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Central nervous system infections (CNSI) disproportionately affect individuals in low-resource settings where diagnosis is challenging; large proportions of patients never receive a confirmed microbiological diagnosis resulting in inadequate management and high mortality. The epidemiology of CNSI varies globally and conventional diagnostics deployed in resource-limited settings have significant limitations, with an urgent need for improved diagnostic strategies. This review describes molecular platforms and other novel diagnostics used in the diagnosis of CNSI that are applicable to resource-limited settings. An extensive literature search of Medline and PubMed was performed. The emphasis is on investigations targeting infections of relevance to resource-limited settings either due to variation in regional CNSI epidemiology or due to increased prevalence in patients with immunosuppression. This includes commercially available multiplex PCR platforms, mycobacterial PCR platforms, and rapid diagnostics tests. To offer a framework for the optimal implementation in clinical settings, existing evidence highlighting the advantages and limitations of available platforms is reviewed. The implementation of molecular platforms and other novel diagnostics has the potential to transform CNSI diagnosis in resource-limited settings, with several examples of successful rollout of novel diagnostics such as Xpert MTB/RIF Ultra and cryptococcal antigen testing. [ABSTRACT FROM AUTHOR]

Point-of-care molecular diagnostics offer solutions to the limited diagnostic availability and accessibility in resource-limited settings. During the COVID-19 pandemic, molecular diagnostics became essential tools for accurate detection and monitoring of SARS-CoV-2. The unprecedented demand for molecular diagnostics presented challenges and catalyzed innovations which may provide lessons for the future selection of point-of-care molecular diagnostics. We searched PubMed from January 2020 to August 2023 to identify lessons learned from the COVID-19 pandemic which may impact the selection of point-of-care molecular diagnostics for future use in sub-Saharan Africa. We evaluated this in the context of REASSURED criteria (Real-time connectivity; Ease of specimen collection; Affordable; Sensitive; Specific; User-friendly; Rapid and robust; Equipment free; and Deliverable to users at the point of need) for point-of-care diagnostics for resource-limited settings. The diagnostic challenges and successes during the COVID-19 pandemic affirmed the importance of the REASSURED criteria but demonstrated that these are not sufficient to ensure new diagnostics will be appropriate for public health emergencies. Capacity for rapid scale-up of diagnostic testing and transferability of assays, data, and technology are also important, resulting in updated REST-ASSURED criteria. Few diagnostics will meet all criteria, and trade-offs between criteria will need to be context-specific. [ABSTRACT FROM AUTHOR]

Myeloproliferative neoplasms (MPN) are a heterogeneous group of clonal hematopoietic stem cell neoplasms characterized by the driver mutations JAK2, CALR, and MPL. These mutations cause constitutive activation of JAK-STAT signaling, which is central to pathogenesis of MPNs. Next-generation sequencing has further expanded the molecular landscape allowing for improved diagnostics, prognostication, and targeted therapy. This review aims to address current understanding of the molecular diagnosis of MPN not only through improved awareness of the driver mutations but also the disease modifying mutations. In addition, other genetic factors such as clonal hematopoiesis of indeterminate potential (CHIP), order of mutation, and mutation co-occurrence are discussed and how these factors influence disease initiation and ultimately progression. How this molecular information is incorporated into risk stratification models allowing for earlier intervention and targeted therapy in the future will be addressed further. The genomic landscape of the MPN has evolved in the last 15 years with integration of next-generation sequencing becoming the gold standard of MPN management. Although diagnostics and prognostication have become more personalized, additional studies are required to translate these molecular findings into targeted therapy therefore improving patient outcomes. [ABSTRACT FROM AUTHOR]

Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens. We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS). PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings. [ABSTRACT FROM AUTHOR]

Precision medicine based on the driver genes mutation status is the current systemic therapeutic paradigm in patients with lung cancer. Next-generation sequencing (NGS) has emerged as a powerful platform for molecular diagnosis by virtue of high-throughput and massively parallel sequencing. Liquid biopsy also enabled the dynamic monitoring and comprehensive profiling of lung cancer in a noninvasive manner. However, challenges remain in the field of technology and clinical applications, especially in the era of immunotherapy. Here, we update the role of NGS in the context of lung cancer screening, molecular diagnosis, predictive and prognostic biomarkers, and guiding personalized treatment. The NGS application for actable genomic alternation has greatly changed the therapeutic landscape in patients with lung cancer including perioperative setting and advanced stage. Meanwhile, emerging evidence has shown the potential of other applications such as early screening and detection, and MRD. However, challenges remain such as the lack of standardized protocols across different platforms and bioinformatics analysis pipelines, and the complexity of interpreting and leveraging numerous genomic mutation messages for therapy selection. Future research is needed to overcome these challenges and expand the applications of NGS to other aspects such as immunotherapy. [ABSTRACT FROM AUTHOR]

