Advances in diagnostic tools for respiratory tract infections : from tuberculosis to COVID-19 - changing paradigms?

Respiratory tract infections (RTIs) are one of the most common reasons for seeking healthcare, but are amongst the most challenging diseases in terms of clinical decision-making. Proper and timely diagnosis is critical in order to optimise management and prevent further emergence of antimicrobial resistance by misuse or overuse of antibiotics. Diagnostic tools for RTIs include those involving syndromic and aetiological diagnosis: from clinical and radiological features to laboratory methods targeting both pathogen detection and host biomarkers, as well as their combinations in terms of clinical algorithms. They also include tools for predicting severity and monitoring treatment response. Unprecedented milestones have been achieved in the context of the COVID-19 pandemic, involving the most recent applications of diagnostic technologies both at genotypic and phenotypic level, which have changed paradigms in infectious respiratory diseases in terms of why, how and where diagnostics are performed. The aim of this review is to discuss advances in diagnostic tools that impact clinical decision-making, surveillance and follow-up of RTIs and tuberculosis. If properly harnessed, recent advances in diagnostic technologies, including omics and digital transformation, emerge as an unprecedented opportunity to tackle ongoing and future epidemics while handling antimicrobial resistance from a One Health perspective. Unprecedented advances have been achieved by improving and applying the latest technologies to key aspects such as epidemiology, contact tracing and diagnostics of respiratory tract infections that need to be properly addressed for global improvement

Deciphering microbiota of acute upper respiratory infections: A comparative analysis of PCR and mNGS methods for lower respiratory trafficking potential

Although it is clinically important for acute respiratory tract (co)infections to have a rapid and accurate diagnosis, it is critical that respiratory medicine understands the advantages of current laboratory methods. In this study, we tested nasopharyngeal samples (n = 29) with a commercially available PCR assay and compared the results with those of a hybridization-capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct \u3c 35 and for mNGS samples it was \u3e40% target coverage, median depth of 1X and RPKM \u3e 10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positively 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterized the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify® Platform (Illumina® Inc, San Diego, CA, USA) for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompromised or immunocompetent with comorbidity respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndrome-based tests, and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration—with promise to reduce morbidity and mortality

Microbiology for Allied Health Students

This open textbook is a remix of Openstax Microbiology, CC-BY 4.0, and created through an Affordable Learning Georgia Round Six Textbook Transformation Grant. The textbook has the following supplemental materials within this repository: This is a collection of instructional materials for the following open textbook and lab manual: Microbiology for Allied Health Students Lab Manual Microbiology for Allied Health Students Instructional Materials Authors\u27 Description: Microbiology for Allied Health Students is designed to cover the scope and sequence requirements for the single semester Microbiology course for non-majors and allied health students. The book presents the core concepts of microbiology with a focus on applications for careers in allied health. The pedagogical features of Microbiology for Allied Health Students make the material interesting and accessible to students while maintaining the career-application focus and scientific rigor inherent in the subject matter. The scope and sequence of Microbiology for Allied Health Students has been developed and vetted with input from numerous instructors at institutions across the U.S. It is designed to meet the needs of most microbiology courses allied health students. With these objectives in mind, the content of this textbook has been arranged in a logical progression from fundamental to more advanced concepts. The opening chapters present an overview of the discipline, with individual chapters focusing on cellular biology as well as each of the different types of microorganisms and the various means by which we can control and combat microbial growth. The focus turns to microbial pathogenicity, emphasizing how interactions between microbes and the human immune system contribute to human health and disease. The last several chapters of the text provide a survey of medical microbiology, presenting the characteristics of microbial diseases organized by body system. Accessible files with optical character recognition (OCR) and auto-tagging provided by the Center for Inclusive Design and Innovation.https://oer.galileo.usg.edu/biology-textbooks/1015/thumbnail.jp

Innovative and rapid antimicrobial susceptibility testing systems

Antimicrobial resistance (AMR) is a major threat to human health worldwide, and the rapid detection and quantification of resistance, combined with antimicrobial stewardship, are key interventions to combat the spread and emergence of AMR. Antimicrobial susceptibility testing (AST) systems are the collective set of diagnostic processes that facilitate the phenotypic and genotypic assessment of AMR and antibiotic susceptibility. Over the past 30 years, only a few high-throughput AST methods have been developed and widely implemented. By contrast, several studies have established proof of principle for various innovative AST methods, including both molecular-based and genome-based methods, which await clinical trials and regulatory review. In this Review, we discuss the current state of AST systems in the broadest technical, translational and implementation-related scope

