Genotyping of Turkish environmental Cryptococcus neoformans var. neoformans isolates by pulsed field gel electrophoresis and mating type

A Landscape of the Genomic Structure of Cryptococcus neoformans in Colombian Isolates

Cryptococcus neoformans species complexes are recognized as environmental fungi responsible for lethal meningoencephalitis in immunocompromised individuals. Despite the vast knowledge about the epidemiology and genetic diversity of this fungus in different regions of the world, more studies are necessary to comprehend the genomic profiles across South America, including Colombia, considered to be the second country with the highest number of Cryptococcosis. Here, we sequenced and analyzed the genomic architecture of 29 Colombian C. neoformans isolates and evaluated the phylogenetic relationship of these strains with publicly available C. neoformans genomes. The phylogenomic analysis showed that 97% of the isolates belonged to the VNI molecular type and the presence of sub-lineages and sub-clades. We evidenced a karyotype without changes, a low number of genes with copy number variations, and a moderate number of single-nucleotide polymorphisms (SNPs). Additionally, a difference in the number of SNPs between the sub-lineages/sub-clades was observed; some were involved in crucial fungi biological processes. Our study demonstrated the intraspecific divergence of C. neoformans in Colombia. These findings provide evidence that Colombian C. neoformans isolates do not probably require significant structural changes as adaptation mechanisms to the host. To the best of our knowledge, this is the first study to report the whole genome sequence of Colombian C. neoformans isolates.

Molecular Markers Reveal Epidemiological Patterns and Evolutionary Histories of the Human Pathogenic Cryptococcus

The human pathogenic Cryptococcus species are the main agents of fungal meningitis in humans and the causes of other diseases collectively called cryptococcosis. There are at least eight evolutionary divergent lineages among these agents, with different lineages showing different geographic and/or ecological distributions. In this review, we describe the main strain typing methods that have been used to analyze the human pathogenic Cryptococcus and discuss how molecular markers derived from the various strain typing methods have impacted our understanding of not only cryptococcal epidemiology but also its evolutionary histories. These methods include serotyping, multilocus enzyme electrophoresis, electrophoretic karyotyping, random amplified polymorphic DNA, restriction fragment length polymorphism, PCR-fingerprinting, amplified fragment length polymorphism, multilocus microsatellite typing, single locus and multilocus sequence typing, matrix-assisted laser desorption/ionization time of flight mass spectrometry, and whole genome sequencing. The major findings and the advantages and disadvantages of each method are discussed. Together, while controversies remain, these strain typing methods have helped reveal (i) the broad phylogenetic pattern among these agents, (ii) the centers of origins for several lineages and their dispersal patterns, (iii) the distributions of genetic variation among geographic regions and ecological niches, (iv) recent hybridization among several lineages, and (v) specific mutations during infections within individual patients. However, significant challenges remain. Multilocus sequence typing and whole genome sequencing are emerging as the gold standards for continued strain typing and epidemiological investigations of cryptococcosis.

Cryptococcus neoformans Recovered From Olive Trees (Olea europaea) in Turkey Reveal Allopatry With African and South American Lineages