This report provides an overview of the highlights of the 12th European Meeting on Molecular Diagnostics held in Noordwijk aan Zee, The Netherlands, 12–14 October 2022. This 3-day conference covered many relevant topics in the field of molecular diagnostics in humans i.e. oncology, infectious diseases, laboratory medicine, pharmacogenetics, pathology, and preventive medicine. Other relevant topics included quality management, laboratory automation, diagnostic preparedness, and lessons learned from the COVID pandemic. More than 400 participants, the majority coming from European countries, attended the meeting. Besides high-quality scientific presentations, more than 40 diagnostic companies presented their latest innovations, altogether in an informal and inspiring ambiance. [ABSTRACT FROM AUTHOR]

Although, in the past few decades molecular diagnostics of parasitic infections have been accepted as first-line diagnostics, laboratories tend to be reluctant of introducing nucleic acid based tests as they dread the validation of laboratory developed tests (LDTs) compliant with ISO1589. This paper describes how to set tailor-made performance characteristics for the validation of laboratory developed tests (LDTs) for the molecular diagnosis of intestinal parasitic infections complying with the ISO 15189 guidelines. Then, just as important, maintaining these tests by daily monitoring, external quality assessment schemes, and reassessment of the test set-up. Tailoring performance characteristics for the validation of LDTs defining criteria that make sense and actually leading to a process of continuous quality improvement in the day-to-day practice of a diagnostic laboratory. It is essential or even obligatory to modify these characteristics, skip, or to add additional characteristics based on personal or changing insights fitted for a specific setting. [ABSTRACT FROM AUTHOR]

Pneumonia is one of the main causes of mortality associated with infectious diseases worldwide. Several challenges have been identified in the management of patients with pneumonia, ranging from accurate and cost-effective microbiological investigations, prompt and adequate therapeutic management, and optimal treatment duration. In this review, an updated summary on the current management of pneumonia patients is provided and the epidemiological issues of infectious respiratory diseases, which in the current pandemic situation are of particular concern, are addressed. The clinical and microbiological approaches to pneumonia diagnosis are reviewed, including discussion about the new molecular assays pointing out both their strengths and limitations. Finally, the current recommendations about antibiotic treatment are examined and discussed depending on the epidemiological contexts, including those with high prevalence of multidrug-resistant bacteria. We claim that rapid diagnostic tests, if well-positioned in the diagnostic workflow and reserved for the subset of patients who could most benefit from these technologies, may represent an interesting and feasible tool to optimize timing of targeted treatments especially in terms of early de-escalation or discontinuation of antibiotic therapy. [ABSTRACT FROM AUTHOR]

Introduction: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged as a novel viral agent that quickly spread worldwide. SARS-CoV-2 is responsible for the human coronavirus disease 2019 (COVID-19) which has claimed hundreds of thousands of lives and had an immeasurable toll on the economy. Currently, most clinical cases are identified by qualitative molecular testing. However, the need for quantitative assessment is gaining traction. Areas covered: In this review, the current state and future perspective of SARS-CoV-2 viral load quantification is presented. Expert opinion: Viral load quantification is a critical measure that informs clinicians of treatment response, actionable viral load levels, and guidance on patient management. Additionally, for pathogens with epidemiological consequences, viral load can provide information to guide infection control measures and policies. While qualitative detection is sufficient to identify cases and initiate containment and mitigation measures in the vast majority of COVID-19 cases, in certain situations, SARS-CoV-2 quantification is needed to assess viral load trending. However, there are obstacles to quantification, including variability in respiratory specimen collection and the lack of commutable reference material. At the same time, the need for quantification for clinical and epidemiological management is growing, especially concerning individuals with prolonged RNA shedding. [ABSTRACT FROM AUTHOR]

