Journal articles: 'Microbiology diagnostics'

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Hawkey, Peter M. "Molecular diagnostics in clinical microbiology." Journal of Infection 40, no. 2 (March 2000): A8—A9. http://dx.doi.org/10.1016/s0163-4453(00)80032-8.

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Patel, Robin, and Brad S. Karon. "Advances Afoot in Microbiology." Journal of Clinical Microbiology 55, no. 7 (May 24, 2017): 1984–88. http://dx.doi.org/10.1128/jcm.00664-17.

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ABSTRACT In 2016, the American Academy of Microbiology convened a colloquium to examine point-of-care (POC) microbiology testing and to evaluate its effects on clinical microbiology. Colloquium participants included representatives from clinical microbiology laboratories, industry, and the government, who together made recommendations regarding the implementation, oversight, and evaluation of POC microbiology testing. The colloquium report is timely and well written (V. Dolen et al., Changing Diagnostic Paradigms for Microbiology , 2017, https://www.asm.org/index.php/colloquium-reports/item/6421-changing-diagnostic-paradigms-for-microbiology?utm_source=Commentary&utm_medium=referral&utm_campaign=diagnostics ). Emerging POC microbiology tests, especially nucleic acid amplification tests, have the potential to advance medical care.

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Obranic, Sonja. "Molecular diagnostics in the clinical microbiology laboratory." Molecular and experimental biology in medicine 2, no. 2 (October 5, 2019): 1–8. http://dx.doi.org/10.33602/mebm.2.2.1.

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Molecular diagnostics is broadly available in clinical microbiology laboratories worldwide, especially for the detection and identification of difficult-to-cultivate microorganisms. The field of clinical microbiology has experienced significant changes over the past decade due to extensive molecular biology research that resulted in novel molecular diagnostics technologies. These new technologies are being introduced in clinical microbiology laboratories with the aim of improving sensitivity, specificity, accuracy and time-to-diagnosis, ensuring valuable data for effective infectious disease clinical management, infection control and surveillance. They have a potential to greatly improve general healthcare, but also present certain challenges, mainly regarding the cost and the proper definition of test ordering and interpretation. This review will discuss the current and potential application of next-generation sequencing, digital PCR and syndromic multiplex molecular assays in clinical microbiology.

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Moser, Claus, Trine Rolighed Thomsen, and Niels Høiby. "Next generation microbiology and cystic fibrosis diagnostics." Current Opinion in Pulmonary Medicine 24, no. 6 (November 2018): 599–605. http://dx.doi.org/10.1097/mcp.0000000000000516.

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Taravati, Parisa, Deborah Lam, and Russell N. Van Gelder. "Role of Molecular Diagnostics in Ocular Microbiology." Current Ophthalmology Reports 1, no. 4 (September 28, 2013): 181–89. http://dx.doi.org/10.1007/s40135-013-0025-1.

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Westblade, Lars F., Alex van Belkum, Adam Grundhoff, George M. Weinstock, Eric G. Pamer, Mark J. Pallen, and W. Michael Dunne. "Role of Clinicogenomics in Infectious Disease Diagnostics and Public Health Microbiology." Journal of Clinical Microbiology 54, no. 7 (February 24, 2016): 1686–93. http://dx.doi.org/10.1128/jcm.02664-15.

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Clinicogenomics is the exploitation of genome sequence data for diagnostic, therapeutic, and public health purposes. Central to this field is the high-throughput DNA sequencing of genomes and metagenomes. The role of clinicogenomics in infectious disease diagnostics and public health microbiology was the topic of discussion during a recent symposium (session 161) presented at the 115th general meeting of the American Society for Microbiology that was held in New Orleans, LA. What follows is a collection of the most salient and promising aspects from each presentation at the symposium.

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Kociolek, Larry K. "Strategies for Optimizing the Diagnostic Predictive Value of Clostridium difficile Molecular Diagnostics." Journal of Clinical Microbiology 55, no. 5 (March 8, 2017): 1244–48. http://dx.doi.org/10.1128/jcm.00147-17.

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ABSTRACT Because nucleic acid amplification tests (NAATs) do not distinguish Clostridium difficile infection (CDI) and asymptomatic C. difficile carriage, the diagnostic predictive value of NAATs is limited when used in patients with a low probability of CDI. In this issue of the Journal of Clinical Microbiology , Truong et al. (J. Clin. Microbiol., 55:1276–1284, 2017, https://doi.org/10.1128/JCM.02319-16 ) report significant reductions in hospital-onset CDI and oral vancomycin utilization at their institution following implementation of a novel intervention that leveraged their clinical bioinformatics resources to prevent C. difficile testing of stools from patients without clinically significant diarrhea and in patients with recent laxative use.

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Paramasivam, Saravanan, and Satish Kumar. "Diagnostic and immunoprophylactic applications of synthetic peptides in veterinary microbiology." Microbiology Research 1, no. 1 (October 26, 2009): 1. http://dx.doi.org/10.4081/mr.2010.e1.

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Chemically synthesized peptides are considered as potential reagents for various applications in biological sciences. They mimic naturally occurring peptides or segments of proteins and have emerged as diagnostic reagents and safe immunogens in animal science. Carefully selected peptides resembling authentic epitopes serve as synthetic antigens in diagnostic tests. Synthetic peptide-based vaccines can elicit antibodies against animal pathogens. The early use of synthetic peptides as a vaccine for foot-and-mouth disease stimulated interest in the development of peptide-based diagnostics and immunoprophylactics. The development of a peptide vaccine for canine parvovirus confirmed the usefulness of peptides as immunoprophylactics. Recently, the advent of the technology for the development of multiple antigenic peptides (MAPs) has provided a well-defined method for the production of highly immunogenic peptides and anti-peptide antibodies. Antibodies raised against major epitopes can be used in the detection of the native antigen (virus) in the enzyme-linked immunosorbent assay (ELISA) and other tests, vindicating the usefulness of peptides for safe, chemically defined, non-infectious diagnostics and immunoprophylactics. This article focuses on the methods for selecting and preparing peptides for the predicted epitopes, their characterization and use, and the application of MAPs.

