Genome editing in the yeast Nakaseomyces delphensis and description of its complete sexual cycle

The environmental yeast Nakaseomyces delphensis is, phylogenetically, the closest known species to Candida glabrata, a major fungal pathogen of humans. C. glabrata is haploid and described as asexual, while N. delphensis is also haploid, but has been described as competent for mating and meiosis. Both genomes contain homologues of all the genes necessary for sexual reproduction and also the genes for Ho-dependent mating-type switching, like Saccharomyces cerevisiae. We first report the construction of genetically engineered strains of N. delphensis, including by CRISPR-Cas 9 gene editing. We also report the description of the sexual cycle of N. delphensis. We show that it undergoes Ho-dependent mating-type switching in culture and that deletion of the HO gene prevents such switching and allows maintenance of stable, separate, MATa and MATalpha haploid strains. Rare, genetically selected diploids can be obtained through mating of haploid strains, mutated or not for the HO gene. In contrast to HO/HO diploids, which behave as expected, Δho/Δho diploids exhibit unusual profiles in flow cytometry. Both types of diploids can produce recombined haploid cells, which grow like the original haploid-type strain. Our experiments thus allow the genetic manipulation of N. delphensis and the reconstruction, in the laboratory, of its entire life cycle.

Efficient Mating-Type Switching in Candida glabrata Induces Cell Death

Candida glabrata is an apparently asexual haploid yeast that is phylogenetically closer to Saccharomyces cerevisiae than to Candida albicans. Its genome contains three MAT-like cassettes, MAT, which encodes either MATa or MATalpha information in different strains, and the additional loci, HML and HMR. The genome also contains an HO gene homolog, but this yeast has never been shown to switch mating-types spontaneously, as S. cerevisiae does. We have recently sequenced the genomes of the five species that, together with C. glabrata, make up the Nakaseomyces clade. All contain MAT-like cassettes and an HO gene homolog. In this work, we express the HO gene of all Nakaseomyces and of S. cerevisiae in C. glabrata. All can induce mating-type switching, but, despite the larger phylogenetic distance, the most efficient endonuclease is the one from S. cerevisiae. Efficient mating-type switching in C. glabrata is accompanied by a high cell mortality, and sometimes results in conversion of the additional cassette HML. Mortality probably results from the cutting of the HO recognition sites that are present, in HML and possibly HMR, contrary to what happens naturally in S. cerevisiae. This has implications in the life-cycle of C. glabrata, as we show that efficient MAT switching is lethal for most cells, induces chromosomal rearrangements in survivors, and that the endogenous HO is probably rarely active indeed.

One small step for a yeast--microevolution within macrophages renders Candida glabrata hypervirulent due to a single point mutation

Candida glabrata is one of the most common causes of candidemia, a life-threatening, systemic fungal infection, and is surpassed in frequency only by Candida albicans. Major factors contributing to the success of this opportunistic pathogen include its ability to readily acquire resistance to antifungals and to colonize and adapt to many different niches in the human body. Here we addressed the flexibility and adaptability of C. glabrata during interaction with macrophages with a serial passage approach. Continuous co-incubation of C. glabrata with a murine macrophage cell line for over six months resulted in a striking alteration in fungal morphology: The growth form changed from typical spherical yeasts to pseudohyphae-like structures – a phenotype which was stable over several generations without any selective pressure. Transmission electron microscopy and FACS analyses showed that the filamentous-like morphology was accompanied by changes in cell wall architecture. This altered growth form permitted faster escape from macrophages and increased damage of macrophages. In addition, the evolved strain (Evo) showed transiently increased virulence in a systemic mouse infection model, which correlated with increased organ-specific fungal burden and inflammatory response (TNFα and IL-6) in the brain. Similarly, the Evo mutant significantly increased TNFα production in the brain on day 2, which is mirrored in macrophages confronted with the Evo mutant, but not with the parental wild type. Whole genome sequencing of the Evo strain, genetic analyses, targeted gene disruption and a reverse microevolution experiment revealed a single nucleotide exchange in the chitin synthase-encoding CHS2 gene as the sole basis for this phenotypic alteration. A targeted CHS2 mutant with the same SNP showed similar phenotypes as the Evo strain under all experimental conditions tested. These results indicate that microevolutionary processes in host-simulative conditions can elicit adaptations of C. glabrata to distinct host niches and even lead to hypervirulent strains.