Cryptococcus species are life-threatening human fungal pathogens that cause cryptococcal meningoencephalitis in both immunocompromised and healthy hosts. The natural environmental niches of Cryptococcus include pigeon (Columba livia) guano, soil, and a variety of tree species such as Eucalyptus camaldulensis, Ceratonia siliqua, Platanus orientalis, and Pinus spp. Genetic and genomic studies of extensive sample collections have provided insights into the population distribution and composition of different Cryptococcus species in geographic regions around the world. However, few such studies examined Cryptococcus in Turkey. We sampled 388 Olea europaea (olive) and 132 E. camaldulensis trees from seven locations in coastal and inland areas of the Aegean region of Anatolian Turkey in September 2016 to investigate the distribution and genetic diversity present in the natural Cryptococcus population. We isolated 84 Cryptococcus neoformans strains (83 MATα and 1 MAT a) and 3 Cryptococcus deneoformans strains (all MATα) from 87 (22.4% of surveyed) O. europaea trees; a total of 32 C. neoformans strains were isolated from 32 (24.2%) of the E. camaldulensis trees, all of which were MATα. A statistically significant difference was observed in the frequency of C. neoformans isolation between coastal and inland areas (P < 0.05). Interestingly, the MAT a C. neoformans isolate was fertile in laboratory crosses with VNI and VNB MATα tester strains and produced robust hyphae, basidia, and basidiospores, thus suggesting potential sexual reproduction in the natural population. Sequencing analyses of the URA5 gene identified at least five different genotypes among the isolates. Population genetics and genomic analyses revealed that most of the isolates in Turkey belong to the VNBII lineage of C. neoformans, which is predominantly found in southern Africa; these isolates are part of a distinct minor clade within VNBII that includes several isolates from Zambia and Brazil. Our study provides insights into the geographic distribution of different C. neoformans lineages in the Mediterranean region and highlights the need for wider geographic sampling to gain a better understanding of the natural habitats, migration, epidemiology, and evolution of this important human fungal pathogen.

Hybrids and hybridization in the Cryptococcus neoformans and Cryptococcus gattii species complexes

The basidiomycetous yeasts of the Cryptococcus neoformans and Cryptococcus gattii species complexes (CNSC and CGSC respectively) are the causative agents of cryptococcosis, a set of life-threatening diseases affecting the central nervous system, lungs, skin, and other body sites of humans and other mammals. Both the CNSC and CGSC can be subdivided into varieties, serotypes, molecular types, and lineages based on structural variations, molecular characteristics and genetic sequences. Hybridization between the haploid lineages within and between the two species complexes is known to occur in natural and clinical settings, giving rise to intraspecific and interspecific diploid/aneuploid hybrid strains. Since their initial discovery in 1977, cryptococcal hybrids have been increasingly discovered in both clinical and environmental settings with over 30% of all cryptococcal infections in some regions of Europe being caused by hybrid strains. This review summarizes the major findings to date on cryptococcal hybrids, including their possible origins, prevalence, genomic profiles and phenotypic characteristics. Our analyses suggest that CNSC and CGSC can be an excellent model system for studying fungal hybridization.

Molecular epidemiology of environmental Cryptococcus species isolates based on amplified fragment length polymorphism

OBJECTIVE

Cryptococcosis is a major opportunistic fungal infection caused by members of the genus Cryptococcus, mainly those belonging to the Cryptococcus neoformans/Cryptococcus gattii species complexes. Here, we report a comprehensive molecular epidemiological study of the environmental distribution of Cryptococcus isolates in Shiraz, Iran with review of litreature.

METHOD

A total of 406 samples were obtained from Eucalyptus trees and 139 samples from pigeon droppings. Cryptococcus species identification and genotyping were performed by amplified fragment length polymorphism (AFLP) fingerprinting sequencing and sequencing of the ITS rDNA region.

RESULTS

Majority of the isolates belonged to the Naganishia taxon (n=69) including N. albida (formerly C. albidus, n=62), N. globosa (formerly C. saitoi, n=4), N. adeliensis (formerly C. adeliensis, n=2), N. diffluens (formerly C. diffluens, n=1), and the identified C. neoformans isolates (n=25) belonged to genotype AFLP1/VNI (n=22) and AFLP1B/VNII (n=3).

CONCLUSION

More research efforts should be employed to isolate C. gattii species complex from environmental niches in Iran and provide additional evidence related to novel molecular types.

