A nested PCR assay to detect DNA in sera for the diagnosis of deep-seated trichosporonosis

Rapid and Simple Detection of Trichosporon asahii by Optimized Colony PCR

Trichosporon asahii is the major pathogen causing invasive trichosporonosis. Conventional methods of its detection are time-consuming or costly and often require complex DNA extraction and purification steps, which hinders rapid clinical diagnosis. In this study, we evaluated colony PCR, which directly uses colonies or trace clinical samples as the template for amplification, for rapid detection of T. asahii infection. Four methods, namely, direct colony, freeze-thaw, glass beads, and enzymolysis, were compared to select the best DNA extraction strategy. We subsequently designed and screened species-specific primers targeting the intergenic spacer 1 (IGS1) of the ribosomal DNA of T. asahii and used them to detect mock infection clinical samples. The species-specific colony PCR based on glass beads proved advantageous, with short procedure time (154.8 ± 0.6 min), good sensitivity (detection limit, 10² CFU/mL), and specificity for T. asahii, indicating that this method can be used for the rapid and simple identification of clinical samples of T. asahii infection.

Prevalence of Streptococcus mutans and Lactobacillus fermentum and their association with caries and dietary habits in preschool Thai children

AIMS

To detect the prevalence of Streptococcus mutans and Lactobacillus fermentum in plaque obtained from severe early childhood caries (S-ECC) and caries-free (CF) groups and to assess any association between their prevalence, feeding habits and oral hygiene practices within each group.

STUDY DESIGN

Sixty-four supra-gingival plaque samples were collected from S-ECC and CF groups (CF = 30, S-ECC = 34). All participants were asked about feeding habits and oral hygiene care behaviour by direct questionnaire.

METHODS

After DNA extraction, S. mutans and L. fermentum were amplified using standard PCR. Nested PCR was performed as a second identification method for S. mutans.

RESULTS

Mean age in CF and S-ECC was 2.29 ± 0.42 and 2.49 ± 0.41 years, respectively. Mean dmft in S-ECC was 4.51 ± 0.72. By standard PCR, no S. mutans was detected in CF group, while 10 % was detected in S-ECC group. By nested PCR, S. mutans was detected for 48 and 50 % in CF and S-ECC, respectively. L. fermentum was detected for 16 and 40 % in CF and S-ECC, respectively.

CONCLUSION

Nested PCR gave a higher detection frequency than standard PCR but not significant (p ≤ 0.05). The prevalence of S. mutans was not different between the two groups, while the prevalence of L. fermentum was significantly associated with S-ECC (p ≤ 0.05).

Development of a peptide nucleic acid probe to Trichosporon species and identification of trichosporonosis by use of in situ hybridization in formalin-fixed and paraffin-embedded (FFPE) sections

In order to identify Trichosporon species in formalin-fixed and paraffin-embedded sections from which visual discrimination of non-glabrata Candida species is mostly ineffective but critical for the choice of antifungals, we tested the usefulness of a newly designed peptide nucleic acid probe (PNA) for in situ hybridization (ISH). Results confirmed the usefulness of ISH with our PNA probe in identifying Trichosporon species from Candida albicans.

Current knowledge of Trichosporon spp. and Trichosporonosis

Trichosporon spp. are basidiomycetous yeast-like fungi found widely in nature. Clinical isolates are generally related to superficial infections. However, this fungus has been recognized as an opportunistic agent of invasive infections, mostly in cancer patients and those exposed to invasive medical procedures. It is possible that the ability of Trichosporon strains to form biofilms on implanted devices, the presence of glucuronoxylomannan in their cell walls, and the ability to produce proteases and lipases are all factors likely related to the virulence of this genus and therefore may account for the progress of invasive trichosporonosis. Disseminated trichosporonosis has been increasingly reported worldwide and represents a challenge for both diagnosis and species identification. Phenotypic identification methods are useful for Trichosporon sp. screening, but only molecular methods, such as IGS region sequencing, allow the complete identification of Trichosporon isolates at the species level. Methods for the diagnosis of invasive trichosporonosis include PCR-based methods, Luminex xMAP technology, and, more recently, proteomics. Treating patients with trichosporonosis remains a challenge because of limited data on the in vitro and in vivo activities of antifungal drugs against clinically relevant species of the genus. Despite the mentioned limitations, the use of antifungal regimens containing triazoles appears to be the best therapeutic approach.

