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

Deep-seated trichosporonosis caused by Trichosporon asahii has a high mortality rate and a very poor prognosis. New species-specific oligonucleotide primers for T. asahii were developed from a sequence analysis of rRNA genes that included the internal transcribed spacer regions. A nested PCR assay with specific primers was used to examine 11 serum samples from 7 patients, who were diagnosed with deep-seated trichosporonosis histologically at autopsy. In addition, Trichosporon cell wall polysaccharide (PS) was detected by a latex agglutination (LA) test. Of 11 samples, seven had a positive LA test, and T. asahii DNA was also detected with the nested PCR assay. Of the four samples in which PS antigen was not detected, the nested PCR of two samples was positive. Our new nested PCR assay may be used as an adjunct to conventional methods for diagnosing T. asahii infection.     

The opportunistic yeast pathogen Trichosporon asahii colonizes the skin of healthy individuals: analysis of 380 healthy individuals by age and gender using a nested polymerase chain reaction assay

Deep-seated trichosporonosis is an opportunistic fungal infection with a poor prognosis and high mortality rate. The major causative agent is Trichosporon asahii; its route of infection is not clear. To elucidate whether this microorganism is part of the cutaneous microbiota, we examined skin samples from 380 healthy Japanese ranging in age from 0 to 82 years using a nested PCR assay. The colonization frequency of T. asahii increased with age up to 13-15 years in male and 30-39 years in female subjects, subsequently decreasing gradually in both sexes until senescence. Of the nine genotypes of the intergenic spacer region of the T. asahii rRNA gene, type 1 predominated (81.7%), followed by types 4 (6.7%) and 6 (5.5%). The distribution of identified genotypes was similar to that for T. asahii isolated from clinical specimens (blood and urine) of patients with deep-seated trichosporonosis and quite different from that of environmental isolates. Additionally, T. asahii DNA was detected stably from skin samples over 1 year. The opportunistic yeast pathogen T. asahii is part of the cutaneous fungal microbiota in humans. Cutaneous T. asahii may be one of the routes through which deep-seated trichosporonosis is acquired, whereas environmental T. asahii is not associated with this infection.     

Phenotypic switching and beta-N-acetylhexosaminidase activity of the pathogenic yeast Trichosporon asahii

The pathogenic yeast Trichosporon asahii is the major causative agent of deep-seated trichosporonosis in immunocompromised patients. Although infection by this microorganism is becoming increasingly frequent, information related to its pathogenicity and virulence factors is still limited. Therefore, we investigated phenotypic switching in colony morphology, and the production of extracellular enzymes as a virulence factor. Sixty-one clinical isolates of T. asahii produced four different morphological types on Sabouraud dextrose agar (SDA): 69% WF (white farinose), 18% WP (white pustular), 10% Y (yellowish white), and 3% WC (white cerebriform). Strains of the three major types (WF, WP, and Y) produced two to five colony types when cultured on SDA at 37 C. The frequency of switching between colony types was 10(-2) to 10(-4), as in Candida albicans and Cryptococcus neoformans. Notably, most of the colonies switched to the smooth (S) type irreversibly, at frequencies of 10(-2) to 10(-3). No secreted aspartic proteinase or phospholipase activity was detected in T. asahii, while beta-N-acetylhexosaminidase activity, which catalyzes the hydrolysis of terminal nonreducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides, was found. Furthermore, enzymatic activity of the S type was significantly greater than that of the parent type in all strains. No other clinically relevant Trichosporon species (T. mucoides, T. inkin, and T. ovoides ) produced this enzyme. These results provide basal information for understanding the pathogenic potential of T. asahii.     