Introduction: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is a major pandemic and continuously emerging due to unclear prognosis and unavailability of reliable detection tools. Older adults are more susceptible to COVID-19 than children showing mature Angiotensin-Converting Enzyme 2 (ACE2), low concentration of immune targets, and comorbid conditions. Several detection platforms have been commercialized to date and more are in pipeline, however, the rate of false-positive results and rapid mutation of SARS-CoV-2 is increasing. Additionally, physiological, and geographical variations of affected individuals are also calling for diagnostic methods optimization. Areas Covered: Extensive information related to the optimization and usefulness of SARS-CoV-2 diagnostic methods based on sensitivity and specificity as definitive and feasible investigative tools is discussed. Moreover, an option of combining laboratory diagnostic methods to improve diagnostic strategies is also proposed and discussed in the comparative section of optimization studies. Expert Opinion: The review article explains the importance of optimization strategies for SARS-CoV-2 detection in children and older adults. There are advancements in COVID-19 detection including CRISPR-based, electrochemical, and optical-based sensing systems. However, the lack of sufficient studies on a comparative evaluation of standardized SARS-CoV-2 diagnostic methods among children and older adults, limit the authentication of commercialized kits. [ABSTRACT FROM AUTHOR]

The group of vascular tumors contains many different entities, and is considered difficult by pathologists, as they often have overlapping histological characteristics. Chromosomal translocations have been identified in ~20% of mesenchymal tumors and are considered the drivers of tumor formation. Many translocations have been discovered over the past decade through next-generation sequencing. This technological advancement has also revealed several recurrent gene fusions in vascular tumors. This review will discuss the various vascular tumors for which recurrent gene fusions have been identified. The gene fusions and the presumed molecular mechanisms underlying tumorigenesis are shown, and potential implications for targeted therapies discussed. The identification of these gene fusions in vascular tumors has improved diagnostic accuracy, especially since several of these fusions can be easily detected using surrogate immunohistochemical markers. The identification of gene fusions in a subset of vascular tumors over the past decade has improved diagnostic accuracy, and has provided the pathologists with novel diagnostic tools to accurately diagnose these often difficult tumors. Moreover, the increased understanding of the underlying molecular mechanisms can guide the development of targeted therapeutic strategies. [ABSTRACT FROM AUTHOR]

Introduction: Point-of-care (POC) tests for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are urgently needed to control the STI epidemic in order to offer patients an immediate diagnoses and accurate treatment before they leave a clinical encounter and thus reduce transmission and sequelae. Nucleic acid amplification tests (NAATs) have increased sensitivity and specificity, but very few POC assays can provide results of such tests within the usual time of the patient visit. Areas covered: This review describes the technology and performance characteristics of the binx health io® [Boston, MA] (binx io) CT/NG assay, a new rapid molecular POC assay. The assay is compared to other available molecular POC tests. We also describe the importance of time to results and assay performance for this POC assay. Expert opinion: The binx io CT/NG assay offers the ability to incorporate the use of POC tests to identify and immediately treat chlamydia and gonococcal infections into the clinical visit, which will provide improved outcomes for patients. Additional implementation studies are needed to optimize the adoption of this new test. [ABSTRACT FROM AUTHOR]

Mycoplasma genitalium (MG) causes frequently asymptomatic STIs. MG prevalence figures are lacking and management is complicated by the lack of etiological diagnostics and high antimicrobial resistance in many countries. Appropriately validated, quality-assured, and FDA-approved MG diagnostic assays have been lacking. The clinical and analytical performance characteristics of the Aptima® MG assay, the first FDA-approved MG nucleic acid amplification test (NAAT), are summarized. Key priorities in the management and control of MG infections are also discussed. Highly sensitive, specific, and quality-assured MG NAATs, e.g. the Aptima MG assay on the automated and flexible Panther® platform, are imperative to improve the management and control of MG infections internationally. This testing, combined with macrolide-resistance testing (not yet available on the Panther platform), offers a rapid, high-throughput, and appropriate diagnosis of MG. Macrolide resistance-guided sequential treatment needs to be implemented for MG infections. Dual antimicrobial therapy, novel antimicrobials and, ideally, a vaccine may become essential. [ABSTRACT FROM AUTHOR]

The merging of molecular diagnostics with personalized medicine has led to a surge in development of molecular-based companion diagnostics. Companion diagnostics, defined as 'a medical device, often an in vitro device, which provides information that is essential for the safe and effective use of a corresponding drug or biological product', are key to the appropriate utilization of several pharmacotherapies; primarily in the area of oncology. While most molecular companion diagnostics are targeted toward oncology, the potential to multiplex assays will contribute to an expansion in the applications of companion diagnostics for an increasing menu of disease states and conditions including areas such as infectious disease, cardiology, and hematology. With this innovation comes the responsibility to ensure molecular companion diagnostic devices are robust and controlled against the detrimental effects of false positive/negative results. Additional important considerations, such as paired development with pharmaceutical companies and adherence to Food and Drug Administration and/or European Union guidelines, must be addressed. While the current number of companion diagnostics is relatively small, as molecular assays continue to be developed as companion diagnostics the world of personalized medicine will advance to meet the needs of an expanding portion of the patient population. [ABSTRACT FROM AUTHOR]