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Lopez-Siles, Mireia, Sylvia H. Duncan, L. Jesús Garcia-Gil, and Margarita Martinez-Medina. "Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics." ISME Journal 11, no. 4 (January 3, 2017): 841–52. http://dx.doi.org/10.1038/ismej.2016.176.

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Yagci, Aysegul Karahasan. "Future trends of molecular diagnostics in clinical microbiology." Current Opinion in Biotechnology 22 (September 2011): S29. http://dx.doi.org/10.1016/j.copbio.2011.05.057.

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Volkov, A. N., L. V. Nacheva, and Yu V. Zakharova. "Molecular genetic techniques in current biomedical research. Part II: PCR applications in diagnostics of human infectious diseases." Fundamental and Clinical Medicine 6, no. 1 (March 29, 2021): 77–85. http://dx.doi.org/10.23946/2500-0764-2021-6-1-77-85.

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Polymerase chain reaction (PCR)-based diagnostics is currently established as a gold standard for the detection of microorganisms. The features of PCR include rapid amplification of DNA and RNA as well as high sensitivity and specificity. In contrast to diagnostic microbiology, PCR diagnostics does not require preliminary culture of the microorganisms for their identification, reducing both time and costs of the diagnostic procedure. The lecture discusses the molecular basis behind the modern technical solutions for the PCR diagnostics of human infectious diseases including multiplex and reverse transcription PCR. We describe the principles of qualitative and quantitative PCR-based detection of pathogens in biological samples and provide the examples of PCR application for solving specific diagnostic scenarios. The lecture is primarily designed for students of biomedical specialties and healthcare professionals using molecular genetic techniques in their practice.

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Steensels, Deborah, Anne Vankeerberghen, and Hans De Beenhouwer. "Towards Multitarget Testing in Molecular Microbiology." International Journal of Microbiology 2013 (2013): 1–6. http://dx.doi.org/10.1155/2013/121057.

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Advantages of PCR assays over more conventional culture-based diagnostics include significantly higher sensitivities and shorter turnaround times. They are particularly useful when patient treatment has already been initiated or for specimens that may contain microorganisms that are slow-growing, difficult to culture, or for which culture methods do not exist. However, due to genome variability, single target testing might lead to false-negative results. This paper focuses on examples from our own experiences and the literature to provide insight into the limitations of single target testing in molecular biology. Lessons learned from these experiences include the careful design of diagnostic assays, preferably multitargeted, the importance of investigating the incidence and epidemiology of infection in detail, the frequent participation in appropriate quality assurance schemes, and the importance of continuous attentiveness by investigators when confronted with inconsistent results. In conclusion, multitargeted testing in microbiological molecular assays should be a rule.

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VANBELKUM, A. "Molecular diagnostics in medical microbiology: yesterday, today and tomorrow." Current Opinion in Pharmacology 3, no. 5 (October 2003): 497–501. http://dx.doi.org/10.1016/s1471-4892(03)00108-5.

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Brink, Adrian John, Chad M. Centner, and Stefan Opperman. "Microbiology Assessments in Critically Ill Patients." Seminars in Respiratory and Critical Care Medicine 43, no. 01 (February 2022): 075–96. http://dx.doi.org/10.1055/s-0041-1741018.

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AbstractThe prevalence of suspected or proven infections in critically ill patients is high, with a substantial attributable risk to in-hospital mortality. Coordinated guidance and interventions to improve the appropriate microbiological assessment for diagnostic and therapeutic decisions are therefore pivotal. Conventional microbiology follows the paradigm of “best practice” of specimen selection and collection, governed by laboratory processing and standard operating procedures, and informed by the latest developments and trends. In this regard, the preanalytical phase of a microbiological diagnosis is crucial since inadequate sampling may result in the incorrect diagnosis and inappropriate management. In addition, the isolation and detection of contaminants interfere with multiple intensive care unit (ICU) processes, which confound the therapeutic approach to critically ill patients. To facilitate bedside enablement, the microbiology laboratory should provide expedited feedback, reporting, and interpretation of results. Compared with conventional microbiology, novel rapid and panel-based diagnostic strategies have the clear advantages of a rapid turnaround time, the detection of many microorganisms including antimicrobial resistant determinants and thus promise substantial improvements in health care. However, robust data on the clinical evaluation of rapid diagnostic tests in presumed sepsis, sepsis and shock are extremely limited and more rigorous intervention studies, focusing on direct benefits for critically ill patients, are pivotal before widespread adoption of their use through the continuum of ICU stay. Advocating the use of these diagnostics without firmly establishing which patients would benefit most, how to interpret the results, and how to treat according to the results obtained, could in fact be counterproductive with regards to diagnostic “best practice” and antimicrobial stewardship. Thus, for the present, they may supplement but not yet supplant conventional microbiological assessments.

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Cho, Sang-Nae, and Patrick J. Brennan. "Tuberculosis: Diagnostics." Tuberculosis 87 (August 2007): S14—S17. http://dx.doi.org/10.1016/j.tube.2007.05.001.

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Delić, Snežana. "Will the COVID-19 pandemic change anything?: A view from the angle of experts in microbiology." Zdravstvena zastita 49, no. 3 (2020): 89–96. http://dx.doi.org/10.5937/zdravzast49-28454.