Genotyping and Antifungal Drug Susceptibility of Trichosporon asahii Isolated from Chinese Patients

As a major pathogenic agent of trichosporonosis, Trichosporon asahii can cause life-threatening infection in immunocompromised patients. In this study, we analyzed the genotypes of the intergenic spacer (IGS) 1 region of the rRNA gene and the antifungal drug susceptibility of eight T. asahii isolates obtained from Chinese patients. Five genotypes were identified from the eight isolates, including three novel genotypes, three genotype 1, and two genotype 4. The eight T. asahii isolates were resistant to amphotericin B, 5-flucytosine, and terbinafine, but were highly sensitive to fluconazole (FLC), itraconazole (ITC), and voriconazole (VRC). The mean minimum inhibitory concentrations (MICs) of FLC and VRC were significantly lower than those reported in most other countries, while that of ITC was slightly higher. Our results suggest that genotypes of the T. asahii isolated from China are different from those of other countries, and azole drugs appeared to be more effective on the Chinese isolates. These results provide new insights into the epidemiology and antifungal treatment for T. asahii.     

Susceptibilities to Amphotericin B, Fluconazole and Voriconazole of Trichosporon Clinical Isolates

A total of 35 Trichosporon isolates were collected from the Taiwan Surveillance of Antimicrobial Resistance of Yeasts (TSARY) project from 1999 to 2006, and their identifications as well as drug susceptibilities were determined. The most frequently isolated species was T. asahii (62.9%), and the most common clinical sample that yielded Trichosporon isolates was urine (37.1%). The etiology of all seven invasive trichosporonosis was T. asahii. For the 22 T. asahii isolates, the MIC(50) and MIC(90) for amphotericin B were 0.25 and 1 μg/mL, respectively. Those for fluconazole were 2 and 4 μg/mL, respectively, and for voriconazole 0.031 and 0.063 μg/mL, respectively. When the intraclass correlation coefficients (ICCs) and agreements were calculated, we found that the MICs of fluconazole obtained from different methods were similar and the inter-method discrepancies were low. Nevertheless, no unanimous MIC of amphotericin B and voriconazole was obtained among different methods.     

阿萨希毛孢子菌生物膜构建及水杨酸干预策略研究

目的在医院内常用生物材料聚氯乙烯（PVC）表面构建阿萨希毛孢子菌的生物膜,评估该生物膜对几种临床抗真菌药物的耐药性,并观察水杨酸是否对阿萨希毛孢子菌生物膜的形成有干预作用。方法菌株鉴定采用API20CAUX并经PCR鉴定复核;使用PVC于RPM11640-MOPS中培养进行阿萨希毛孢子菌生物膜构建;MIC测定采用法国生物梅里埃公司ATB Fungus-3真菌药敏试剂条以及微量液体稀释法,并观察水杨酸对生物膜构建的影响。结果阿萨希毛孢子菌可以通过几个不连续阶段在聚氯乙烯表面形成生物膜,且已使用PVC块上附着的生物膜细胞比未使用PVC块上黏附的生物膜细胞明显密集;固着相即生物膜细胞的MIC比浮游相成倍提高;24h两性霉素B的MIC〉512μ/ml,且经两性霉素B的药物刺激后,阿萨希毛孢子明显可见芽管延长,菌丝交织;水杨酸作用后阿萨希毛孢子菌的菌丝明显变短,孢子短小。结论介入性器械可以作为阿萨希毛孢子菌生物膜构建的黏附基质,使微生物群体黏附于细胞外多聚材料表面而造成持续播散感染,因此生物膜干预对阿萨希毛孢子菌深部感染的治疗有很重要的意义。     

Nosocomial infection due to Trichosporon asahii: clinical revision of 22 cases

Twenty two cases of nosocomial infection caused by Trichosporon asahii, detected during a period of six years (1999-2005) is described. The patients were predominantly males with an average age of 47.3 years-old. The predominant diseases in the study group were respiratory insufficiency, cancer, diabetes, chronic renal insufficiency, cirrhosis and AIDS. The main predisposing conditions were antibiotic therapy, mechanical ventilation, urethral catheterization, catheter, corticoids, transplant, immunosuppressive therapy, chemotherapy, granulocytopenia, surgical procedures and continuous ambulatory peritoneal dialysis. The most used antifungal drugs were fluconazole and amphotericin B. In some cases several antifungals were administered. Five patients did not receive antifungal treatment, and one patient received granulocyte colony stimulating factor (G-CSF). Nine patients showed clinical improvement, nine died and the progress of four patients is unknown. T. asahii is an emergent pathogen in patients with immunodeficiency and its presence in these type hosts can not be considered colonization, as there is an important risk of invasive infection. So, in susceptible patients to develop trichosporonosis it is advisable to take into consideration this disease especially in intensive clinical care units.     

