Introducing a molecular test into the clinical microbiology laboratory: development, evaluation, and validation

Evaluation of four different DNA extraction methods in coagulase-negative staphylococci clinical isolates

Currently there are several methods to extract bacterial DNA based on different principles. However, the amount and the quality of the DNA obtained by each one of those methods is highly variable and microorganism dependent, as illustrated by coagulase-negative staphylococci (CoNS) which have a thick cell wall that is difficult to lyse. This study was designed to compare the quality and the amount of CoNS DNA, extracted by four different techniques: two in-house protocols and two commercial kits. DNA amount and quality determination was performed through spectrophotometry. The extracted DNA was also analyzed using agarose gel electrophoresis and by PCR. 267 isolates of CoNS were used in this study. The column method and thermal lyses showed better results with regard to DNA quality (mean ratio of A260/280 = 1.95) and average concentration of DNA (), respectively. All four methods tested provided appropriate DNA for PCR amplification, but with different yields. DNA quality is important since it allows the application of a large number of molecular biology techniques, and also it's storage for a longer period of time. In this sense the extraction method based on an extraction column presented the best results for CoNS.

Molecular diagnosis in clinical parasitology: When and why?

Microscopic detection and morphological identification of parasites from clinical specimens are the gold standards for the laboratory diagnosis of parasitic infections. The limitations of such diagnostic assays include insufficient sensitivity and operator dependence. Immunoassays for parasitic antigens are not available for most parasitic infections and have not significantly improved the sensitivity of laboratory detection. Advances in molecular detection by nucleic acid amplification may improve the detection in asymptomatic infections with low parasitic burden. Rapidly accumulating genomic data on parasites allow the design of polymerase chain reaction (PCR) primers directed towards multi-copy gene targets, such as the ribosomal and mitochondrial genes, which further improve the sensitivity. Parasitic cell or its free circulating parasitic DNA can be shed from parasites into blood and excreta which may allow its detection without the whole parasite being present within the portion of clinical sample used for DNA extraction. Multiplex nucleic acid amplification technology allows the simultaneous detection of many parasitic species within a single clinical specimen. In addition to improved sensitivity, nucleic acid amplification with sequencing can help to differentiate different parasitic species at different stages with similar morphology, detect and speciate parasites from fixed histopathological sections and identify anti-parasitic drug resistance. The use of consensus primer and PCR sequencing may even help to identify novel parasitic species. The key limitation of molecular detection is the technological expertise and expense which are usually lacking in the field setting at highly endemic areas. However, such tests can be useful for screening important parasitic infections in asymptomatic patients, donors or recipients coming from endemic areas in the settings of transfusion service or tertiary institutions with transplantation service. Such tests can also be used for monitoring these recipients or highly immunosuppressed patients, so that early preemptive treatment can be given for reactivated parasitic infections while the parasitic burden is still low.

Utilization management in microbiology

The available literature concerning utilization management in the clinical microbiology laboratory is relatively limited compared with that for high-volume, automated testing in the central Core Laboratory. However, the same strategies employed elsewhere in the clinical laboratory operation can be applied to utilization management challenges in microbiology, including decision support systems, application of evidence-based medicine, screening algorithms and gatekeeper functions. The results of testing in the microbiology laboratory have significant effects on the cost of clinical care, especially costs related to antimicrobial agents and infection control practices. Consequently many of the successful utilization management interventions described in clinical microbiology have targeted not just the volume of tests performed in the laboratory, but also the downstream costs of care. This article will review utilization management strategies in clinical microbiology, including specific examples from our institution and other healthcare organizations.

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The literature on utilization management in the microbiology laboratory is limited.

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Utilization management strategies employed in core laboratory can be applied to microbiology.

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Many utilization interventions in microbiology target the use of antimicrobial agents.