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The COVID-19 pandemic has shaken the majority of health systems around the world, pointing out that it is necessary to invest in the modern equipment for molecular diagnostics, as well as to provide an adequate space within microbiological laboratories for this form of diagnostics, according to the standards that are required for such procedures. It is also necessary to increase the number of specialists within the field of medical microbiology, especially in those laboratories where the lack of experts is at an alarming level. Investing in the diagnostic branches of medicine (and microbiology, as well) provides the optimal health protection: fast and correct diagnosis, the application of the adequate antimicrobial therapy as soon as possible, resulting in greater chances for curing. Furthermore, this leads to fewer hospital days and fewer deathly outcomes, while for infirmary patients this means a faster diagnostic procedure and a decrease in the number of specialist examinations, which are sometimes unnecessary. During the Covid-19 pandemic, The Section of Microbiologists of the Serbian Medical Society as well as the Institute for Microbiology and Immunology of the Faculty of Medicine of Belgrade University, have made themselves available to the Ministry of Health of The Republic of Serbia for the identification of potential laboratory capacities and for conducting necessary experts training, for doctors specialists and for laboratory technicians, as well. Although new technologies develop fast and the laboratory work becomes automated, in theory and in practice as well, an educated expert in medical microbiology still presents the main pillar that stands up for a precise, modern, quick and high-quality diagnosis of infective pathogens, especially those with pandemic potential.

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Kaprou, Georgia D., Ieva Bergšpica, Elena A. Alexa, Avelino Alvarez-Ordóñez, and Miguel Prieto. "Rapid Methods for Antimicrobial Resistance Diagnostics." Antibiotics 10, no. 2 (February 20, 2021): 209. http://dx.doi.org/10.3390/antibiotics10020209.

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Antimicrobial resistance (AMR) is one of the most challenging threats in public health; thus, there is a growing demand for methods and technologies that enable rapid antimicrobial susceptibility testing (AST). The conventional methods and technologies addressing AMR diagnostics and AST employed in clinical microbiology are tedious, with high turnaround times (TAT), and are usually expensive. As a result, empirical antimicrobial therapies are prescribed leading to AMR spread, which in turn causes higher mortality rates and increased healthcare costs. This review describes the developments in current cutting-edge methods and technologies, organized by key enabling research domains, towards fighting the looming AMR menace by employing recent advances in AMR diagnostic tools. First, we summarize the conventional methods addressing AMR detection, surveillance, and AST. Thereafter, we examine more recent non-conventional methods and the advancements in each field, including whole genome sequencing (WGS), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) spectrometry, Fourier transform infrared (FTIR) spectroscopy, and microfluidics technology. Following, we provide examples of commercially available diagnostic platforms for AST. Finally, perspectives on the implementation of emerging concepts towards developing paradigm-changing technologies and methodologies for AMR diagnostics are discussed.

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Klyushkin, I. V., K. T. Valeeva, and E. E. Krasnoshchekova. "Modern laboratory equipment." Kazan medical journal 74, no. 3 (June 15, 1993): 239–40. http://dx.doi.org/10.17816/kazmj64732.

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With the creation of new measuring instruments equipped with automation elements and powerful computer systems, the prospect of a qualitatively new level of laboratory diagnostics has arisen. Currently, large diagnostic laboratories are being equipped with equipment from well-known companies in Japan, USA, Germany, Austria, Switzerland. Research opportunities in the field of hematology, clinical biochemistry, immunology, microbiology have expanded significantly.

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Mislovičová, Danica, Peter Gemeiner, Anna Kozarova, and Tibor Kožár. "Lectinomics I. Relevance of exogenous plant lectins in biomedical diagnostics." Biologia 64, no. 1 (January 1, 2009): 1–19. http://dx.doi.org/10.2478/s11756-009-0029-3.

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AbstractThis review focuses on utilization of plant lectins as medical diagnostic reagents and tools. The lectin-related diagnostic is aimed at detection of several diseases connected to alteration of the glycosylation profiles of cells and at identification of microbial and viral agents in clinical microbiology. Certain lectins, proposed for or used as diagnostic tools could even recognize those cellular determinants, which are not detected by available antibodies. Broad information is presented on the lectinomics field, illustrating that lectin diagnostics might become practical alternative to antibody-based diagnostic products. In addition, the rising trend of lectin utilization in biomedical diagnostics might initiate a development of innovative methods based on better analytical technologies. Lectin microarray, a rapid and simple methodology, can be viewed as an example for such initiative. This technology could provide simple and efficient screening tools for analysis of glycosylation patterns in biological samples (cellular extracts, tissues and the whole cells), allowing thus personalized detection of changes associated with carbohydrate-related diseases.

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Shipitsyna, Е. V., О. V. Budilovskaya, and А. М. Savitcheva. "Nucleic acid sequence—based amplification (nasba) and its application in obstetrical and gynecological practice." Journal of obstetrics and women's diseases 54, no. 2 (October 1, 2005): 83–89. http://dx.doi.org/10.17816/jowd82490.

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Method of isothermal amplification of nucleic acids NASBA {Nucleic Acid SequenceBased Amplification) is becoming widely used in diagnostic molecular microbiology including diagnostics of infections in pregnant women and newborn infants. NASBA method possesses the unique ability to amplify RNA target selectively in the presence of DNA target of identical sequence, which determines its main application areas: diagnosis of RNA viruses, investigation of bacterial and viral gene expression, diagnosis of bacterial infections based on 16S rRNA detection. In the article the principle and the main steps of the method as well as some applications in diagnostic microbiology are reviewed. In addition, a comparative evaluation of NASBA and other amplification techniques such as polymerase chain reaction (PCR) and reversetranscriptase PCR (RTPCR) is presented.

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Evans, Jason V. "Automation and Molecular Diagnostics: a New Era in Clinical Microbiology." American Society for Clinical Laboratory Science 32, no. 4 (January 21, 2020): ascls.2019001883. http://dx.doi.org/10.29074/ascls.2019001883.