Evolution is not limited to making new species emerge and others perish over the millennia. It is also a central force in shorter-term interactions between microbes and hosts. A good example can be found in fungi, which are an underestimated cause of human diseases. Some fungi exist as commensals, and have adapted well to life on human epithelia. But as facultative pathogens, they face a different, hostile environment. We tested the ability of C. glabrata, a pathogen closely related to baker's yeast, to adapt to macrophages. We found that by adaptation, it changed its growth type completely. This allowed the fungus to escape the phagocytes, and increased its virulence in a mouse model. Sequencing the complete genome revealed surprisingly few mutations. Further analyses allowed us to detect the single mutation responsible for the phenotype, and to recreate it in the parental strain. Our work shows that fungi can adapt to immune cells, and that this adaptation can lead to an increased virulence. Since commensals are continuously exposed to host cells, we suggest that this ability could lead to unexpected phenotype changes, including an increase in virulence potential.

Comparative genomics of emerging pathogens in the Candida glabrata clade

BACKGROUND

Candida glabrata follows C. albicans as the second or third most prevalent cause of candidemia worldwide. These two pathogenic yeasts are distantly related, C. glabrata being part of the Nakaseomyces, a group more closely related to Saccharomyces cerevisiae. Although C. glabrata was thought to be the only pathogenic Nakaseomyces, two new pathogens have recently been described within this group: C. nivariensis and C. bracarensis. To gain insight into the genomic changes underlying the emergence of virulence, we sequenced the genomes of these two, and three other non-pathogenic Nakaseomyces, and compared them to other sequenced yeasts.

RESULTS

Our results indicate that the two new pathogens are more closely related to the non-pathogenic N. delphensis than to C. glabrata. We uncover duplications and accelerated evolution that specifically affected genes in the lineage preceding the group containing N. delphensis and the three pathogens, which may provide clues to the higher propensity of this group to infect humans. Finally, the number of Epa-like adhesins is specifically enriched in the pathogens, particularly in C. glabrata.

CONCLUSIONS

Remarkably, some features thought to be the result of adaptation of C. glabrata to a pathogenic lifestyle, are present throughout the Nakaseomyces, indicating these are rather ancient adaptations to other environments. Phylogeny suggests that human pathogenesis evolved several times, independently within the clade. The expansion of the EPA gene family in pathogens establishes an evolutionary link between adhesion and virulence phenotypes. Our analyses thus shed light onto the relationships between virulence and the recent genomic changes that occurred within the Nakaseomyces.

SEQUENCE ACCESSION NUMBERS

Nakaseomyces delphensis: CAPT01000001 to CAPT01000179Candida bracarensis: CAPU01000001 to CAPU01000251Candida nivariensis: CAPV01000001 to CAPV01000123Candida castellii: CAPW01000001 to CAPW01000101Nakaseomyces bacillisporus: CAPX01000001 to CAPX01000186.

