Loop-mediated isothermal amplification method targeting the lytA gene for detection of Streptococcus pneumoniae

It is difficult to separate Streptococcus pneumoniae from the genotypically similar species Streptococcus mitis and Streptococcus oralis, which are commensals of the human oral cavity. A novel nucleic acid amplification technique, loop-mediated isothermal amplification (LAMP), which amplifies DNA under isothermal conditions (63 degrees C) with high specificity, efficiency, and rapidity, was examined regarding its applicability for detecting S. pneumoniae. An S. pneumoniae-specific LAMP primer targeting the lytA gene was designed. The primer specificity was validated using 10 Streptococcus and 7 non-Streptococcus species. Within 60 min, the assay could detect 10 or more copies of purified S. pneumoniae DNA with a sensitivity 1,000 times that of conventional PCR. Clinical isolates of 21 other strains (3 S. oralis, 17 S. mitis, and 1 Streptococcus species) that harbor virulence-factor-encoding genes (lytA or ply) were tried to differentiate S. pneumoniae. The detection of S. pneumoniae in clinical isolates was more selective using the LAMP method than using conventional PCR. Therefore, LAMP appears to be a sensitive and reliable means of diagnosing S. pneumoniae infection.     

Evaluation of an indirect haemagglutination kit for the rapid serological diagnosis of Mycoplasma pneumoniae infections.

A recently introduced indirect haemagglutination kit for the detection of Mycoplasma pneumoniae antibodies is compared with the standard method complement fixation. It is concluded that the kit provides a rapid, simple, and moderately sensitive means of detecting antibodies and, in some cases, enables these to be detected in the early, acute stage of infection.     

For the proposition: for the diagnosis of viral infections, commercial assays provide more reliable results than do in-house assays

It cannot be disputed that in-house ('home brew') assays have a part to play in the diagnosis of emerging or evolving infections such as avian influenza H5N1. In such circumstances, diagnostic companies can provide Research Use Only (RUO) or analyte specific reagents (ASR) to facilitate development. In contrast, the provision of commercial assays is governed by regulatory approval and subject to regular audit by the relevant regulatory bodies to ensure continued quality process throughout the continuum of product management. From initial design, through to post-launch support, the process has to meet the requirements of the USA Food and Drug Administration (FDA) Quality System Regulation (FDA, 1996) as well as that of the international quality standards, for example ISO 9001 (Int. Standard ISO 9001, 2000). Because of the quality policies that are implemented in the commercial environment, I will argue that, where available, commercial assays should replace in-house methods in order to ensure long term reliability of results.     

Against the proposition: for the diagnosis of viral infections, commercial assays provide more reliable results than do in-house assays

There are no differences inherent in the design of commercial or in-house assays and their early development is similar. The same principles apply and it is on the same criteria of accuracy, reproducibility and clinical relevance of results that all assays are judged. However, if there is sufficient uptake of a commercial assay, its strengths and any flaws soon become apparent and it will only be the best commercial assays that remain in the market. For the in-house assays it is through comparability studies and external quality assessment (EQA) schemes that the best can be demonstrated, albeit this information is only accessible initially to the EQA provider and the laboratories using the assays. The EQA results described here support my supposition that, for the diagnosis of viral infections, commercial assays do not provide more reliable results than do in-house assays.     

Loop-mediated isothermal amplification for rapid and reliable diagnosis of tuberculous meningitis

Diagnosis of tuberculous meningitis (TBM) is often difficult. A reliable, simple, and rapid diagnostic test that can be performed in any standard laboratory could be helpful in TBM diagnosis. In this study, a loop-mediated isothermal amplification assay (LAMP) was evaluated to rapidly detect and diagnose TBM infection and was compared to the performance of nested PCR. Six specific primers were used to recognize the IS6110 genomic sequence from Mycobacterium tuberculosis, which included one forward outer primer, one reverse outer primer, two respective inner primers, and two loop primers. The optimum reaction temperature and time were 63°C and 60 min, respectively. Nested PCR was performed targeting the IS6110 region from M. tuberculosis using a commercial kit. The LAMP method yielded a sensitivity of 88.23% and a specificity of 80%, compared to the nested-PCR assay, which yielded a sensitivity of 52.9% and a specificity of 90% for TBM diagnosis. Comparative experiments showed that the LAMP assay is a rapid, sensitive, and specific method to detect TBM infection and that it is superior to the nested-PCR assay. LAMP is very simple, and it can be performed in any laboratory and in rural settings.     