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Baselski, Vickie S. "The Role of Molecular Diagnostics in the Clinical Microbiology Laboratory." Clinics in Laboratory Medicine 16, no. 1 (March 1996): 49–60. http://dx.doi.org/10.1016/s0272-2712(18)30286-5.

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Booth, Stephanie A., Michael A. Drebot, Graham A. Tipples, and Lai King Ng. "Application of DNA Array Technology for Diagnostic Microbiology." Canadian Journal of Infectious Diseases 11, no. 6 (2000): 291–94. http://dx.doi.org/10.1155/2000/127160.

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Microarrays or DNA chips have been hailed as the ultimate experimental tool for research, drug discovery and diagnostics. They have the potential to perform a multitude of molecular tests simultaneously and to produce a wealth of information from a single clinical sample. Applications include genotyping, expression analysis and sequencing (1-4). The aim of this review is to provide a brief summary of current microarray technology and highlight the many ways in which it is being developed for use in clinical microbiology laboratories.

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Holcomb, Zachary E., Ephraim L. Tsalik, Christopher W. Woods, and Micah T. McClain. "Host-Based Peripheral Blood Gene Expression Analysis for Diagnosis of Infectious Diseases." Journal of Clinical Microbiology 55, no. 2 (October 19, 2016): 360–68. http://dx.doi.org/10.1128/jcm.01057-16.

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ABSTRACTEmerging pandemic infectious threats, inappropriate antibacterial use contributing to multidrug resistance, and increased morbidity and mortality from diagnostic delays all contribute to a need for improved diagnostics in the field of infectious diseases. Historically, diagnosis of infectious diseases has relied on pathogen detection; however, a novel concept to improve diagnostics in infectious diseases relies instead on the detection of changes in patterns of gene expression in circulating white blood cells in response to infection. Alterations in peripheral blood gene expression in the infected state are robust and reproducible, yielding diagnostic and prognostic information to help facilitate patient treatment decisions.

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Branson, Bernard M. "HIV Diagnostics." Infectious Disease Clinics of North America 33, no. 3 (September 2019): 611–28. http://dx.doi.org/10.1016/j.idc.2019.04.001.

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Bernal-Martínez, Leticia, Ana Alastruey-Izquierdo, and Manuel Cuenca-Estrella. "Diagnostics and susceptibility testing inAspergillus." Future Microbiology 11, no. 2 (February 2016): 315–28. http://dx.doi.org/10.2217/fmb.15.140.

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Grigoryev, Aleksey Nikolayevich. "CURRENT STATE OF THE PROBLEM OF THE LABORATORY DIAGNOSTICS OF UROGENITAL TRICHOMONIASIS." Journal of obstetrics and women's diseases 62, no. 1 (March 15, 2013): 32–41. http://dx.doi.org/10.17816/jowd62132-41.

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The laboratory diagnostics of urogenital trichomoniasis is an actual problem of modern microbiology of infections of the reproductive tract. In the review, literature data on methods of microbiological diagnostics of trichomoniasis are presented, which include microscopy of wet mount and stained preparations, culture techniques, immunological methods and nucleic acid amplification tests.

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Webster, John, Monica A. Kehoe, Elisse Nogarotto, Linda Falconer, Nerida Jane Donovan, and Toni A. Chapman. "Using Genomics to Design a Pathovar-Specific Loop-Mediated Isothermal Amplification (LAMP) Assay, for the Improved Detection of Xanthomonas citri pv. citri." Microorganisms 10, no. 6 (June 2, 2022): 1153. http://dx.doi.org/10.3390/microorganisms10061153.

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The ability to swiftly respond to pathogen incursions relies heavily on fast and accurate diagnostics. Current published assays for citrus bacterial canker do not target Xanthomonas citri pv. citri, the causative agent, with high specificity when testing Australian samples. While the current diagnostics are useful in countries where canker is endemic, the detection of canker in Australia requires an emergency response. Close relatives to X. citri pv. citri found in Australia may generate false positives with the current recommended diagnostic assays. Therefore, we developed a more specific detection tool for citrus bacterial canker to provide greater diagnostic confidence for surveillance and eradication efforts. We used genomic comparisons of 161 Xanthomonad genomes and identified and confirmed genomic regions specific for X. citri pv. citri by performing local alignments of unique regions to reference genomes. We then developed loop-mediated isothermal amplification primers and validated them against a panel of 190 isolates to confirm specificity. Our diagnostic assay showed 100% corroboration with the concurrently developed multiplex primers and represents an improved diagnostic method capable of effective citrus bacterial canker identification.

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Mruh, V. M., O. F. Mruh, O. V. Rymsha, O. K. Stukan, and N. V. Shchepina. "Interdisciplinary integration of microbiology and psychiatry in diagnostics of progressive paralysis." Reports of Vinnytsia National Medical University 24, no. 1 (May 18, 2020): 134–37. http://dx.doi.org/10.31393/reports-vnmedical-2020-24(1)-26.

