Development of molecular tests for the detection of ILAR and latent viruses in fruit trees

The detection throughout the year of latent and ILAR viruses in fruit tress by classical serological tests appear to be unreliable. We have developed RT-PCR tests for a reliable detection of latent and ILAR viruses in fruit trees. These assays were then simplified to allow the direct use of crude plant extracts instead of total RNA preparations, and the analyses of pooled samples. In this way, such RT-PCR protocols are suitable for a routine diagnosis of latent and ILAR viruses in fruit tree certification.     

Are molecular tools solving the challenges posed by detection of plant pathogenic bacteria and viruses?

Plant pathogenic bacteria, phytoplasmas, viruses and viroids are difficult to control, and preventive measures are essential to minimize the losses they cause each year in different crops. In this context, rapid and accurate methods for detection and diagnosis of these plant pathogens are required to apply treatments, undertake agronomic measures or proceed with eradication practices, particularly for quarantine pathogens. In recent years, there has been an exponential increase in the number of protocols based on nucleic-acid tools being those based on PCR or RT-PCR now routinely applied worldwide. Nucleic acid extraction is still necessary in many cases and in practice inhibition problems are decreasing the theoretical sensitivity of molecular detection. For these reasons, integrated protocols that include the use of molecular techniques as screening methods, followed by confirmation by other techniques supported by different biological principles are advisable. Overall, molecular techniques based on different types of PCR amplification and very especially on real-time PCR are leading to high throughput, faster and more accurate detection methods for the most severe plant pathogens, with important benefits for agriculture. Other technologies, such as isothermal amplification, microarrays, etc. have great potential, but their practical development in plant pathology is still underway. Despite these advances, there are some unsolved problems concerning the detection of many plant pathogens due to their low titre in the plants, their uneven distribution, the existence of latent infections and the lack of validated sampling protocols. Research based on genomic advances and innovative detection methods as well as better knowledge of the pathogens' lifecycle, will facilitate their early and accurate detection, thus improving the sanitary status of cultivated plants in the near future.     

Interlaboratory quality control in gynecologic cytopathology using the novel CONQUISTADOR software. Interobserver reproducibility in the Latin American screening study

OBJECTIVE: The recently developed software (CONQUISTADOR), capable of computing all intralaboratory and interlaboratory quality control (QC) indicators, was used to evaluate the diagnostic agreement among 4 cytology laboratories participating in the LAMS Study. STUDY DESIGN: The study was an interlaboratory exchange of specially designed 5 slide sets, each comprising 20 (conventional cytology) slides. At the first step, 80 slides (with "clear-cut" cases) were divided into four sets (A, B, C, D) of 20 specimens, each including inadequate and negative cases as well as in different proportions of all diagnostic TBS 2001 categories. In the second round, a fifth set (E) of 20 slides ("difficult cases") was designed, with all diagnostic categories, ASC and AGC included. Common measures of reproducibility (kappa and weighted kappa), accuracy (SE, SP, PPV, NPV) and 3 indices of diagnostic variability were calculated for sets A-D and set E, separately. RESULTS: For the 5 slide sets together, the weighted kappa was 0.8 (95% CI 0.76-0.85), which is the lower limit of the "almost perfect" ranking of kappa statistics, indicating an excellent interlaboratory agreement. The interlaboratory reproducibility was lower only for the difficult set (E). Similarly, the sensitivity for set E (70.0%) was lower than that (92.1%) for sets A-D. The diagnostic variability indices were not substantially different between the difficult (set E) and clearcut (sets A-D) cases. CONCLUSION: High interlaboratory reproducibility was obtained for sets A-D ("clear-cut" cases), while more interlaboratory variation was evident in the difficult samples. The new CONQUISTADOR software is a valuable tool in calculating the indicators needed in this intralaboratory and interlaboratory.     