Introduction: Monogenic diabetes is a subset of diabetes characterized by the presence of single-gene mutations and includes neonatal diabetes mellitus and maturity-onset diabetes of the young. Due to the genetic etiology of monogenic diabetes, molecular genetic testing can be used for diagnosis and classification. Areas covered: In addition to first-generation molecular analyses, many large clinical laboratories are transitioning to multiplexed next-generation sequencing panels to simultaneously assess patients for several of the most common genetic mutations seen in monogenic diabetes. With expanded development and adoption of next-generation sequencing panels, particularly in reference to laboratory settings, diagnostic testing for monogenic diabetes has the potential to be more accessible to the patient population. Expert opinion: Although molecular diagnostic testing is becoming increasingly prevalent, it is crucial to identify patients most likely to benefit from molecular testing versus those whose disease can be diagnosed and characterized with more traditional, less costly laboratory analyses. The continuous evolution of clinical molecular testing will be echoed in the clinical laboratory analysis of monogenic diabetes and continue to improve the diagnostic capabilities for monogenic diabetes mellitus. [ABSTRACT FROM AUTHOR]

Introduction: Chlamydia trachomatis and Neisseria gonorrhoeae infection rates continue to rise worldwide. Increasing screening of the largely asymptomatic infections is critical for timely and effective disease control. Laboratory solutions that can handle increasing volumes and generate highly accurate test results are needed in reference labs that provide the majority of chlamydia/gonorrhea testing. Areas covered: This review will describe the Roche cobas CT/NG assay performed on the cobas 6800/8800 system. The instrument features will be described as will the performance of the assay. Expert opinion: The high throughput cobas 6800/8800 can be integrated with clinical chemistry, hematology and immunology systems which will increase reference lab efficiency. The broad menu, ease of expansion with lab developed tests, in combination with features that support lab efficiencies and cost management while assuring high sensitivity and specificity, make this a uniquely effective diagnostic tool. [ABSTRACT FROM AUTHOR]

Introduction: Trichomonas vaginalis and Mycoplasma genitalium are highly prevalent sexually transmitted pathogens that may be asymptomatic or may cause cervicitis and pelvic inflammatory disease in women and urethritis in men. Our limited understanding of the epidemiology of these infections has been hampered by a lack of diagnostic capacity, but the new cobas® TV/MG assay runs on the cobas® 6800/8800 platform offers a solution to this gap in our current diagnostic capacity. Areas covered: This article will describe what we know about the epidemiology and impact of untreated infections with these organisms as well as current recommendations for testing. The features and performance of the cobas 6800/8800 and the TV/MG assay will be described based on the emerging data related to this assay. Expert commentary: Molecular diagnostics for trichomonas and mycoplasma that can be performed on a high-throughput system with the flexibility to order only those tests required are needed in order to reduce the burden of disease and of consequences of undiagnosed infections caused by these pathogens. As a result of the complexities in the needs for testing in different populations, sample-specific flexibility in test ordering is an absolute need in the molecular laboratory. [ABSTRACT FROM AUTHOR]

Background: Molecular diagnostic tests for HBV, HCV and HIV-1 and other pathogens are widely used for clinical management. Practical issues related to workflow and labor requirements need to be characterized to inform selection of the most appropriate system. Research design and methods: We compared the workflow of two high-throughput systems: cobas 6800 (Roche) and Panther (Hologic), using average mid-size laboratory test volumes for five different assays (HIV-1, HBV, HCV, HPV or TV, and CT/NG). Results: Set-up time, time to first results, time to last results, and total hands-on time for cobas 6800 was 0.40, 2.47, 7.12, and 0.98 hours, respectively; on the Panther system, these times were 0.75, 2.7, 9.1, and 1.48 hours. Fifty-seven samples had results available at the first time point on cobas 6800 compared to 5 samples on the Panther system. The Panther system required more manual steps including several with potential risks of contamination or error. The number of reagents items required was 5 for cobas 6800 and 40 for the Panther system. Conclusions: Both systems provided a high level of automation. The cobas 6800 platform had shorter start up, time to first result, time to last result and hands-on times than the Panther system. [ABSTRACT FROM AUTHOR]

