孢子丝菌病快速诊断方法的探究

目的研究申克孢子丝菌DNA提取方法;探索申克孢子丝茵的种特异性引物,运用聚合酶链反应方法鉴定申克孢子丝菌;从而为临床孢子丝茵病的分子诊断奠定基础。方法用Viscozyme L酶替代液氮研磨破壁提取孢子丝菌的基因组DNA;根据申克孢子丝茵钙调蛋白基因序列设计一对寡核苷酸引物,分别对52株申克孢子丝菌及3种6株普通真茵的基因组DNA进行PCR扩增。结果用Viscozyme L酶替代液氮研磨破壁成功提取出孢子丝菌的基因组DNA。特异性引物对52株申克孢子丝菌可扩增出一条约430 bp的片段,而对念珠菌、曲霉、黑霉基因组DNA扩增结果均为阴性。结论用Viscozyme L酶替代液氮研磨破壁提取孢子丝菌基因组DNA与传统的CTAB法相比不仅操作更简便,而且避免了液氮研磨过程中难于避免的污染。运用我们所设计的特异性引物,结合PCR方法对申克孢子丝菌进行分子鉴定,结果显示不仅该引物对申克孢子丝菌特异、敏感而且该方法简便、快捷;可用于申克孢子丝菌病的临床诊断。     

实时荧光PCR检测巴西孢子丝菌的实验方法的建立

目的建立一种快速、特异、灵敏的荧光PCR方法检测巴西孢子丝菌。方法比对NCBI数据库中所有巴西孢子丝菌内转录间隔区(internal transcribed spacer, ITS)序列,在保守区域设计并合成特异性引物和探针,建立并优化荧光PCR检测方法。对优化后的方法使用标准浓度核酸进行扩增效率、灵敏度及特异度评价。通过巴西孢子丝菌小鼠感染模型,与组织培养比较,对本研究中的方法进行评价。结果建立的实时荧光PCR方法对巴西孢子丝菌的检测限为100fg。该方法对申克孢子丝菌、球形孢子丝菌、其他常见致病真菌28种、常见细菌3种以及人类基因组和小鼠基因组扩增结果均为阴性,特异度为100%。对巴西孢子丝菌感染小鼠脑、肝、肺、脾、肾及淋巴结检测与培养结果相一致。结论本研究建立的荧光PCR方法可快速、灵敏、特异地鉴定巴西孢子丝菌,并能够有效的对感染小鼠模型标本进行检测,有助于孢子丝菌病的早期特异性病原学诊断。     

特比萘芬治愈儿童鼻翼孢子丝菌病1例

目的报道1例发生在4岁儿童鼻翼的孢子丝菌病。方法刮取病变组织接种到沙堡弱培养基培养,并对培养出的病原菌进行形态学鉴定和ITS区序列分析。结果病变组织在沙堡弱培养基25℃培养长出黑褐色菌落,25℃小培养后光镜及扫描电镜下见菌丝细长,分枝分隔,合轴式产孢形成的成簇和沿菌丝两侧排列,分生孢子卵圆形。提取真菌总DNA用PCR方法扩增ITS序列,测序后登录GeneBank进行比对,该菌与申克孢子丝菌菌株KMU3360ITS区碱基序列一致性达99%,鉴定为申克孢子丝菌。内服联合局部应用特比萘芬治疗6个月后皮损完全消退。结论确诊1例儿童鼻翼的孢子丝菌病,内服联合局部应用特比萘芬治疗儿童孢子丝菌病疗效良好。     

1株多重耐药申克孢子丝菌感染的治疗

报道1例由多重耐药申克孢子丝菌引起的面部孢子丝菌病。患者61岁男性,面部皮疹2 a余,先后口服伊曲康唑、特比萘芬和氟康唑治疗16个月无效。患者皮损经真菌镜检和培养确诊为孢子丝菌病,分离的申克孢子丝菌体外药敏试验显示其菌丝相和酵母相对上述三种药物均不敏感。给予患者口服10%碘化钾溶液治疗3个月获得痊愈。     

