Rapid identification of Candida species in oral rinse solutions by PCR

A Preliminary Pilot Study: Metabolomic Analysis of Saliva in Oral Candidiasis

Early detection of oral candidiasis is essential. However, most currently available methods are time-consuming and useful only for screening patients. Previous studies on the relationship between oral candidiasis and saliva have focused on saliva volume and not on its components. Therefore, to clarify the effects of oral candidiasis on salivary metabolites, the relationship between salivary components and oral candidiasis was investigated by comparing the salivary metabolites of oral candidiasis patients and those not previously diagnosed with candidiasis. Forty-five participants visiting our university hospital were included and classified into two groups, the Candida group and the control group, based on the Candida detection test results. The unstimulated saliva was collected using the spitting method over 15 min, and the stimulated saliva was collected using the gum-chewing method over 10 min. The saliva volume was measured, and the saliva samples were frozen and analyzed metabolomically. Metabolome analysis revealed 51 metabolites with peak detection rates exceeding 50%. There was no significant difference in age and sex between the Candida and control groups. In the Candida group, five metabolites (tyrosine, choline, phosphoenolpyruvate, histidine, and 6-phosphogluconate) were significantly elevated in the unstimulated, two (octanoic acid and uridine monophosphate(UMP)) were significantly increased, and four (ornithine, butyrate, aminovalerate and aminolevulinate) were significantly decreased in the stimulated saliva. This study suggests the possibility of identifying metabolites specific to patients with oral candidiasis, which could aid prompt diagnosis.

GhPLP2 Positively Regulates Cotton Resistance to Verticillium Wilt by Modulating Fatty Acid Accumulation and Jasmonic Acid Signaling Pathway

Patatin-like proteins (PLPs) have non-specific lipid acyl hydrolysis (LAH) activity, which can hydrolyze membrane lipids into fatty acids and lysophospholipids. The vital role of PLPs in plant growth and abiotic stress has been well documented. However, the function of PLPs in plant defense responses against pathogens is still poorly understood. Here, we isolated and identified a novel cotton (Gossypium hirsutum) PLP gene GhPLP2. The expression of GhPLP2 was induced upon treatment with Verticillium dahliae, the signaling molecules jasmonic acid (JA) and ethylene (ETH) in cotton plants. Subcellular localization revealed that GhPLP2 was localized to the plasma membrane. GhPLP2-silenced cotton plants were more susceptible to infection by V. dahliae, while the overexpression of GhPLP2 in Arabidopsis enhanced its resistance to V. dahliae, which was apparent as mild symptoms, and a decrease in the disease index and fungal biomass. The hypersensitive response, deposition of callose, and H₂O₂ accumulation triggered by V. dahliae elicitor were reduced in GhPLP2-silenced cotton plants. The overexpression of GhPLP2 in Arabidopsis resulted in the accumulation of linoleic acid (LA, 18:2) and α-linolenic acid (ALA, 18:3) and facilitated the biosynthesis of JA and JA-mediated defensive responses. GhPLP2 silencing in cotton plants consistently reduced the accumulation of linoleic acid (LA, 18:2) and α-linolenic acid (ALA, 18:3) and suppressed the biosynthesis of JA and the defensive responses mediated by JA. These results indicate that GhPLP2 is involved in the resistance of cotton to V. dahliae by maintaining fatty acid metabolism pools for JA biosynthesis and activating the JA signaling pathway.

GhPLP2 Positively Regulates Cotton Resistance to Verticillium Wilt by Modulating Fatty Acid Accumulation and Jasmonic Acid Signaling Pathway

