Viable quantitative PCR for assessing the response of Candida albicans to antifungal treatment

Cell Viability Assays for Candida auris

Cell viability assays are useful for assessing the efficacy of antifungal therapeutics and disinfection strategies in vitro. In recent years these assays have been fundamental for the testing of conventional and novel therapies against the nosocomial fungal pathogen Candida auris. Here we provide detailed descriptions of methods for assessing cellular viability of Candida auris in vitro, such as metabolic assays (XTT and resazurin), colony-forming unit counting, live/dead quantitative PCR, and fluorescent staining for microscopic analyses.

Detection of Viable Zygosaccharomyces rouxii in Honey and Honey Products via PMAXX-qPCR

In order to establish a fast detection method for the living Zygosaccharomyces rouxii (Z. rouxii) cells in honey and honey products, the performance of propidium monoazide bromide (PMA) and enhanced propidium monoazide bromide (PMAXX) combined with real-time PCR for detecting living cells of Z. rouxii was compared. PMAXX was chosen as the added agent because of its better performance. The optimal concentration of PMAXX was found to be 76.92 μM in cell solution (the cell concentration was 1.0 × 108 CFU/mL). The LODs of PMAXX-qPCR in detecting Z. rouxii in pure MEA and honey solution were found to be 103 and 101 CFU/mL, respectively. Living Z. rouxii cells in 18 real honey samples were detected using this PMAXX-qPCR method and compared with the plate count method. The two methods showed consistent detection results in ten negative samples. In the other eight plate count zero but PMAXX-qPCR-positive samples, further verification experiments showed that six of the PMAXX-qPCR-positive samples contained viable but nonculturable (VBNC) Z. rouxii, while the other two PMAXX-qPCR-positive samples may have contained DNA contamination of Z. rouxii. This method is not only fast and sensitive but also can detect both culturable and viable but nonculturable Z. rouxii. This study provides a promising fast and culture-independent method for the detection of living Z. rouxii cells in honey and honey products.

Chamomile Extract versus Clotrimazole Vaginal Cream in Treatment of Vulvovaginal Candidiasis: A Randomized Double-Blind Control Trial

Objectives

Vulvovaginal candidiasis (VVC) treatment is advised for all women due to its symptoms and complications. In this study, the standard treatment, clotrimazole, was compared with chamomile extract cream in outpatient clinics.

Methods

We recruited 73 women with VVC, who were randomly allocated into two groups, clotrimazole versus chamomile extract cream. After two weeks of treatment with the same criteria, cheese-like vaginal discharge, itching and burning sensations, strawberry cervix, and recovery percentage was evaluated.

Results

Thirty patients in each group were analyzed. There was no significant difference in age and number of pregnancies between groups (p = 0.85 and 0.09, respectively). Comparing before and after treatment, cheese like discharge (p < 0.001), itching (p < 0.001), burning (p < 0.001) had significantly improved in both groups. Further, the recovery percentage was not significantly different between groups (88.9% vs 75% in the chamomile vs clotrimazole groups, respectively).

Conclusion

Chamomile is as effective as clotrimazole in VVC treatment; a higher percentage of women who used this medication recovered, although this did not reach significance. In addition, no complications were reported in either group.

Quantitative and specific detection of viable pathogens on a portable microfluidic chip system by combining improved propidium monoazide (PMAxx) and loop-mediated isothermal amplification (LAMP)

An accurate and specific detection of viable Candida albicans (C. albicans) in vaginal discharge is crucial for the diagnosis of vulvovaginal candidiasis (VVC) and assessment of antifungal effects. In this study, improved propidium monoazide (PMAxx) and loop-mediated isothermal amplification (LAMP) were used for the first time to distinguish between viable and dead C. albicans. A portable microfluidic chip system was developed to detect multiple viable pathogens in parallel. The consumption of samples and reagents in per reaction cell were only 0.94 μL, less than 1/25 of the conventional 25 μL Eppendorf tubular test method, both significantly reducing testing cost and greatly simplifying the detection of multiple viable pathogens. The concentration of PMAxx was optimized against C. albicans at 4.0 log CFU mL^-1 to 5.0 log CFU mL^-1, and 1 μM PMAxx was proven to be suitable for the detection of C. albicans in clinical samples. When testing mixtures containing different ratios of viable to dead C. albicans, PMAxx-LAMP could circumvent the signal arising from dead cells and, therefore, reflected the abundance of viable cells precisely. Furthermore, the suitability of this technique to evaluate the effects of antifungal agents, including clotrimazole, miconazole, and tioconazole, was assessed. Finally, the viability of Escherichia coli (E. coli) and C. albicans were detected on the portable microfluidic chip system. PMAxx-LAMP based portable microfluidic chip system was determined to be a feasible technique for assessing the viability of multiple pathogens in gynecology and might provide insights into new VVC treatment strategies.