Differential diagnosis of trichosporonosis using conventional histopathological stains and electron microscopy

AIMS

Although Trichosporon is a causative pathogen of white piedra and summer-type hypersensitivity pneumonitis, fatal disseminated trichosporonosis cases have recently been increasing. However, Trichosporon is often confused with other fungi, especially Candida, in pathological specimens. The aim was to determine the utility of histopathological stains and electron microscopy for diagnosing trichosporonosis.

METHODS AND RESULTS

Autopsy cases of trichosporonosis, candidiasis, aspergillosis and cryptococcosis were investigated using histopathological stains and electron microscopy. Using Grocott's method, Trichosporon was weakly detected compared with other fungi. In contrast, diluted periodic acid methenamine silver (PAM) stain clearly enhanced the intensity of staining of Trichosporon compared with Candida. Furthermore, Alcian blue and colloidal iron stains predominantly detected Trichosporon. Electron microscopy after staining with diluted PAM demonstrated that Trichosporon has a variety of hyphal sizes and laminar deposition of rough silver granules, whereas Candida has uniform pseudohyphae and fine granules. The average diameter and population area of the granules were significantly higher in Trichosporon compared with Candida (P<0.01). Meanwhile, the laminar structure was preserved in the cell walls of Trichosporon without silver stains, whereas a low-density structure was observed in Candida.

CONCLUSIONS

Histopathological staining patterns and electron microscopic findings can facilitate the diagnosis of trichosporonosis.

Supplemental utility of nested PCR for the pathological diagnosis of disseminated trichosporonosis

Disseminated trichosporonosis is known to be a severe opportunistic mycosis and has a high mortality rate. In autopsy cases, it is often difficult to diagnose as trichosporonosis because the causative Trichosporon species are pathologically similar to other fungi, especially the Candida species. Immunohistochemical analysis is essential for the differential diagnosis, but an antibody to Trichosporon is not available commercially. In the present study, we investigated the supplemental utility of nested polymerase chain reaction (PCR) for the pathological diagnosis of trichosporonosis from formalin-fixed and paraffin-embedded tissues. Total DNA was purified from 30 major organs in three autopsy cases, and Trichosporon DNA was specifically amplified by nested PCR using three sets of primers. Of 22 organs in which Grocott's stain was positive for fungal infection, 170- and 259-bp PCR products were detected in 20 (91%) and 12 (55%) organs, respectively. In short-term fixation (about 1 day), these bands were highly detected in ten (100%) and nine (90%) organs, whereas the detection efficiency tended to decrease after long-term fixation and decalcification. No PCR product of 412 bp was detected in any organs. These findings suggest that nested PCR from short-term-fixed tissues is useful for supportive pathological diagnosis of disseminated trichosporonosis.

Real-time PCR assay to detect DNA in sera for the diagnosis of deep-seated trichosporonosis

Deep-seated trichosporonosis due to Trichosporon asahii is life-threatening and has high mortality. A real-time PCR assay to detect T. asahii DNA in sera for diagnosis of this fungal infection was developed. The assay showed a higher sensitivity than polysaccharide antigen detection method. Our new real-time PCR assay may be used for diagnosing deep-seated trichosporonosis due to T. asahii.

Susceptibility patterns and molecular identification of Trichosporon species

The physiological patterns, the sequence polymorphisms of the internal transcriber spacer (ITS), and intergenic spacer regions (IGS) of the rRNA genes and the antifungal susceptibility profile were evaluated for their ability to identify Trichosporon spp. and their specificity for the identification of 49 clinical isolates of Trichosporon spp. Morphological and biochemical methodologies were unable to differentiate among the Trichosporon species. ITS sequencing was also unable to differentiate several species. However, IGS1 sequencing unambiguously identified all Trichosporon isolates. Following the results of DNA-based identification, Trichosporon asahii was the species most frequently isolated from deep sites (15 of 25 strains; 60%). In the main, other Trichosporon species were recovered from cutaneous samples. The majority of T. asahii, T. faecale, and T. coremiiforme clinical isolates exhibited resistance in vitro to amphotericin B, with geometric mean (GM) MICs >4 mug/ml. The other species of Trichosporon did not show high MICs of amphotericin B, and GM MICs were <1 mug/ml. Azole agents were active in vitro against the majority of clinical strains. The most potent compound in vitro was voriconazole, with a GM MIC Collapse

