Real-time detection of common microbial volatile organic compounds from medically important fungi by Selected Ion Flow Tube-Mass Spectrometry (SIFT-MS)

We describe a new method, Selected Ion Flow Tube-Mass Spectrometry (SIFT-MS) for the rapid and sensitive real-time detection and quantification of volatile organic compounds from medically important fungi, grown on a range of laboratory media. SIFT-MS utilises the chemical ionisation reactions of mass-selected ions to characterise volatile organic compounds (VOCs) that are produced as metabolites from fungi. This technique has the distinct advantage over others in that it readily detects low molecular weight, reactive volatiles, and allows for real-time, quantitative monitoring. The fungi examined in this study were Aspergillus flavus, Aspergillus fumigatus, Candida albicans, Mucor racemosus, Fusarium solani, and Cryptococcus neoformans grown on or in malt extract agar, Columbia agar, Sabouraud's dextrose agar, blood agar, and brain-heart infusion broth. Common metabolites (ethanol, methanol, acetone, acetaldehyde, methanethiol, and crotonaldehyde) were detected and quantified. We found the fingerprint of volatiles, in terms of presence and quantity of volatiles to be strongly dependent on the culture medium, both in terms of variety and quantity of volatiles produced, but may form the basis for species specific identification of medically important fungi.     

Medically important fungi found in hallux nails of university students from Cali, Colombia

The presence of medically important fungi was studied in hallux nails scrapings obtained from 504 students (204 males, 300 females) of three universities in Cali. Specimens were examined by direct microscopic examination and fungal culture. Medically important fungi were found in 49 (9.7%) students, 24 (4.8%) had onychomycosis while the rest did not have nail lesions. Trichophyton rubrum was the most commonly isolated fungi in students with lesions, where as T. mentagrophytes predominated in healthy nails. Most of the students with fungi were males. The prevalence of fungi was higher in individuals between 26 and 35 years. No association was observed between fungi and practicing sports or undergoing pedicures. These results suggest that dermatophytes can be found in healthy hallux nails, which can be reservoirs of pathogenic fungi.     

A decision-based key to determine the most appropriate protocol for the preservation of fungi

The long-term preservation of valuable fungal cultures can be achieved in several ways and the choice of methodology can be problematical. Firstly, there is the decision whether to use a public service culture collection or `in-house' facilities. Secondly, the wide variety of preservation methods available often leads to confusion about which protocol(s) are best suited for specific fungi. No method can be universally applied to all fungi. Some species are notoriously difficult to preserve, whilst other fungi can be preserved by almost any method. A decision-based key has been devised, which uses questions related to fungal characters and user facilities and economics to determine the most appropriate method for long-term preservation of cultures. This key should facilitate the decisions of microbiologists when considering preservation of important fungal cultures.     

医学昆虫的病原真菌

昆虫病原真菌在自然环境中对害虫数量起着抑制作用,在害虫的微生物防治中也占有独特的地位。长期以来,在应用昆虫病原真菌防治人畜害虫方面研究进展较为缓慢,六十年代以来才有较大的发展。本文介绍了近十年的发展概况,并讨论了影响这个研究领域迅速发展的原因及病原真菌在生物防治中应用的潜力。认为尽管至今对这类真菌了解还较少,但通过今后加强有关方面的研究工作,其应用前景是广阔的。     

医学昆虫的病原真菌*

昆虫病原真菌在自然环境中对害虫数量起着抑制作用,在害虫的微生物防治中也占有独特的地位。长期以来,在应用昆虫病原真菌防治人畜害虫方面研究进展较为缓慢,六十年代以来才有较大的发展。本文介绍了近十年的发展概况,并讨论了影响这个研究领域迅速发展的原因及病原真菌在生物防治中应用的潜力。认为尽管至今对这类真菌了解还较少,但通过今后加强有关方面的研究工作,其应用前景是广阔的。     

Immunoglobulins in defense, pathogenesis, and therapy of fungal diseases

Only two decades ago antibodies to fungi were thought to have little or no role in protection against fungal diseases. However, subsequent research has provided convincing evidence that certain antibodies can modify the course of fungal infection to the benefit or detriment of the host. Hybridoma technology was the breakthrough that enabled the characterization of antibodies to fungi, illuminating some of the requirements for antibody efficacy. As discussed in this review, fungal-specific antibodies mediate protection through direct actions on fungal cells and through classical mechanisms such as phagocytosis and complement activation. Although mechanisms of antibody-mediated protection are often species-specific, numerous fungal antigens can be targeted to generate vaccines and therapeutic immunoglobulins. Furthermore, the study of antibody function against medically important fungi has provided fresh immunological insights into the complexity of humoral immunity that are likely to apply to other pathogens.     