Comparison of real-time and nested PCR assays for detection of herpes simplex virus DNA

We performed a real-time PCR assay to detect herpes simplex virus (HSV) DNA, and compared it prospectively with a nested PCR assay in 164 clinical samples (109 cerebrospinal fluid and 55 sera) from patients suspected of having neonatal HSV infection or HSV encephalitis. In 25 of 164 samples, HSV DNA was detected by the nested PCR assay. All samples positive for HSV DNA in the nested PCR assay were also positive in the real-time PCR assay, and all but two samples negative for HSV DNA in the nested assay were negative in the real-time assay. The real-time PCR assay thus had a sensitivity of 100% and a specificity of 99%, when compared with the nested assay. Sequential assays in a case of disseminated HSV showed that a decrease in HSV DNA paralleled clinical improvement. Quantification of HSV DNA by real-time PCR was useful for diagnosing and monitoring patients with HSV encephalitis and neonatal HSV infection.     

阿萨希毛孢子菌的溶血活性及生物膜形成能力与其基因型关系研究

目的 分析临床分离自尿路感染患者的阿萨希毛孢子菌的体外溶血活性及生物膜形成能力与其基因型的关系,为临床诊治提供依据.方法 玻璃珠法提取总DNA,并采用PCR技术利用IGS1区特异性引物确定其基因型别;同时,平板法和XTT还原比色法分别检测阿萨希毛孢子菌的溶血活性及生物膜形成能力,并分析其与基因型的关系.结果 10株分离自尿路感染的阿萨希毛孢子菌基因型分别属于Ⅰ、Ⅲ、Ⅳ,其中以Ⅳ型为主;所分离菌株均具有不同程度的溶血活性;除1例分离株外,其余各分离株均具有在聚苯乙烯表面形成生物膜的能力;基因型Ⅲ型菌株具有较强的溶血活性和生物膜形成能力.结论 分离自尿路感染患者的10株阿萨希毛孢子菌以Ⅳ型为主,而其中Ⅲ型菌株表现出较强的溶血活性和生物膜形成能力.     

用实时荧光PCR方法鉴定转基因玉米T14/T25

本研究以实时荧光PCR技术鉴定商业化种植的转基因玉米T14/T25品系。根据转基因玉米T14/T25转入的外源基因质粒图谱,设计转基因引物和探针进行PCR和实时荧光PCR检测,建立了转基因玉米品系鉴定的实时荧光PCR方法。实验结果表明,用TaqMan探针可检测到T14/T25产生的荧光信号,而对其他玉米品系则检测不到荧光信号,为转基因产品的鉴定检测提供了新方法。Abstract: To identify genetically modified (GM) maize T14/T25 lines, a real-time fluorescent PCR (RTF PCR) assay was performed in this study. Primers and Taqman probes specific for inserted genes in the T14/T25 were used to conduct the real-time fluorenscent (RTF) PCR and PCR assays. The RTF PCR method was established to detect and identify GM maize lines. The results show that the TaqMan probe could identify T14/T25 maize used, while other GM and NO-GM maize didn’t be detected. The RTF PCR could be a new method for detecting other genetically modified organism.     

Antifungal pharmacodynamic characteristics of amphotericin B against Trichosporon asahii, using time-kill methodology

We determined the MIC of amphotericin B against 45 Trichosporon asahii isolates from various clinical and environmental sources, and used in vitro time-kill methods to characterize the relationship between amphotericin B concentrations and MIC for four representative T. asahii isolates. Amphotericin B had concentration-dependent antifungal activity. MICs ranged from 0.5 to 16 microg/ml, and most T. asahii isolates (76%, 34/45) were inhibited at safely achievable amphotericin B serum concentrations (< or = 2 microg/ml). However, 40% (18/45) of isolates were not killed at these concentrations (MFCs from 1.0 to 32 microg/ml). At concentrations > or = 2 x MIC, amphotericin B exhibited fungicidal activity (< 99.9% reduction in CFU) over a 12-hr time-period; the maximal effect was achieved at > or =4 x MIC. Susceptibility testing confirmed the resistance of T. asahii to amphotericin B, and in vitro pharmacodynamic results also suggest that amphotericin B is not suitable therapy for T. asahii infection.     