Radioimmunologic analysis for the rapid diagnosis of arbovirus infections

The employment of radioimmunoassay (RIA) allows arbovirus infections to be diagnosed at an early stage of the illness. In the present study the best variant of RIA was determined with regard to its practical use in rapid diagnosis of some arbovirus infections and its superiority over CFT, HI, IHA, IF. The method was shown to be highly specific and sensitive for qualitative studies of specimens from natural foci of arboviruses and for timely diagnosis of human illnesses.     

Comparison of two rapid commercial tests with complement fixation for serologic diagnosis of Mycoplasma pneumoniae infections.

The complement fixation (CF) test is the current reference serologic test for the diagnosis of Mycoplasma pneumoniae infection. However, it is reported to be insensitive and nonspecific, and it is labor intensive. To determine if a faster and more sensitive diagnosis of M. pneumoniae could be obtained, we examined 50 paired serum samples from patients with suspected M. pneumoniae infection by the CF test and two commercial rapid antibody detection kits, the Remel M. pneumoniae immunoglobulin G (IgG)-IgM antibody test system (Remel, Lenexa, Kans.) and the Seradyn Color Vue M. pneumoniae IgG-IgM kit (Seradyn, Indianapolis, Ind.). The Remel test, a 5-min qualitative immunobinding assay, detected antibodies in three patient serum samples with CF titers of 32 and in all but one sample with titers of > or = 64. The Seradyn test, a 40-min qualitative agglutination test, was less sensitive than CF or Remel. The Seradyn test was positive in 68% of cases, compared with 94 and 96% of cases tested by CF or Remel, respectively. Both commercial tests are faster and less technically demanding to perform than is the CF test.     

Development of a novel MALDI-TOF MS-based bile solubility test for rapid discrimination of Streptococcus pneumoniae

Differentiation of Streptococcus pneumoniae from other Streptococcus mitis group streptococci (SMGS) remains challenging despite the introduction of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). While the bile solubility test (BST) provides most reliable discrimination of pneumococci, its practical implementation is limited by subjective visual interpretation and frequent inconclusive results. We aimed to develop a rapid confirmation BST based on direct-on-target MALDI-TOF MS assay. After establishment of optimal test conditions, test performance was evaluated on 36 consecutive clinical SMGS isolates. Colony material was suspended and pipetted onto a MALDI target. After drying, sodium deoxycholate in different concentrations (2%, 5%, and 10 %) was added. Incubation for 30 min (at room temperature or 35 °C) was followed by liquid removal and spot washing. After adding 70 % formic acid, spots were overlaid with matrix and measured (MALDI Biotyper smart, Bruker). The absence of microbial spectra (Biotyper score <1.7) in samples with sodium deoxycholate indicated efficient removal of bacterial biomass due to bile solubility, thus, identifying pneumococci. In contrast, scores ≥1.7 were interpreted as lack of bile solubility and confirmation as viridans streptococci other than S. pneumoniae. Highest test accuracy was achieved applying 5% sodium deoxycholate at 35 °C and 10 % sodium deoxycholate at room temperature. These test conditions provided 100 % sensitivity and 100 % specificity for discrimination of S. pneumoniae. The developed MALDI-TOF MS-based BST is an easy-to-perform assay with minimum hands-on time and objective readout. The promising results of this proof-of-principle study warrant confirmation with large collections of epidemiologically diverse strains.     