Molecular characterization of Cryptococcus neoformans isolated from the environment in Beijing, China

The molecular type of environmental Cryptococcus neoformans in Beijing was not clear. Our study aims to reveal the molecular characterization of C. neoformans complex from environment in Beijing, China. A total of 435 samples of pigeon droppings from 11 different homes in Beijing were collected from August to November in 2015. Pigeon droppings were inoculated onto caffeic acid cornmeal agar (CACA) to screen C. neoformans complex. Bruker Biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was performed for species identification. Serotype and mating type was determined by specific primers. Restriction fragment length polymorphisms of URA5 (URA5-RFLP) were applied to genotype. Multi-locus sequence typing (MLST) was done for further identification and sequence type (ST) determination. Altogether, 81 isolates of C. neoformans AFLP1/VNI were recognized from 435 pigeon droppings in this study. The positive rate for C. neoformans AFLP1/VNI from pigeon droppings in different homes varied from 5.0% to 52.6%, the average was 20.2%. All of these cryptococcal strains were serotype A, MATα. They were genotyped as VNI by URA5-RFLP and were confirmed by MLST. No other molecular types of C. neoformans and Cryptococcus gattii isolates were isolated. Their STs were identified as ST 31 (n = 54, 66.7%), followed by ST 53 (n = 10), ST 191 (n = 8), ST 5 (n = 5), ST 57 (n = 3), and ST 38 (n = 1). We concluded that not only clinical but also environmental isolates of C. neoformans need to be investigated more deeply and more extensively. The virulence difference between ST 5 and ST 31 need to be explored in the future.

Fluconazole alters the polysaccharide capsule of Cryptococcus gattii and leads to distinct behaviors in murine Cryptococcosis

Cryptococcus gattii is an emergent human pathogen. Fluconazole is commonly used for treatment of cryptococcosis, but the emergence of less susceptible strains to this azole is a global problem and also the data regarding fluconazole-resistant cryptococcosis are scarce. We evaluate the influence of fluconazole on murine cryptococcosis and whether this azole alters the polysaccharide (PS) from cryptococcal cells. L27/01 strain of C. gattii was cultivated in high fluconazole concentrations and developed decreased drug susceptibility. This phenotype was named L27/01F, that was less virulent than L27/01 in mice. The physical, structural and electrophoretic properties of the PS capsule of L27/01F were altered by fluconazole. L27/01F presented lower antiphagocytic properties and reduced survival inside macrophages. The L27/01F did not affect the central nervous system, while the effect in brain caused by L27/01 strain began after only 12 hours. Mice infected with L27/01F presented lower production of the pro-inflammatory cytokines, with increased cellular recruitment in the lungs and severe pulmonary disease. The behavioral alterations were affected by L27/01, but no effects were detected after infection with L27/01F. Our results suggest that stress to fluconazole alters the capsule of C. gattii and influences the clinical manifestations of cryptococcosis.

Cryptococcus gattii VGIII isolates causing infections in HIV/AIDS patients in Southern California: identification of the local environmental source as arboreal

Ongoing Cryptococcus gattii outbreaks in the Western United States and Canada illustrate the impact of environmental reservoirs and both clonal and recombining propagation in driving emergence and expansion of microbial pathogens. C. gattii comprises four distinct molecular types: VGI, VGII, VGIII, and VGIV, with no evidence of nuclear genetic exchange, indicating these represent distinct species. C. gattii VGII isolates are causing the Pacific Northwest outbreak, whereas VGIII isolates frequently infect HIV/AIDS patients in Southern California. VGI, VGII, and VGIII have been isolated from patients and animals in the Western US, suggesting these molecular types occur in the environment. However, only two environmental isolates of C. gattii have ever been reported from California: CBS7750 (VGII) and WM161 (VGIII). The incongruence of frequent clinical presence and uncommon environmental isolation suggests an unknown C. gattii reservoir in California. Here we report frequent isolation of C. gattii VGIII MATα and MATa isolates and infrequent isolation of VGI MATα from environmental sources in Southern California. VGIII isolates were obtained from soil debris associated with tree species not previously reported as hosts from sites near residences of infected patients. These isolates are fertile under laboratory conditions, produce abundant spores, and are part of both locally and more distantly recombining populations. MLST and whole genome sequence analysis provide compelling evidence that these environmental isolates are the source of human infections. Isolates displayed wide-ranging virulence in macrophage and animal models. When clinical and environmental isolates with indistinguishable MLST profiles were compared, environmental isolates were less virulent. Taken together, our studies reveal an environmental source and risk of C. gattii to HIV/AIDS patients with implications for the >1,000,000 cryptococcal infections occurring annually for which the causative isolate is rarely assigned species status. Thus, the C. gattii global health burden could be more substantial than currently appreciated.