几种不同基质对阿萨希毛孢子菌形成生物膜影响的初步观察

目的观察不同基质对阿萨希毛孢子菌生物膜形成能力的影响。方法在聚芳脂、聚苯乙烯、聚氯乙烯上构建阿萨希毛孢子菌生物膜,在生物膜形成过程中采用XTT法对其活性进行定量分析,倒置显微镜和扫描电镜下观察不同基质上阿萨希毛孢子菌生物膜形态特征。结果 3种基质上均能形成阿萨希毛孢子菌生物膜,且形成广泛的的生物膜。比较成熟期不同基质上形成生物膜的活性有差别(F=14.743,P0.01),活性由高到低为聚芳脂=聚氯乙烯聚苯乙烯。倒置显微镜和扫描电镜下观察发现聚芳脂、聚氯乙烯形成的生物膜可见孢子、菌丝、假菌丝结构,聚苯乙烯上形成以孢子为主要结构的微生物群落。结论阿萨希毛孢子菌可在聚芳脂、聚苯乙烯、聚氯乙烯上形成生物膜,但形成生物膜的能力不同。聚芳脂、聚氯乙烯比聚苯乙烯更易于真菌的黏附;且以菌丝、假菌丝为主要结构的微生物群落活力比单纯孢子的活力强。     

Nosocomial urinary infection due to Trichosporon asahii. First two cases in Chile

We present two cases of nosocomial urinary tract infection due to Trichosporon asahii in intensive care unit patients with bladder catheter from two hospitals in Santiago, Chile. Both patients had an several catheters and bacterial infections that required the use of antibiotic therapy. One strain showed in vitro resistance to amphotericin B. Both strains were susceptible to fluconazole, but presented MIC with dose-dependent susceptibility to ketoconazole and itraconazole. This is the first report showing T. asahii as urinary tract infection agent in Chile.     

基于PubMed数据库毛孢子菌病临床研究文献计量学分析

目的分析国际毛孢子菌病文献概貌,了解毛孢子菌病临床相关研究现状,为更好地开展毛孢子菌临床研究提供思路和依据。方法利用汤森路透TDA软件分析PubMed数据库收录的毛孢子菌病临床相关文献的时间、国家、期刊、作者和高频主题词分布,并获得作者合作网络图。结果临床毛孢子菌病相关文献始于1970年,经过1981～1992年的快速增长期后,近年来数量增长不明显。日本在临床毛孢子菌病研究领域具有领先优势,美国、印度、巴西、法国和中国内地发文量也较多。刊载毛孢子菌病临床研究文献最多的期刊是《日本胸部疾病杂志》（Nihon Kyobu Shikkan Gakkai Zasshi,Japa—nese Journal of Thoracic Diseases）和《临床微生物学杂志》（Journal of Clinical Microbiology）。发文量最多的作者分别是熊本大学医学部的Ando M、Araki S和琦玉医科大学的Sakata T。毛孢子菌病的高频主题词涉及毛孢子菌病的诊治、宿主免疫和毛孢子菌致病机制等。结论日本和美国仍是相关领域的研究大国,但近5a来,更多的中国科研团队加入到这一研究领域,提高了我国学者的学术影响力。侵袭性毛孢子菌病的诊治是临床毛孢子菌病研究的主要关注点。     

Cloning of the lanosterol 14-α-demethylase ( ERG11 ) gene in Trichosporon asahii: a possible association between G453R amino acid substitution and azole resistance in T. asahii