Introduction: Gastric cancer (GC) is the fifth most common cancer and confers the second-highest mortality among other cancers. Improving the survival rates of GC patients requires prompt and accurate diagnosis and effective treatment which is often preceded by the poorly understood pathogenic mechanisms. Area covered: This literature review aims to summarize current understanding of genetic and molecular alterations that promote carcinogenesis including (1) activation of oncogenes, (2) overexpression of growth factors, receptors and matrix metalloproteinases, (3) inactivation of tumor suppressor genes, DNA repair genes, and cell adhesion molecules and (4) alterations of cell-cycle regulators that regulate biological characteristics of cancer cells. Moreover, the significance of molecular biomarkers such as micro-RNAs (miRNAs) and long non-coding RNAs (lncRNAs) and advanced molecular techniques including droplet digital polymerase chain reaction (ddPCR), quantitative PCR (qPCR) and next-generation sequencing (NGS) are also discussed. Expert opinion: A GC-specific panel of biomarkers based on the NGS or ddPCR has the potential for diagnosis, prognosis, and monitoring treatment response in GC patients. Despite the requirements for validation in larger population in clinical studies, race-specific differences in the gene panel have also to be examined by performing the clinical trials in subjects with different races. [ABSTRACT FROM AUTHOR]

Introduction: Big Data technologies instilled an informational perspective to our understanding of the world. However, fundamental issues such as the management and storage of data can create privacy concerns. Heterogeneous types of data pose challenges in reproducibility and standardization. It is now an opportunity for us to help the health-care professionals, educators, and policy-makers understand the impact of Big Data, and steer the development roadmap to positively impact the molecular diagnostic industry. Area covered: In this review, we discuss the latest trends in applying Big Data to several key areas of molecular diagnostics: metagenomics, Mendelian disease screening, personalized medicine, and metabolomics. The limitations of utilizing bioinformatics and Big Data analytic tools are also summarized. We further propose an action plan on how to prepare a new generation of health-care professionals to step into the age of Big Data through a tailor-made bioinformatics training program. Expert opinion: In order to cope with the development of these powerful technologies, issues of ethics, regulations, and data format standardization are urgently needed. Besides, a long-term planning to train medical scientists, pathologists, and specialists on bioinformatics is necessary. It is an appropriate time to review all these issues before implementing these tests for patients' diagnosis, prognosis and treatment efficacy. [ABSTRACT FROM AUTHOR]

Introduction: Metabolomics, the study of metabolites, is a promising research field for cancers. The metabolic pathway in a tumor cell is different from a normal tissue cell. There are two approaches to study the metabolism, targeted and untargeted. The general approach is that metabolomic data are interpreted by bioinformatics tools correlating with metabolomic databases to obtain significant findings. With the use of specific analysis tools, such as nuclear magnetic resonance (NMR) and mass spectrometer (MS) combined with chromatography, metabolic profile or metabolic fingerprint of various biological specimens could be obtained. The applications of metabolomics are used to discover potential cancer biomarkers and monitor the metastatic state, therapeutic and drug response for better patient management. Areas covered: In this review, the author introduce metabolomics and discuss the use of metabolomics approaches in different cancers, including the study of colorectal cancer, prostate cancer, liver cancer, pancreatic cancer and breast cancer using NMR and MS. Expert opinion: Knowledge on the molecular basis of cancer metabolism and its potential clinical applications has been improving recently. However, there are still many challenges for the technological development and integration of metabolomics with other omics spaces such as genomics. In the near future, it is expected that metabolomics will play an important role in cancer molecular diagnostics. [ABSTRACT FROM AUTHOR]

Introduction: An update on the uses and applications of the non-cross-linking (NCL) hybridization assay based on the spectral modulation of gold nanoparticles (AuNPs) are presented, emphasizing DNA and RNA detection. Areas covered: Nanotechnology is strongly impacting the way we address diagnostics and therapeutics. In fact, nanoscale devices and particles have been used in a variety of platforms for improved biosensing and, more interestingly, for molecular diagnostics. AuNPs have been used in a great diversity of DNA and RNA detection strategies that are based on their nanoscale properties. Their unique optical properties have put them at the forefront of colorimetric sensing platforms. Among these, those relying on the NCL mechanism using DNA-modified AuNPs have shown remarkable versatility and simplicity for molecular detection of human pathogens, identification of single base alterations at the basis of human disease, gene expression, among others. Application of the NCL assay to molecular diagnostics will be discussed considering the challenges for validation and clinically relevant targets. Expert commentary: Integration of the NCL approach using AuNPs into chip biosensing platforms, projecting miniaturization and portability, will be addressed in terms of the future, i.e. clinical validation and translation to market. [ABSTRACT FROM AUTHOR]