Application of morphometry in tumor pathology

The application of morphometry in tumor pathology is discussed, e.g., its use in studying the biology of tumors, in creating tumor classification(s), in creating methods for the identification of a tumor in the diagnostic context, and in characterizing diagnostic histopathology in absolute terms. In traditional subjective diagnostic histopathology, reproducibility can be defined satisfactorily, but the definition of accuracy is ambiguous; in morphometric histopathology, a satisfactory definition is found for both concepts but it may be difficult to separate them in practice. Morphometric histopathology can study parameters measured from sections or parameters derived from the primary measurements through calculations. In the histopathology of tumors, the following parameters have turned out to be specially valuable: densitometric measurements of nuclei, nuclear area, perimeter and form factors, nucleolar parameters, the number of mitotic cells per area, the cellularity, the volume fraction of the epithelium, and parameters associated with the fraction of tumor tissue in the sample. The standard deviation or other moments of the distribution of these measurements can be more relevant than the mean values of the results. This indicates that more attention should be given to sampling rules, which are important in defining the efficiency of the methods. For rational application of morphometric methods, it is very important to make a distinction between group morphometry and diagnostic morphometry. The latter engenders numerous sources of variation (variation in section thickness, variation in tissue processing, variation in the techniques of measurement, interobserver variation, interlaboratory variation, variation due to subjective interpretation, etc.), which are usually better controlled in group morphometry. The influence on morphometric parameters of variation in section thickness and tissue shrinkage during processing are discussed.     

Molecular diagnostics of clinically important staphylococci

Bacterial species of the genus Staphylococcus known as important human and animal pathogens are the cause of a number of severe infectious diseases. Apart from the major pathogen Staphylococcus aureus, other species until recently considered to be nonpathogenic may also be involved in serious infections. Rapid and accurate identification of the disease-causing agent is therefore prerequisite for disease control and epidemiological surveillance. Modern methods for identification and typing of bacterial species are based on genome analysis and have many advantages compared to phenotypic methods. The genotypic methods currently used in molecular diagnostics of staphylococcal species, particularly of S. aureus, are reviewed. Attention is also paid to new molecular methods with the highest discriminatory power. Efforts made to achieve interlaboratory reproducibility of diagnostic methods are presented.     

Circulating microRNAs in the identification of biological fluids: A new approach to standardization of expression-based diagnostics

Molecular profiling of normal tissues is a regular and necessary step when developing systems for expression analyses in biological samples, including diagnostic panels for various diseases and conditions. Yet there are still no rigorous criteria to allow precise typing of normal tissues. A main problem is that the methods employed in diagnostic expression testing are difficult to standardize. While various technologies, instruments, and reagents are available, universal protocols of handling biological material are lacking, thus impairing the reproducibility of data from independent studies. The review describes a new approach to standardizing circulating microRNA studies in forensic biology, which has relatively recently (7–8 years ago) come to employ RNA markers in molecular typing of tissues and biological fluids. Forensic biology is now one of the few disciplines where several panels of tissue mRNA markers have been developed within a short period of time and a number of specific microRNA markers have been established and validated for several biological fluids. To allow their successful use, new protocols have been combined with the available, rigidly standardized system of genetic personal identification. Although a ready diagnostic product has still not been obtained with this well-working approach, the apparent efficiency of the standardization methods clearly demonstrates that the problem is possible to solve in other biomedical fields, including those where RNA-based diagnostic protocols are still under development.     

Expert examination of the immunogenic activity and toxicity of the pertussis component of adsorbed and non-adsorbed diphtheria-tetanus-pertussis vaccines. Results of interlaboratory investigations under the WHO project "Reactogenicity and Toxicity of DPT Vaccines"

