Conventional Methods for the Diagnosis of Dermatophytosis

Dermatophytes are keratinolytic fungi responsible for a large variety of diseases that can affect glabrous skin, nails and hair. In many cases, the diagnosis is not clinically obvious, and mycological analysis is required. This includes both direct microscopic examination and cultures. First of all, clinical specimens have to be sampled according to localization and characteristics of the lesions. Direct microscopic examination is usually performed using clearing reagents (KOH or Amman's chloral-lactophenol), but its sensitivity may be greatly enhanced by the use of stains or fluorochromes such as Congo red or Calcofluor white. Histological analysis is an efficient method, but it is constraining for the patients and, as direct examination, it does not allow precise identification of the pathogen. Cultures are therefore needed, and specific culture media may be used to overcome the growth of rapidly growing contaminating moulds which may hamper the recovery of dermatophytes. Identification at the species level which may be useful to initiate an appropriate treatment or for setting prophylactic measures, relies on macroscopic and microscopic morphology. Subcultures on culture media which stimulate conidiation and, for some species, the production of pigments, are often necessary. Additionally, in case of atypical isolates, some biochemical or physiological tests may be performed such as the search for urease activity or the in vitro hair perforation test. However, their contribution to species identification is rather limited, and progress is still needed for the development of biochemical or immunological tests allowing an accurate identification at the species level, pending for the availability of molecular biology-based kits.     

Skin diseases associated with Malassezia species in humans. Clinical features and diagnostic criteria

Malassezia yeasts not only cause the well known pityriasis versicolor and folliculitis, but also play an important role in other skin diseases, including seborrheic dermatitis and atopic dermatitis. The presence of Malassezia yeasts may be confirmed by direct microscopic examination and cultures of skin scrapings. In pityriasis versicolor the direct microscopic examination is the rapidest and surest test for confirming the clinical diagnosis. The preparation will show a cluster of globose budding spores with thick or double wall and short hyphae. For detecting Malassezia in the other diseases the cultures is preferable. Culture is useful both for confirming the clinical diagnosis and for epidemiological investigations. The identification of the Malassezia species is not easy. The microscopic observation of the colony direct towards the identification of Malassezia species, but it is not enough to identify the colonies definitely. Several biochemical tests are necessary for a precise identification, such as catalase reaction, growth on media without lipid sources, ability to utilize hydrophilic emulsifiers as sole lipid source, esculin test, tryptophan test.     

New methods for the detection of orthopedic and other biofilm infections

The detection and identification of bacteria present in natural and industrial ecosystems is now entirely based on molecular systems that detect microbial RNA or DNA. Culture methods were abandoned, in the 1980s, because direct observations showed that <1% of the bacteria in these systems grew on laboratory media. Culture methods comprise the backbone of the Food and Drug Administration-approved diagnostic systems used in hospital laboratories, with some molecular methods being approved for the detection of specific pathogens that are difficult to grow in vitro. In several medical specialties, the reaction to negative cultures in cases in which overt signs of infection clearly exist has produced a spreading skepticism concerning the sensitivity and accuracy of traditional culture methods. We summarize evidence from the field of orthopedic surgery, and from other medical specialties, that support the contention that culture techniques are especially insensitive and inaccurate in the detection of chronic biofilm infections. We examine the plethora of molecular techniques that could replace cultures in the diagnosis of bacterial diseases, and we identify the new Ibis technique that is based on base ratios (not base sequences), as the molecular system most likely to fulfill the requirements of routine diagnosis in orthopedic surgery.     

Listeria: growth,phenotypic differentiation and molecular microbiology

The identification of Listeria species is based on a limited number of biochemical markers, among which absence or presence of hemolysis and arylamidase are used to differentiate between L. monocytogenes and L. innocua. The CAMP (Christie, Atkins, Munch-Petersen) test must be interpreted with caution. Chromogenic media are based on both the specific chromogenic detection of phosphatidylinositol phospholipase C and the xylose fermentation and give specific and direct identification of L. monocytogenes and L. ivanovii. Isolates of L. monocytogenes with atypical properties require tools of molecular biology for final identification. Serotyping, although not allowing speciation, serves a useful purpose for confirming the genus diagnosis Listeria. Polymerase chain reaction is particularly useful when prior administration of antimicrobial agents compromises culture. For clinical specimens the importance of trying to isolate the pathogen as a prerequisite for an epidemiological work-up and finally for prevention of further cases cannot be overstressed.     