1例皮肤播散型孢子丝菌病的分离菌株的基因鉴定

孢子丝菌病是由申克孢子丝菌及其卢里变种感染引起的皮肤、皮下组织和附近淋巴系统的亚急性和慢性感染,偶可播散至全身引起多系统损害。该病遍布全世界,我国孢子丝菌病主要是由申克孢子丝菌引起。孢子丝菌一般生存在土壤和植物上,人的皮肤接触带菌植物或土壤后可引起感染。临床上主要表现为固定型和淋巴管型孢子丝菌病,皮肤播散型孢子丝菌病少见。现认为机体感染申克孢子丝菌引起的不同的临床型别与机体免疫状态、申克孢子丝菌的致病力及其基因差异相关[1-2]。我     

皮内与腹腔接种不同来源菌株对实验性小鼠孢子丝菌病的影响

目的将不同来源的申克孢子丝菌菌株接种于免疫抑制处理后的小鼠皮内及腹腔,造成其实验性感染,观察其感染情况,研究不同菌株及不同接种途径对小鼠孢子丝菌病的影响。方法分别在小鼠皮内和腹腔注射孢子丝菌菌悬液0.1ml,约含1×107个孢子,观察3周。观察结束时处死小鼠取其血、脑、肺、肝、脾、肾、肠系膜、睾丸、腹膜进行真菌培养和组织病理检查。结果皮内和腹腔接种不同来源菌株的小鼠各器官感染率各不相同。播散株皮内接种组、固定株腹腔接种组、播散株腹腔接种组的各器官平均感染率分别为16.05%、18.89%、58.73%。播散株腹腔接种组与其他二组之间差异均有显著性,脾和睾丸是最易受累的器官。结论不同来源菌株可能毒力不同,播散型菌株具有更强的侵袭性。脾脏可能在宿主抗孢子丝菌感染中具有重要作用。     

申克孢子丝菌感染诊治1例

通过1例16岁女孩由申克孢子丝菌导致的皮下孢子丝菌病,口服伊曲康唑治疗有效,回顾申克孢子丝菌的实验室检验方法 ,以此来提高孢子丝菌感染的诊断水平。     

皮肤淋巴管型孢子丝菌病1例

报道1例皮肤淋巴管型孢子丝菌病。患者女,79岁,农民。左上肢皮肤红斑结节线状分布,疼痛瘙痒不适两月余。皮损病理及PAS染色提示真菌感染,对皮损和脓液进行真菌镜检,结果为阴性。真菌培养、小培养及对培养阳性菌落进行分子生物学鉴定提示申克孢子丝菌。诊断:皮肤淋巴管型孢子丝菌病。予口服伊曲康唑胶囊0.2g/次,2次/d,治疗1个月后明显改善。     

子宫颈感染孢子丝菌1例

目的探讨双相真菌申克孢子丝菌(复合体)子宫颈感染的临床特点,为进一步提高实验室及临床诊断水平提供资料。方法分析1例申克孢子丝菌(复合体)子宫颈感染临床表现与实验室诊断过程,检索近年来国内外主要文献进行复习。结果患者阴道分泌物镜检见成团的革兰染色阳性、圆形、卵圆形孢子,较球菌大,较酵母样真菌孢子小。37℃血平皿培养,形成边缘不齐、表面有褶皱、干燥、有韧性不易挑取的白色菌落;革兰氏染色镜下见染色阳性酵母样芽生孢子。25℃SDA培养,形成中心有白色褶皱,周围绒毛样的丝状真菌菌落形态,直接涂片镜检见大量有隔菌丝、孢子。上述特征符合申克孢子丝菌。国内外文献检索,申克孢子丝菌感染多为皮肤局限性、肺炎、骨关节等病例,偶有累及局部淋巴结的病例,仅少数艾滋病等免疫力极度低下患者为全身播散性感染。结论申克孢子丝菌所致子宫颈感染罕见,掌握其在人体内与不同条件下培养菌落的特征有助于及时诊断。     

鼻部固定型孢子丝菌病1例

报道1例猫抓后引起的固定型孢子丝菌病.患者男,16岁,皮损表现为鼻翼部位的增生物,其上覆有脓痂.临床上易与细菌感染混淆,但根据患者的病史、临床表现、病理、真菌镜检及培养诊断为申克孢子丝菌引起的孢子丝菌病.患者在应用7个月的碘化钾结合特比萘芬软膏外用治疗后,皮损完全消失.     

