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.     

Evaluation of a reverse line blot assay for genotyping common human rotaviruses

To allow high-throughput genotyping of group A rotaviruses (RVA) in a routine surveillance setting, we developed a reverse line blotting method for the determination of the most common human RVA G- and P-genotypes: G1–G4, G9, G12, P[4], P[6] and P[8]. Using the reverse line blotting method on 951 clinical RVA positive feces samples, in 905 (95%) of the samples the G-genotyping yielded a result while in 945 (99%) of the samples the P-genotyping was successful. Comparison of the reverse line blotting-method as it is used currently to a sequence based method for genotyping RVAs showed an agreement of 96% for single strain infections (75 out of 78) but only 48% for mixed infections (10 out of 21).     

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.     

Evaluation of a novel microplate colorimetric hybridization genotyping assay for human papillomavirus

Persistent infection with high-risk human papillomavirus (HR-HPV) has been associated with cervical cancer. Developing assays for the identification of these viral types is of great importance for monitoring patients and controlling strategies. The development of the MCHA (microplate colorimetric hybridization assay), a PCR-based method for identifying six of the most common HR-HPV types (HPV 16, 18, 31, 33, 39 and 45) is described. The MCHA combines the amplification with the GP5+/GP6+ consensus primers followed by PCR reverse hybridization with specific probes and detection through a colorimetric assay. The performance of the MCHA was evaluated using 108 DNA samples typed previously by the PapilloCheck^®. The agreement between both methods was 69.4% for HPV 16; 79.1% for HPV 45; 82.4% for HPV 18; 93.6% for HPV 31; 87.9% for HPV 33, and 17.6% for HPV 39. The assay had higher sensitivity than the Papillocheck^®, particularly for identifying HPV 16 and 18. The MCHA seemed to be sensitive and specific for the identification of the most prevalent HPV types in invasive cervical cancer, HPV 16, 18, 45, 33 and 31. It requires low-cost reagents and common laboratory apparatus.     

Evaluation of a polymerase chain reaction reverse hybridization line probe assay for the detection and identification of medically important fungi in bronchoalveolar lavage fluids.

An assay system in which polymerase chain reaction (PCR) amplification of the ITS-1 region of ribosomal DNA (rDNA) is combined with a reverse-hybridization line probe assay (LiPA) was used for the identification of six Candida species and four Aspergillus species in pure cultures of clinical isolates, as well as in bronchoalveolar lavage (BAL) fluid samples from 42 patients with various underlying diseases. The results were compared with the results obtained with conventional routine identification methods as well as with a commercial enzyme-linked immunosorbent assay (ELISA) galactomannan detection assay and an Aspergillus-specific PCR. No discrepancies between the PCR-LiPA system and routine methods were found for pure cultures of Candida and Aspergillus species except in the case of Aspergillus versicolor. In BAL fluid samples in which Candida species were cultured, the PCR-LiPA system identified more species than did the routine methods. When routine analyses of patient samples were supplemented by adding data obtained by repurifying and re-identifying cultures and by taking isolates obtained from other body sites into account, the results agreed with PCR-LiPA system results in 81% of the cases (34/42). Most of the remaining discrepancies (6/8) involved cases in which such supplementary data were not available. In BAL fluid samples from which A. fumigatus was cultured, the agreement between the PCR-LiPA system and the routine methods was low. Only 2 of 11 BAL samples shown to contain A. fumigatus in ELISA and genus-specific PCR assays were positive in PCR-LiPA system. The PCR-LiPA system enables the simultaneous detection and identification of different fungal species present in pure or mixed populations within 6 h in a single assay. Optimization is required, however, before it is useful as a diagnostic tool in the clinical microbiology laboratory.     

