膜芯片技术检测泌尿生殖道沙眼衣原体、淋病奈瑟菌和3种支原体的方法学研究

目的建立和评价一个新的多重PCR．反向线点杂交技术（RIJB）快速同时检测泌尿生殖道沙眼衣原体（Ct）、淋病奈瑟菌（坛）和3种支原体感染的方法。方法分别选择Ct隐蔽质粒和Ng16SrRNA基因设计两对特异性引物，以支原体内转录间隔序列（ITS）设计一对支原体属通用引物，生物素标记下游引物。构建三重PCR同时扩增Ct、Ng、解脲脲原体（仇）、微小脲原体（跏）、人型支原体（Mh）等菌DNA，然后与固定在尼龙膜上的各特异性寡核苷酸探针杂交。并对142份经荧光定量PCR（FQ-PCR）检测0和坛的性病高危人群标本，以及45份经支原体液体培养法鉴定的标本进行检测。结果多重PCR可同时扩增Ct、Ng、Uu、Up和Mh标准菌株DNA，其PCR产物的片段长度为208～408bp。97份FQ-PCRCt阳性标本中有93份经多重PCR-RLB检测为Ct阳性，45份FQ-PCRCt阴性标本中35份多重PCR-RLB阴性。41份FQ-PCRNg阳性标本中34份多重PCR-RLBNg阳性，101份FQ-PCRNg阴性标本中98份多重PCR-RLB阴性。其中36份经多重PCR-RLB检测为混合感染。32份支原体液体培养阳性标本中28份多重PCR-RLB阳性，13份支原体培养阴性标本经多重PCR-RLB检测均为阴性。结论多重PCR-RLB可快速同时检测Ct、Ng、Uu、Up和Mh，为性传播疾病的临床诊断提供了一种可靠的方法。     

A new combination of RT-PCR and reverse dot blot hybridization for rapid detection and identification of potyviruses

Three degenerate primers, located at the NIb and CP gene regions, were designed for potyvirus detection. Using these primer pairs, 1.0-1.2 kb cDNA fragments of the 3'-terminal region of six potyviruses were successfully amplified from infected plant tissues. RT-PCR products were sequenced and found to be derived from the expected viruses. To identify further these potyviruses, sequences located between the 3' end of the NIb gene and the 5' end of the CP gene were chosen to design a series of species-specific probes. The probes were prepared by PCR with species-specific primers, immobilized onto nylon membrane, and then hybridized with DIG-labeled RT-PCR products amplified by potyvirus degenerate primers. The results suggested that species-specific cDNA probes plus reverse dot blot hybridization was able to identify correctly different species of potyviruses in single as well as mixed infections.     

聚合酶链反应结合反向线点杂交技术在检测及鉴定真菌性鼻窦炎常见致病曲霉菌中的应用

目的 探讨聚合酶链反应结合反向线点杂交(PCR/RLB)技术在检测和鉴定真菌性鼻窦炎(FS)常见致病曲霉菌中应用的可行性.方法 收集首都医科大学附属北京同仁医院2009年5月至2010年2月住院手术的FS患者活检石蜡包埋组织26例和活检新鲜组织8例,全部病例进行了病理学真菌检查、真菌培养及真菌ITS2区测序;提取各标本中真菌的DNA,用真菌特异性引物行PCR扩增,针对真菌的ITS2区设计曲霉菌种特异性探针,用5根曲霉菌种特异性探针与PCR产物进行反向线点杂交;将PCR/RLB与ITS2区测序、真菌培养及病理学检查的结果进行比较.阳性对照为5株曲霉菌株,阴性对照为真菌培养为非曲霉的石蜡包埋组织.结果 活检标本病理学检查均可见菌丝;真菌培养14例阳性(41.2％);测序16例(47.1％)得到结果;PCR/RLB鉴定34例均得出鉴定结果:黄曲霉14例,烟曲霉10例,黑曲霉4例,构巢曲霉1例,黄曲霉和烟曲霉同时阳性3例,烟曲霉与黑曲霉同时阳性2例.结论 PCR/RLB技术可以对FS常见致病曲霉菌进行检测及鉴定,与病理组织学检查、真菌培养及DNA测序方法相比较,具有经济省时、敏感性高、特异性强、高通量等优势.     