Molecular Diagnosis of Yeast Infections

PURPOSE OF REVIEW

The use of molecular tests to aid the diagnosis of invasive yeast infection, in particular invasive candidosis, has been described for over two decades, yet widespread application is limited, and diagnosis remains heavily dependent on classical microbiology. This article will review developments from the past decade in attempt to build on existing knowledge. It will highlight clinical performance and limitations while reviewing developments on recognized procedures; it will also provide insight into novel approaches incorporated in response to clinical demand (e.g. C. auris and antifungal resistance) or technological advances (e.g. next-generation sequencing).

RECENT FINDINGS

Limited methodological standardization and, until recently, unavailability of commercial options have hindered the integration of molecular diagnostics for yeasts. The development of certain, novel commercial methods has received considerable evaluation allowing a greater understanding of individual assay performance, but widespread multicentre evaluation of most commercial kits is lacking. The detection of emerging pathogens (e.g. C. auris) has been enhanced by the development of molecular tests. Molecular methods are providing a better understanding of the mycobiome, mechanisms of resistance and epidemiology/phylogeny.

SUMMARY

Despite over two decades of use, the incorporation of molecular methods to enhance the diagnosis of yeast infections remains limited to certain specialist centres. While the development of commercial tests will provide stimulus for broader application, further validation and reduced costs are required. Over the same period of time, Aspergillus PCR has become more widely accepted driven by international efforts to standardize methodology; it is critical that yeast PCR follows suit. Next-generation sequencing will provide significant information on the mycobiome, antifungal resistance mechanism and even broad-range detection directly from the specimen, which may be critical for the molecular detection of yeasts other than Candida species, which is currently limited.

Propidium Monoazide Improves Quantification of Resting Spores of Plasmodiophora brassicae with qPCR

Plasmodiophora brassicae, which causes clubroot of Brassica crops, persists in soil as long-lived resting spores. Quantitative polymerase chain reaction (qPCR) analysis is often used to quantify resting spores but does not distinguish between DNA of viable and nonviable spores. The impact of pretreating spores with propidium monoazide (PMA), which inhibits amplification of DNA from nonviable microorganisms, was assessed in several experiments. Spore suspensions from immature and mature clubs were heat treated; then, PMA-PCR analyses and bioassays were performed to assess spore viability. Prior to heat treatment, assessments comparing PMA-PCR to qPCR for mature spores were similar, indicating that most of these spores were viable. However, only a small proportion (<26%) of immature spores were amplified in PMA-PCR. Bioassays demonstrated that clubroot severity was much higher in plants inoculated with mature spores than with immature spores. Heat treatment produced little or no change in estimates of mature spores from qPCR but spore estimates from PMA-PCR and clubroot severity in bioassays were both substantially reduced. Estimates of spore concentration with PMA-PCR were less consistent for immature spores. To facilitate use of PMA-PCR on infested soil, a protocol for extracting spores from soil was developed that provided higher extraction efficiency than the standard methods.

Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation

Introduction and Purpose

Propidium monoazide (PMA)-pretreatment has increasingly been applied to remove the bias from dead or damaged cell artefacts, which could impact the microbiota analysis by high-throughput sequencing. Our study aimed to determine whether a PMA-pretreatment coupled with high-throughput sequencing analysis provides a different picture of the airway mycobiome and bacteriome.

Results and Discussion

We compared deep-sequencing data of mycobiota and microbiota of 15 sputum samples from 5 cystic fibrosis (CF) patients with and without prior PMA-treatment of the DNA-extracts. PMA-pretreatment had no significant effect on the entire and abundant bacterial community (genera expressed as operational taxonomic units (OTUs) with a relative abundance greater than or equal to 1%), but caused a significant difference in the intermediate community (less than 1%) when analyzing the alpha biodiversity Simpson index (p = 0.03). Regarding PMA impact on the airway mycobiota evaluated for the first time here; no significant differences in alpha diversity indexes between PMA-treated and untreated samples were observed. Regarding beta diversity analysis, the intermediate communities also differed more dramatically than the total and abundant ones when studying both mycobiome and bacteriome. Our results showed that only the intermediate (or low abundance) population diversity is impacted by PMA-treatment, and therefore that abundant taxa are mostly viable during acute exacerbation in CF. Given such a cumbersome protocol (PMA-pretreatment coupled with high-throughput sequencing), we discuss its potential interest within the follow-up of CF patients. Further studies using PMA-pretreatment are warranted to improve our “omic” knowledge of the CF airways.