Use of the Agilent 2100 bioanalyzer for rapid and reproducible molecular typing of Streptococcus pneumoniae

Restriction fragment length polymorphism (RFLP) analysis is an economic and fast technique for molecular typing but has the drawback of difficulties in accurately sizing DNA fragments and comparing banding patterns on agarose gels. We aimed to improve RFLP for typing of the important human pathogen Streptococcus pneumoniae and to compare the results with the commonly used typing techniques of pulsed-field gel electrophoresis and multilocus sequence typing. We designed primers to amplify a noncoding region adjacent to the pneumolysin gene. The PCR product was digested separately with six restriction endonucleases, and the DNA fragments were analyzed using an Agilent 2100 bioanalyzer for accurate sizing. The combined RFLP results for all enzymes allowed us to assign each of the 47 clinical isolates of S. pneumoniae tested to one of 33 RFLP types. RFLP analyzed using the bioanalyzer allowed discrimination between strains similar to that obtained by the more commonly used techniques of pulsed-field gel electrophoresis, which discriminated between 34 types, and multilocus sequence typing, which discriminated between 35 types, but more quickly and with less expense. RFLP of a noncoding region using the Agilent 2100 bioanalyzer could be a useful addition to the molecular typing techniques in current use for S. pneumoniae, especially as a first screen of a local population.     

E-cadherin gene mutations provide a genetic basis for the phenotypic divergence of mixed gastric carcinomas

Inactivation of the E-cadherin gene has been described previously in gastric carcinomas. In the present study, we investigated the alterations of the E-cadherin gene in gastric carcinomas and analyzed the relationship between such alterations and the histotypes of the tumors. We performed PCR/single-strain conformation polymorphism mutation screening and loss of heterozygosity analysis of the E-cadherin gene in a series of 26 gastric carcinomas, including 10 "pure" intestinal, 10 "pure" diffuse, and 6 mixed gastric carcinomas, the latter with intestinal and diffuse components. Fifteen mutations of the E-cadherin gene were identified in 12 cases (46.2%). Mutations included 10 missense mutations, 7 of which occurred in sequences coding for calcium binding motifs, 3 splice site mutations, 1 nonsense mutation, and 1 frameshift deletion. We found mutations of the E-cadherin gene in 7 of 10 "pure" diffuse carcinomas (70.0%) and in 5 of 6 mixed carcinomas (83.3%). No mutations were found in "pure" intestinal carcinomas. In mixed carcinomas, inactivating E-cadherin mutations were exclusively observed in the diffuse component of the tumors. We conclude that E-cadherin inactivation is significantly related with the diffuse histotype in gastric carcinomas, not only in "pure" diffuse carcinomas but also in the diffuse component of mixed tumors. To the best of our knowledge, this is the first report advancing a genetic basis for the phenotypic divergence of mixed gastric carcinomas.     

A rapid and reliable immunofluorescent method for the identification of common virus infections of the skin

Summary Improvements to the immunofluorescent identification of common virus infections of the skin are described. These include preliminary incubation of the clinical specimen in tissue cultures of mixed cell type for 16 hours; transfer of the cells from the original container to microscope slides; incorporation of a counterstain into the immunofluorescent serum; modifications to the standard exciter filters on the fluorescence microscope.These changes in technique produce excellent, easily read specimens within 24 hours in which the cellular elements have normal morphology and in which the common pathogenic viruses of the skin can easily be identified. The virus-infected cells are recognized from their green immunofluorescent staining, and contrast well against a background of red-brown negative cells. The method eliminates the dangers which are inherent in the direct immunofluorescent examination of skin-scrapings.     