Introduction: Chronic liver disease due to viral hepatitis continues to be a major global health concern. Timely diagnosis and treatment will prevent cirrhosis, risk of hepatocellular carcinoma (HCC), and requirement for liver transplantation. Numerous serum biomarkers are available for viral hepatitis that are helpful in diagnosis, measuring severity, progression of disease, evaluating the best therapeutic options, and monitoring antiviral treatment response. Determining the clinical use of available diagnostic tests can be challenging for the health care provider. Areas covered: This review article attempts to summarize the established and emerging serological markers for diagnosis and managing viral hepatitis. The literature search was performed in February 2018 and included MEDLINE and Embase databases for recent relevant literature on biomarkers for viral hepatitis. Expert Commentary: Despite the discovery of several candidate biomarkers, translating these to clinical practice in viral hepatitis and HCC remains challenging. While limited availability of the new biomarkers in prevalent geographic areas and significant cost remain major obstacles, there have been exciting developments in this field. Understanding the detection limits and sensitivity of these markers and translating them into clinical use is important in management of viral hepatitis and complications of liver disease such as cirrhosis and hepatocellular cancer. [ABSTRACT FROM AUTHOR]

Introduction: Chlamydia trachomatis (chlamydia) is the most commonly diagnosed bacterial sexually transmitted infection (STI) worldwide. The advancement of molecular techniques has made chlamydia diagnostics infinitely easier. However, molecular techniques lack the information on chlamydia viability. Where in routine diagnostics the detection of chlamydia DNA or RNA might suffice, in other patient scenarios, information on the viability of chlamydia might be essential. Areas covered: In this review, the authors discuss the specific strengths and limitations of currently available methods to evaluate chlamydia viability: conventional cell culture, messenger RNA (mRNA) detection and viability-PCR (V-PCR). PubMed and Google Scholar were searched with the following terms: Chlamydia trachomatis, Treatment failure, Anal chlamydia, Microbial viability, Culture, Viability-PCR, Messenger RNA, and Molecular diagnostics Expert commentary: Several techniques are currently available to determine chlamydia viability and thus the clinical relevance of a positive test result in clinical samples. Depending on the underlying research question, all three discussed techniques have their merits when testing for viability. However, mRNA methods show the most promise in determining the presence of a true infection, in case the chlamydia reticulate body can be specifically detected. Further research is needed to understand how to best apply viability testing in current chlamydia diagnostics. [ABSTRACT FROM AUTHOR]

Introduction: A century of advances in infectious disease diagnosis and treatment changed the face of medicine. However, challenges continue to develop including multi-drug resistance, globalization that increases pandemic risks, and high mortality from severe infections. These challenges can be mitigated through improved diagnostics, and over the past decade, there has been a particular focus on the host response. Since this article was originally published in 2015, there have been significant developments in the field of host response diagnostics, warranting this updated review. Areas Covered: This review begins by discussing developments in single biomarkers and pauci-analyte biomarker panels. It then delves into ‘omics, an area where there has been truly exciting progress. Specifically, progress has been made in sepsis diagnosis and prognosis; differentiating viral, bacterial, and fungal pathogen classes; pre-symptomatic diagnosis; and understanding disease-specific diagnostic challenges in tuberculosis, Lyme disease, and Ebola. Expert Commentary: As ‘omics have become faster, more precise, and less expensive, the door has been opened for academic, industry, and government efforts to develop host-based infectious disease classifiers. While there are still obstacles to overcome, the chasm separating these scientific advances from the patient’s bedside is shrinking. [ABSTRACT FROM AUTHOR]

Introduction: Acquired immunodeficiency syndrome(AIDS) is a kind of acquired disease that breaks down the immune system. Human immunodeficiency virus (HIV) is the causative agent of AIDS. By the end of 2016, there were 36.7 million people living with HIV worldwide. Early diagnosis can alert infected individuals to risk behaviors in order to control HIV transmission. Infected individuals are also benefited from proper treatment and management upon early diagnosis. Thanks to the public awareness of the disease, the annual increase of new HIV infections has been slowly declining over the past decades. The advent of molecular diagnostics has allowed early detection and better management of HIV infected patients. Areas covered: In this review, the authors summarized and discussed the current and future technologies in molecular diagnosis as well as the biomarkers developed for HIV infection. Expert Commentary: A simple and rapid detection of viral load is important for patients and doctors to monitor HIV progression and antiretroviral treatment efficiency. In the near future, it is expected that new technologies such as digital PCR and CRISPR-based technology will play more important role in HIV detection and patient management. [ABSTRACT FROM AUTHOR]