A new semi-nested PCR protocol to amplify large 18S rRNA gene fragments for PCR-DGGE analysis of soil fungal communities

The analysis of soil fungal communities by molecular fingerprinting and subsequent identification of the underlying populations require the amplification of a phylogenetically informative gene fragment. In this study we tested the reliability and suitability of the previously published fungal primer combination (NS1/FR1-GC) that amplifies almost the entire 18S rRNA gene for the DGGE analysis of fungal communities in soil samples from 36 sites. This direct PCR system failed to amplify the fragment of interest from the total DNA extracted from most of the soils tested. Thus, we developed a new semi-nested PCR system based on the initial amplification of over 1,700 bp of the 18S rRNA gene with a new primer combination, followed by a subsequent amplification with NS1/FR1-GC. By means of the PCR approach developed in this study distinct 18S rRNA gene amplicons could be reproducibly generated for all soil samples. Amplification tests with 101 soil fungal isolates showed that with the new semi-nested system 18S rRNA gene fragments could be obtained from more fungi than with the direct approach. The subsequent DGGE separation of community amplicons resulted in a high resolution and revealed reproducible complex soil fungal communities specific for each site, despite a minor variability between replicates of the same sample. The semi-nested PCR system developed in this study, coupled with DGGE fingerprinting, offers a robust, reliable and sensitive tool for the analysis of soil fungal community structure.     

Development of a species-specific AFLP-based SCAR marker for authentication of black muntjac (Muntiacus crinifrons)

Black muntjac is a rare and endangered deer endemic to eastern China. Due to the economic and pharmaceutical value of the meat, antlers and skin, the species has chronically suffered from poaching though it is regarded as the state key protected animal. To provide an effective molecular method for authentication of tissue specimen (such as meat, skin etc.) of the species, we developed a Sequence Characterized Amplified Region (SCAR) derived from a species specific Amplification Fragment Length Polymorphism (AFLP) marker. Initially, a 707-bp species specific DNA fragment of the animal was detected by a pair of AFLP primers (Ep7/Mp8). Subsequently, a species-specific primer pair (P-F/P1-R) was designed based on the specific AFLP fragment sequence, obtaining a 298-bp SCAR for the species. Finally, the reliability of the SCAR primers was verified by two separate PCRs using the designed SCAR primers and a cyt b universal primer pair. As expected, all black muntjac samples presented two bands but the others failed to produce the SCAR by merely showing one band. Our results indicated that the SCAR primers developed in this study may provide a useful tool for forensic authentication of black muntjac samples though further testing with larger sample sizes is warranted.     

Detection of bacterial and mycoplasma contamination in cell cultures by polymerase chain reaction

A fast and simple method to detect bacterial and especially mycoplasma contamination in tissue culture by means of polymerase chain reaction (PCR) amplification is described. In a first step the universal primer pairs P1/P2 (190-bp fragment) and P3/P4 (120-bp fragment) directed to different conserved parts of the prokaryotic 16S rRNA gene are used. A positive signal after amplification on cell culture DNA with these primers provides an indication of bacterial infection. Using the internal primers IP1, IP3 and IP'3 complementary to a part of the V4 and V8 variable regions of the 16S rRNA gene, in combination with a universal primer, cultures contaminated with mycoplasma could be identified. Six mycoplasma species, typical contaminants in tissue cultures, were investigated: Mycoplasma orale, M. fermentans, M. arginini, M. hyorhinis, M. hominis and Aeromonas laidlawii. This mycoplasma test is an easy, specific and sensitive assay which should be extremely useful in any tissue culture setting.     

16S/18S/ITS扩增子高通量测序引物的生物信息学评估和改进

【背景】在过去的十几年里,基于核糖体RNA基因的扩增子测序技术被广泛用于各种生态系统中微生物群落的多样性检测。扩增子测序的使用极大地促进了土壤、水体、空气等环境中微生物生态的相关研究。【目的】随着高通量测序技术的不断发展和参考数据库的不断更新,针对不同的环境样本的引物选择和改进仍然需要更深入的校验。【方法】本文收集了目前在微生物群落研究中被广泛采用的标记基因扩增通用引物,包括16S rRNA基因扩增常用的8对通用引物和2对古菌引物、9对真菌转录间隔区(internal transcribed spacer,ITS)基因扩增引物,以及18S rRNA基因扩增的4对真核微生物通用引物和1对真菌特异性引物。这些引物中包括了地球微生物组计划(Earth Microbiome Project,EMP)推荐的2对16S rRNA基因扩增引物、1对ITS1基因扩增引物和1对18S rRNA基因扩增引物。采用最近更新的标准数据库对这些引物进行了覆盖度和特异性评价。【结果】EMP推荐的引物依然具有较高的覆盖度,而其他引物在覆盖度及对特定环境或类群的特异性上也各有特点。此外,最近有研究对这些通用引物进行了一些改进,而我们也发现,一个碱基的变化都可能会导致评价结果或扩增产物发生明显变化,简并碱基的引入既可以覆盖更多的物种,但同时也会在一定程度上降低关注物种的特异性。【结论】研究结果为微生态研究中标记基因的引物选择提供了一个广泛的指导,但在关注具体科学问题时,引物的选择仍需数据指导与实验尝试。     