Patatin-like proteins (PLPs) have non-specific lipid acyl hydrolysis (LAH) activity, which can hydrolyze membrane lipids into fatty acids and lysophospholipids. The vital role of PLPs in plant growth and abiotic stress has been well documented. However, the function of PLPs in plant defense responses against pathogens is still poorly understood. Here, we isolated and identified a novel cotton (Gossypium hirsutum) PLP gene GhPLP2. The expression of GhPLP2 was induced upon treatment with Verticillium dahliae, the signaling molecules jasmonic acid (JA) and ethylene (ETH) in cotton plants. Subcellular localization revealed that GhPLP2 was localized to the plasma membrane. GhPLP2-silenced cotton plants were more susceptible to infection by V. dahliae, while the overexpression of GhPLP2 in Arabidopsis enhanced its resistance to V. dahliae, which was apparent as mild symptoms, and a decrease in the disease index and fungal biomass. The hypersensitive response, deposition of callose, and H₂O₂ accumulation triggered by V. dahliae elicitor were reduced in GhPLP2-silenced cotton plants. The overexpression of GhPLP2 in Arabidopsis resulted in the accumulation of linoleic acid (LA, 18:2) and α-linolenic acid (ALA, 18:3) and facilitated the biosynthesis of JA and JA-mediated defensive responses. GhPLP2 silencing in cotton plants consistently reduced the accumulation of linoleic acid (LA, 18:2) and α-linolenic acid (ALA, 18:3) and suppressed the biosynthesis of JA and the defensive responses mediated by JA. These results indicate that GhPLP2 is involved in the resistance of cotton to V. dahliae by maintaining fatty acid metabolism pools for JA biosynthesis and activating the JA signaling pathway.

Clonal evolution of Candida albicans, Candida glabrata and Candida dubliniensis at oral niche level in health and disease

Background:Candida species have long been recognised as aetiological agents of opportunistic infections of the oral mucosa, and more recently, as players of polymicrobial interactions driving caries, periodontitis and oral carcinogenesis.

Methods: We studied the clonal structure of Candida spp. at oral niche resolution in patients (n = 20) with a range of oral health profiles over 22 months. Colonies from oral micro-environments were examined with multilocus sequencing typing.

Results:Candida spp. identified were C. albicans, C. glabrata and C. dubliniensis. Increased propensity for micro-variations giving rise to multiple diploid strain types (DST), as a result of loss of heterozygosity, was observed among C. albicans clade 1 isolates compared to other clades. Micro-variations among isolates were also observed in C. dubliniensis contra to expectations of stable population structures for this species. Multiple sequence types were retrieved from patients without clinical evidence of oral candidosis, while single sequence types were isolated from oral candidosis patients.

Conclusion: This is the first study to describe the clonal population structure, persistence and stability of Candida spp. at oral niche level. Future research investigating links between Candida spp. clonality and oral disease should recognise the propensity to micro-variations amongst oral niches in C. albicans and C. dubliniensis identified here.

Quantification of Bacteria in Mouth-Rinsing Solution for the Diagnosis of Periodontal Disease

This study aimed to evaluate the feasibility of diagnosing periodontitis via the identification of 18 bacterial species in mouth-rinse samples. Patients (n = 110) who underwent dental examinations in the Department of Periodontology at the Veterans Health Service Medical Center between 2018 and 2019 were included. They were divided into healthy and periodontitis groups. The overall number of bacteria, and those of 18 specific bacteria, were determined via real-time polymerase chain reaction in 92 mouth-rinse samples. Differences between groups were evaluated through logistic regression after adjusting for sex, age, and smoking history. There was a significant difference in the prevalence (healthy vs. periodontitis group) of Aggregatibacter actinomycetemcomitans (2.9% vs. 13.5%), Treponema denticola (42.9% vs. 69.2%), and Prevotella nigrescens (80% vs. 2.7%). Levels of Treponema denticola, Prevotella nigrescens, and Streptococcus mitis were significantly associated with severe periodontitis. We demonstrated the feasibility of detecting periopathogenic bacteria in mouth-rinse samples obtained from patients with periodontitis. As we did not comprehensively assess all periopathogenic bacteria, further studies are required to assess the potential of oral-rinsing solutions to indicate oral infection risk and the need to improve oral hygiene, and to serve as a complementary method for periodontal disease diagnosis.

Role of antimicrobial photodynamic therapy in reducing whole salivary oral yeasts colonization in type-2 diabetic and non-diabetic patients with and without dental implants

OBJECTIVE

The aim was to assess the impact of antimicrobial photodynamic therapy (aPDT) in reducing whole salivary oral yeasts colonization in type-2 diabetic and non-diabetic patients with dental implants.