Since the DPT vaccine is broadly used for the prevention of diphtheria, tetanus and pertussis' its preparations should meet special quality requirements. The present study was aimed at evaluating the reproducibility of laboratory methods utilized to assess the protective activity and toxicity of the pertussis component as well as at examining the feasibility of expert estimations of product quality to enhance the validity of findings. The results of interlaboratory comparative examination of quality parameters of the tested preparations revealed that the routine laboratory quality control methods were not sufficiently standardized as their application in different laboratories did not always produce identical results. The WHO criteria to evaluate the toxicity of pertussis vaccines are far from perfect since vaccines with pronounced toxicity can only be distinguished from those with moderate to mild toxicity after the administration to tested mice of vaccines at a single infant dose of 0.5 ml. To enhance the reproducibility of methods employed in the laboratory, appropriate standard specimens of the preparation should be used serving as a measure of different quality parameters; all test conditions should be also standardized as far as possible. To enable objective quality evaluation of medical biological preparations, the degree of experiment reproducibility should be regularly verified in interlaboratory tests on an international scale as well as inside those countries which have several manufacturers of a given preparation. It appears expedient to set up an international system of expert evaluation of quality of biological preparations by appointing several regional and national centres which meet the requirements for expert laboratories.     

Intercalibration of ecotoxicity testing protocols with Artemia franciscana

The brine shrimp, Artemia spp., is widely used in ecotoxicology as a target biological model. Although several protocols were available in the early 1980s, only the 24-h acute mortality toxicity test was evaluated in a European intercalibration exercise during that period. Nevertheless, documentation of standard methods serving to provide specifications, guidelines or detailed characteristics of the 24-h protocol is still unavailable. This paper present the results of an intercalibration study of three toxicity-testing protocols using Artemia franciscana: (a) the 24-h static acute mortality test, (b) the 48-h static hatching test and (c) the 14-d static-renewal long-term mortality test. A first tier of experiments was conducted by a reference laboratory, which investigated the repeatability of the three methods. The feasibility and reproducibility of these protocols were then investigated by an intercomparison exercise involving 11 participants for the acute mortality test, seven for the acute hatching test and nine for the long-term mortality test. Protocols were tested on reference toxicants (copper sulphate pentahydrate and sodium dodecyl sulphate). The coefficients of variation were <20% and <50% for intra- and interlaboratory activities, respectively. These results encourage the standardization of the proposed methods and their use as regulatory procedures.     

The role of flow cytometry in medical mycology

The alarming increase in fungal diseases among hospitalized patients is a serious problem as these infections often have poor prognosis because of delayed diagnosis and lack of proper therapy. The rapid laboratory diagnosis of these diseases still remains problematic. The areas of concern include accurate identification of pathogenic fungi, rapid testing of their susceptibility to antifungals, and reliable determination of their interrelatedness to other clinical isolates. In the past few decades, flow cytometry has proven to be an adaptive technology platform for diagnostics. The applications encompass identification, serotyping, genotyping, susceptibility testing, and molecular pathogenesis studies. The recent revolution in the miniaturizing and customizing of instrumentation has now made this technology more accessible and affordable. In the near future, it is imperative to develop standardized protocols by means of interlaboratory comparisons and to share reagents for reproducibility studies. Flow cytometry remains highly attractive as an integrated application for myriad tasks in medical mycology laboratories.     

Comparison of different biochemical and molecular methods for the identification of Vibrio parahaemolyticus

AIMS: Multicentre evaluation of biochemical and molecular methods for the identification of Vibrio parahaemolyticus. METHODS AND RESULTS: For the biochemical identification methods, API 20E and API 20NE and Alsina's scheme were evaluated in intra- and interlaboratory tests in order to determine the accuracy and concordance of each method. Both in intra- and interlaboratory tests, the Alsina's scheme showed the highest sensitivity (86% of correct identifications in the interlaboratory test). False-positive results were obtained by all methods (specificity was 95% for API 20E, 73% for API 20NE and 84% for Alsina's scheme) and concordance varied from 65% of API 20NE to 84% of API 20E. For the molecular identifications, polymerase chain reaction (PCR) for the detection of toxR gene, tl gene and pR72H fragment were tested on 30 strains by two laboratories. The PCR for toxR showed the highest inclusivity (96%), exclusivity (100%) and concordance (97%). CONCLUSIONS: Among the biochemical identification methods tested, the Alsina's scheme gave more reliable results; however, in order to avoid false-positive results, all the biochemical identifications should be confirmed by means of molecular methods. SIGNIFICANCE AND IMPACT OF THE STUDY: Availability of an efficient identification method of Vibrio parahaemolyticus to use in official control of fisheries products.     