[Prevalence of opportunistic digestive parasitic infections in Kinshasa, Democratic Republic of Congo. Results of a preliminary study in 50 AIDS patients]

In the Democratic Republic of Congo (DRC), as in many African countries, AIDS and its procession of opportunistic infections are a major cause of morbidity and mortality. In Kinshasa, the estimated prevalence rate of HIV-infected persons is between 4 and 5%, corresponding to more than 200,000 people. Due to the lack of trained laboratory personnel and appropriate diagnostic equipment, no local investigation has been carried out to determine the prevalence of the opportunistic digestive parasitic infection in HIV-infected persons. As a step to obtaining this information that is needed for implementation of an adequate care policy, a preliminary investigation was carried out in Paris, France on 50 stool samples from 50 AIDS-patients hospitalized in 3 reference hospitals in Kinshasa. Eleven patients (22%) had digestive symptoms with a diarrhea syndrome. Further study using specialized techniques demonstrated 2 cases of digestive infection related to opportunistic parasites (4%). The first involved a Cryptosporidium sp. The second represented the first case of Enterocytozoon bieneusi infection reported in the literature from the DRC.

Molecular identification of Cryptococcus neoformans serotypes

Cryptococcus neoformans is a fungal pathogen that causes life-threatening infections primarily in immunocompromised hosts. Based on the genetic characteristics and serologic properties of capsular polysaccharides, three varieties and five serotypes have been defined: C. neoformans var. neoformans (serotype D), C. neoformans var. grubii (serotype A), hybrid serotype AD, and C. neoformans var. gattii (serotypes B and C). Epidemiologic features, such as geographic distribution and ecologic niche, and clinical characteristics have been shown to be associated with serotypes. At the present time, serotyping is based on agglutination tests with either commercial or "homemade" antisera or on immunofluorescence assays using a monoclonal antibody directed against the capsule polysaccharide. In this paper, we describe two molecular methods (PCR-restriction enzyme analysis and length polymorphism analysis) for C. neoformans serotype identification. Both are based on the sequence characteristics of a fragment of the CAP59 gene required for capsule biosynthesis. Testing of 72 C. neoformans strains including representatives of the five serotypes demonstrated the reliability of these methods.

Application of microsatellite typing for the investigation of a cluster of cases of Candida albicans candidaemia

A cluster of cases of Candida albicans candidaemia in a surgical intensive care unit was investigated. The probability of such a cluster during a single month was highly significant compared with the frequency of candidaemia in the previous year. A molecular typing method, based on length analysis of three (EF3, CDC3, HIS3) microsatellite-containing regions, was used to investigate isolates from patients in and outside the ward. This demonstrated the involvement of different strains, indicating the absence of cross-transmission among patients. Results of microsatellite typing can be obtained almost in real-time, which is particularly useful in an outbreak context.

Invasive Saccharomyces infection: a comprehensive review

BACKGROUND

Saccharomyces cerevisiae (also known as "baker's yeast" or "brewer's yeast") is mostly considered to be an occasional digestive commensal. However, since the 1990s, there have been a growing number of reports about its implication as an etiologic agent of invasive infection. A particular feature of such infections is their association with a probiotic preparation of Saccharomyces boulardii (a subtype of S. cerevisiae) for treatment various diarrheal disorders.

METHODS

We collected published case reports, through May 2005, of invasive Saccharomyces infection by use of a Medline query. Epidemiological and clinical charts and therapeutic strategies were analyzed.

RESULTS

We found 92 cases of Saccharomyces invasive infection. Predisposing factors were similar to those of invasive candidiasis, with intravascular catheter and antibiotic therapy being the most frequent. Blood was the most frequent site of isolation (for 72 patients). S. boulardii accounted for 51.3% of fungemias and was exclusively isolated from blood. Compared with patients infected with S. cerevisiae, patients infected with S. boulardii were more frequently immunocompetent and had a better prognosis. Saccharomyces invasive infection was clinically indistinguishable from an invasive candidiasis. Overall, S. cerevisiae clinical isolates exhibited low susceptibility to amphotericin B and azole derivatives. However, global outcome was favorable in 62% of the cases. Treatment with intravenous amphotericin B and fluconazole, in combination with central vascular catheter removal, were effective therapeutic options.

CONCLUSION

Saccharomyces organisms should now be added to the growing list of emerging fungal pathogens. Special caution should be taken regarding the use of S. boulardii probiotic preparations.