METHODS

Type-2 diabetic and self-reported non-diabetic patients were included. Participants were divided into the following groups: Group-1: Type-2 diabetic patients with dental implants; Group-2: Non-diabetic patients with dental implants; Group-3: Type-2 diabetic patients without dental prostheses; Group-4: Non-diabetic patients without dental prostheses. In each group, participants were subdivided into 2-sub-groups. In the test-subgroup, participants received routine oral hygiene maintenance instructions (OHMI) and underwent full mouth disinfection using aPDT; and in the control-group, participants received OHMI alone. Unstimulated whole saliva samples were collected, hemoglobin A1c levels were measured and yeast colonization was assessed at baseline and at 3-months' follow-up in all groups. Sample-size estimation was done and group-comparisons were done. P-values <0.01 were considered statistically significant.

RESULTS

At baseline, the mean oral yeasts colonization was significantly higher among patients in Group-1 (P < 0.001) and 3 (P < 0.001) compared with individuals in groups 2 (P < 0.001) and 4 (P < 0.001). At baseline and at 3-months of follow-up, the mean HbA1c levels and oral yeasts colonization were significantly higher among patients in Group-1 (P < 0.001) and 3 (P < 0.001) compared with individuals in groups 2 (P < 0.001) and 4 (P < 0.001).

CONCLUSION

In the short-term, routine OHMI with adjunct aPDT is more effective in reducing whole salivary oral yeasts counts than OHMI alone in patients with and without dental implants.

Relationship Between the Quantity of Oral Candida and Systemic Condition/Diseases of the Host: Oral Candida Increases with Advancing Age and Anemia

BACKGROUND

The impact of host systemic conditions/diseases on the prosperity of oral Candida colonies remains unclear. The aim of the present study was to investigate whether a relationship exists between the quantity of oral Candida and the systemic condition/diseases of the host.

PATIENTS AND METHODS

The cross-sectional relationship between Candida mannan concentrations and health check-up results was analyzed in consideration of local conditions that influence the prevalence of oral Candida.

RESULTS

Candida mannan concentrations correlated with age, the number of untreated decayed teeth, number of prosthetic teeth, salivary pH, HbA1c, and the red blood cell count in a univariate analysis. In a multivariate analysis, Candida mannan concentrations correlated with age, the number of untreated decayed teeth, number of prosthetic teeth, salivary pH, and the red blood cell count. Candida mannan concentrations were higher in subjects older than 80 years, with a higher number of either untreated or prosthetic teeth, with a lower salivary pH, and with a decreased red blood cell count. Mannan concentrations were slightly higher in subjects with elevated HbA1c.

CONCLUSIONS

The present results suggest a close relationship between the quantity of oral Candida and the systemic condition/diseases of the host. Oral Candida may increase in immunocompromised hosts.

A sensitive and a rapid multiplex polymerase chain reaction for the identification of Candida species in concentrated oral rinse specimens in patients with diabetes

OBJECTIVES

Oral candidiasis is being frequently recognized in patients with diabetes, and is associated with multiple pathogens including Candida albicans, Candida parapsilosis, Candida glabrata and Candida tropicalis. The aim of this study was to evaluate a usefulness of a Multiplex Polymerase Chain Reaction as a rapid diagnostic tool for identification of four oral Candida pathogens in patients with diabetes.

MATERIALS AND METHODS

A multiplex PCR was optimized to identify four Candida species in concentrated oral rinse samples. Common reverse primer, ITS4 and four species-specific forward primers targeting ITS1 and ITS2 regions of yeast genome were used. Species-specific single amplicon were detected by agarose gel electrophoresis. Performance efficacy of multiplex PCR was compared with phenotypic identification.