Use of PCR and reverse line blot hybridization macroarray based on 16S-23S rRNA gene internal transcribed spacer sequences for rapid identification of 34 mycobacterium species

The aim of this study was to develop a PCR and reverse line blot hybridization (PCR-RLB) macroarray assay based on 16S-23S rRNA gene internal transcribed spacer sequences for the identification and differentiation of 34 mycobacterial species or subspecies. The performance of the PCR-RLB assay was assessed and validated by using 78 reference strains belonging to 55 Mycobacterium species, 219 clinical isolates which had been identified as mycobacteria by high-performance liquid chromatography or gas chromatography, three skin biopsy specimens from patients with suspected leprosy which had been shown to contain acid-fast bacilli, and isolates of 14 nonmycobacterial species. All mycobacteria were amplified in the PCR and hybridized with a genus-specific probe (probe MYC). The 34 species-specific probes designed in this study hybridized only with the corresponding Mycobacterium species. The mycobacterial PCR-RLB assay is an efficient tool for the identification of clinical isolates of mycobacteria; it can reliably identify mixed mycobacterial cultures and M. leprae in skin biopsy specimens.     

Rapid antigen detection assay for identification of Chlamydia trachomatis infection.

A rapid antigen detection test was compared with direct fluorescent-antibody staining and with tissue culture isolation for the detection of Chlamydia trachomatis infections in 507 women. The sensitivities observed were 75, 76, and 84%, respectively, with specificities of > 99%.     

Detection and identification of eight Trichinella genotypes by reverse line blot hybridization

A reverse line blot (RLB) assay was developed to identify different Trichinella genotypes. The RLB assay accomplishes detection and specific identification of the different Trichinella genotypes and relies on hybridization of the amplified 5S ribosomal DNA intergenic spacer regions to specific, membrane-bound oligonucleotide probes. After one single amplification, we were able to detect and genetically identify six sibling species, i.e., T. spiralis, T. britovi, T. nativa, T. murrelli, T. nelsoni, and T. pseudospiralis, and two additional Trichinella genotypes, T6 and T8. Twenty-four Trichinella strains of different genotypes were unequivocally identified evaluated using one simple PCR-based assay based on single larvae. This assay allows the specific identification of Trichinella species without the need to passage larvae in laboratory animals.     

New method for simultaneous species-specific identification of equine strongyles (nematoda, strongylida) by reverse line blot hybridization

The ability of a reverse line blot (RLB) assay to identify 13 common species of equine small strongyles (cyathostomins) and to discriminate them from three Strongylus spp. (large strongyles) was demonstrated. The assay relied on the specific hybridization of PCR-amplified intergenic spacer DNA fragments of the nuclear ribosomal DNA to membrane-bound species-specific probes. All cyathostomins examined were unequivocally identified and simultaneously discriminated from each other and from three large strongyles (Strongylus edentatus, Strongylus equinus, and Strongylus vulgaris). This assay will enable the accurate and rapid identification of equine cyathostomins irrespective of their life cycle stage, opening important avenues for a better understanding of their biology and epidemiology and of the pathogenesis of cyathostomin-associated disease. In particular, this RLB method promises to be a powerful diagnostic tool to determine the roles of individual species in the pathogenesis of mixed infections and to elucidate some aspects of cyathostominosis. Also, it could represent a basic step toward the development of a rapid and simple molecular test for the early detection of drug-resistant genotypes of horse strongyle species.     