Rapid Diagnosis of Bloodstream Infections with PCR Followed by Mass Spectrometry

Achieving a rapid microbiological diagnosis is crucial for decreasing morbidity and mortality of patients with a bloodstream infection, as it leads to the administration of an appropriate empiric antimicrobial therapy. Molecular methods may offer a rapid alternative to conventional microbiological diagnosis involving blood culture. In this study, the performance of a new technology that uses broad-spectrum PCR coupled with mass spectrometry (PCR/ESI-MS) was evaluated for the detection of microorganisms directly from whole blood. A total of 247 whole blood samples and paired blood cultures were prospectively obtained from 175 patients with a suspicion of sepsis. Both sample types were analyzed using the PCR/ESI-MS technology, and the results were compared with those obtained by conventional identification methods. The overall agreement between conventional methods and PCR/ESI-MS performed in blood culture aliquots was 94.2% with 96.8% sensitivity and 98.5% specificity for the molecular method. When comparing conventional methods with PCR/ESI-MS performed in whole blood specimens, the overall agreement was 77.1% with 50% sensitivity and 93.8% specificity for the molecular method. Interestingly, the PCR/ESI-MS technology led to the additional identification of 13 pathogens that were not found by conventional methods. Using the PCR/ESI-MS technology the microbiological diagnosis of bloodstream infections could be anticipated in about half of the patients in our setting, including a small but significant proportion of patients newly diagnosed. Thus, this promising technology could be very useful for the rapid diagnosis of sepsis in combination with traditional methods.     

Comparison of Dermatophyte PCR Kit with Conventional Methods for Detection of Dermatophytes in Skin Specimens

The laboratory diagnosis of dermatophytosis is usually based on direct microscopic examination and culturing of clinical specimens. A commercial polymerase chain reaction kit (Dermatophyte PCR) has had favorable results when used for detection of dermatophytes and identification of Trichophyton rubrum in nail specimens. This study investigated the efficacy of the Dermatophyte PCR kit for detecting dermatophytosis in 191 hair or skin specimens from patients with suspected dermatophytosis. PCR was positive for 37 % of samples, whereas 31 and 39 % of the specimens were positive by culturing and direct microscopy, respectively. The sensitivity, specificity, positive predictive value, and negative predictive value for PCR analysis were 83, 84, 71, and 91 %, respectively. The sensitivity of the PCR test was higher in specimens obtained from skin (88 %) than in those obtained from hair (58 %), while the specificity remained almost the same (84 and 86 % for skin and hair, respectively). Our results show that the Dermatophyte PCR kit is a promising diagnostic tool for detection of dermatophytosis in skin samples, providing clinicians with a rapid diagnosis.     

真菌感染的实验室诊断研究进展

随着易感人群逐渐增多,对临床真菌感染标本的快速检测及真菌培养的分离鉴定日益重要。所幸目前有新的检测方法用来辅助早期诊断及指导经验性的抗真菌治疗。主要的进展集中在对标本的真菌抗原直接检测方面(如半乳甘露聚糖和β-葡聚糖);假丝酵母产色培养基等快速培养鉴定法;微生物生化自动分析系统(VITEK2)和显微扫描(MicroScan)等生化自动检测平板;多肽核苷酸原位杂交,特异性的大范围聚合酶链反应(PCR)检测以及针对临床标本或培养阳性标本直接DNA测序技术。     

非侵袭性真菌性鼻窦炎的实验室诊断及致病菌分析

目的 探讨非侵袭性真菌性鼻窦炎的实验室诊断方法,分析其致病菌,为鼻窦炎合并真菌感染的临床诊断、治疗提供依据。方法 对我院临床及鼻内镜下所诊断的10例真菌性鼻窦炎患者,鼻内镜手术时直接吸取病变的鼻窦黏膜及窦腔内容物,通过直接镜检、真菌培养、传统鉴定及分子生物学鉴定和组织病理学检查对其进行检查。结果 10例病例中,直接镜检阳性者8例;病理学检查可见真菌菌丝或者孢子者8例;接种培养及基因鉴定阳性者5例（感染菌株包括2例烟曲霉复合体、1例杂色曲霉、1例枝孢样枝孢霉、1例帚霉）。不同方法检测出的阳性病例并非完全重叠。结论 真菌镜检、真菌培养、真菌分子生物学鉴定、组织病理学检查在诊断真菌感染时可以互补,有助于明确诊断及发现新菌株。     