RESULTS

Out of 100 oral rinse samples, 72 were culture positive and of these 43 were at risk of oral Candida infection (>600cfu/ml). Multiple Candida species including C. albicans, C. parapsilosis and C. tropicalis were identified in 22 samples which had risk of oral Candida infection. In total, 85 patients were positive for Candida by multiplex PCR and of them 49 had multiple Candida species. All 43 colonized specimens were also positive by multiplex PCR. C. albicans was the most predominant organism (75/85) followed by C. parapsilosis (47/85), C. tropicalis (17/85) and C. glabrata (6/85). In specimens with multiple species, the two most common organisms were C. albicans and C. parapsilosis. Multiplex PCR yielded a sensitivity of 10 Candida cells/ml of oral rinse sample.

CONCLUSIONS

Multiplex PCR is found to be rapid, sensitive and specific than phenotypic identification methods in discriminating multiple Candida species in oral rinse specimens.

Host factors and clinical outcomes of Candida colonization in critically ill patients

This study aimed to describe factors and outcomes associated with Candida colonization of critically ill patients. This was a cross-sectional study conducted over 2 weeks in the intensive care unit (ICU) of a tertiary care hospital at the Texas Medical Center, Houston, TX. All Candida samples were prospectively collected with demographic and clinical data collected retrospectively. We examined 48 patients, 32 (67%) were colonized with Candida spp; 25 (52.1%) patients were isolated with Candida albicans and 18 (37.5%) were isolated with a non-albicans species, mostly commonly Candida glabrata. A multivariate analysis identified proton pump inhibitor administration at admission to ICU [odds ratio 5.66; 95% confidence interval 1.12-28.5] as associated with colonization. Patients colonized with Candida had a significantly longer length of ICU and hospital stays (7.6 ± 6.6 vs. 4.2 ± 2.6 days, P = 0.01 and 14.9 ± 12.9 vs. 7.5 ± 6.7 days, P = 0.02, respectively). Clonality testing between C. albicans and C. glabrata strains identified indistinguishable strains among the patient cohort. These data provide additional information on Candida colonization in critically ill patients.

Evaluation of chromogenic media and seminested PCR in the identification of Candida species

Identification of Candida cultured from various clinical specimens to the species level is increasingly necessary for clinical laboratories. Although sn PCR identifies the species within hours but its cost-effectiveness is to be considered. So there is always a need for media which help in the isolation and identification at the species level. The study aimed to evaluate the performance of different chromogenic media and to compare the effectiveness of the traditional phenotypic methods vs. seminested polymerase chain reaction (sn PCR) for identification of Candida species. One hundred and twenty seven Candida strains isolated from various clinical specimens were identified by conventional methods, four different chromogenic media and sn PCR. HiCrome Candida Differential and CHROMagar Candida media showed comparably high sensitivities and specificities in the identification of C. albicans, C. tropicalis, C. glabrata and C. krusei. CHROMagar Candida had an extra advantage of identifying all C. parapsilosis isolates. CHROMagar-Pal’s medium identified C. albicans, C. tropicalis and C. krusei with high sensitivities and specificities, but couldn’t identify C. glabrata or C. parapsilosis. It was the only medium that identified C. dubliniensis with a sensitivity and specificity of 100%. Biggy agar showed the least sensitivities and specificities. The overall concordance of the snPCR compared to the conventional tests including CHROMAgar Candida in the identification of Candida species was 97.5%. The use of CHROMAgar Candida medium is an easy and accurate method for presumptive identification of the most commonly encountered Candida spp.

Salivary diagnostics: a brief review

Early detection of disease plays a crucial role for treatment planning and prognosis. Saliva has great potential as a diagnostic fluid and offers advantage over serum and other biological fluids by an economic and noninvasive collection method for monitoring of systemic health and disease progression. The plethora of components in this fluid can act as biomarkers for diagnosis of various systemic and local diseases. In this review paper, we have emphasized the role of salivary biomarkers as diagnostic tools.