Quality in the molecular microbiology laboratory

In the clinical microbiology laboratory advances in nucleic acid detection, quantification, and sequence analysis have led to considerable improvements in the diagnosis, management, and monitoring of infectious diseases. Molecular diagnostic methods are routinely used to make clinical decisions based on when and how to treat a patient as well as monitor the effectiveness of a therapeutic regime and identify any potential drug resistant strains that may impact on the long term patient treatment program. Therefore, confidence in the reliability of the result provided by the laboratory service to the clinician is essential for patient treatment. Hence, suitable quality assurance and quality control measures are important to ensure that the laboratory methods and service meet the necessary regulatory requirements both at the national and international level. In essence, the modern clinical microbiology laboratory ensures the appropriateness of its services through a quality management system that monitors all aspects of the laboratory service pre- and post-analytical-from patient sample receipt to reporting of results, from checking and upholding staff competency within the laboratory to identifying areas for quality improvements within the service offered. For most European based clinical microbiology laboratories this means following the common International Standard Organization (ISO9001) framework and ISO15189 which sets out the quality management requirements for the medical laboratory (BS EN ISO 15189 (2003) Medical laboratories-particular requirements for quality and competence. British Standards Institute, Bristol, UK). In the United States clinical laboratories performing human diagnostic tests are regulated by the Centers for Medicare and Medicaid Services (CMS) following the requirements within the Clinical Laboratory Improvement Amendments document 1988 (CLIA-88). This chapter focuses on the key quality assurance and quality control requirements within the modern microbiology laboratory providing molecular diagnostics.

Rethinking approaches to improve the utilization of nucleic acid amplification tests for detection and characterization of influenza A in diagnostic and reference laboratories

Influenza A virus (IFVA) is a significant cause of respiratory infections worldwide and was also responsible for a recent pandemic in 2009. Laboratory identification of IFVA can guide antiviral therapy, assist in cohorting of patients and prevent antibiotic use. Characterization of the virus can track the emergence of novel strains, identify resistance and determine how circulating strains match with vaccine components. The gold standard for detection and characterization of IFVA is nucleic acid amplification technology (e.g., reverse transcriptase PCR [RT-PCR]), which must contend with a constantly evolving viral genome. Although molecular technology has been available for over two decades, there is still an operational gap between assay design and utilization of these tests for the diagnosis and characterization of IFVA. This review will discuss issues surrounding the implementation and use of RT-PCR for the identification and characterization of IFVA, and speculate on why RT-PCR has not been used more widely in clinical laboratories or moved closer to the patient. Newer, less widely used technologies that may change our laboratory practices will be identified and the authors will close with an attempt to identify some future applications of RT-PCR-based technologies for the detection and characterization of IFVA.

FilmArray, an automated nested multiplex PCR system for multi-pathogen detection: development and application to respiratory tract infection

The ideal clinical diagnostic system should deliver rapid, sensitive, specific and reproducible results while minimizing the requirements for specialized laboratory facilities and skilled technicians. We describe an integrated diagnostic platform, the "FilmArray", which fully automates the detection and identification of multiple organisms from a single sample in about one hour. An unprocessed biologic/clinical sample is subjected to nucleic acid purification, reverse transcription, a high-order nested multiplex polymerase chain reaction and amplicon melt curve analysis. Biochemical reactions are enclosed in a disposable pouch, minimizing the PCR contamination risk. FilmArray has the potential to detect greater than 100 different nucleic acid targets at one time. These features make the system well-suited for molecular detection of infectious agents. Validation of the FilmArray technology was achieved through development of a panel of assays capable of identifying 21 common viral and bacterial respiratory pathogens. Initial testing of the system using both cultured organisms and clinical nasal aspirates obtained from children demonstrated an analytical and clinical sensitivity and specificity comparable to existing diagnostic platforms. We demonstrate that automated identification of pathogens from their corresponding target amplicon(s) can be accomplished by analysis of the DNA melting curve of the amplicon.

Recommended principles and practices for validating clinical molecular pathology tests

CONTEXT

The use of DNA- and RNA-based tests continues to grow for applications as varied as inherited disease, infectious disease, cancer, identity testing, human leukocyte antigen typing, and pharmacogenetics. Progress is driven in part by the huge growth in knowledge about the molecular basis of disease coupled with advancements in technologic capabilities. In addition to requirements for clinical utility, every molecular test also may have limitations that must be carefully considered before clinical implementation. Analytic and clinical performance characteristics as well as test limitations are established and documented through the process of test validation.

OBJECTIVE

To describe the established principles of test validation, along with relevant regulations in the United States, in order to provide a rational approach to introducing molecular tests into the clinical laboratory.

DATA SOURCES

PubMed review of published literature, published guidelines, and online information from national and international professional organizations.

CONCLUSIONS

These resources and recommendations provide a framework for validating clinical tests.