In vitro culture of fibroblast-like cells from postmortem skin of Katahdin sheep stored at 4��C for different time intervals

Live animals have been produced recently from animal tissues preserved for decades at frozen temperatures with or without cryoprotectants. However, the tissues in these studies were cryopreserved within few hours of animal death to obtain culturable live cells as nuclear donors. How long the tissues can be left unfrozen after animal death, without losing the viability and potential to in vitro culture with comparable morphology and proliferative rate as the fresh tissues, is not completely understood. To understand this phenomenon, ear skin samples from individual sheep (n=3) were procured from slaughter plant and stored at 4 °C. After various intervals (2, 8, 24, 32, 48, and 56 h after slaughter), 2-3 mm(2) pieces (n=10) of skin samples were cultured for 12 d on two dishes (60 mm) for each sheep. Outgrowth of fibroblast-like cells was observed as early as day 4 of culture and was visible on dishes of all time points including 56 h by day 10. The number of outgrowing cells decreased with increasing time interval between animal slaughter and culture initiation. Secondary cultures were successfully established for all the time points. All cultures proliferated well and were apparently normal. Passage 2 cultures of 2 h and 56 h interval for one of the three sheep were compared for their growth pattern and proliferation rates. The population doubling time of 2 h and 56 h intervals was 33.12 and 34.8 h, respectively, and both the lines exhibited similar cell morphology and an "S"-shaped growth curve. These results suggest that skin tissues of sheep and perhaps other animal species with superior traits are effectively preserved at cellular level at least for 56 h at normal refrigerating conditions, without need of complicated cryopreservatives/cryotanks that are usually not available at small farms.     

Polymerase chain reaction as a sensitive and rapid method for specific detection of Mycoplasma pneumoniae in clinical samples

The fast diagnosis of Mycoplasma primary atypical pneumonia is impaired by the lack of routinely available culture methods for isolation of Mycoplasma pneumoniae from clinical specimens. Likewise, serological methods commonly used for diagnosis are insensitive and non-specific. In this study, we have established and applied the polymerase chain reaction (PCR) technique to detect M. pneumoniae DNA in clinical samples originating from the respiratory tract. The PCR results were compared with those from culture and serology tests. To standardize the detection of M. pneumoniae by PCR, we first used DNA from culture grown organisms and clinical samples seeded with M. pneumoniae. PCR amplification was performed with M. pneumoniae-specific primers to amplify 144, 153 and 631 bp DNA fragments by using primer pairs MP5-1/MP5-2, P1-178/P1-331 and P1-178/P1-809, respectively. The amplification of the 631 bp DNA fragment was found to be most sensitive for the detection of M. pneumoniae. Using the most sensitive PCR, a total of 47 respiratory specimens from patients suspected of community acquired pneumonia were tested. While none of the specimens were positive for M. pneumoniae in culture, 6 specimens gave positive results by PCR. In 4 out of the 5 PCR positive samples tested serologically, the results were supported by elevated levels of anti-mycoplasma IgG/IgM/IgA. Thus, these results suggest that PCR is the most sensitive method to detect M. pneumoniae in clinical specimens.     