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MESH Headings

• Amphotericin B/pharmacology
• Antifungal Agents/pharmacology
• Argentina/epidemiology
• DNA, Fungal/analysis
• DNA, Fungal/genetics
• DNA, Intergenic/analysis
• DNA, Intergenic/genetics
• DNA, Ribosomal/analysis
• DNA, Ribosomal/genetics
• DNA, Ribosomal Spacer/analysis
• DNA, Ribosomal Spacer/genetics
• Disease Susceptibility
• Drug Resistance, Fungal/genetics
• Humans
• Microbial Sensitivity Tests
• Phylogeny
• Polymorphism, Genetic
• RNA, Fungal/analysis
• RNA, Fungal/genetics
• RNA, Ribosomal/analysis
• RNA, Ribosomal/genetics
• Retrospective Studies
• Sequence Analysis, DNA
• Spain/epidemiology
• Trichosporon/classification
• Trichosporon/drug effects
• Trichosporon/genetics
• Trichosporon/growth & development
• Trichosporon/isolation & purification
• Trichosporon/physiology

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Affiliation(s)

Juan L Rodriguez-Tudela Servicio de Micología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
Teresa M Diaz-Guerra
Emilia Mellado
Virginia Cano
Cecilia Tapia
Alexander Perkins
Alicia Gomez-Lopez
Laura Rodero
Manuel Cuenca-Estrella

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Characterization of Trichosporon species isolated from clinical specimens in Kuwait

Invasive trichosporonosis is an emerging infection of severely immunocompromised patients. It is principally caused by Trichosporon asahii, although some other species of the genus have also been implicated in the aetiology. In this work, 29 clinical isolates of Trichosporon species recovered from 29 different patients over a 6-year period were studied for phenotypic and genotypic characteristics. Two morphotypes were recognized on the basis of colony characteristics. The colonies of 25 isolates appeared flat and centrally wrinkled, while the other four isolates appeared dry and irregularly folded or verrucosed. Based on substrate assimilation profiles, all 29 isolates were identified as T. asahii using the Vitek 2 system. However, PCR amplification of rRNA gene sequences identified only 25 of the 29 isolates as T. asahii. The identity of the remaining four isolates was established as Trichosporon asteroides by direct DNA sequencing of the internally transcribed spacer (ITS)-1 and ITS-2 regions in the rRNA gene fragment amplified by PCR using panfungal primers. Fingerprinting carried out by randomly amplified polymorphic DNA analysis showed genotypic heterogeneity among the 25 T. asahii and four T. asteroides isolates. These data suggest that T. asahii is the major species associated with clinical specimens in Kuwait.

Nested PCR for detection of mutans streptococci in dental plaque

AIMS

Mutans streptococci such as Streptococcus mutans and Streptococcus sobrinus have been implicated in human dental caries. In an attempt to develop a rapid and sensitive method for detecting Strep. mutans and Strep. sobrinus in dental plaque, a nested PCR amplification based on the 16S rRNA gene was employed.

METHODS AND RESULTS

A universal set of PCR primers for bacterial 16S rRNA gene was introduced for the first PCR, and then two sets of primers specific for the 16S rRNA gene sequences of either Strep. mutans or Strep. sobrinus were used for the second PCR. Eighteen plaque samples were analyzed, and a nested PCR was shown to be more sensitive for detecting Strep. mutans and Strep. sobrinus than direct PCR.

CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY

The 16S rRNA gene-based nested PCR method is a rapid and sensitive method for the detection of mutans streptococci, and may also be suitable for carrying out large-scale studies on the cariogenicity of mutans streptococci.

A review of nucleic acid-based diagnostic tests for systemic mycoses with an emphasis on polymerase chain reaction-based assays

Nucleic acid-based assays have good potential to complement and enhance the sensitivity and rapidity of conventional methods used in diagnostic mycology. The majority of molecular tests are polymerase chain reaction (PCR)-based assays focusing mainly on the detection of Candida and Aspergillus spp. from clinical samples. DNA extraction and purification procedures should be standardized and can be facilitated by using commercial extraction kits. In general, protocols that target multi-copy genes provide the greatest sensitivity. Objective endpoint assessments of PCR tests using enzyme-linked immunosorbent assays (ELISA) or commercial quantitative systems are capable of rapidly detecting and identifying Candida and Aspergillus spp. Sequencing of PCR products can be used to confirm the identity of amplicons. In cases of suspected invasive aspergillosis, PCR should be performed on both blood and bronchoalveolar lavage fluid to maximize test sensitivity and the positive predictive value. At least two blood specimens should be tested if PCR is undertaken on blood samples alone. In situ hybridization techniques have been used with success to identify fungi in tissue specimens. The wide application of PCR-based assays relies on the introduction of standardized protocols following their evaluation in multicentre, prospective studies.