天然菌斑生物被膜中变形链球菌、远缘链球菌和血链球菌的荧光原位检测

目的 检测菌斑生物被膜初期形成过程中的变形链球菌(Streptpcoccus mutans)、远缘链球菌(Streptpcoccus sobrinus)和血链球菌(Streptpcoccus sanguis).方法 从植入釉质磨片表面获得完整的菌斑生物被膜标本,应用激光共聚焦扫描显微镜和荧光原位杂交技术相结合的方法,对天然菌斑生物被膜形成初期的变形链球菌、远缘链球菌和血链球菌进行原位的、实时的动态观察,通过连续断层扫描及三维重建,观察这3种菌在天然菌斑生物被膜中的空间分布,测量3种细菌的扫描厚度.实验中的扫描厚度结果采用方差分析方法进行统计处理,SPSS11.5统计软件辅助完成,α设在0.05.结果 在激光共聚焦扫描显微镜下观察生物被膜呈三维立体结构,形态多样,生物被膜内层和外层细菌较稀疏,中间层较密集,细菌之间可见许多黑色空隙,贯穿整个生物被膜.菌斑生物被膜变形链球菌、远缘链球菌和血链球菌在菌斑生物被膜形成初期的平均扫描厚度随时间延长而增加,1 h时平均扫描厚度分别为20.43、11.50、14.76 μm,到24 h时平均厚度最大,分别为70.25、75.40、79.98 μm.结论 应用荧光原位杂交技术结合激光共聚焦扫描显微镜,可以快速、灵敏地检测出菌斑生物被膜变形链球菌、远缘链球菌和血链球菌.     

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。     

Use of PCR and reverse line blot hybridization assay for rapid simultaneous detection and serovar identification of Chlamydia trachomatis

The aim of this study was to develop and evaluate multiplex and nested PCR-reverse line blot (RLB) hybridization assays for detection and serovar identification of Chlamydia trachomatis. Two sets of primers targeting the VD2 region of the omp1 gene and one set targeting the cryptic plasmid were designed for use in multiplex (both targets) and nested PCR (omp1 only). For the RLB assay, labeled omp1 amplicons were hybridized to a membrane containing probes specific for 15 C. trachomatis serovars. The assays were used to test 429 clinical specimens, which had been previously tested for C. trachomatis using the COBAS AMPLICOR system. Specimens were tested without knowledge of the COBAS AMPLICOR result. Of 205 specimens that were positive by COBAS AMPLICOR, 201 (98%) were positive by multiplex PCR-RLB and 188 (92%) were also positive by omp1 nested PCR-RLB. In addition, three of 224 COBAS AMPLICOR-negative specimens were positive by omp1 nested PCR-RLB. One hundred sixty-six of 191 (87%) specimens in which C. trachomatis serovars were identified contained only one serovar and 25 (13%) contained two or three serovars. Serovars D, E, and F were found in 31 (16%), 83 (43%), and 51 (27%) specimens, respectively. Serovar E (41%) was the most commonly identified single serovar. Serovars J and K were found alone uncommonly (<2% each), but 18 of 25 (72%) specimens with multiple C. trachomatis serovars contained one or both (10 specimens) of these serovars. The nested (ompI) PCR-RLB is a specific and sensitive method for simultaneous detection and serovar identification of C. trachomatis, which can reliably identify mixed C. trachomatis serovars. It is suitable for use in epidemiological studies.     

Evaluation of a novel line probe assay to detect resistance to pyrazinamide,a key drug used for tuberculosis treatment

ObjectivesThe development of rapid molecular diagnostic assays for pyrazinamide (PZA) resistance is considered technically challenging as mutations are highly diverse, scattered along the full length of the pncA gene and not all are associated with PZA resistance. We evaluated the performance of the novel Genoscholar PZA-TB II line probe assay (PZA-LPA2; NIPRO Corporation, Japan).MethodsTo evaluate the applicability of the PZA-LPA2 in clinical settings, we compared the performance of the PZA-LPA2 to a composite reference standard pncA Sanger and Illumina sequencing plus phenotypic susceptibility testing on a panel of 87 Mycobacterium tuberculosis isolates from World Health Organization (WHO) drug resistance surveys, harbouring mutations previously classified as associated or not associated with resistance according to data from peer-reviewed literature. In addition, the PZA-LPA2 was challenged against a selection of isolates with lineage-specific and non-resistance-associated mutations, for which the frequency among clinical isolates is unknown, and tested directly on 59 sputum extracts.ResultsFor the survey isolates, the PZA-LPA2 reached an overall agreement with the composite reference of 97.6% (80/82) or 94.3% (82/87) excluding or including heteroresistance, respectively. The PZA-LPA2 failed on 8.5% (5/59) of clinical samples; among valid results, 100% (14/14) sensitivity and 100% (7/7) specificity was reached relative to pncA Sanger sequencing.ConclusionsThe PZA-LPA2 represents a valid and rapid alternative for indirect PZA susceptibility testing. Preliminary findings on clinical samples show promise for direct testing. Further studies are needed to assess the clinical risk of missing heteroresistance and falsely detecting lineage-specific, silent and nonassociated mutations.     