Simultaneous detection and identification of Candida, Aspergillus, and Cryptococcus species by reverse line blot hybridization

We report on a reverse line blot (RLB) assay, utilizing fungal species-specific oligonucleotide probes to hybridize with internal transcribed spacer 2 region sequences amplified using a nested panfungal PCR. Reference and clinical strains of 16 Candida species (116 strains), Cryptococcus neoformans (five strains of Cryptococcus neoformans var. neoformans, five strains of Cryptococcus neoformans var. grubii, and six strains of Cryptococcus gatti), and five Aspergillus species (68 strains) were all correctly identified by the RLB assay. Additional fungal species (16 species and 26 strains) not represented on the assay did not exhibit cross-hybridization with the oligonucleotide probes. In simulated clinical specimens, the sensitivity of the assay for Candida spp. and Aspergillus spp. was 10(0.5) cells/ml and 10(2) conidia/ml, respectively. This assay allows sensitive and specific simultaneous detection and identification of a broad range of fungal pathogens.     

TestPack Chlamydia, a new rapid assay for the direct detection of Chlamydia trachomatis.

TestPack Chlamydia (Abbott Laboratories) is a rapid enzyme immunoassay for the direct antigen detection of Chlamydia trachomatis in endocervical specimens. The assay is self-contained, requires no specialized equipment, and yields results in less than 30 min. The clinical performance of TestPack Chlamydia versus chlamydial cell culture was evaluated with a total of 1,694 paired endocervical specimens. Discordant samples were further investigated by immunofluorescent staining and by Chlamydiazyme immunoassay, with confirmatory procedures. The sensitivity of TestPack Chlamydia with less-than-48-h-old specimens was 76.5%, while culture sensitivity was 86.7%. TestPack Chlamydia specificity was determined to be 99.5%. These results indicate that TestPack Chlamydia is an accurate test for chlamydial infection, with a positive predictive value of 96.2%. This assay is suitable for low-volume chlamydial testing in physician offices, clinics, and smaller laboratories.     

Use of a multiplex PCR-based reverse line blot (mPCR/RLB) hybridisation assay for the rapid identification of bacterial pathogens.

The aim of this study was to develop a sensitive and reliable method for the molecular identification of pathogenic bacteria. A multiplex PCR-based reverse line blot (mPCR/RLB) hybridisation assay was developed and evaluated for the rapid identification of 24 systemic and respiratory bacterial pathogens in routine diagnosis. All species-specific probes designed for the RLB hybridised with amplified DNA only from the corresponding species. Sensitivity limits of the mPCR/RLB assay varied among the 24 target organisms from 0.05 pg to 0.5 ng of genomic DNA. The sensitivity of the assay was 2 x 10(2) CFU/mL for Streptococcus pneumoniae and 6 x 10(2) CFU/mL for Escherichia coli. The specificity of each probe was tested against 24 species. There were no cross-reactions among any of the 43 probes. The mPCR/RLB assay appeared to be a useful alternative tool for the molecular identification of common pathogens.     

Molecular diagnosis of Old World cutaneous leishmaniasis and species identification by use of a reverse line blot hybridization assay

Reverse line blot hybridization assays (RLB) have been used for the rapid diagnosis and genotyping of many pathogens. The leishmaniases are caused by a large number of species, and rapid, accurate parasite characterization is important in deciding on appropriate therapy. Fourteen oligonucleotide probes, 2 genus specific and 12 species specific (2 specific for Leishmania major, 3 for L. tropica, 1 for L. infantum, 3 for L. donovani, and 3 for L. aethiopica), were prepared by using DNA sequences in the internal transcribed spacer 1 (ITS1) region of the rRNA genes. Probe specificity was evaluated by amplifying DNA from 21 reference strains using biotinylated ITS1 PCR primers and the RLB. The genus-specific probes, PP and PP3′, recognized all Leishmania species examined, while the species-specific probes were able to distinguish between all the Old World Leishmania species. Titrations using purified parasite DNA showed that the RLB is 10- to 100-fold more sensitive than ITS1 PCR and can detect <0.1 pg DNA. The RLB was compared to kinetoplast DNA (kDNA) and ITS1 PCR by using 67 samples from suspected cutaneous leishmaniasis (CL) patients in Israel and the West Bank. The RLB accurately identified 58/59 confirmed positive samples as CL, a result similar to that found by kDNA PCR (59/59) and better than that by ITS1 PCR (50/59). The positive predictive value and negative predictive value of the RLB were 95.1% and 83.3%, respectively. L. major or L. tropica was identified by the RLB in 55 of the confirmed positive cases, a level of accuracy better than that of ITS1 PCR with restriction fragment length polymorphism (42/59). Thus, RLB can be used to diagnose and characterize Old World CL.     