Lanosterol 14-α-demethylase ( Erg11 protein; Erg11p ), encoded by the ERG11 gene, is the primary target of azoles. Recently, a change in affinity of this enzyme for azoles has been reported as a resistance mechanism in several fungal species. Trichosporon asahii ( T.?asahii) is susceptible to fluconazole (FLC). This report identified the ERG11 gene of T.?asahii (NCBI accession; HQ176415). The Erg11p of T.?asahii, presumed from the DNA sequence, was closely related to the Erg11p of Cryptococcus neoformans. Furthermore, a FLC-susceptible strain was cultured in medium containing FLC at concentrations from 4.0 to 16?μg?mL(-1) in order to analyze the development of FLC resistance in T.?asahii. The degree of resistance was related to the FLC concentration of the growth medium. One highly resistant strain that was cultured in the medium containing 16?μg?mL(-1) FLC contained 1 point mutation (G1357C) that caused a single amino acid substitution at G453R. This amino acid is highly conserved among major fungal pathogens, and it is in a region very close to the heme-binding domain, which is characteristic of the cytochrome P450 superfamily, the primary target for the azole class of antifungal agents. This amino acid substitution may have caused the high resistance to azoles in T.?asahii.     

Development of a real-time PCR assay with an internal amplification control for the screening of Shiga toxin-producing Escherichia coli in foods

Aims:  To develop and evaluate a real-time PCR assay incorporating an internal amplification control (IAC) suitable for the screening of Shiga toxin (Stx)-producing Escherichia coli (STEC) in foods.
Methods and Results:  A competitive IAC was constructed and included in an stx -specific real-time PCR assay. Coupled to 18-h enrichment and automated DNA extraction, the assay could reliably detect the presence of STEC in minced meats inoculated at 10 CFU per 25 g. Its performance was evaluated on 415 minced beef and 112 raw milk cheese samples and compared with that of a PCR-ELISA method. Fifty-three minced meats and 31 cheeses were found stx -positive, giving 98·3% and 93·75% concordance, respectively, with the PCR-ELISA reference method.
Conclusions:  A highly sensitive stx -specific real-time PCR method including an IAC was developed, facilitating monitoring of false-negative results due to PCR inhibitors.
Significance and Impact of the Study:  Combined with automated DNA extraction, the stx -IAC real-time PCR assay represents a suitable method for rapid screening of STEC in foods.     

A rapid and direct real time PCR-based method for identification of Salmonella spp

The aim of this work was the validation of a rapid, real-time PCR assay based on TaqMan technology for the unequivocal identification of Salmonella spp. to be used directly on an agar-grown colony. A real-time PCR system targeting at the Salmonella spp. invA gene was optimized and validated through a four times repeated blind experiment performed in two different laboratories including 50 Salmonella spp. with representative strains from each of the 5 different Salmonella subgenera and 30 non-Salmonella strains. Both parameters DeltaR(n) (fluorescence intensity of template through a normalized reporter value) and C(T) (cycle at which the fluorescence intensity achieved a pre-established threshold) were analyzed. Overall mean DeltaR(n) and C(T) values for Salmonella strains (2.14+/-0.87 and 15.30+/-0.90, respectively) were statistically different from values for non-Salmonella strains, allowing the establishment of cut-off DeltaR(n) and C(T) values based on 95% confidence intervals that allowed the correct identification of all strains tested in each independent experiment. The accuracy of this assay in terms of inclusivity and exclusivity was 100%. Moreover, the PCR system proved to be especially convenient because the pre-mix containing all PCR reagents except for the bacterial cells could be kept at -20 degrees C for at least 1 month before its use. The optimized TaqMan real-time PCR assay is a useful, simple and rapid method for routine identification of Salmonella spp., irrespective of the particular subgenus.     