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Annotation. The article argues the importance of interdisciplinary integration of theoretical and clinical disciplines in the preparation of a doctor. The purpose of the work is to ensure the formation of an integrated system of knowledge, skills and practical skills necessary to justify the diagnosis of neurosyphilis of syphilis, methods of laboratory diagnostics and etiological therapy of progressive paralysis, which are laid down when studying a course of Microbiology and are fixed when mastering the educational discipline of Psychiatry and Narcology. Over the past 30 years, an increase in the incidence of syphilis has been observed throughout the world, and the number of cases of neurosyphilis and late forms of the disease has been increasing. This can be attributed to the late visits of patients to the doctor, the widespread uncontrolled unqualified treatment and the frequent association of syphilis and HIV infection. The main clinical signs of progressive paralysis are cognitive impairment, impaired regulation of voluntary activity, emotional and behavioral disorders, pseudo-neurotic symptoms, uncriticality, pathognomonic and nonspecific neurological disorders. For diagnosis, neuropsychological scales are used as screening techniques. As a rule, the diagnosis is confirmed by positive standard serological reactions: the Wassermann complement binding reaction, the pale treponema immobilization reaction, and the immune fluorescence reaction. For the diagnosis of late and latent forms of syphilis, the result of which is the development of progressive paralysis, Wassermann reaction with cerebrospinal fluid is also used. From modern studies, enzyme immunoassay and the molecular genetic method, the Lange reaction are used. Of great importance are laboratory indicators of the presence of inflammatory phenomena and neuroimaging methods. Thus, reliable diagnosis of progressive paralysis using the clinical anamnestic method, neuropsychological scales, laboratory methods of research and assessment of neurological status will help to solve the main task of the doctor — to help the patient by prescribing reasonable etiotropic and pathogenetic therapy.

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Perry, John D. "A Decade of Development of Chromogenic Culture Media for Clinical Microbiology in an Era of Molecular Diagnostics." Clinical Microbiology Reviews 30, no. 2 (January 25, 2017): 449–79. http://dx.doi.org/10.1128/cmr.00097-16.

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SUMMARYIn the last 25 years, chromogenic culture media have found widespread application in diagnostic clinical microbiology. In the last decade, the range of media available to clinical laboratories has expanded greatly, allowing specific detection of additional pathogens, includingPseudomonas aeruginosa, group B streptococci,Clostridium difficile,Campylobacterspp., andYersinia enterocolitica. New media have also been developed to screen for pathogens with acquired antimicrobial resistance, including vancomycin-resistant enterococci, carbapenem-resistantAcinetobacterspp., andEnterobacteriaceaewith extended-spectrum β-lactamases and carbapenemases. This review seeks to explore the utility of chromogenic media in clinical microbiology, with particular attention given to media that have been commercialized in the last decade. The impact of laboratory automation and complementary technologies such as matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is also assessed. Finally, the review also seeks to demarcate the role of chromogenic media in an era of molecular diagnostics.

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Assama Riaz, Dinali Obeysekera, and Kelsie Ruslow. "Total lab automation in microbiology: An overview of BD Kiestra InoqulA and Copan WASP." Open Access Research Journal of Biology and Pharmacy 1, no. 1 (March 30, 2021): 07–015. http://dx.doi.org/10.53022/oarjbp.2021.1.1.0011.

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Total Laboratory Automation (TLA) is the future of laboratory diagnostics due to its efficiency, reproducibility, better turnaround time (TATs), precision, sensitivity, and specificity. Microbiology is generally considered a human dependent field and still, most of the microbiology world is confused with TLA implementation. Two better-claimed technologies BD Kiestra InoqulA and Copan WASP have emerged as a well satisfactory solution of microbiology automation in the last decade. Here we design a practical approach and reviewed all studies of BD Kiestra InoqulA and Copan WASP, assessed microbiology samples in a healthcare setting.

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Nowakowska, Karolina, Emilia Królewicz, Andrzej Gamian, and Wojciech Barg. "Basophil activation test in allergy diagnostics." Postępy Higieny i Medycyny Doświadczalnej 74 (December 11, 2020): 548–55. http://dx.doi.org/10.5604/01.3001.0014.5766.

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The prevalence of allergic diseases in Poland and in the world continues to rise in recent years. The most commonly used methods for diagnosing IgE – dependent allergies are skin prick testing (SPT) and assessment of specific IgE (sIgE) directed against specific allergens. However, both methods have some disadvantages and the obtained results may be inconsistent. In particular, routine diagnostic tests are not always effective for some drugs and foods. Consequently, additional laboratory tools should be used. Basophil activation test (BAT) based on flow cytometry is a promising diagnostic method. The present paper demonstrates the usefulness and effectiveness of BAT protocols in allergy diagnosis in scientific research. In comparison to routinely used diagnostic methods, BAT is an expensive and complicated laboratory tool. However, it offers the possibility to efficiently and effectively recognize allergies. Introducing BAT into routine diagnostics in allergology is problematic because this method has not yet been standardized and validated. Therefore, there is a justified need to continue research in this field. If standardized and validated, BAT may offer a reasonable improvement in allergy diagnostics in the future.

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Verma, R., and S. Sood. "Gonorrhoea diagnostics: An update." Indian Journal of Medical Microbiology 34, no. 2 (April 2016): 139–45. http://dx.doi.org/10.4103/0255-0857.180278.

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Azar, Marwan M., and Chadi A. Hage. "Laboratory Diagnostics for Histoplasmosis." Journal of Clinical Microbiology 55, no. 6 (March 8, 2017): 1612–20. http://dx.doi.org/10.1128/jcm.02430-16.

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ABSTRACTThe diagnosis of histoplasmosis is based on a multifaceted approach that includes clinical, radiographic, and laboratory evidence of disease. The gold standards for laboratory diagnosis include demonstration of yeast on pathological examination of tissue and isolation of the mold in the culture of clinical specimens; however, antigen detection has provided a rapid, noninvasive, and highly sensitive method for diagnosis and is a useful marker of treatment response. Molecular methods with improved sensitivity on clinical specimens are being developed but are not yet ready for widespread clinical use. This review synthesizes currently available laboratory diagnostics for histoplasmosis, with an emphasis on complexities of testing and performance in various clinical contexts.

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Pandori, Mark W., and Bernard M. Branson. "2010 HIV Diagnostics Conference." Expert Review of Anti-infective Therapy 8, no. 6 (June 2010): 631–33. http://dx.doi.org/10.1586/eri.10.48.

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Murray, Patrick R. "Laboratory automation impact on antimicrobial resistance." Microbiology Australia 40, no. 2 (2019): 66. http://dx.doi.org/10.1071/ma19019.