Non–Culture-Based Methods for the Diagnosis of Invasive Candidiasis

Given the limitations of current fungal diagnostics, the use of non–culture-based methods for the diagnosis of invasive candidiasis (IC) is highly warranted. The implementation of molecular diagnostic strategies could permit the timely onset of appropriate therapy and may be expected to pave the way for improved clinical outcome of IC. Polymerase chain reaction (PCR) may have higher sensitivity for the diagnosis of IC than conventional blood cultures. The detection of fungal antigens generally requires a large fungal burden, and the presence of fungus-specific antibodies may not correlate with the underlying diseases. Therefore, the combined mannan and anti-mannan antibody testing is recommended. No single test has been shown convincingly to compensate for all the limitations of culture. Real-time PCR coupled with fungal culture and/or antigen detection will likely be required to significantly ameliorate the diagnostic problems in IC.     

Diagnosis of American foulbrood in honey bees: a synthesis and proposed analytical protocols

Worldwide, American foulbrood (AFB) is the most devastating bacterial disease of the honey bee (Apis mellifera). Because the distinction between AFB and powdery scale disease is no longer considered valid, the pathogenic agent has recently been reclassified as one species Paenibacillus larvae, eliminating the subspecies designations Paenibacillus larvae subsp. larvae and Paenibacillus larvae subsp. pulvifaciens. The creamy or dark brown, glue-like larval remains of infected larvae continue to provide the most obvious clinical symptom of AFB, although it is not conclusive. Several sensitive and selective culture media are available for isolation of this spore-forming bacterium, with the type of samples that may be utilized for detection of the organism being further expanded. PCR methods for identification and genotyping of the pathogen have now been extensively developed. Nevertheless, biochemical profiling, bacteriophage sensitivity, immunotechniques and microscopy of suspect bacterial strains are entirely adequate for routine identification purposes.     

Genomics and Proteomics as Compared to Conventional Phenotypic Approaches for the Identification of the Agents of Invasive Fungal Infections

There is overwhelming evidence that prompt diagnosis coupled with timely instigation of appropriate antifungal therapy are critical determinants of clinical outcome in invasive fungal infections. However, since the clinical symptoms of infection are often nonspecific, the number and diversity of potential aetiological agents is vast, and many fungi exhibit species-specific differences in antifungal susceptibility, the accurate identification of the responsible pathogen is a cornerstone of the therapeutic decision pathway. Traditionally, identification was achieved by examination of the phenotypic characteristics of the fungus obtained in pure culture, ideally from a normally sterile site/sample. However, this standard culture-based approach lacks sensitivity and obtaining appropriate specimens for culture is often difficult. Moreover, numerous recent studies have demonstrated the existence of clinically relevant cryptic species within well-established morphospecies that can not be differentiated by phenotypic methods. Here we discuss recent advances in genomic and proteomic approaches for the rapid and accurate identification of the principal pathogenic fungi associated with invasive fungal infections.     

Laboratory diagnosis of melioidosis: Past,present and future

Melioidosis is an emerging, potentially fatal disease caused by Burkholderia pseudomallei, which requires prolonged antibiotic treatment to prevent disease relapse. However, difficulties in laboratory diagnosis of melioidosis may delay treatment and affect disease outcomes. Isolation of B. pseudomallei from clinical specimens has been improved with the use of selective media. However, even with positive cultures, identification of B. pseudomallei can be difficult in clinical microbiology laboratories, especially in non-endemic areas where clinical suspicion is low. Commercial identification systems may fail to distinguish between B. pseudomallei and closely related species such as Burkholderia thailandensis. Genotypic identification of suspected isolates can be achieved by sequencing of gene targets such as groEL which offer higher discriminative power than 16S rRNA. Specific PCR-based identification of B. pseudomallei has also been developed using B. pseudomallei-specific gene targets such as Type III secretion system and Tat-domain protein. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolutionary technique for pathogen identification, has been shown to be potentially useful for rapid identification of B. pseudomallei, although existing databases require optimization by adding reference spectra for B. pseudomallei. Despite these advances in bacterial identification, diagnostic problems encountered in culture-negative cases remain largely unresolved. Although various serological tests have been developed, they are generally unstandardized “in house” assays and have low sensitivities and specificities. Although specific PCR assays have been applied to direct clinical and environmental specimens, the sensitivities for diagnosis remain to be evaluated. Metabolomics is an uprising tool for studying infectious diseases and may offer a novel approach for exploring potential diagnostic biomarkers. The metabolomics profiles of B. pseudomallei culture supernatants can be potentially distinguished from those of related bacterial species including B. thailandensis. Further studies using bacterial cultures and direct patient samples are required to evaluate the potential of metabolomics for improving diagnosis of melioidosis.     