Application of real-time PCR for quantitative detection of Clostridium botulinum type A toxin gene in food

The TaqMan real-time PCR method for the quantitative detection of C. botulinum type A was developed based on sequence-specific hybridization probes. The validity of this assay was verified by using 10 genera of 20 strains, including reference strains of C. botulinum types A, B, C, D, E and F. The detection limit of this assay was evaluated on C. botulinum type A, using a 10-fold dilution series of DNA and spores . The DNA and spores were detected up to level of 0.1 ng/ml and 10(2)spores/ml, respectively. Spore spiked food sample preparation prior to the real-time PCR was performed by two methods, heat treatment and GuSCN. The detection limits after heat treatment showed 10(2) spores/ml for spiked sausage slurry, and 10(3) spores/ml for spiked canned corn slurry, while detection limits after GuSCN precipitation showed 10(2) spores/ml in both sausage and canned corn. Therefore the real-time PCR assay after GuSCN precipitation is useful for the quantification of C. botulinum type A because it showed identical CT values in both pure spore solutions and food slurries. We suggest that quantitative analysis of C. botulinum type A by TaqMan real-time PCR can be a rapid and accurate assessment method for botulinal risk in food samples.     

Detection of Trichinella spiralis, T. britovi and T. pseudospiralis in muscle tissue with real-time PCR

Infections caused by Trichinella species occur throughout the world in many wild and domestic animals resulting in trichinellosis in men. In Europe, domestic pigs are predominantly infected by three Trichinella species: T. spiralis, T. britovi and T. pseudospiralis. Present methods for detection of Trichinella spp. (compressorium method, artificial digestion) do not always sufficiently recognize Trichinella larvae and these techniques are labor-intensive, time consuming and do not differentiate isolates on the species level since there are no distinguishing morphological features. Additionally, conventional PCRs cannot quantify numbers of larvae in infectious material. In order to better meet these requirements, we developed a real-time PCR assay for the accurate, rapid and specific identification of the three common European species of the genus Trichinella. The assay targets the large subunit of the mitochondrial rRNA (rrnL) and enables sensitive determination and discrimination of larvae in muscle tissue samples. The real-time PCR assay was developed and validated using reference and field strains from T. spiralis, T. britovi and T. pseudospiralis. In the described real-time PCR assay, the melting points of specific amplificates were always discernable via the melting curve from melting points of unspecific amplificates. This is important for the methods workflow because only C(T) values connected with the additional melting curve analysis allow a distinction of the individual species with confidence. The sensitivity of the technique enabled detection down to 0.1 Trichinella larva per gram meat sample. High disruption levels of tissues by mincing generally resulted in higher sensitivities than protocols without mincing. With its short completion time as well as accurate and specific detection of selected species this assay could become a convenient tool for the fast detection of Trichinella larvae in meat.     

Quantification of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens strains in the plant rhizosphere by real-time PCR

A real-time PCR SYBR green assay was developed to quantify populations of 2,4-diacetylphloroglucinol (2,4-DAPG)-producing (phlD+) strains of Pseudomonas fluorescens in soil and the rhizosphere. Primers were designed and PCR conditions were optimized to specifically amplify the phlD gene from four different genotypes of phlD+ P. fluorescens. Using purified genomic DNA and genomic DNA extracted from washes of wheat roots spiked with bacteria, standard curves relating the threshold cycles (C(T)s) and copies of the phlD gene were generated for P. fluorescens strains belonging to genotypes A (Pf-5), B (Q2-87), D (Q8r1-96 and FTAD1R34), and I (FTAD1R36). The detection limits of the optimized real-time PCR assay were 60 to 600 fg (8 to 80 CFU) for genomic DNA isolated from pure cultures of P. fluorescens and 600 fg to 6.0 pg (80 to 800 CFU, corresponding to log 4 to 5 phlD+ strain CFU/rhizosphere) for bacterial DNA extracted from plant root washes. The real-time PCR assay was utilized to quantify phlD+ pseudomonads in the wheat rhizosphere. Regression analysis of population densities detected by real-time PCR and by a previously described phlD-specific PCR-based dilution endpoint assay indicated a significant linear relationship (P = 0.0016, r2 = 0.2). Validation of real-time PCR assays with environmental samples was performed with two different soils and demonstrated the detection of more than one genotype in Quincy take-all decline soil. The greatest advantage of the developed real-time PCR is culture independence, which allows determination of population densities and the genotype composition of 2,4-DAPG producers directly from the plant rhizospheres and soil.