Development and clinical validation of a molecular diagnostic assay to detect CTX-M-type beta-lactamases in Enterobacteriaceae

Enterobacterial isolates producing CTX-M beta-lactamases have recently emerged worldwide in the community and hospital settings. Because of the significant public health implications, the spread of organisms producing CTX-M enzymes merits close monitoring with enhanced surveillance efforts. A molecular diagnostic assay using two different sets of primers simultaneously for the detection of all bla(CTX-M)-like beta-lactamase genes was developed. This assay repeatedly demonstrated 100% sensitivity, specificity and positive and negative predictive values for detecting different CTX-M enzymes in well-characterised strains that included producers of VEB-, TEM- and SHV-type extended-spectrum beta-lactamases (ESBLs) and plasmid-mediated AmpC enzymes. The majority (132/240; 55%) of ESBL-producing enterobacterial isolates recovered in the Calgary Health Region during 2003 and 2004 were positive for bla(CTX-M) genes, including 81 (61%) positive for the CTX-M-9 group, 49 (37%) for the CTX-M-1 group, and two (2%) for the CTX-M-2 group. The CTX-M-specific PCR assay was reproducible and easy to use. It can be introduced in a clinical or reference laboratory to track and monitor the spread of organisms producing CTX-M enzymes in the community and hospital settings.

Integrating molecular biology into the veterinary curriculum

The modern discipline of molecular biology is gaining increasing relevance in the field of veterinary medicine. This trend must be reflected in the curriculum if veterinarians are to capitalize on opportunities arising from this field and direct its development toward their own goals as a profession. This review outlines current applications of molecular-based technologies that are relevant to the veterinary profession. In addition, the current techniques and technologies employed within the field of molecular biology are discussed. Difficulties associated with teaching a subject such as molecular biology within a veterinary curriculum can be alleviated by effectively integrating molecular topics throughout the curriculum, pitching the subject at an appropriate depth, and employing varied teaching methods throughout.

Laboratory diagnosis of invasive aspergillosis

Invasive aspergillosis occurs in a wide range of clinical scenarios, is protean in its manifestations, and is still associated with an unacceptably high mortality rate. Early diagnosis is critical to a favourable outcome, but is difficult to achieve with current methods. Deep tissue diagnostic specimens are often difficult to obtain from critically ill patients. Newer antifungal agents exhibit differential mould activity, thus increasing the importance of establishing a specific diagnosis of invasive aspergillosis. For these reasons, a range of alternate diagnostic strategies have been investigated. Most investigative efforts have focused on molecular and serological diagnostic techniques. The detection of metabolites produced by Aspergillus spp and a range of aspergillus-specific antibodies represent additional, but relatively underused, diagnostic avenues. The detection of galactomannan has been incorporated into diagnostic criteria for invasive aspergillosis, reflecting an increased understanding of the performance, utility, and limitations of this technique. Measurement of (1,3)-beta-D glucan in blood may be useful as a preliminary screening tool for invasive aspergillosis, despite the fact that this antigen can be detected in a number of other fungi. There have been extensive efforts directed toward the detection of Aspergillus spp DNA, but a lack of technical standardisation and relatively poor understanding of DNA release and kinetics continues to hamper the broad applicability of this technique. This review considers the application, utility, and limitations of the currently available and investigational diagnostic modalities for invasive aspergillosis.

A VP3/VP1 gene polymerase chain reaction assay for detection of chicken anemia virus in broiler samples

A PCR assay was designed for amplification of the highly conserved VP3 gene and a 5' region of the VP1 gene, for the diagnosis of CAV in organ samples of broiler flocks suspected of chicken infectious anemia. A comparison of the VP3/VP1 PCR with in vivo virus isolation revealed 100% agreement of the results, with 13 positive and 3 negative samples in both assays, indicating that the VP3/VP1 PCR is a specific diagnostic method. Tissues from additional 24 broiler chicken flocks, with CAV-like lesions and clinical history were then tested only by the VP3/VP1 PCR and a reference PCR with published primers for the VP1 gene. Nineteen samples resulted positive and one negative in both PCR, while another 4 samples were positive only in the VP3/VP1 PCR. These results indicate that the VP3/VP1 PCR is a sensitive, specific diagnostic test, suitable as an alternative to the expensive and time consuming in vivo virus isolation method, specially considering the difficult diagnosis of CAV strains not readily adaptable to MSB-1 cell culture.