Novel, ultrasensitive, Q-beta replicase-amplified hybridization assay for detection of Chlamydia trachomatis.

A sensitive, nonisotopic hybridization assay termed "dual capture" is described. The assay rapidly and specifically detects very low levels of target nucleic acids and organisms. The assay is based on the principles of sandwich hybridization, reversible target capture, and Q-Beta replicase amplification. The assay can be completed in less than 4 h, and in the described model format, it detects Chlamydia trachomatis rRNA or rDNA. Up to 96 samples can be analyzed simultaneously. The assay employs two types of probes: a test-specific capture probe, which mediates the cycling of the target probe complex on and off derivatized magnetic beads, and a replicatable RNA detector molecule containing a sequence complementary to and adjacent to the capture probe site on the target. Following reversible target capture, detection of the signal is accomplished by replication of the detector molecule by Q-Beta replicase in the presence of propidium iodide. A specific assay signal can be detected from as few as 1,000 molecules above the background. In a limited study of 94 urogenital samples the assay detected five of the six culture-positive samples and did not detect the C. trachomatis target in 85 of the 88 culture-negative samples.     

A rapid immunoperoxidase assay for the detection of specific IgG antibodies to Chlamydia trachomatis

A technique, using indirect immunoperoxidase antibody (IPA), was developed for the detection of IgG antibody to Chlamydia trachomatis. The IPA technique employs glass slides with air-dried and acetone-fixed C trachomatis infected cells, which can be stored at -70 degrees C and used for several months. Antibody titres detected by IPA were comparable to those detected by the indirect fluorescent antibody technique.     

Duplex PCR system for simultaneous detection of Neisseria gonorrhoeae and Chlamydia trachomatis in clinical specimens.

AIMS--To evaluate the use of a duplex polymerase chain reaction (PCR) assay for the simultaneous detection of Neisseria gonorrhoeae and Chlamydia trachomatis in clinical samples. METHODS--Genital swab specimens were obtained from both China (203 swabs) and Hong Kong (202 swabs). N gonorrhoeae and C trachomatis were detected in each specimen with a number of tests including enzyme immunoassays (IDEIA) and PCR assays using both single and double primer pairs. The primer pair for N gonorrhoeae was derived from the cppB gene on its cryptic plasmid and the PCR product was 390 base pairs long. For C trachomatis, the PCR product was 473 base pairs long, resulting from amplification of a sequence in the common 7.4 kilobase plasmid present in all serovars. For N gonorrhoeae, PCR results were also compared with those obtained by culture and Gram's smear of the discharges. RESULTS--For the 203 specimens collected in China, similar numbers of positive results (177) were obtained by both Gonozyme and duplex PCR for the detection of N gonorrhoeae. No discrepant results were found among the cultured specimens when Gonozyme and duplex PCR were compared. C trachomatis was detected in 47 specimens by duplex PCR, but was detected in only 28 by IDEIA. Of the 202 Hong Kong specimens, 46 were positive for N gonorrhoeae, detected by both Gonozyme and duplex PCR; 34 were positive for C trachomatis, 25 of which were detected by IDEIA and the remainder by duplex PCR. CONCLUSIONS--The duplex PCR assay is a satisfactory diagnostic tool for the simultaneous detection of N gonorrhoeae and C trachomatis in clinical swab samples. Further evaluation is suggested.     