Chitinases: in agriculture and human healthcare

Abstract

Biological control of phytopathogenic fungi and insects continues to inspire the research and development of environmentally friendly bioactive alternatives. Potentially lytic enzymes, chitinases can act as a biocontrol agent against agriculturally important fungi and insects. The cell wall in fungi and protective covers, i.e. cuticle in insects shares a key structural polymer, chitin, a β-1,4-linked N-acetylglucosamine polymer. Therefore, it is advantageous to develop a common biocontrol agent against both of these groups. As chitin is absent in plants and mammals, targeting its metabolism will signify an eco-friendly strategy for the control of agriculturally important fungi and insects but is innocuous to mammals, plants, beneficial insects and other organisms. In addition, development of chitinase transgenic plant varieties probably holds the most promising method for augmenting agricultural crop protection and productivity, when properly integrated into traditional systems. Recently, human proteins with chitinase activity and chitinase-like proteins were identified and established as biomarkers for human diseases. This review covers the recent advances of chitinases as a biocontrol agent and its various applications including preparation of medically important chitooligosaccharides, bioconversion of chitin as well as in implementing chitinases as diagnostic and prognostic markers for numerous diseases and the prospect of their future utilization.     

A Review of Soybean (Glycine max) Seed,Pod, and Flower Mycofloras in North America,with Methods and a Key for Identification of Selected Fungi

A review of the fungi associated with soybean seeds, pods, or flowers was conducted in North America. Species of Deuteromycetes are the most common fungi in each of the soybean flower organs followed by the Ascomycetes and Phycomycetes which comprise about one-fourth of the total mycoflora. Eighty genera and about 135 or more species occur in seeds, pods, or flowers. With regard to numbers of taxa from separate mycofloras, 63 genera and about 108 or more species occur in seeds, 65 genera and about 88 or more species occur in pods, and 36 genera and approximately 47 or more species occur in flowers. Most of the fungi which occur in flowers can be cultured from pods, and the majority of those fungi occur in seeds. Methods for and a key are provided for the identification of the 30 most important selected fungi. This revised version was published online in June 2006 with corrections to the Cover Date.     

Noisy neighbourhoods: quorum sensing in fungal–polymicrobial infections

Quorum sensing was once considered a way in which a species was able to sense its cell density and regulate gene expression accordingly. However, it is now becoming apparent that multiple microbes can sense particular quorum‐sensing molecules, enabling them to sense and respond to other microbes in their neighbourhood. Such interactions are significant within the context of polymicrobial disease, in which the competition or cooperation of microbes can alter disease progression. Fungi comprise a small but important component of the human microbiome and are in constant contact with bacteria and viruses. The discovery of quorum‐sensing pathways in fungi has led to the characterization of a number of interkingdom quorum‐sensing interactions. Here, we review the recent developments in quorum sensing in medically important fungi, and the implications these interactions have on the host's innate immune response.     

Identification of medically significant fungal genera by polymerase chain reaction followed by restriction enzyme analysis

Rapid non-culture-dependent assays for identification of fungi quicken diagnosis and prompt treatment of invasive fungal disease. Fungal DNA extracts from pure cultures of the most frequently isolated fungal pathogens belonging to the Genera Aspergillus, Candida and Cryptococcus along with less common pathogenic Genera were amplified with the general fungal primer pair internal transcribed spacer-1/4. Subsequently, the amplicon was digested with the restriction endonucleases MspI, HaeIII, HinfI and EcoRI in order to generate genus- or species-specific patterns for identification of the fungus. HinfI produced indistinguishable fingerprints for all Aspergillus species tested. MspI produced species-specific patterns for: Cryptococcus neoformans, Cryptococcus non-neoformans, Candida albicans and Candida tropicalis. EcoRI succeeded in differentiating penicillia from aspergilli and cryptococci from Candida spp. It is concluded that this procedure can differentiate genera and occasionally species of medically important fungi and that following the necessary validation experiments, it can be used directly on clinical samples to assist prompt diagnosis of systemic fungal infections.     