The Black Yeasts: an Update on Species Identification and Diagnosis

Purpose of review

Black yeast-like fungi are capable of causing a wide range of infections, including invasive disease. The diagnosis of infections caused by these species can be problematic. We review the changes in the nomenclature and taxonomy of these fungi, and methods used for detection and species identification that aid in diagnosis.

Recent findings

Molecular assays, including DNA barcode analysis and rolling circle amplification, have improved our ability to correctly identify these species. A proteomic approach using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has also shown promising results. While progress has been made with molecular techniques using direct specimens, data are currently limited.

Summary

Molecular and proteomic assays have improved the identification of black yeast-like fungi. However, improved molecular and proteomic databases and better assays for the detection and identification in direct specimens are needed to improve the diagnosis of disease caused by black yeast-like fungi.

     

PCR Amplification and Species Determination of Microsporidia in Formalin-Fixed Feces after Immunomagnetic Separation

The term microsporidia is used to describe several species of opportunistic protozoan parasites. Encephalitozoon intestinalis and Enterocytozoon bieneusi have been found in stools of more than 40% of AIDS patients with diarrhea. Diagnosis of infection with these small protozoans has been difficult, and until recently their occurrence has not been well documented. Formalin is widely used to preserve clinical specimens, but due to the nature of the fixation process, subsequent analysis, especially analysis by the PCR, is difficult. This study evaluated methods used to prepare formalin-fixed fecal specimens for PCR amplification of microsporidial DNA. Two methods were devised to allow PCR detection and subsequent identification of microsporidia in formalin-fixed fecal specimens to the species level. One method involved immunomagnetic separation to concentrate microsporidial spores from fecal specimens. In the second method Chelex resin (Bio-Rad, Hercules, Calif.) was used to remove inhibitory substances, followed by a DNA concentration step. Both methods resulted in reproducible, confirmed detection of microsporidia in formalinized fecal specimens and subsequent species determination by PCR sequencing. The detection sensitivity was two in vitro culture-derived spores (Encephalitozoon intestinalis) for the direct PCR. The reproducible detection sensitivity for DNA amplification from formalin-fixed fecal samples was 200 spores for either the Chelex method or the immunomagnetic bead separation method. Thus, we developed two methods for rapid, inexpensive detection of microsporidial spores in formalin-fixed fecal specimens.     

Identification to the species level of the plant pathogens Phytophthora and Pythium by using unique sequences of the ITS1 region of ribosomal DNA as capture probes for PCR ELISA

The ribosomal internal transcribed spacer 1 region was sequenced for 10 species of Pythium and eight species of Phytophthora. Alignment of the sequences revealed considerable sequence microheterogeneity, which was utilized to prepare a capture probe of unique sequence for each species. The capture probes were tested by PCR ELISA, combining the sensitivity and specificity of the polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA). The probes were entirely species specific, enabling the detection and identification of the amplified DNA of species from individual cultures or from mixed samples of the DNAs of two different species. This approach to species identification, which provides a molecular technology to process large numbers of samples and still identify the fungi with a high level of confidence, may greatly reduce the resources and the time of highly trained specialists currently needed to identify these important species of plant pathogenic fungi.     

DNA barcoding and morphology reveal two common species in one: Pimpla molesta stat. rev. separated from P. croceipes (Hymenoptera, Ichneumonidae)

Correct species identification is the basis of ecological studies. Nevertheless, morphological examination alone may not be enough to tell species apart. Here, our integrated molecular and morphological studies demonstrate that the relatively widespread and common neotropical parasitoid wasp Pimpla croceipes Cresson, 1874 (Hymenoptera: Ichneumonidae: Pimplinae) actually consists of two distinct species. The name Pimpla molesta (Smith, 1879), stat. rev. is available for the second species. The two species were identified by DNA barcoding and minor differences in morphology and colouration. Our results support the previous notions that DNA barcoding can complement morphological identification and aid the discovery of cryptic species complexes.     