Clinical and microbiological diagnosis of oral candidiasis

Introduction: Candidiasis or oral candidiasis is the most frequent mucocutaneous mycosis of the oral cavity. It is produced by the genus Candida, which is found in the oral cavity of 53% of the general population as a common commensal organism. One hundred and fifty species have been isolated in the oral cavity, and 80% of the isolates correspond to Candida albicans, which can colonize the oral cavity alone or in combination with other species. Transformation from commensal organism to pathogen depends on the intervention of different predisposing factors that modify the microenvironment of the oral cavity and favor the appearance of opportunistic infection. The present study offers a literature review on the diagnosis of oral candidiasis, with the purpose of establishing when complementary microbiological techniques for the diagnosis of oral candidiasis should be used, and which techniques are most commonly employed in routine clinical practice in order to establish a definitive diagnosis. Materials and methods: A Medline-PubMed, Scopus and Cochrane search was made covering the last 10 years. Results: The diagnosis of oral candidiasis is fundamentally clinical. Microbiological techniques are used when the clinical diagnosis needs to be confirmed, for establishing a differential diagnosis with other diseases, and in cases characterized by resistance to antifungal drugs. Biopsies in turn are indicated in patients with hyperplastic candidiasis. Staining (10% KOH) and culture (Sabouraud dextrose agar) are the methods most commonly used for diagnosing primary candidiasis. Identification of the individual species of Candida is usually carried out with CHROMagar Candida®. For the diagnosis of invasive candidiasis, and in cases requiring differentiation between C. albicans and C. dubliniensis, use is made of immunological and genetic techniques such as ELISA and PCR.

Key words:Clinical, oral candidiasis, microbiology.

Oral candidiasis: Species identification and their antifungal susceptibility pattern in cancer patients receiving radiation therapy

Introduction:Radiotherapy-induced hyposalivation encourages oralCandidacolonization that often leads to oral/pharyngeal candidiasis. The objective of this study was to identify theCandidaspecies in lesions of oropharyngeal candidiasis in patients undergoing radiotherapy for head and neck cancers and to find out antifungal susceptibility pattern.

Material and methods:Swabs were collected from 60 patients who developed lesions suggestive of oral candidiasis at the end of 1st week of radiation therapy. Antifungal susceptibility of each of the isolated species was done using disc diffusion method following CLSI guidelines.

Results: Candidawas isolated in 13 cases.C.albicans(7) was the most predominant species; a small number of other species have also been identified. Few strains (3) ofCandidashowed variable resistance to the commonly used antifungal drugs.

Discussion:The colonization ofCandidamay lead to development of infections with drug-resistant strains, and hence the patients receiving radiation for head and neck cancers should undergo microbiological study for oral candidiasis.

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

BACKGROUND

Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as those representing eukaryotic organisms.

RESULTS

Here we introduce CloVR-ITS, an automated pipeline for comparative analysis of internal transcribed spacer (ITS) pyrosequences amplified from metagenomic DNA isolates and representing fungal species. This pipeline performs a variety of steps similar to those commonly used for 16S rRNA amplicon sequence analysis, including preprocessing for quality, chimera detection, clustering of sequences into operational taxonomic units (OTUs), taxonomic assignment (at class, order, family, genus, and species levels) and statistical analysis of sample groups of interest based on user-provided information. Using ITS amplicon pyrosequencing data from a previous human gastric fluid study, we demonstrate the utility of CloVR-ITS for fungal microbiota analysis and provide runtime and cost examples, including analysis of extremely large datasets on the cloud. We show that the largest fractions of reads from the stomach fluid samples were assigned to Dothideomycetes, Saccharomycetes, Agaricomycetes and Sordariomycetes but that all samples were dominated by sequences that could not be taxonomically classified. Representatives of the Candida genus were identified in all samples, most notably C. quercitrusa, while sequence reads assigned to the Aspergillus genus were only identified in a subset of samples. CloVR-ITS is made available as a pre-installed, automated, and portable software pipeline for cloud-friendly execution as part of the CloVR virtual machine package (http://clovr.org).

CONCLUSION

The CloVR-ITS pipeline provides fungal microbiota analysis that can be complementary to bacterial 16S rRNA and total metagenome sequence analysis allowing for more comprehensive studies of environmental and host-associated microbial communities.