Evolutionary affiliations within the superfamily of ketosynthases reflect complex pathway associations

Abstract Type I polyketide synthases are known to produce a wide range of medically and industrially important polyketides. The ketosynthase (KS) domain is required for the condensation of an extender unit onto the growing polyketide chain during polyketide biosynthesis. KSs represent a superfamily of complex biosynthetic pathway-associated enzymes found in prokaryotes, fungi, and plants. Although themselves functionally conserved, KSs are involved in the production of a structurally diverse range of metabolites. Degenerate oligonucleotide primers, designed for the amplification of KS domains, amplified KS domains from a range of organisms including cyanobacterial and dinoflagellates. KS domains detected in dinoflagellate cultures appear to have been amplified from the less than 3-μm filtrate of the nonaxenic culture. Phylogenetic analysis of sequences obtained during this study enabled the specific identification of KS domains of hybrid or mixed polyketide synthase/peptide synthetase complexes, required for the condensation of an extender unit onto an amino acid starter unit. The primer sets described in this study were also used for the detection of novel KS domains directly from environmental samples. The ability to predict function based on primary molecular structure will be critical for future discovery and rational engineering of polyketides.     

Genomic approaches to fungal pathogenicity

Within a few years, the genome sequences of a large number of medically and agriculturally important fungi will be known. With this resource come the promises of genomic approaches to study pathogenicity and host-fungus interactions. Genomics is particularly attractive for these questions, as conventional genetic and biochemical approaches are limited in many pathogenic fungi. Recent work has applied signature-tagged mutagenesis and DNA microarray analysis to virulence studies in several fungal species, and novel approaches, such as protein arrays and genomic deletion libraries, are being developed in Saccharomyces cerevisiae and have significant potential in other fungi. High-throughput gene-discovery approaches should greatly increase our understanding of fungal pathogenesis.     

MALDI‐TOF‐MS‐based species identification and typing approaches in medical mycology

MALDI‐TOF MS‐based species identification has found its place in many clinical routine diagnostic laboratories over the past years. Several well‐established commercial systems exist and these allow precise analyses not only among bacteria, but also among clinically important yeasts. This methodology shows higher precision than biochemical and microscopic methods at significantly reduced turnaround times. Furthermore, the differentiation of different filamentous fungi including most dermatophytes and zygomycetes has been established. The direct identification of yeasts from blood culture bottles will be possible in a routine fashion with new standardized procedures. In addition to species identification, the MALDI‐TOF MS technology offers several further possibilities, like assays to detect or predict resistance phenotypes in fungi as well as subtyping approaches to detect clinically relevant subgroups. The differences between the commercial systems are discussed with respect to fungi and an overview of their performances provided. Factors influencing outcome of MALDI‐TOF‐based species identification are discussed.     

丛枝菌根真菌培养方法研究进展

文章结合最新研究成果着重从十个不同的层面对丛枝菌根真菌(AM真菌)的培养方法研究做了较为系统的介绍与评述。认为活体宿主植物盆栽培养法是最简单、最容易、也是最可靠的AM真菌培养方法,玻璃珠分室培养可方便地将培养基质与AM真菌分开,能获得纯净的AM真菌菌体,具有其它方法不可替代的作用,AM真菌单孢无菌的分室Ri T-DNA转型胡萝卜根双重离体培养是获得AM真菌纯净菌体和研究AM真菌遗传、生理、生化等特性的理想方法,以此方法为基础,在根室中补充碳源、在菌丝生长室置换培养基、多次收获菌体的转型根改良双重培养法是提高某些AM真菌孢子产量的力荐方法。     

Prospects of the use of chromosomal transformation for the identification of the causative agent melioidosis

Prospects for the use of chromosomal transformation for the identification of Pseudomonas pseudomallei and some other medically important Pseudomonas species are considered. The method is simple, reproducible and highly specific. It permits the screening of a great number of cultures and can facilitate further study of the biology of P. pseudomallei and the epidemiology of melioidosis.     