Experience in managing a large-scale rescreening of Papanicolaou smears and the pros and cons of measuring proficiency with visual and written examinations

Experiences in a large-scale interlaboratory rescreening of Papanicolaou smears are detailed, and the pros and cons of measuring proficiency in cytology are discussed. Despite the additional work of the rescreening project and some psychological and technical problems, it proved to be a useful measure of the laboratory's performance as a whole. One problem to be avoided in future similar studies is the creation of too many diagnostic categories. Individual testing and certification have been shown to be accurate predictors of proficiency. For cytology, such tests require a strong visual component to test interpretation and judgment skills, such as by the use of glass slides or photomicrographs. The potential of interactive videodisc technology for facilitating cytopathologic teaching and assessment is discussed.     

A comparison of RT-PCR-based assays for the detection of HAV from shellfish

The hepatitis A virus (HAV) is the most common cause of viral infection linked to shellfish consumption. The lack of correlation between the fecal coliform indicators and the presence of enteric viruses in shellfish and their harvesting waters points to the need for molecular methods to detect viruses. We compared two RT-PCR based techniques currently available for the detection of the hepatitis A virus (HAV) in shellfish. Both approaches involve extraction of viral particles by glycine buffer and concentration of virus particles by one or two PEG precipitation steps. One procedure involves as RNA extraction method the use of oligo (dT) cellulose to select poly (A) RNA, and the other uses a system in which total RNA is bound on silica membrane. Comparison of the two RT-PCR based methods highlighted the efficiency of the first approach which is less time-consuming and technically demanding than the second.     

PCR detection of Cryptosporidium parvum in environmental samples—a review of published protocols and current developments

Since 1991 more than 30 PCR protocols have been published, which show a potential to replace the current microscopic detection method for Cryptosporidium parvum in environmental samples and food. This review provides a synoptic comparison of these protocols with respect to the following features: isolation and purification of oocysts from tested matrices, elimination of free DNA, viability and infectivity assessment, release of nucleic acids, nucleic acid extraction, type of PCR (PCR, RT-PCR, internal-standard-PCR, in situ PCR, TaqMan-PCR), primary product detection, additional specificity control, secondary product detection, reported sensitivity, cross-reaction with other Cryptosporidium species, and target and sequence information such as amplicon length, primer sequences, multiple copy target, presence of strain-specific differences in the amplicon, GenBank accession numbers and gene function. The results demonstrate that problems like PCR inhibition, viability assessment, and the requirement of an extreme sensitivity have been solved. PCR assays would be most valuable to control presence-absence standards in defined matrix volumes, and the setup of such standards would very much contribute to a rapid introduction of this awaited technology into routine monitoring of environmental, water and food samples, and to a further standardization of the various protocols. It can be expected that satisfactory solutions for quantification will be found for a growing number of PCR-based assays. Systematic field evaluation and interlaboratory studies will complement our present knowledge of these methods in the near future. Received 5 May 1998/ Accepted in revised form 7 September 1998     

Biosafety of plant viruses for human and animals

Currently, virions and virus-like particles (VLPs) of plant viruses are considered as the basis for the development of new biotechnologies for human and veterinary medicine, including production of modern and safe vaccines, targeted delivery systems, and novel diagnostic preparations, as well as for production of therapeutic proteins in plants. Despite the fact that plant viruses cannot replicate in vertebrates, there are data that they are able to reproduce one or another phase of the infectious cycle in mammalian cells. Moreover, it was shown that plant viruses can be permanently present in a human and animal organism and can use it as a vector. In the review, the results of biocompatibility, toxicity, teratogenicity, and distribution of plant viruses are presented. Based on recent data, it can be affirmed that plant viruses are safe for humans and animals. It was shown that the virions are biodegradable and are easily eliminated from an organism of laboratory animals. Furthermore the virions and VLPs of plant viruses are highly immunogenic and presentation of antigenic determinant of human and animal pathogens on their surface allow to simulate a safe viral particle that is able to replace live attenuated vaccines.