Serologic diagnosis of chlamydial and Mycoplasma pneumoniae infections

The diagnosis of Chlamydia trachomatis infection can be based either on direct detection of the organism or its components or indirectly by measuring antibodies as markers of the individual's response to the infection. The latter is currently of limited value. Neither IgG or IgA antibodies can be used to diagnose current genital infection by Chlamydia trachomatis or to exclude such an infection. There is no solid ground as yet for the use of IgA antibodies as a marker of persistant or unresolved infection. Commercial tests in the Elisa format based on peptides from the MOMP of Chlamydia trachomatis are available and show good specificities and sensitivities. Hsp60 seems to have a unique role in the development of tubal scarring and antibodies to chsp60 could predict tubal factor infertility. Serology is the main diagnostic tool for the diagnosis of Mycoplasma pneumoniae infection. The serologic assays are the complement fixation test (CF), immunofluorescence, the microparticle agglutination and recently EIAs. The CF test is still used for serodiagnosis of Mycoplasma pneumoniae infection because of the sensitivity of 90%. Single titer of >or= 64 are considered to be indicative of recent infection. A number of commercial EIAs have been developped. The difficulty for IgG interpretation is a definition of a cutoff value for discriminating infected and healthy subjects. Most of the IgM assays show good diagnostic sensitivities and are valuable tools for the early diagnosis of Mycoplasma pneumoniae infection in children. There are no wholly satisfactory serological methods for diagnosis of Chlamydia pneumoniae infection. Problems arise from the high background of IgG antibody prevalence, the lack of standardized testing methods.     

Sensitive and specific method for rapid identification of Streptococcus pneumoniae using real-time fluorescence PCR

Molecular surveillance of pathogens has shown the need for rapid and dependable methods for the identification of organisms of clinical and epidemiological importance. As the leading cause of community-acquired pneumonia, Streptococcus pneumoniae was used as a model organism to develop and refine a real-time fluorescence PCR assay and enhanced DNA purification method. Seventy clinical isolates of S. pneumoniae, verified by latex agglutination, were screened against 26 negative control clinical isolates employing a TaqMan assay on a thermocycler (LightCycler). The probe, constructed from the lytA gene, correctly detected all S. pneumoniae genomes without cross-reaction to negative controls. The speed and ease of this approach will make it adaptable to identification of many bacterial pathogens and provide potential for adaptation to direct detection from patient specimens.     

Management of antibiotic-resistant Streptococcus pneumoniae infections and the use of pneumococcal conjugate vaccines

The epidemiology of Streptococcus pneumoniae , a major cause of meningitis, pneumonia, bacteraemia and acute otitis media in both children and adults, has been altered by the availability of the seven-valent pneumococcal conjugate vaccine (PCV7) and selection pressure from broad-spectrum antibiotics. In Spain, the rates of antimicrobial consumption and resistance are high; of all S. pneumoniae isolates collected between 2001 and 2003, 9.2% were penicillin-resistant and 26.4% were penicillin-intermediate. These rates were even higher in children aged ≤4 years; 52.3% of isolates were penicillin-resistant or penicillin-intermediate. Serogroup 14 comprises nearly 9% of pneumococcal strains and exhibits the highest resistance to penicillin (69%). Since the introduction of PCV7 in Madrid, the isolates collected from hospitalized children aged <15 years from 21 hospitals revealed that only 8% of cases involving S. pneumoniae isolates were due to PCV7 serotypes, and no PCV7 vaccination failures were identified. These isolates demonstrated low rates of penicillin–non-susceptible and erythromycin–non-susceptible strains. Among multiresistant strains, serotype 19A was identified as most important. Although the recent WHO position paper on childhood immunizations speaks to the growing resistance of pneumococci, antibiotic resistance in Spain is noted to be decreasing and must be evaluated in conjunction with global studies.     