A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses

BACKGROUND

Recent studies posit a reciprocal dependency between the microbiomes associated with humans and indoor environments. However, none of these metagenome surveys has considered the viability of constituent microorganisms when inferring impact on human health.

RESULTS

Reported here are the results of a viability-linked metagenomics assay, which (1) unveil a remarkably complex community profile for bacteria, fungi, and viruses and (2) bolster the detection of underrepresented taxa by eliminating biases resulting from extraneous DNA. This approach enabled, for the first time ever, the elucidation of viral genomes from a cleanroom environment. Upon comparing the viable biomes and distribution of phylotypes within a cleanroom and adjoining (uncontrolled) gowning enclosure, the rigorous cleaning and stringent control countermeasures of the former were observed to select for a greater presence of anaerobes and spore-forming microflora. Sequence abundance and correlation analyses suggest that the viable indoor microbiome is influenced by both the human microbiome and the surrounding ecosystem(s).

CONCLUSIONS

The findings of this investigation constitute the literature's first ever account of the indoor metagenome derived from DNA originating solely from the potential viable microbial population. Results presented in this study should prove valuable to the conceptualization and experimental design of future studies on indoor microbiomes aimed at inferring impact on human health.

Antimicrobial Activity of Rhoeo discolor Phenolic Rich Extracts Determined by Flow Cytometry

Traditional medicine has led to the discovery of important active substances used in several health-related areas. Phytochemicals in Rhoeo discolor extracts have proven to have important antimicrobial activity. In the present study, our group determined the antimicrobial effects of extracts of Rhoeo discolor, a plant commonly used in Mexico for both medicinal and ornamental purposes. We evaluated the in vitro activity of phenolic rich extracts against specifically chosen microorganisms of human health importance by measuring their susceptibility via agar-disc diffusion assay and flow cytometry: Gram-positive Listeria innocua and Streptococcus mutans, Gram-negative Escherichia coli and Pseudomonas aeruginosa, and lastly a fungal pathogen Candida albicans. Ten different extracts were tested in eight different doses on all the microorganisms. Analytical data revealed a high content of phenolic compounds. Both agar-disc diffusion assay and flow cytometry results demonstrated that Pseudomonas aeruginosa was the least affected by extract exposure. However, low doses of these extracts (predominantly polar), in a range from 1 to 4 μg/mL, did produce a statistically significant bacteriostatic and bactericidal effect on the rest of the microorganisms. These results suggest the addition of certain natural extracts from Rhoeo discolor could act as antibacterial and antimycotic drugs or additives for foods and cosmetics.

Dead or alive: molecular assessment of microbial viability

Nucleic acid-based analytical methods, ranging from species-targeted PCRs to metagenomics, have greatly expanded our understanding of microbiological diversity in natural samples. However, these methods provide only limited information on the activities and physiological states of microorganisms in samples. Even the most fundamental physiological state, viability, cannot be assessed cross-sectionally by standard DNA-targeted methods such as PCR. New PCR-based strategies, collectively called molecular viability analyses, have been developed that differentiate nucleic acids associated with viable cells from those associated with inactivated cells. In order to maximize the utility of these methods and to correctly interpret results, it is necessary to consider the physiological diversity of life and death in the microbial world. This article reviews molecular viability analysis in that context and discusses future opportunities for these strategies in genetic, metagenomic, and single-cell microbiology.

Use of propidium monoazide for the enumeration of viable Oenococcus oeni in must and wine by quantitative PCR

Malolactic fermentation is an important step in winemaking, but it has to be avoided in some cases. It's carried out by lactic acid bacteria belonging mainly to the genus Oenococcus, which is known to be a slow growing bacterium. Classical microbiological methods to enumerate viable cells of Oenococcus oeni in must and wine take 7-9 days to give results. Moreover, RT-qPCR technique gives accurate quantitative results, but it requires time consuming steps of RNA extraction and reverse transcription. In the present work we developed a fast and reliable quantitative PCR (qPCR) method to enumerate cells of Oenococcus oeni, directly, in must and wine. For the first time we used a propidium monoazide treatment of samples to enumerate only Oenococcus oeni viable cells. The detection limit of the developed method is 0.33 log CFU/mL (2.14 CFU/mL) in must, and 0.69 log CFU/mL (4.90 CFU/mL) in wine, lower than that of the previously developed qPCR protocols.