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Antibiotic resistance in common bacterial pathogens, such as Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae, has significantly limited the therapeutic options available for management of infectious diseases. While the indiscriminant use of broad spectrum antibiotics is a significant contributing factor, a more fundamental problem exists. Diagnostic microbiology test results have historically been available too late to be useful. This is, in part, due to the nature of the test methods and in part due to workflow practices in the laboratory. Thus, patients remain on empiric treatments that are frequently ineffective or unnecessarily too broad spectrum1,2. Microscopy and bacterial cultures are mainstays in the microbiology lab, using techniques developed more than 100 years ago. Although microbiologists speak with pride about the ‘art' of their science, the clinical value of the diagnostic tests is frequently lost because of the delays in reporting results with these ‘traditional' approaches. Fortunately, the practice of clinical microbiology is undergoing a dramatic transformation with the introduction of molecular diagnostics, primarily for rapid diagnosis of infections caused by viruses and difficult to grow bacteria, MALDI-TOF mass spectrometry for identification of bacteria, mycobacteria and fungi, and automation of all practices in bacteriology.

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Bigge, Richard, Boyke Bunk, Wolfram Rudolph, Florian Gunzer, Sina Coldewey, Thomas Riedel, and Percy Schröttner. "Comparative Study of Different Diagnostic Routine Methods for the Identification of Acinetobacter radioresistens." Microorganisms 10, no. 9 (August 31, 2022): 1767. http://dx.doi.org/10.3390/microorganisms10091767.

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Recent publications indicate that A. radioresistens can cause infections in humans, even though it is rarely reported in routine diagnostics. However, the fact that it is infrequently detected may be explained by the misidentification of the species by conventional methods. It is also likely that A. radioresistens is not considered clinically relevant and therefore not consistently included in diagnostic results. To elucidate the medical significance of this probably clinically underestimated bacterial species, we created a well-documented reference strain collection of 21 strains collected in routine diagnostics. For further analysis of A. radioresistens, it is essential to know which methods can be used to achieve a trustworthy identification. We, therefore, compared three methods widely used in routine diagnostics (MALDI-TOF MS, VITEK 2, and sequencing of housekeeping genes) in terms of secure and reliable identification of A. radioresistens. As reference methods, whole genome-based approaches were applied. VITEK 2 led to misidentification for four strains. However, MALDI-TOF MS and sequencing of housekeeping genes led to reliable and robust identifications.

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Tretjak, Anna Timofeevna, Lubov Pavlovna Vostokova, and Aleksey Borisovich Chukhlovin. "Role and place of DNA diagnostics in infection clinics." Pediatrician (St. Petersburg) 4, no. 4 (December 15, 2013): 84–92. http://dx.doi.org/10.17816/ped4484-92.

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The review article is addressed to general pediatricians. It considers common approaches, technical principles and applications of DNA polymerase chain reaction (PCR) usage in clinical microbiology. Comparative significance of immunological (antigen-based) and PCR/nucleic acid based diagnostics for detection of various viral, protozoan and bacterial infections is discussed. PCR applications are considered for diagnostics of different infectious diseases, e. g., viral hepatitis, sexually transmitted diseases, some zoonotic infections.

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Peeling, Rosanna W. "Evaluating diagnostics: STIs." Nature Reviews Microbiology 4, S12 (December 2006): S1. http://dx.doi.org/10.1038/nrmicro1561.

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Ridley, Robert G. "Evaluating diagnostics: VL." Nature Reviews Microbiology 5, S11 (November 2007): S1. http://dx.doi.org/10.1038/nrmicro1765.

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Clemens, John D. "Evaluating diagnostics: dengue." Nature Reviews Microbiology 8, S12 (December 2010): S1. http://dx.doi.org/10.1038/nrmicro2461.

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Lyzikov, A. N., A. L. Kalinin, A. A. Kozlovsky, and E. M. Butenkova. "OPTIMIZATION OF TRAINING AT THE FACULTY OF DIAGNOSTIC MEDICINE IN THE CONTEXT OF THE CODE ON EDUCATION OF THE REPUBLIC OF BELARUS." Health and Ecology Issues, no. 4 (December 28, 2011): 132–37. http://dx.doi.org/10.51523/2708-6011.2011-8-4-25.

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Objective: to study the facilities of higher, further and postgraduate training in the specialty «Diagnostic Medicine» at Gomel State Medical University. Material and methods. The professional competencies were analyzed in accordance with the standard on stage I of higher education in the specialty of Diagnostic Medicine OS RB 79 01 04 - 2007 and were compared with those as a result of training at Magistrature, Clinical Residency and retraining of the graduates of the Faculty of Diagnostic medicine (DMF) in accordance with the Common Сlassifier of the Republic of Belarus (ССRB). The educational opportunities and ways to improve the training were evaluated in connection with the introduction of the Code on Education of the Republic of Belarus. Results. The Standard clearly formulates the potential of higher medical training in four specialties of diagnostic specialization: clinical laboratory diagnostics, performance of laboratory research at the departments of laboratory service in centers for hygiene and epidemiology, radiation and functional diagnostics and asserts the list of medical knowledge and skills of a physician in these areas. DMF graduates can continue their training at the departments with a high demand for scientifically-pedagogical workers in the following magistrature specialties: «Human anatomy», «Pathophysiology, Physiology», «Biochemistry», «Microbiology, virology», «Histology, cytology, cell biology», «Public health and health care». The clinical residency makes it possible to receive additional education in all the specialties in accordance with the Standard. The Faculty trains highly qualified scientific personnel, the graduates having specialized in Diagnostic Medicine get training in the field of seven postgraduate specialties available at the University: «Biochemistry», «Physiology», «Pathophysiology», «Anatomy», «Public health and health care», «Clinical Laboratory Diagnostics», «Parasitology». Conclusion. The training at the Faculty as a whole corresponds to the principle of lifelong educational opportunities in accordance with the Code on Education of the Republic of Belarus. There are not such clinical specialties at the Magistrature as Radiation Diagnostics. Certain areas of training should obtain more potential for taking an internship in Diagnostic Medicine: functional diagnostics, ultrasound diagnosis, pathological anatomy. The best graduates will be able to continue their training at postgraduate school in the fundamental medical subjects, as well as in one clinical specialty, i.e. clinical laboratory diagnostics.