Analysis of the macrolide resistance gene in penicillin-resistant Streptococcus pneumoniae

We examined the penicillin and macrolide resistance of 496 strains of Streptococcus pneumoniae (S. pneumoniae) isolated at Showa University Hospital from November 2004 to May 2005. According to the classification established by the Clinical and Laboratory Standards Institute, the ratio of penicillin susceptible S. pneumoniae (PSSP) was 25.8%, penicillin intermediate S. pneumoniae was 35.9% and penicillin resistant S. pneumoniae (PRSP) was 38.3%. The ratios of macrolide resistant S. pneumoniae were 85.3% for erythromycin and 76.2% for clarithromycin. S. pneumoniae strains were isolated mainly from pediatric patients, and the ratios of PRSP were similar between outpatients (39.8%) and inpatients (45.6%). We screened for mutations in pbp1a, pbp2b and pbp2x, and the retention rate of the macrolide resistance genes, ermB and mefA in 90 strains isolated in the same period. Seventy two strains had at least one mutation in the pbp genes. Interestingly, some of the penicillin susceptible strains had one or two pbp mutations, suggesting a progressive genetic acquirement of penicillin resistance. In screening for retention of the macrolide resistance genes, we found that 42 strains(46.7%) had ermB, 19 strains (21.1%) had mefA and 13 strains (14.4%) had both ermB and mefA. The possession of resistance genes and the minimal inhibitory concentration indicate that the resistance to erythromycin and clarithromycin were induced by ermB or mefA, and the resistance to clindamycin was induced only by ermB. Among the 72 strains with pbps mutations, 65 strains (90.3%) had ermB or mefA or both. Together, these results show that the strains with pbp mutations were being selected and, after acquiring the macrolide resistance gene, transform to multidrug resistant S. pneumoniae.     

The autolysin-encoding gene (lytA) of Streptococcus pneumoniae displays restricted allelic variation despite localized recombination events with genes of pneumococcal bacteriophage encoding cell wall lytic enzymes.

The lytA-encoded autolysin (N-acetylmuramoyl-L-alanine amidase) of Streptococcus pneumoniae is believed to play an important role in the pathogenesis of pneumococcal infection and has been identified as a putative vaccine target. Allelic diversity of lytA in an extensive collection of clinical isolates was assessed by restriction fragment length polymorphism and confirmatory sequencing studies. Genetic diversity within lytA is limited, especially compared to the high levels of diversity seen in other pneumococcal virulence factor genes, although small blocks generating mosaic structure were identified. Sequence comparisons with genes encoding cell wall lytic enzymes of pneumococcal bacteriophage suggest that localized recombination events have occurred between host lytA and these bacteriophage genes. These results confirm earlier suggestions that recombination between DNA encoding bacteriophage autolytic enzymes and chromosomally encoded lytA might be important in the evolution of lytA. The implications of these findings for understanding the evolution of lytA and the potential utility of LytA as a vaccine target are discussed.     

Chemiluminescent immunoenzymatic assay for rapid diagnosis of viral infections

Current methods of viral diagnosis have been criticized for slowness and insensitivity. However, immunoassay may provide the desired increase in the speed of diagnosis without sacrificing accuracy. This report describes the efficacy of the detection of viral antigen by means of an absorptiometric enzyme-linked immunoassay (ELISA) or by a chemiluminescent enzyme-linked immunoassay (CELISA). Human cytomegalovirus was detected in clinical specimens or culture fluid with comparable sensitivity by CELISA and by viral isolation but with 50 times lesser sensitivity by ELISA. Similarly, herpes simplex virus was detected in clinical specimens with markedly greater sensitivity by CELISA than by ELISA. These findings indicate that the detection of appropriate viruses by CELISA may be a practical alternative to their isolation in cell culture.     

New technique (the NOW test) for rapid detection of Streptococcus pneumoniae in the nasopharynx

Although the NOW test was originally introduced as a rapid pneumococcal antigen detection test for use with urine samples, it was successfully adapted to nasopharyngeal samples in the present study. The sensitivity, specificity, positive predictive value, and negative predictive value of the test were 92.2, 97.7, 95.9, and 95.5%, respectively. These results demonstrate that nasopharyngeal colonization with Streptococcus pneumoniae can be documented within 15 min of sample collection.