镰刀菌分子鉴定与重要应用的研究进展

镰刀菌(Fusarium sp.)在土壤及动植物体内广泛分布。由于其形态变异大,有关镰刀菌的分类一直是一个难题。随着PCR技术发展,镰刀菌的分子标记和rDNA分析等鉴定方法的建立,提高了镰刀菌形态学鉴定的准确性,为镰刀菌进一步研究和应用奠定了基础。镰刀菌能产生多种重要的酶类,包括纤维酶、果胶酶和木聚糖水解酶等。通过生物转化可获得重要药物或药物中间体,因此具有潜在商业价值。镰刀菌能降解多种环境污染物,在环境保护中具有重要潜力。特别是能通过生物转化生产生物乙醇,解决能源危机问题。本文较详细地介绍了镰刀菌的鉴定和产酶情况,对镰刀菌产生的主要酶的性质、作用以及在生产生物乙醇方面的应用进行了详细综述。     

A web-based identification programme for Pythium species

The genus Pythium, with slightly over 140 described species, has been classified traditionally with other filamentous, coenocytic, sporangia-producing fungi as “Phycomycetes”. However, with recent advances in chemical, ultrastructural and molecular studies, Pythium spp. are now considered as “fungus-like organisms” or “pseudo-fungi” and are placed in the kingdom Chromista or kingdom Stramenopila, distinct from the true fungi or the kingdom Fungi. There is no comprehensive web-based identification key available for the identification of all described Pythium species. This article describes a web-based identification tool (which has been described by the authors under the name of Fungid) that uses morphological features. For the isolate in question, the software compares the unknown isolate with near to 90 known species submitted in the database. One or more than one species is suggested to the user by the software.     

Secretomes of medically important fungi reflect morphological and phylogenetic diversity

Secretome represents a main target for understanding the mechanisms of fungal adaptation. In the present study, we focus on the secretomes of fungi associated with infections in humans and other mammals in order to explore relationships between the diverse morphological and phylogenetic groups. Almost all the mammalian pathogenic fungi analyzed have secretome sizes smaller than 1000 proteins and, secreted proteins comprise between 5% and 10% of the total proteome. As expected, the correlation pattern between the secretome size and the total proteome was similar to that described in previous secretome studies of fungi. With regard to the morphological groups, minimum secretome sizes of less than 250 secreted proteins and low values for the fraction of secreted proteins are shown in mammalian pathogenic fungi with reduced proteomes such as microsporidia, atypical fungi and some species of yeasts and yeast-like fungi (Malassezia). On the other hand, filamentous fungi have significantly more secreted proteins and the highest numbers are present in species of filamentous fungi that also are plant or insect pathogens (Fusarium verticilloides, Fusarium oxysporum and Basidiobolus meristosporus). With respect to phylogeny, there are also variations in secretome size across fungal subphyla: Microsporidia, Taphrinomycotina, Ustilagomycotina and Saccharomycotina contain small secretomes; whereas larger secretomes are found in Agaricomycotina, Pezizomycotina, Mucoromycotina and Entomophthoromycotina. Finally, principal component analysis (PCA) was conducted on the complete secretomes. The PCA results revealed that, in general, secretomes of fungi belonging to the same morphological group or subphyla cluster together. In conclusion, our results point out that in medically important fungi there is a relationship between the secretome and the morphological group or phylogenetic classification.     

Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens

According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.     

浅部真菌病1948份临床标本的真菌学分析

目的 通过对浅部真菌病患者临床送检标本的病原真菌菌种进行系统分析,了解感染及病原真菌的分布情况。方法 采用直接镜检、培养及真菌鉴定等方法对临床送验标本进行检验和鉴定,大部分标本鉴定到种。结果 1948份临床送验标本中,直接涂片镜检阳性率53．41％,培养阳性率40．28％,而镜检＋培养的阳性率为66．98％。对上述3种方法的真菌检出率进行比较,均存在显著差异（χ^2检验P均〈0．005）。在培养的1944份标本中,共分离出18个属,36种真菌,其中,红色毛癣菌24．52％、须癣毛癣菌16．48％、白念珠菌12．64％。结论 ①镜检结合培养的阳性率显著高于单一的镜检或培养的阳性率。②在患者即时的真菌镜检阴性时,应选择培养方法进一步检测,不轻易排除浅部真菌病感染可能。③皮肤癣菌居患者浅部真菌病致病菌首位,而白念珠菌及酵母类菌也是重要病原菌。