The environmentally-acquired human pathogen C. gattii is responsible for ongoing and expanding outbreaks in the Western United States and Canada. C. gattii comprises four distinct molecular types: VGI, VGII, VGIII, and VGIV. Molecular types VGI, VGII, and VGIII have been isolated from patients and animals throughout the Western US. The Pacific Northwest and Canadian outbreak is primarily caused by C. gattii VGII. VGIII is responsible for ongoing infections in HIV/AIDS patients in Southern California. However, only two environmental C. gattii isolates have ever been identified from the Californian environment: CBS7750 (VGII) and WM161 (VGIII). We sought to collect environmental samples from areas that had confirmed reports of clinical or veterinary infections. Here we report the isolation of C. gattii VGI and VGIII from environmental soil and tree samples. C. gattii isolates were obtained from three novel tree species: Canary Island pine, American sweetgum, and a Pohutukawa tree. Genetic analysis provides robust evidence that these environmental isolates are the source of human infections.

Electrophoretic karyotyping of Cryptococcus neoformans AD-hybrid strains

This study investigated the differences in genome structure between haploid serotype A and D isolates and AD-hybrid strains of Cryptococcus neoformans, and the correlation between the karyotype of A and D strains with their mating ability. The electrophoretic karyotyping of 16 AD-hybrid, eight haploid serotype-A MATalpha, and eight haploid serotype-D MATalphaC. neoformans isolates was performed. These 32 isolates presented, two by two, the same genotype and flow cytometry profile. Five clusters were identified, each including VNI (serotype A), VNIV (serotype D) haploid strains and VNIII AD hybrids. Similarly, mating types were also randomly distributed in the five clusters. In addition, AD-hybrid isolates, with double content of DNA, showed only a slight increase in both the number of chromosomal bands and the calculated genome size compared with haploid isolates. Data support the hypothesis that hybrid isolates are aneuploids (2n+x) rather than eudiploids (2n). In addition, a set of six mating type a strains were karyotyped and then used for mating experiments carried out crossing the haploid isolates with similar or different karyotype profile strains. Isolates with completely different karyotype were able to mate confirming that meiosis occurred even in the presence of chromosomes of different lengths.

Isolation ofCryptococcus neoformansvar.neoformansserotype D from Eucalypts in South Brazil

Cryptococcus neoformans causes the second most common opportunistic infection in patients with AIDS. In Brazil, 4.5% of the AIDS-related opportunistic infections are caused by C. neoformans and all varieties are recognized as etiological agents of cryptococcosis. This pathogen is a ubiquitous environmental yeast, commonly associated with avian excreta and decaying wood, especially Eucalypt species. The aim of the present study was to search for C. neoformans in Eucalypts and analyze the genotypic diversity of the obtained isolates by RAPD and PCR fingerprinting. All obtained isolates have been C. neoformans var. neoformans, serotype D molecular type VNIV. Serotype D, was isolated from 3 (37.5%) out of 8 cities surveyed in the South Brazilian state Rio Grande do Sul. Nine (9%) out of 99 environmental samples were obtained from Eucalypt species, Eucalyptus calmadulensis and Eucalyptus tereticornis. Molecular analysis using RAPD and PCR-fingerprinting revealed very little genetic diversity in the obtained cryptococcal serotype D isolates. To our knowledge this is the first report of the isolation of serotype D from Eucalyptus trees in Brazil. More studies are required in order to establish the ecological significance of this finding.