Evaluation of a modified reverse line blot assay for detection and typing of human papillomavirus

Detection and typing of human papillomaviruses (HPVs) are requested by clinicians with growing frequency as part of the overall management of patients. A new method using consensus L1 amplification and a reverse line blot hybridization detection method has been described for broad spectrum HPV genotype identification. This method involves hybridization at 53 degrees C in a shaking water bath, which many laboratories might find cumbersome. We describe a modified hybridization step, using a dry-air incubator, that simplifies the detection protocol. Overall, comparable results were obtained by the modified, more easily performed protocol, indicating that laboratories might validate and use this modified method.     

Combination of PCR targeting the VD2 of omp1 and reverse line blot analysis for typing of urogenital Chlamydia trachomatis serovars in cervical scrape specimens

In this study we developed and evaluated a new PCR-based typing assay, directed to the VD2 region of the omp1 gene, for the detection and typing of urogenital Chlamydia trachomatis infections. A nested VD2 PCR-reverse line blot (RLB) assay was developed for the typing of nine different urogenital serovars of C. trachomatis. The assay developed was tested with reference strains of C. trachomatis serovars and cervical scrapes of 86 Colombian women previously found to be positive for C. trachomatis by using plasmid PCR. Two sets of primers directed to the VD2 region of the omp1 gene of C. trachomatis were designed, and fragments of 220 and 166 bp were generated in the primary and nested PCRs, respectively. In addition, an RLB assay was developed to identify nine different urogenital serovars of C. trachomatis (Ba, D, E, F, G, H, I, J, and K) and group controls, including group B (Ba, D, and E), group C (I, J, K, and H), and an intermediate group (F and G). Using this assay, we were able to type 81 of the 86 samples (94.2%). Of these samples, 91.3% were single C. trachomatis infections, and 8.7% were multiple infections. The most common serovars identified were serovars D (22.2%), F (18.5%), G (13.6%), and E (12.3%). Of the women with multiple C. trachomatis infections, >50% contained both serovars D and E. The nested VD2 PCR-RLB developed is a simple, fast, and specific method for the identification of individual urogenital C. trachomatis serovars previously detected by using plasmid PCR. Moreover, it is an appropriate method for studying multiple C. trachomatis infections and for use in large epidemiological studies.     

Reverse line blot hybridization assay for identification of medically important fungi from culture and clinical specimens

We evaluated a combined panfungal PCR-reverse line blot (RLB) hybridization assay based on internal transcribed spacer 1 (ITS1) and ITS2 region polymorphisms to identify 159 Candida, Cryptococcus neoformans, and Aspergillus isolates (22 species). Its utility to identify fungal pathogens directly from 27 clinical specimens was also determined. ITS sequence analysis was performed to resolve discrepant identifications or where no RLB result was obtained. Species-specific ITS2- and ITS1-based probes correctly identified 155 of 159 isolates (98%) and 149 (93.7%) isolates, respectively. All strains were unambiguously differentiated with the exception of cross-reactivity between the Candida norvegensis probe and Candida haemulonii DNA product. Species identification of the pathogen was made for all 21 specimens (sensitivity of 100%) where species-specific probes were included in the RLB; however, there was no ITS2 probe-based hybridization signal for two specimens. Results were concordant with the culture results for 18 (85.7%) specimens. The assay was able to provide species identification in the absence of a culture result (two specimens) and to detect mixed infection (one specimen). The results indicate that the RLB assay is capable of reliably detecting yeasts and Aspergillus spp. in clinical specimens and that the incorporation of both ITS1- and ITS2-targeted probes is required for optimal sensitivity. The test has potential utility in the early diagnosis of invasive fungal infection, since "fungal" DNA was detected in all 27 specimens. Prior to incorporation of probes to detect other fungal species, ITS sequencing may be performed to achieve species identification.