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Poelman, Randy, Johan van der Meer, Corina van der Spek, Annelies Riezebos-Brilman, Marjolein Knoester, Coretta Van Leer-Buter, Alexander W. Friedrich, and Hubert G. Niesters. "Improved diagnostic policy for respiratory tract infections essential for patient management in the emergency department." Future Microbiology 15, no. 8 (May 2020): 623–32. http://dx.doi.org/10.2217/fmb-2019-0119.

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Aim: Establishing an optimal diagnostic policy for patients with respiratory tract infections, at the emergency department (ED) of a university hospital in The Netherlands. Methods: Adult patients were sampled at admission, during the respiratory season (2014–2015). The FilmArray-RP was implemented at the clinical virology laboratory. Diagnostics were provided from 8 am to 10 pm, weekends included. Results: 436/492 (89%) results were available while patients were still at the ED. Median TAT from admission to test result was 165 min (IQR: 138–214). No antibiotics were prescribed in 94/207 (45%) patients who tested positive for a virus. 185/330 (56%) hospitalized patients did not need admission with isolation measures. The value-based measure, expressed in euro–hour (€h), increased to tenfold compared with previous policy. Conclusion: An optimal policy is essential for patient management, by providing timely, reliable diagnostics.

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BODROSSY, L., and A. SESSITSCH. "Oligonucleotide microarrays in microbial diagnostics." Current Opinion in Microbiology 7, no. 3 (June 2004): 245–54. http://dx.doi.org/10.1016/j.mib.2004.04.005.

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OLCHAWA, ANNA, BEATA KRAWCZYK, and ANNA BRILLOWSKA-DĄBROWSKA. "New PCR Test for Detection of Candida glabrata Based on the Molecular Target Chosen by the RAPD Technique." Polish Journal of Microbiology 62, no. 1 (2013): 81–84. http://dx.doi.org/10.33073/pjm-2013-011.

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Rapid, reliable diagnosis is a necessary condition for the successful treatment of infections. Such diagnostic assays are continually being developed. The paper presents a method for selecting the molecular target for PCR-based diagnostics based on the comparison of RAPD patterns. A sequence encoding Candida glabrata CBS138 hypothetical protein was selected. The limit of detection for PCR and real-time PCR reactions with DNA extracted from blood samples spiked with Candida glabrata was estimated at 1 CFU/ml. The application of the assays developed in this study would thus seem to be promising as a complementary method in the diagnostics of C. glabrata infections.

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Bajinka, Ousman, Khalid A Abdelhalim, and Guven Ozdemir. "The Inconsistences of Quantitative Real Time Polymerase Chain Reaction in Diagnostics Microbiology." ACTA SCIENTIFIC MICROBIOLOGY 1, no. 2 (February 1, 2018): 27–31. http://dx.doi.org/10.31080/asmi.2018.01.0016.

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Masyukova, S. A., V. V. Mordovtseva, Inna V. Ilina, E. G. Sanakoeva, Z. A. Alieva, D. V. Grebenyuk, and E. I. Gubanova. "Hidradenitis suppurativa: clinic and diagnostics (part 2)." Russian Journal of Skin and Venereal Diseases 19, no. 3 (June 15, 2016): 154–58. http://dx.doi.org/10.18821/1560-9588-2016-19-3-154-158.

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The data on the clinical features and course of suppurative hidradenitis characterized by severe course and a tendency to relapse are presented. To select the treatment strategy the scale of the severity and staging process are proposed. The atypical localization of purulent suppurative hidradenitis and follicular occlusion tetrad, which also includes conglobata acne, folliculitis sycosiformis atrophicans / exfoliating scalp cellulitis and pilonidal abscess are described. It is proved that manifestation of suppurative hidradenitis are phenotypically heterogeneous. The role of genetic, comorbid factors, metabolic and hormonal disorders, as well as the role of the immune system in the development of the disease are discused. For the diagnosis index Sartorius (Sartorius score), microbiology, immunohistochemistry and other research methods, which largely determine the tactics of treatment of severe dermatosis were used.

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Pankhurst, Louise, Louissa Macfarlane-Smith, James Buchanan, Luke Anson, Kerrie Davies, Lily O’Connor, Helen Ashwin, et al. "Can rapid integrated polymerase chain reaction-based diagnostics for gastrointestinal pathogens improve routine hospital infection control practice? A diagnostic study." Health Technology Assessment 18, no. 53 (August 2014): 1–167. http://dx.doi.org/10.3310/hta18530.