Treatment of Candida famata bloodstream infections: case series and review of the literature

OBJECTIVES

Candida famata (also known as Debaryomyces hansenii and Torulopsis candida) is a commensal yeast found in cheese, dairy products and the environment. C. famata accounts for 0.2%-2% of invasive candidiasis. The purpose of this study was to provide an overview of the treatment of C. famata bloodstream infections.

METHODS

The clinical course of two hospitalized patients who developed C. famata fungaemia within 2 weeks of each other was summarized along with available data regarding in vitro susceptibility patterns, genotyping and clinical outcomes of these cases compared with the published literature.

RESULTS AND CONCLUSIONS

C. famata appears to exhibit reduced susceptibility to echinocandins and azoles, particularly in the setting of prior antifungal exposure. The removal of indwelling central venous catheters and prompt initiation of therapy with liposomal amphotericin B is recommended for successful treatment of C. famata fungaemia, particularly in immunocompromised patients. These cases also help provide justification for routine antifungal susceptibility testing in patients with candidaemia to guide optimal antifungal therapy.

Oral candidosis in lichen planus: the diagnostic approach is of major therapeutic importance

OBJECTIVES

Candida albicans is the most common fungal pathogen in humans, but other Candida species cause candidosis. Candida species display significant differences in their susceptibility to antimycotic drugs. Patients with symptomatic or erythematous oral lichen planus (OLP) commonly have Candida infection requiring correct identification of Candida species in order to initiate adequate antimycotic therapy. Therefore, conventional cytosmear and culture tests were compared with genetic diagnostics on oral rinse followed by agar culture and material collected by cytobrush from OLP patient mucosal lesion.

METHODS

The genetic approach was validated on a reference panel of 60 well-defined unrelated fungal species. The study included 37 OLP patients. Oral candidosis (OC) was established based on clinical signs of OC and/or oral mucosal symptoms and at least one hypha in lesional cytosmear. Antimycotic treatment was initiated after OC diagnosis, and symptomatic treatment was initiated in no-candidosis situations.

RESULTS

The composition of Candida species in oral rinse/culture test was different from that of lesional cytobrush sampling as more non-albicans species were detected by the latter. Unexpectedly, Candida dubliniensis was found to be overrepresented among patients with a history of antimycotic treatment indicating unintentional iatrogen selection. Of the 22 OLP patients receiving treatment, 27% of these should have been offered alternative therapy based on the improved diagnostic approach.

CONCLUSION

This study highlights the importance of lesional sampling in OLP patients with suspected OC.

CLINICAL RELEVANCE

Correct fungal identification is critical in order to initiate adequate antimycotic therapy, thus minimizing iatrogen selection of non-albicans species.

Insights into Candida tropicalis nosocomial infections and virulence factors

Candida tropicalis is considered the first or the second non-Candida albicans Candida (NCAC) species most frequently isolated from candidosis, mainly in patients admitted in intensive care units (ICUs), especially with cancer, requiring prolonged catheterization, or receiving broad-spectrum antibiotics. The proportion of candiduria and candidemia caused by C. tropicalis varies widely with geographical area and patient group. Actually, in certain countries, C. tropicalis is more prevalent, even compared with C. albicans or other NCAC species. Although prophylactic treatments with fluconazole cause a decrease in the frequency of candidosis caused by C. tropicalis, it is increasingly showing a moderate level of fluconazole resistance. The propensity of C. tropicalis for dissemination and the high mortality associated with its infections might be strongly related to the potential of virulence factors exhibited by this species, such as adhesion to different host surfaces, biofilm formation, infection and dissemination, and enzymes secretion. Therefore, the aim of this review is to outline the present knowledge on all the above-mentioned C. tropicalis virulence traits.