The appropriateness of clinical microbiology laboratory investigations : a retrospective study of the cost and clinical relevance of specimen management and processing

Each year, NHS clinical laboratories carry out more than 700 million laboratory tests, of which 50 million are microbiology investigations. Several studies have shown that between 25% and 40% of all tests sent to the laboratory are unnecessary, and up to 46% of ordered microbiology tests are inappropriate. In light of these accounts, the present study was undertaken to evaluate the process of microbiology specimen management in order to assess microbiology test utilisation and the appropriateness of the test ordering processes. The study focussed on respiratory tract specimens using sputum microbiology as a model for the microbiology service inappropriate test utilisation. The overall main aim of this study was to determine the appropriateness of clinical microbiology test utilisation, its clinical relevance and cost-effectiveness, hence recommend better utilisation strategies. A total of 15,941 respiratory tract samples from Barts and The London NHS Trust were randomly selected from the years 2004/05 and analysed retrospectively. Seven hundred microbiology laboratory request forms from patients for whom respiratory tract cultures were requested over a three month period were examined in detail. These requests were derived from 511 sputum specimens, 100 throat swabs, 63 ear swabs and 76 samples from other respiratory tract sites. 641 (91%) of microbiology test requisition forms were completed, provided all requested details by the service users and were therefore considered as appropriate microbiology test requisitions. 660 (94%) of those examined stated the patient’s clinical diagnosis and only in 65 (13%) of these patients was the stated diagnosis as respiratory tract infection. Sixty percent of sputum specimens examined were considered as poor quality. Forty percent of respiratory specimens were reported as culture positive, based on the local hospital criteria of microbiology test reporting. In sputum culture, 39% was reported as culture positive; however, less than 18% were positive with recognised respiratory pathogens, whilst 27% of throat swabs were reported as culture positive, of which 67% had throat pathogens. From the beginning of this study and before, there were no microbiology test comments and interpretation of test results provided with the test result reporting. The test turnaround time of respiratory microbiology results reported within three days in 2004/2005 was only 20%. The total inappropriate respiratory specimens processed locally were 9,575. Extrapolating from our results, this suggests that 2,153,977 nationally were inappropriate in NHS hospitals in 2004/2005. The total cost of inappropriate respiratory microbiology test use was approximately £152,000 in local NHS hospitals. Extrapolating from our results, this suggests that £23,900, 000 nationally was the total cost of inappropriate tests in the NHS hospitals. Following implementation of this study, follow up studies in 2006 and onwards indicated that there has been an improvement in the quality of the microbiology service. The number of good quality sputum specimens was 69% compared to 40% in 2004/2005. While the total microbiology test turnaround time that was reported within three days in 2009/2010 was more than 94%. From mid 2006 onwards, test interpretation comments have been used in all microbiology test result reporting. The total workload of respiratory tract microbiology activity decreased from 18,915/year to 16,651/year over the years 2004/2005 to 2007/2008, which is down nearly 8%. Analysis of the findings showed that the usefulness of culture results was limited by the collection of inappropriate specimens, and lack of clinical information on the microbiology request form. The crucial importance of the role of clinical and nursing staff is stressed if the clinical relevance of sputum culture is to be maximised. The increasing introduction of electronic pathology test requests gives new opportunities to restrict the collection of inappropriate specimens and make substantial savings in resources, both in the ward and the laboratory. This type of study and audit can give invaluable information about the rationale behind testing, and the appropriateness of sampling and transport time. Appropriate measures for corrective actions can be identified.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Ten Issues for Updating in Community-Acquired Pneumonia: An Expert Review

Community-acquired pneumonia represents the third-highest cause of mortality in industrialized countries and the first due to infection. Although guidelines for the approach to this infection model are widely implemented in international health schemes, information continually emerges that generates controversy or requires updating its management. This paper reviews the most important issues in the approach to this process, such as an aetiologic update using new molecular platforms or imaging techniques, including the diagnostic stewardship in different clinical settings. It also reviews both the Intensive Care Unit admission criteria and those of clinical stability to discharge. An update in antibiotic, in oxygen, or steroidal therapy is presented. It also analyzes the management out-of-hospital in CAP requiring hospitalization, the main factors for readmission, and an approach to therapeutic failure or rescue. Finally, the main strategies for prevention and vaccination in both immunocompetent and immunocompromised hosts are reviewed