Development of oligonucleotide primers for the specific PCR-based detection of the most frequent Enterobacteriaceae species DNA using wec gene templates

Oligonucleotide primers were designed for the PCR-based detection of the wec gene cluster involved in the biosynthetic pathway leading to the production of enterobacterial common antigen (ECA). Escherichia coli DNA was detected using wec A, wec E, and wec F gene primers. The wec A primers were specific for E. coli. The wec E and wec F primers enabled the detection of the most frequent species of the Enterobacteriaceae found in blood and urine specimens as well as in water. The sensitivity of the assay was approximately 1.2 x 102 bacteria/mL of water. Thus, these primers represent an important step in the molecular diagnosis of major Enterobacteriaceae infections. Their role in the routine testing of contamination in drinking water and food may prove to be very useful. The DNA of Enterobacteriaceae species is detected in a first step PCR, followed by specific identification of important pathogens like E. coli O157, Shigella spp., Salmonella spp., and Yersinia spp.     

Shotgun lipidomics of phosphoethanolamine-containing lipids in biological samples after one-step in situ derivatization

This article presents a novel methodology for the analysis of ethanolamine glycerophospholipid (PE) and lysoPE molecular species directly from lipid extracts of biological samples. Through brief treatment of lipid extracts with fluorenylmethoxylcarbonyl (Fmoc) chloride, PE and lysoPE species were selectively derivatized to their corresponding carbamates. The reaction solution was infused directly into the ion source of an electrospray ionization mass spectrometer after appropriate dilution. The facile loss of the Fmoc moiety dramatically enhanced the analytic sensitivity and allowed the identification and quantitation of low-abundance molecular species. A detection limitation of attomoles (amoles) per microliter for PE and lysoPE analysis was readily achieved using this technique (at least a 100-fold improvement from our previous method) with a >15,000-fold dynamic range. Through intrasource separation and multidimensional mass spectrometry array analysis of derivatized species, marked improvements in signal-to-noise ratio, molecular species identification, and quantitation can be realized. The procedure is both simple and effective and can be extended to analyze many other lipid classes or other cellular metabolites by adjustments in specific derivatization conditions. Thus, through judicious derivatization, a new dimension exploiting specific functional reactivities in each lipid class can be used in conjunction with shotgun lipidomics to penetrate farther into the low-abundance regime of cellular lipidomes.     

Molecular taxonomy in pholcid spiders (Pholcidae, Araneae): evaluation of species identification methods using CO1 and 16S rRNA

The identification of species using molecular characters is a promising approach in alpha taxonomy and in any discipline depending on reliable assignment of specimens. Previous studies have shown the feasibility of the method, but considerable controversy persists. In this study, we use pholcid spiders in an effort to address two main issues. First, we evaluate and calibrate molecular species (re-)identification within a closely related group of organisms by using specimens that are morphologically unambiguously either conspecific or not. Species limits hypothesized a priori based on morphology were almost universally reconstructed by both mitochondrial markers used. Second, we focus on species identification methodology in a morphology-calibrated scenario, i.e. on how to assess the quality of a dataset and of the method used to obtain distance estimates (e.g. choice of markers, alignment strategy, type of distance data). We develop a number of statistical estimators permitting the measurement and communication of the clarity of species boundaries in a dataset and discuss their benefits and drawbacks. We propose that box plots rather than histograms are the superior tool for graphically illustrating taxonomic signal and that the median is a more appropriate measure of central tendency than the mean. Applying the suggested tools to our data, we propose that in molecular species identification, indel-related alignment uncertainties may often be even advantageous (by accentuating taxonomy-relevant information) and we conclude that — at least for our dataset — 16S is better suited to taxonomy than CO1.     

Extensive set of mitochondrial LSU rDNA-based oligonucleotide probes for the detection of common airborne fungi

Fungi exist in every indoor and outdoor environment. Many fungi are toxigenic or pathogens that may cause various public health concerns. Rapid and accurate detection and identification of fungi require specific markers. In this study, partial mitochondrial large subunit rDNA was amplified and sequenced from 32 fungal strains representing 31 species from 14 genera. Based on the sequence variation pattern, 26 oligonucleotide probes were designed for their discrimination. The specificity of the probes was evaluated through homology search against GenBank database and hybridization examination on 38 fungal strains. The 26 probes were verified as highly specific to 20 fungal species. A two-step detection procedure through PCR followed by probe hybridization gave ten-fold increase in detection sensitivity than single-step PCR assay and would be a practical approach for environmental sample screening. The probes developed in this study can be applied in clinical diagnosis and environmental monitoring of fungal agents.