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BackgroundEvery year approximately 5000–9000 patients are admitted to a hospital with diarrhoea, which in up to 90% of cases has a non-infectious cause. As a result, single rooms are ‘blocked’ by patients with non-infectious diarrhoea, while patients with infectious diarrhoea are still in open bays because of a lack of free side rooms. A rapid test for differentiating infectious from non-infectious diarrhoea could be very beneficial for patients.ObjectiveTo evaluate MassCode multiplex polymerase chain reaction (PCR) for the simultaneous diagnosis of multiple enteropathogens directly from stool, in terms of sensitivity/specificity to detect four common important enteropathogens:Clostridium difficile,Campylobacterspp.,Salmonellaspp. and norovirus.DesignA retrospective study of fixed numbers of samples positive forC. difficile(n = 200),Campylobacterspp. (n = 200),Salmonellaspp. (n = 100) and norovirus (n = 200) plus samples negative for all these pathogens (n = 300). Samples were sourced from NHS microbiology laboratories in Oxford and Leeds where initial diagnostic testing was performed according to Public Health England methodology. Researchers carrying out MassCode assays were blind to this information. A questionnaire survey, examining current practice for infection control teams and microbiology laboratories managing infectious diarrhoea, was also carried out.SettingMassCode assays were carried out at Oxford University Hospitals NHS Trust. Further multiplex assays, carried out using Luminex, were run on the same set of samples at Leeds Teaching Hospitals NHS Trust. The questionnaire was completed by various NHS trusts.Main outcome measuresSensitivity and specificity to detectC. difficile,Campylobacterspp.,Salmonellaspp., and norovirus.ResultsNucleic acids were extracted from 948 clinical samples using an optimised protocol (200Campylobacterspp., 199C. difficile, 60S. enterica, 199 norovirus and 295 negative samples; some samples contained more than one pathogen). Using the MassCode assay, sensitivities for each organism compared with standard microbiological testing ranged from 43% to 94% and specificities from 95% to 98%, with particularly poor performance forS. enterica. Relatively large numbers of unexpected positives not confirmed with quantitative PCR were also observed, particularly forS. enterica,Giardia lambliaandCryptosporidiumspp. As the results indicated thatS. entericadetection might provide generic challenges to other multiplex assays for gastrointestinal pathogens, the Luminex xTag®gastrointestinal assay was also run blinded on the same extracts (937/948 remaining) and on re-extracted samples (839/948 with sufficient material). ForCampylobacterspp.,C. difficileand norovirus, high sensitivities (> 92%) and specificities (> 96%) were observed. ForS. enterica, on the original MassCode/Oxford extracts, Luminex sensitivity compared with standard microbiological testing was 84% [95% confidence interval (CI) 73% to 93%], but this dropped to 46% on a fresh extract, very similar to MassCode, with a corresponding increase in specificity from 92% to 99%. Overall agreement on the per-sample diagnosis compared with combined microbiology plus PCR for the main four/all pathogens was 85.6%/64.7%, 87.0%/82.9% and 89.8%/86.8% for the MassCode assay, Luminex assay/MassCode extract and Luminex assay/fresh extract, respectively. Luminex assay results from fresh extracts implied that 5% of samples did not represent infectious diarrhoea, even though enteropathogens were genuinely present. Managing infectious diarrhoea was a significant burden for infection control teams (taking 21% of their time) and better diagnostics were identified as having major potential benefits for patients.ConclusionsOverall, the Luminex xTag gastrointestinal panel showed similar or superior sensitivity and specificity to the MassCode assay. However, on fresh extracts, this test had low sensitivity to detect a key enteric pathogen,S. enterica; making it an unrealistic option for most microbiology laboratories. Extraction efficiency appears to be a major obstacle for nucleic acid-based tests for this organism, and possibly the whole Enterobacteriaceae family. To improve workflows in service microbiology laboratories, to reduce workload for infection control practitioners, and to improve outcomes for NHS patients, further research on deoxyribonucleic acid-based multiplex gastrointestinal diagnostics is urgently needed.FundingThe Health Technology Assessment programme of the National Institute for Health Research.

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Messacar, Kevin, Sarah K. Parker, James K. Todd, and Samuel R. Dominguez. "Implementation of Rapid Molecular Infectious Disease Diagnostics: the Role of Diagnostic and Antimicrobial Stewardship." Journal of Clinical Microbiology 55, no. 3 (December 28, 2016): 715–23. http://dx.doi.org/10.1128/jcm.02264-16.

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ABSTRACT New rapid molecular diagnostic technologies for infectious diseases enable expedited accurate microbiological diagnoses. However, diagnostic stewardship and antimicrobial stewardship are necessary to ensure that these technologies conserve, rather than consume, additional health care resources and optimally affect patient care. Diagnostic stewardship is needed to implement appropriate tests for the clinical setting and to direct testing toward appropriate patients. Antimicrobial stewardship is needed to ensure prompt appropriate clinical action to translate faster diagnostic test results in the laboratory into improved outcomes at the bedside. This minireview outlines the roles of diagnostic stewardship and antimicrobial stewardship in the implementation of rapid molecular infectious disease diagnostics.

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Tang, Yi-Wei, Gary W. Procop, and David H. Persing. "Molecular diagnostics of infectious diseases." Clinical Chemistry 43, no. 11 (November 1, 1997): 2021–38. http://dx.doi.org/10.1093/clinchem/43.11.2021.

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Abstract Over the past several years, the development and application of molecular diagnostic techniques has initiated a revolution in the diagnosis and monitoring of infectious diseases. Microbial phenotypic characteristics, such as protein, bacteriophage, and chromatographic profiles, as well as biotyping and susceptibility testing, are used in most routine laboratories for identification and differentiation. Nucleic acid techniques, such as plasmid profiling, various methods for generating restriction fragment length polymorphisms, and the polymerase chain reaction (PCR), are making increasing inroads into clinical laboratories. PCR-based systems to detect the etiologic agents of disease directly from clinical samples, without the need for culture, have been useful in rapid detection of unculturable or fastidious microorganisms. Additionally, sequence analysis of amplified microbial DNA allows for identification and better characterization of the pathogen. Subspecies variation, identified by various techniques, has been shown to be important in the prognosis of certain diseases. Other important advances include the determination of viral load and the direct detection of genes or gene mutations responsible for drug resistance. Increased use of automation and user-friendly software makes these technologies more widely available. In all, the detection of infectious agents at the nucleic acid level represents a true synthesis of clinical chemistry and clinical microbiology techniques.

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Journal articles on the topic 'Microbiology diagnostics'

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