biostudies-literature
Project description:BackgroundBlastocystis species (sp.) are gastrointestinal protozoan parasites with high prevalence rates worldwide. Blastocystis sp. show extensive genetic diversity with 17 different subtypes (STs) described to date. A few studies have investigated the prevalence and STs of Blastocystis sp. in Makkah, Saudi Arabia. Therefore, we aimed in this study to identify and characterize subtypes of Blastocystis sp. in the City of Makkah, Saudi Arabia.MethodsStool samples were collected from 140 patients who presented to King Abdulaziz Hospital, Hera General Hospital and Modern Medical Center in Saudi Arabia. Different microscopic examination methods of patients' stools and molecular analyses (using primers targeting SSU rRNA gene) were performed to identify and characterize STs of Blastocystis sp.ResultsOur microscopic examination of stool samples showed that 96/140 patients (68.6%) had Blastocystis sp. infection. Clinical examination of infected patients revealed that 81 patients were symptomatic, whereas 15 were asymptomatic. Next, we isolated DNA from Blastocystis sp.-positive stool samples followed by PCR amplification of small-subunit ribosomal RNA (SSU rRNA) gene and sequence analysis. Our sequence analysis showed that subtype 3 (ST3) was the most prevalent (53.13%) followed by subtype 1 (ST1) (45.83%), whereas subtype 2 (ST2) was the least prevalent (1.04%). Moreover, our results showed that all three STs resulted in more symptomatic than asymptomatic cases. Finally, we identified novel haplotypes which comprised of 8 ST3, 6 ST1, and one ST2 haplotypes.ConclusionOur identification of several haplotypes in patients' stools confirms the genetic diversity of Blastocystis sp. and may explain the reported low host specificity and differential pathogenicity of Blastocystis sp. We believe that additional molecular epidemiological and genomic studies are needed to understand the prevalence and pathogenicity of different subtypes in humans and animal hosts.
| S-EPMC8963194 | biostudies-literature
Project description:PURPOSE: To catalog mutations that underlie retinitis pigmentosa (RP) in Saudi Arabia using a representative sample. METHODS: Fifty-two patients with RP were recruited and their homozygosity mapping, with or without linkage analysis, was used to suggest the causative genes followed by bidirectional sequencing. RESULTS: Mutations were identified in 94% of our study cohort, including seven that were novel. CONCLUSIONS: Homozygosity mapping is an extremely robust approach in the study of retinitis pigmentosa in the setting of high rates of consanguinity. BBS3 mutations can rarely present as nonsyndromic RP.
| S-EPMC2786884 | biostudies-literature
Project description:The contribution of genetic factors to the development of breast cancer in the admixed and consanguineous population of the western region of Saudi Arabia is thought to be significant as the disease is early onset. The current protocols of continuous clinical follow-up of relatives of such patients are costly and cause a burden on the usually over-stretched medical resources. Discovering the significant contribution of BRCA1/2 mutations to breast cancer susceptibility allowed for the design of genetic tests that allows the medical practitioner to focus the care for those who need it most. However, BRCA1/2 mutations do not account for all breast cancer susceptibility genes and there are other genetic factors, known and unknown that may play a role in the development of such disease. The advent of whole-exome sequencing is offering a unique opportunity to identify the breast cancer susceptibility genes in each family of sufferers. The polymorphisms/mutations identified will then allow for personalizing the genetic screening tests accordingly. To this end, we have performed whole-exome sequencing of seven breast cancer patients with positive family history of the disease using the Agilent SureSelect™ Whole-Exome Enrichment kit and sequencing on the SOLiD™ platform.We have identified several coding single nucleotide variations that were either novel or rare affecting genes controlling DNA repair in the BRCA1/2 pathway.The disruption of DNA repair pathways is very likely to contribute to breast cancer susceptibility in the Saudi population.
| S-EPMC4315159 | biostudies-literature