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In conjunction with the Candida and Candidiasis meeting, Microbiology Society is bringing together research on Candida biology – species that are major causes of infectious disease in AIDS patients, cancer chemotherapy patients, premature infants, etc. The polymorphic yeast Candida albicans is the most important fungal pathogen in humans. Beyond the clinics, basic research in this organism deals with a variety of topics of interest, like the genetics and molecular biology behind antifungal drug resistance; the molecular determinants of endurance to nutritional, pH and oxidative stress imposed by the host defences; or its interactions with both the host epithelia and bacterial partners that share the mucosal microbiota with the fungus. This collection of research articles published on diverse aspects of Candida biology showcases the journals’ range of Candida research. This collection is open for submissions across our portfolio. Authors are invited to submit on any aspect of Candida research. Upon submission, please indicate that your manuscript is to be considered for the Candida collection.

Collection Contents

9 results

    • Comparing genomic variant identification protocols for

      Genomic analyses are widely applied to epidemiological, population genetic and experimental studies of pathogenic fungi. A wide range of methods are employed to carry out these analyses, typically without including controls that gauge the accuracy of variant prediction. The importance of tracking outbreaks at a global scale has raised the urgency of establishing high-accuracy pipelines that generate consistent results between research groups. To evaluate currently employed methods for whole-genome variant detection and elaborate best practices for fungal pathogens, we compared how 14 independent variant calling pipelines performed across 35 isolates from 4 distinct clades and evaluated the performance of variant calling, single-nucleotide polymorphism (SNP) counts and phylogenetic inference results. Although these pipelines used different variant callers and filtering criteria, we found high overall agreement of SNPs from each pipeline. This concordance correlated with site quality, as SNPs discovered by a few pipelines tended to show lower mapping quality scores and depth of coverage than those recovered by all pipelines. We observed that the major differences between pipelines were due to variation in read trimming strategies, SNP calling methods and parameters, and downstream filtration criteria. We calculated specificity and sensitivity for each pipeline by aligning three isolates with chromosomal level assemblies and found that the GATK-based pipelines were well balanced between these metrics. Selection of trimming methods had a greater impact on SAMtools-based pipelines than those using GATK. Phylogenetic trees inferred by each pipeline showed high consistency at the clade level, but there was more variability between isolates from a single outbreak, with pipelines that used more stringent cutoffs having lower resolution. This project generated two truth datasets useful for routine benchmarking of variant calling, a consensus VCF of genotypes discovered by 10 or more pipelines across these 35 diverse isolates and variants for 2 samples identified from whole-genome alignments. This study provides a foundation for evaluating SNP calling pipelines and developing best practices for future fungal genomic studies.

    • increases the pathogenicity of during polymicrobial infection of larvae

      This study detailed the responses of larvae to disseminated infection caused by co-infection with and . Doses of (1×10 larva) and (1×10 larva) were non-lethal in mono-infection but when combined significantly (<0.05) reduced larval survival at 24, 48 and 72 h relative to larvae receiving (2×10 larva) alone. Co-infected larvae displayed a significantly higher density of larva compared to larvae infected solely with . Co-infection resulted in dissemination throughout the host and the appearance of large nodules. Co-infection of larvae with and (2×10 larva) resulted in an increase in the density of circulating haemocytes compared to that in larvae infected with only . Proteomic analysis of co-infected larval haemolymph revealed increased abundance of proteins associated with immune responses to bacterial and fungal infection such as cecropin-A (+45.4-fold), recognition proteins [e.g. peptidoglycan-recognition protein LB (+14-fold)] and proteins associated with nodule formation [e.g. Hdd11 (+33.3-fold)]. A range of proteins were also decreased in abundance following co-infection, including apolipophorin (−62.4-fold), alpha-esterase 45 (−7.7-fold) and serine proteinase (−6.2-fold). Co-infection of larvae resulted in enhanced proliferation of compared to mono-infection and an immune response showing many similarities to the innate immune response of mammals to infection. The utility of larvae for studying polymicrobial infection is highlighted.

    • sp. nov. and sp. nov., two yeast species in the / clade

      During studies on the yeast communities associated with rotting wood in the Xishuangbanna Tropical Rainforest in PR China, four novel yeast strains were found. Phylogenetic analysis based on the concatenated sequences of the D1/D2 domains of the large subunit rRNA gene and the ITS regions showed that these strains represented two novel species in the / clade. The novel species, represented by strains NYNU 17948 and NYNU 17981, formed a clade with and , with 1–1.8% sequence divergence in the D1/D2 domains and 8.9–10% sequence divergence in the ITS regions. The other novel species, represented by NYNU 17105 and NYNU 17763, is most closely related to with 0.7 % sequence divergence in the D1/D2 domains and 6.9 % sequence divergence in the ITS regions. The two novel species could be distinguished from their closest described species in terms of physiological traits. The two novel species are described as sp. nov. (holotype NYNU 17948) and sp. nov. (holotype NYNU 17763).

    • Characterization of the mechanism and impact of staphylokinase on the formation of Candida albicans and Staphylococcus aureus polymicrobial biofilms

      Purpose. Candida albicans and Staphylococcus aureus can be co-isolated in biofilm-associated infections. However, treatments have not been well established due to a lack of antibiofilm strategies. Hence, this study aims to characterize the mechanism and impact of Staphylokinase (Sak) on fungal-bacterial polymicrobial biofilms.

      Methodology. Sak generation levels were obtained via chromogenic analysis. C. albicans and S. aureus polymicrobial biofilm formation and integrity were analysed using a bright-field microscope and scanning electron microscopy (SEM). Metabolic mitochondrial activity, growth rate and adhesive capacity were also measured. Quantification real-time RT-PCR (qRT-PCR) was carried out to evaluate the expression levels of biofilm-related genes. Furthermore, the biofilm inhibitory potential of Sak alone or combined with antimicrobials was investigated.