Introduction: Antimicrobial resistance is a growing global public health threat. The complexities of antimicrobial resistance in gram-negative bacteria such as Escherichia coli pose significant diagnostic and therapeutic challenges. Molecular diagnostics are emerging in this field.Areas covered: The authors review the clinical importance of pathogenic E. coli and discuss the mechanisms of resistance to common antibiotics used to treat these infections. We review the literature on antimicrobial susceptibility testing and discuss the current state of phenotypic as well as molecular methodologies. Clinical vignettes are presented to highlight how molecular diagnostics may be used for patient care.Expert commentary: The future use of molecular diagnostics for detection of antimicrobial resistance will be tailored to the context, whether hospital epidemiology, infection control, antibiotic stewardship, or clinical care. Further clinical research is needed to understand how to best apply molecular diagnostics to these settings. [ABSTRACT FROM AUTHOR]

Introduction: Acute respiratory tract infections due to influenza A/B and respiratory syncytial virus (RSV) are major causes of morbidity and mortality globally. Rapid tests for detection of these pathogens include antigen detection point of care tests (POC) and newer easy to use molecular tests. From experience, these assays improve both laboratory workflow and assay interpretation issues. However, the question of the benefits of using rapid test technology compared to routine laboratory testing for respiratory viral pathogens is still often asked. Areas covered: Specifically, this review aims to; 1) identify clinical/patient indicators that can be measured prior to and following the implementation of rapid diagnostic test for influenza and RSV, 2) provide multiple perspectives on the extent of impact of a rapid diagnostic test, including direct and indirect outcomes, and 3) identify the technological advancements in the development of rapid testing, demonstrating a timeline that transitions from antigen-based assays to molecular assays. Expert commentary: Key benefits to the use of either antigen-based or molecular rapid tests for patient care, patient flow within institutions, as well as laboratory utilization are identified. Due to improved test characteristics, the authors feel that rapid molecular tests have greater benefits than antigen-based detection methods. [ABSTRACT FROM PUBLISHER]

Introduction: Hearing loss (HL) is the most common birth defect in industrialized countries with far-reaching social, psychological and cognitive implications. It is an extremely heterogeneous disease, complicating molecular testing. The introduction of next-generation sequencing (NGS) has resulted in great progress in diagnostics allowing to study all known HL genes in a single assay. The diagnostic yield is currently still limited, but has the potential to increase substantially. Areas covered: In this review the utility of NGS and the problems for comprehensive molecular testing for HL are evaluated and discussed. Expert commentary: Different publications have proven the appropriateness of NGS for molecular testing of heterogeneous diseases such as HL. However, several problems still exist, such as pseudogenic background of some genes and problematic copy number variant analysis on targeted NGS data. Another main challenge for the future will be the establishment of population specific mutation-spectra to achieve accurate personalized comprehensive molecular testing for HL. [ABSTRACT FROM PUBLISHER]

Introduction: Chlamydia, gonorrhea and trichomonas are the most common curable STI. improved access to testing could reduce infection rates and prevent sequelae. nucleic acid amplification tests are the recommend class of diagnostic assay for these infections which are often asymptomatic. Areas covered: A description of the BD MAX™ System (MAX) and the BD MAX CT/GC/TV assay is provided along with data from a large US clinical trial. The capacity of the system for other tests and for lab developed assays is also described. Expert commentary: The CT/GC/TV assay on the MAX is a triplex PCR assay suitable for use with female urine and vaginal or endocervical swab samples. Male urine can be tested by ordering the CT/GC results but has not yet been evaluated for trichomonas. The assay performance characteristics are similar to those of assays run on high-throughput platforms with sensitivity ≥91.5% and specificity ≥98.6% for all analytes. Screening with the CT/GC/TV assay can be combined with testing for vaginitis which would provide a greater depth of coverage for common co-infections. The throughput is moderate (1–48 samples per 8-hour shift) but the menu includes assays beyond STI pathogens making this a suitable platform for moderate volume laboratories. [ABSTRACT FROM PUBLISHER]