INNO-LiPA和直接测序法检测HBV耐药突变的比较

目的比较INNO-LiPA HBV DRv2和直接测序法检测HBV耐药突变的准确性和灵敏性。方法选取41例接受阿德福韦或聚乙二醇干扰素α-2a救援治疗并在治疗过程中（治疗48周和72周时）进行INNO-LiPA HBV DRv2耐药检测的拉米夫定耐药患者,共收集到101份足量的血清,采用直接测序法进行拉米夫定和阿德福韦耐药检测。分析HBV聚合酶第80、173、180、181、204和236位点的耐药突变情况,并与INNO-LiPA耐药检测的结果进行对比。结果 INNO-LiPA HBV DRv2和直接测序法检测204位点耐药结果对比,完全符合率为73.8%（62/84）,部分符合率为23.8%（20/84）,总体符合率达到97.6%（82/84）。其他位点总体符合率也多在95%以上。另外INNO-LiPA比直接测序法有更高的灵敏度,对混合感染的检出率（46.4%）明显高于直接测序法（23.8%）,其总体耐药检出率也高于直接测序法。结论 INNO-LiPA方法在灵敏度和准确性上均优于直接测序法,而且操作简便、快捷,能够提供更多的信息量,在科研和临床上都有很好的应用前景。     

A rapid colorimetric assay for the determination of IL-2-producing helper T cell frequencies

Interleukin 2 (IL-2) activity is tested in conditioned media by assessing its ability to support proliferation of selected IL-2 dependent T cell lines, conventionally measured by [3H]thymidine incorporation. Here, we compare this [3H]thymidine uptake test for measuring IL-2 activity with a rapid and sensitive colorimetric method which is based on the ability of viable cells to cleave 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT). The sensitivity of the colorimetric method was dependent on the indicator cell line used, being greatest with the cytotoxic T cell line 16 (CTLL-16). The colorimetric method is at least as sensitive as [3H]thymidine uptake tests, does not rely on radioactivity, and is ideally suited to screen large numbers of individual samples for IL-2 activity. The latter point was demonstrated by calculating IL-2-producing helper T cell frequencies in heterogeneous murine lymphocyte populations: in this assay, splenic T cells were clonally expanded under limiting dilution conditions and supernatants conditioned by these in vitro growing T cell clones were tested for IL-2 activity with the colorimetric method. This allowed us to obtain reliable estimates of the frequency of progenitor cells of IL-2-producing T cell clones in various populations.     

Agreement between CBNAAT,liquid culture and line probe assay for detection of Mycobacterium tuberculosis and anti-tubercular drug resistance in extrapulmonary samples

PurposeCartridge based nucleic acid amplification test (CBNAAT) has been endorsed by the WHO as the screening test for diagnosing extrapulmonary tuberculosis (EPTB). In the present study we report the agreement between CBNAAT (Xpert MTB/RIF), liquid culture (LC) and line probe assay (LPA) for diagnosis of Mycobacterium tuberculosis and detection of drug resistance among EPTB cases.MethodsThe EP samples were subjected to CBNAAT (Xpert MTB/RIF, Cepheid, USA) and wherever possible, to LC (MGIT 960, Becton Dickinson, USA) followed sequentially by first line and second line-LPA (FL-LPA, SL-LPA, Hain Lifescience, Germany) on the isolates.ResultsTotal 566/4080 (13.9%) EP samples were detected positive for M. tuberculosis on CBNAAT. Aspirates from lymph nodes were most often positive (11/30; 36.6%), followed by pus (240/873; 27.5%) and CSF samples (166/104; 15.8%). The detection of M. tuberculosis was more in adults than children except in tissue biopsy samples. Rifampicin resistance was also higher among adults except CSF in which resistance was more in children. Total 185 of 566 (32.7%) CBNAAT positive and 770 of 3510 (21.9%) CBNAAT negative samples could be cultured of which 110/185 (59.4%) and 33/770 (4.3%) respectively turned positive. FL-LPA and SL-LPA of 143 culture isolates showed that 27 isolates had drug resistance, of which 3 (2.1%) were XDR, 11 (7.7%) were Pre-XDR (FQ) and 13 (9.1%) were MDR. Of these 27 resistant isolates, 12 were negative by CBNAAT and two were mislabeled as Rifampicin sensitive or indeterminate based on the unique RpoB gene mutation patterns on LPA. The positive and negative agreements between LC and CBNAAT for detection of M. tuberculosis were 67.1% and 92.7% respectively and between LPA and CBNAAT for rifampicin resistance detection were 98.9% and 92.9% respectively.ConclusionsFor EPTB, CBNAAT should be accompanied with LC wherever possible irrespective of the CBNAAT result.