      Results. Sak production levels varied, ranging from 0.130 to 0.648. A strong decrease of biomass, metabolic activity andearly stage growth rate was demonstrated in the Sak-treated group. SEM showed S. aureus attached on hyphae of C. albicans in sporadic small microcolonies after Sak treatment. Moreover, the gene expression levels of HWP1, EFG1 and NRG1 were significantly altered, while no obvious difference was observed in ALS3. Finally, Sak had a notable impact on mature polymicrobial biofilms alone or when combined with vancomycin and fluconazole.

      Conclusion.The effect induced by Sak to C. albicans and S. aureus polymicrobial biofilms is caused by decreased biomass, biofilm integrity, metabolic activity and early stage growth rate. Alterations of gene expression levels were consistent with Sak-induced phenotypic change. Combined treatment strategies are essential for optimal activities against fungal-bacterial polymicrobial biofilms.

    • Candida africana in recurrent vulvovaginal candidiasis (RVVC) patients: frequency and phenotypic and genotypic characteristics

      Purpose. Up to 75 % of all women develop vulvovaginal candidiasis (VVC), with symptoms such as vulvar erythema, pruritus and abnormal vaginal discharge. Despite the global distribution of Candida africana, its role in recurrent vulvovaginal candidiasis (RVVC) is still unclear and requires further investigation. Here, we report on the frequency of C. africana among clinical isolates from patients with RVVC in Bushehr in southern Iran.

      Methodology. Isolated Candida strains were identified by ITS-PCR-RFLP. Hyphal wall protein 1 (HWP1) was amplified to differentiate C. africana and the resulting sequences were subjected to phylogenetic analyses with a view to identifying similarities and differences in nucleotides.

      Results. Ten out of 119 strains originally identified as C. albicans turned out to be C. africana. Pairwise nucleotide alignment of HWP1 DNA sequences showed 100 % similarity between C. africana strains. Inter-species variation between Iranian C. africana HWP1 sequences and the only three available C. africana type sequences in GenBank revealed 99.7–100 % nucleotide similarity. Phylogenetic analysis of the HWP1 DNA sequences of 10 Iranian C. africana isolates, the 3 C. africana sequences available in GenBank and 2 representative Iranian C. albicans sequences revealed that all 11 Iranian C. africana strains formed a well-supported cluster separated from the remaining C. africana.

      Conclusion. In our sample, C. africana was only isolated from 7.8 % of the patients with RVVC. While size polymorphisms in HPW1 genes allowed us to differentiate C. africana from C. albicans, no evidence of sequence variation within the Iranian C. africana isolates was observed.

    • Clioquinol is a promising preventive morphological switching compound in the treatment of Candida infections linked to the use of intrauterine devices

      Purpose. Candida biofilm infections are frequently linked to the use of biomaterials and are of clinical significance because they are commonly resistant to antifungals. Clioquinol is an antiseptic drug and is effective against multidrug-resistant Candida. We investigated the effect of clioquinol and two other 8-hydroxyquinoline derivatives on Candida biofilm.

      Methodology. The ability to inhibit biofilm formation, inhibit preformed biofilm and remove established biofilms was evaluated using in vitro assays on microtitre plates. The action of clioquinol on biofilm in intrauterine devices (IUDs) was also investigated, describing the first protocol to quantify the inhibitory action of compounds on biofilms formed on IUDs.

      Results. Clioquinol was found to be the most effective 8-hydroxyquinoline derivative among those tested. It prevented more than 90 % of biofilm formation, which can be attributed to blockade of hyphal development. Clioquinol also reduced the metabolic activity of sessile Candida but the susceptibility was lower compared to planktonic cells (0.031–0.5 µg ml required to inhibit 50 % planktonic cells and 4–16 µg ml to inhibit 50 % preformed biofilms). On the other hand, almost complete removal of biofilms was not achieved for the majority of the isolates. Candida spp. also showed the ability to form biofilm on copper IUD; clioquinol eradicated 80–100 % of these biofilms.

      Conclusion. Our results indicate a potential application in terms of biomaterials for 8-hydroxyquinoline derivatives. Clioquinol could be used as a coating to prevent morphological switching and thus prevent biofilm formation. Furthermore, clioquinol may have future applications in the treatment of Candida infections linked to the use of IUDs.

    • sp. nov., a -xylose-fermenting yeast species isolated from peat in a tropical peat swamp forest

      Three strains (DMKU-XE11, DMKU-XE15 and DMKU-XE20) representing a single novel anamorphic and -xylose-fermenting yeast species were obtained from three peat samples collected from Khan Thulee peat swamp forest in Surat Thani province, Thailand. The strains differed from each other by one to two nucleotide substitutions in the sequences of the D1/D2 region of the large subunit (LSU) rRNA gene and zero to one nucleotide substitution in the internal transcribed spacer (ITS) region. Phylogenetic analysis based on the combined sequences of the ITS and the D1/D2 regions showed that the three strains represented a single species that was distinct from the other related species in the / clade. The three strains form a subclade with the other species including , and was the most closely related species, with 2.1–2.4 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene, and 3.8–4.0 % nucleotide substitutions in the ITS region. The three strains (DMKU-XE11, DMKU-XE15 and DMKU-XE20) were assigned as a single novel species, which was named sp. nov. The type strain is DMKU-XE11 (=CBS 15219=TBRC 7764). The MycoBank number for sp. nov. is MB 824179.

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