Species-specific detection of hydrocarbon-utilizing bacteria

Rapid detection and quantitative assessment of specific microbial species in environmental samples is desirable for monitoring changes in ecosystems and for tracking natural or introduced microbial species during bioremediation of contaminated sites. In the interests of developing rapid tests for hydrocarbon-degrading bacteria, species-specific PCR primer sets have been developed for Pseudomonas aeruginosa, Stentrophomonas (Xanthomonas) maltophilia, and Serratia marsescens. Highly variable regions of the 16S rRNA gene were used to design these primer sets. The amplification products of these primer sets have been verified and validated with hemi-nested PCR and with ligase chain reaction (LCR) techniques, and have been applied to the analyses of environmental water samples. These species-specific primer sets were also chosen to amplify in conjunction with a universal set of PCR primers chosen from highly conserved neighboring sequences in the same gene. These multiplex or competitive PCR procedures enable testing with an internal marker and/or the quantitative estimation of the relative proportion of the microbial community that any one of these species occupies. In addition, this universal PCR primer set amplified the same size amplicon from a wide spectrum of procaryotic and eucaryotic organisms and may have potential in earth biota analyses.     

Molecular tools for isolate and community studies of Pyrenomycete fungi

The Pyrenomycetes, defined physiologically by the formation of a flask-shaped fruiting body present in the sexual form, are a monophyletic group of fungi that consist of a wide diversity of populations including human and plant pathogens. Based on sequence analysis of 18S ribosomal DNA (rDNA), rDNA regions conserved among the Pyrenomycetes but divergent among other organisms were identified and used to develop selective PCR primers and a highly specific primer set. The primers presented here were used to amplify large portions of the 18S rDNA as well as the entire internal transcribed spacer (ITS) region (ITS 1, 5.8S rDNA, and ITS 2). In addition to database searches, the specificity of the primers was verified by PCR amplification of DNA extracted from pure culture isolates and by sequence analysis of fungal rDNA PCR-amplified from environmental samples. In addition, denaturing gradient gel electrophoresis (DGGE) analyses were performed on closely related Colletotrichum isolates serving as a model pathogenic genus of the Pyrenomycetes. Although both ITS and 18S rDNA DGGE analyses of Colletotrichum were consistent with a phylogeny established from sequence analysis of the ITS region, DGGE analysis of the ITS region was found to be more sensitive than DGGE analysis of the 18S rDNA. This study introduces molecular tools for the study of Pyrenomycete fungi by the development of two specific primers, demonstration of the enhanced sensitivity of ITS-DGGE for typing of closely related isolates and application of these tools to environmental samples.     

Assessment of amplicons in the DNA from boiled tissue by PCR and AP-PCR amplification

Polymerase chain reaction (PCR) is a technique sensitive enough to amplify small DNA fragments a billion-fold. The generation of amplicons either by PCR with a set of oligo primers or by arbitrarily primed AP-PCR with a single oligonucleotide primer is based on the availability of intact template and priming sites. With these approaches, it is possible to generate specific and random amplicons to assess the extent of damage to DNA caused by any of the physical, chemical, or environmental factors. We report the amplification of sex chromosome and autosome specific loci in the buffalo (Bubalus bubalis) genome by symmetrical and AP-PCR performed on DNA samples isolated from the muscle tissues that were boiled (treated) for different lengths of time. No difference was noticed in the amplification profile of DNA cooked for various lengths 0f time. However, after HinfI treatment, AP-PCR amplification of these DNAs revealed more bands on agarose gel than unrestricted samples. The successful amplification of the DNA samples isolated from the boiled tissues is attributed to the intactness of the amplicons. This suggests that despite storage for more than a year and subsequent heat treatment to the muscle tissues, the DNA remains a good substrate for PCR and AP-PCR amplification. Relevance of this work in the context of DNA probe technology is discussed.     

Design and evaluation of PCR primers for analysis of bacterial populations in wine by denaturing gradient gel electrophoresis

Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal DNA (rDNA) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. While using PCR-DGGE to examine the bacteria in wine fermentations, we noted that several commonly used PCR primers for amplifying bacterial 16S rDNA also coamplified yeast, fungal, or plant DNA present in samples. Unfortunately, amplification of nonbacterial DNA can result in a masking of bacterial populations in DGGE profiles. To surmount this problem, we developed two new primer sets for specific amplification of bacterial 16S rDNA in wine fermentation samples without amplification of eukaryotic DNA. One primer set, termed WLAB1 and WLAB2, amplified lactic acid bacteria, while another, termed WBAC1 and WBAC2, amplified both lactic acid bacterial and acetic acid bacterial populations found in wine. Primer specificity and efficacy were examined with DNA isolated from numerous bacterial, yeast, and fungal species commonly found in wine and must samples. Importantly, both primer sets effectively distinguished bacterial species in wine containing mixtures of yeast and bacteria.