Pathogenesis and treatment of oral candidosis

Oral infections caused by yeast of the genus Candida and particularly Candida albicans (oral candidoses) have been recognised throughout recorded history. However, since the 1980s a clear surge of interest and associated research into these infections have occurred. This has largely been due to an increased incidence of oral candidosis over this period, primarily because of the escalation in HIV-infection and the AIDS epidemic. In addition, changes in medical practice leading to a greater use of invasive clinical procedures and a more widespread use of immunosuppressive therapies have also contributed to the problem. Whilst oral candidosis has previously been considered to be a disease mainly of the elderly and very young, its occurrence throughout the general population is now recognised. Candida are true ‘opportunistic pathogens’ and only instigate oral infection when there is an underlying predisposing condition in the host. Treatment of these infections has continued (and in some regards continues) to be problematic because of the potential toxicity of traditional antifungal agents against host cells. The problem has been compounded by the emergence of Candida species other than C. albicans that have inherent resistance against traditional antifungals. The aim of this review is to give the reader a contemporary overview of oral candidosis, the organisms involved, and the management strategies that are currently employed or could be utilised in the future.

Oral Candida carriage of patients attending a dental clinic in Braga, Portugal

BACKGROUND

The ability of the Candida species to colonize surfaces can be considered as a risk factor for oral infection.

AIMS

To establish oral Candida carriage in patients attending a dental clinic in Braga, Portugal.

METHODS

A total of 97 patients were analysed. Swab samples were collected and directly cultured onto CHROMagar Candida. Representative yeasts were identified by polymerase chain reaction.

RESULTS

From the samples analysed 54.6% (n=53) were Candida positive, and Candida albicans was the most frequently isolated species, accounting for 79% of all the species identified. Non-C. albicans Candida (NCAC) species recovered included Candida parapsilosis, Candida glabrata, Candida tropicalis, and Candida guilliermondii. There was a lack of association between the presence of C. albicans or NCAC species, and age, gender, or prostheses wearing in this population. In 17% of the cases (n=9), polymicrobial cultures, with two different Candida species, were identified.

CONCLUSIONS

This study shows a high Candida carriage rate among this population, thus pointing to the relevance of an accurate diagnostic approach in Candida species identification.

Antifungal drug resistance of oral fungi

Fungi comprise a minor component of the oral microbiota but give rise to oral disease in a significant proportion of the population. The most common form of oral fungal disease is oral candidiasis, which has a number of presentations. The mainstay for the treatment of oral candidiasis is the use of polyenes, such as nystatin and amphotericin B, and azoles including miconazole, fluconazole, and itraconazole. Resistance of fungi to polyenes is rare, but some Candida species, such as Candida glabrata and C. krusei, are innately less susceptible to azoles, and C. albicans can acquire azole resistance. The main mechanism of high-level fungal azole resistance, measured in vitro, is energy-dependent drug efflux. Most fungi in the oral cavity, however, are present in multispecies biofilms that typically demonstrate an antifungal resistance phenotype. This resistance is the result of multiple factors including the expression of efflux pumps in the fungal cell membrane, biofilm matrix permeability, and a stress response in the fungal cell. Removal of dental biofilms, or treatments to prevent biofilm development in combination with antifungal drugs, may enable better treatment and prevention of oral fungal disease.

Characterization of the oral fungal microbiome (mycobiome) in healthy individuals

The oral microbiome-organisms residing in the oral cavity and their collective genome-are critical components of health and disease. The fungal component of the oral microbiota has not been characterized. In this study, we used a novel multitag pyrosequencing approach to characterize fungi present in the oral cavity of 20 healthy individuals, using the pan-fungal internal transcribed spacer (ITS) primers. Our results revealed the "basal" oral mycobiome profile of the enrolled individuals, and showed that across all the samples studied, the oral cavity contained 74 culturable and 11 non-culturable fungal genera. Among these genera, 39 were present in only one person, 16 genera were present in two participants, and 5 genera were present in three people, while 15 genera (including non-culturable organisms) were present in >/=4 (20%) participants. Candida species were the most frequent (isolated from 75% of participants), followed by Cladosporium (65%), Aureobasidium, Saccharomycetales (50% for both), Aspergillus (35%), Fusarium (30%), and Cryptococcus (20%). Four of these predominant genera are known to be pathogenic in humans. The low-abundance genera may represent environmental fungi present in the oral cavity and could simply be spores inhaled from the air or material ingested with food. Among the culturable genera, 61 were represented by one species each, while 13 genera comprised between 2 and 6 different species; the total number of species identified were 101. The number of species in the oral cavity of each individual ranged between 9 and 23. Principal component (PCO) analysis of the obtained data set followed by sample clustering and UniFrac analysis revealed that White males and Asian males clustered differently from each other, whereas both Asian and White females clustered together. This is the first study that identified the "basal mycobiome" of healthy individuals, and provides the basis for a detailed characterization of the oral mycobiome in health and disease.