Introduction:Current laboratory testing of Lyme borreliosis mostly relies on serological methods with known limitations. Diagnostic modalities enabling direct detection of pathogen at the onset of the clinical signs could overcome some of the limitations. Molecular methods detecting borrelial DNA seem to be the ideal solution, although there are some aspects that need to be considered. Areas covered:This review represent summary and discussion of the published data obtained from literature searches from PubMed and The National Library of Medicine (USA) together with our own experience on molecular diagnosis of Lyme disease. Expert commentary:Molecular methods are promising and currently serve as supporting diagnostic testing in Lyme borreliosis. Since the field of molecular diagnostics is under rapid development, molecular testing could become an important diagnostic modality. [ABSTRACT FROM PUBLISHER]

This report provides an overview of the highlights of the 12 th European Meeting on Molecular Diagnostics held in Noordwijk aan Zee, The Netherlands, 12-14 October 2022. This 3-day conference covered many relevant topics in the field of molecular diagnostics in humans i.e. oncology, infectious diseases, laboratory medicine, pharmacogenetics, pathology, and preventive medicine. Other relevant topics included quality management, laboratory automation, diagnostic preparedness, and lessons learned from the COVID pandemic. More than 400 participants, the majority coming from European countries, attended the meeting. Besides high-quality scientific presentations, more than 40 diagnostic companies presented their latest innovations, altogether in an informal and inspiring ambiance.

Introduction: HSV-1 and HSV-2 are among the most common causes of sexually transmitted infections (stis) globally. these infections are strongly associated with increased risk of hiv acquisition and rare, but devastating, neonatal disease. available treatment options can reduce HSV transmission and improve quality of life. accurate diagnosis early in disease can improve patient management. Areas covered: This paper describes the clinical manifestations of HSV infection often used for clinical diagnostic purposes. The paper then describes the evolution of laboratory diagnostic assays. Serology, culture and molecular diagnostics are described since all are currently in use. The features and performance characteristics of the cobas 4800 HSV1 and HSV2 Test (cobas HSV) on the cobas 4800® system (cobas 4800) are described in detail. Expert commentary: Diagnosis of HSV has historically been unreliable or technically difficult, but the availability of molecular assays such as the cobas HSV test for detection and typing of herpes can improve our ability to correctly manage this disease. Utilization of tools such as the cobas HSV assay may help shorten the time to accurate diagnosis and treatment thus potentially reducing the risk of transmission and the global burden of HSV. [ABSTRACT FROM PUBLISHER]

Introduction:Identification of allograft injury, including acute clinical and subclinical injury, is vital in increasing the longevity of the transplanted organ. Acute rejection, which occurs as a result of a variety of immune and non-immune factors including the infiltration of immune cells and antibodies to the donor specific epitopes, poses a significant risk to the organ. Recent years have marked an increase in the discovery of new genomic, transcriptomic, and proteomic biomarkers in molecular diagnostics, which offer better potential for personalized management of the transplanted organ by providing earlier detection of rejection episodes. Areascovered:This review was compiled from key word searches of full-text publications relevant to the field. Expertcommentary:Many of the recent advancements in the molecular diagnostics of allograft injury show much promise, but before they can be fully realized further validation in larger sample sets must be conducted. Additionally, for better informed therapeutic decisions, more work must be completed to differentiate between different causes of injury. Moreover, the diagnostics field is looking at methodologies that allow for multiplexing, the ability to identify multiple targets simultaneously, in order to provide more robust biomarkers and better understanding. [ABSTRACT FROM PUBLISHER]

Introduction: Fusion of BCR-ABL1 genes causes chronic myeloid leukemia (CML). As a reliable marker of disease burden, it also serves as the target of tyrosine kinase inhibitors (TKIs). New more sensitive molecular diagnostic tools for BCR-ABL1 can contribute to therapeutic decision-making, especially in considering drug discontinuation for patients enjoying prolonged deep molecular response. Areas covered: Several novel platforms are transforming CML molecular diagnostics to enable faster point-of-care devices, better understanding of clonal diversity and resistance mutations. Here, we review these molecular platforms, knowing implementation in other hematological malignancies will ensue. Expert commentary: Treatment with TKI in CML is the first example of a highly effective targeted therapy. Monitoring of BCR-ABL1 mRNA is standard in assessing disease burden being highly predictive of outcomes recommended by both European LeukemiaNet (ELN) and National Comprehensive Cancer Network (NCCN); however, studies has demonstrated poor adherence to these recommendations. In both clinical practice and assay performance, further optimizing of BCR-ABL1 monitoring can be envisioned including point-of-care methods for increased availability of rapid, standardized testing and increasingly sensitive molecular assays that allow for quantification of MRD and detecting resistance mutations. [ABSTRACT FROM PUBLISHER]