Characterization of the oral fungal microbiome (mycobiome) in healthy individuals

The oral microbiome–organisms residing in the oral cavity and their collective genome–are critical components of health and disease. The fungal component of the oral microbiota has not been characterized. In this study, we used a novel multitag pyrosequencing approach to characterize fungi present in the oral cavity of 20 healthy individuals, using the pan-fungal internal transcribed spacer (ITS) primers. Our results revealed the “basal” oral mycobiome profile of the enrolled individuals, and showed that across all the samples studied, the oral cavity contained 74 culturable and 11 non-culturable fungal genera. Among these genera, 39 were present in only one person, 16 genera were present in two participants, and 5 genera were present in three people, while 15 genera (including non-culturable organisms) were present in ≥4 (20%) participants. Candida species were the most frequent (isolated from 75% of participants), followed by Cladosporium (65%), Aureobasidium, Saccharomycetales (50% for both), Aspergillus (35%), Fusarium (30%), and Cryptococcus (20%). Four of these predominant genera are known to be pathogenic in humans. The low-abundance genera may represent environmental fungi present in the oral cavity and could simply be spores inhaled from the air or material ingested with food. Among the culturable genera, 61 were represented by one species each, while 13 genera comprised between 2 and 6 different species; the total number of species identified were 101. The number of species in the oral cavity of each individual ranged between 9 and 23. Principal component (PCO) analysis of the obtained data set followed by sample clustering and UniFrac analysis revealed that White males and Asian males clustered differently from each other, whereas both Asian and White females clustered together. This is the first study that identified the “basal mycobiome” of healthy individuals, and provides the basis for a detailed characterization of the oral mycobiome in health and disease.

We characterized the fungal microbiome (mycobiome) of the oral cavity in healthy individuals. Our results demonstrate that the fungal component of the oral microbiome is diverse as revealed by the presence of 74 culturable and 11 non-culturable fungal genera in the oral cavity. A total of 101 species were identified, with between 9 and 23 culturable species present in each person. Fifteen genera (which included four known pathogenic fungi and non-culturable organisms) were present in ≥20% of the tested samples; Candida species were the most frequently obtained genera, isolated from 75% of all study participants, followed by Cladosporium (65%), Aureobasidium, Saccharomycetales (50% for both), Aspergillus (35%), Fusarium (30%), and Cryptococcus (20%). The remaining fungi detected in the oral wash samples represent organisms likely originating from the environment. This is the first study that identified the “basal mycobiome” of healthy individuals, and provides the basis for a detailed characterization of the oral mycobiome in health and disease.

Salivary Genomics, Transcriptomics and Proteomics: The Emerging Concept of the Oral Ecosystem and their Use in the Early Diagnosis of Cancer and other Diseases

There is an increasingly growing interest world-wide for the genomics, transcriptomics and proteomics of saliva and the oral cavity, since they provide a non-invasive source of unprecedently rich genetic information. The complexity of oral systems biology goes much beyond the human genome, transcriptome and proteome revealed by oral mucosal cells, gingival crevicular fluid, and saliva, and includes the complexity of the oral microbiota, the symbiotic assembly of bacterial, fungal and other microbial flora in the oral cavity. In our review we summarize the recent information on oral genomics, transcriptomics and proteomics, of both human and microbial origin. We also give an introduction and practical advice on sample collection, handling and storage for analysis. Finally, we show the usefulness of salivary and oral genomics in early diagnosis of cancer, as well as in uncovering other systemic diseases, infections and oral disorders. We close the review by highlighting a number of possible exploratory pathways in this emerging, hot research field.