Clinical metagenomics.

Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health.

Covid-19 Pandemic: Through the Lens of Science, a Painstaking Review.

BACKGROUND: Coronavirus disease 2019 (COVID-19) has imperiled human lives and global infrastructure since the emergence of SARS-CoV-2 in China. The current review meticulously summarizes the COVID-19 pandemic situation through the lens of science from the inception of the outbreak to the current progression, which is valuable to mitigate the current pandemic situation. METHODS: We reviewed all the relevant literature available on PubMed, Web of Sciences, Google Scholar, and World Health Organization (WHO) website related to COVID-19 from the inception of the outbreak to 18 June 2020. We selected ninety different scientific studies and reports to compile the current review. RESULTS: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a betacoronavirus with four major structural proteins encoded by S, M, E, and N genes and distinct in morphology. The potential provenance of SARS-Cov-2 is zoonotic, and it binds to the host cell receptors by spike protein. The SARS-CoV-2 infectious cycle carries on through direct contact, air, inanimate objects, and contaminated surfaces. The reproductive number (R0) of SARS-CoV-2 is 2 to 3.5, representing that one infected patient can spread this virus to two to three people. An expeditious laboratory diagnosis has a pivotal role in patient management and prevention. Due to the lack of definitive treatment, symptomatic medication regimen and supportive organ therapies are adapted for debilitated patients. CONCLUSIONS: Nucleoside analogs and protease-inhibitors have approved to attenuate the viral infection until the discovery of a specific drug. The other treatment strategies comprise antimalarial drugs, monoclonal antibodies, and glucocorticoids. The use of alcoholic scrubs, sodium hypochlorite, masks, social distancing, and quarantine the affected individual is inevitable to eradicate the infection vector and to break the transmission path.

Laboratory practical to study the differential innervation pathways of urinary tract smooth muscle.

In the mammalian lower urinary tract, there is a reciprocal relationship between the contractile state of the bladder and urethra. As the bladder fills with urine, it remains relaxed to accommodate increases in volume, while the urethra remains contracted to prevent leakage of urine from the bladder to the exterior. Disruptions to the normal contractile state of the bladder and urethra can lead to abnormal micturition patterns and urinary incontinence. While both the bladder and urethra are smooth-muscle organs, they are differentially contracted by input from cholinergic and sympathetic nerves, respectively. The laboratory practical described here provides an experiential approach to understanding the anatomy of the lower urinary tract. Several key factors in urinary tract physiology are outlined, e.g., the bladder is contracted by activation of the parasympathetic pathway via cholinergic stimulation on muscarinic receptors, whereas the urethra is contracted by activation of the sympathetic pathway via adrenergic stimulation on α1-adrenoceptors. This is achieved by measuring the force generated by bladder and urethra smooth muscle to demonstrate that acetylcholine contracts the smooth muscle of the bladder, whereas adrenergic agonists contract the urethral smooth muscle. An inhibition of these effects is also demonstrated by application of the muscarinic receptor antagonist atropine and the α1-adrenergic receptor blocker phentolamine. A list of suggested techniques and exam questions to evaluate student understanding on this topic is also provided.

Sourcebook update: intestinal smooth muscle contractility and autonomic control.

This laboratory practical requires first-year students to anticipate the effects of drugs active at cholinergic and adrenergic receptors on gut motility in order to design experiments during an authentic inquiry exercise. Rather than specifying a strict sequence of drug additions that aim to provide ideal demonstrations of pharmacological and physiological antagonism, I have instead designed switches into the drugs provided and set students, working in small teams, the task of identifying the switched drugs, an inquiry activity. To extend the teamwork aspect, laboratory reports were submitted by the student teams rather than individual students. Staff observed that discussions within the teams were stimulated by the inquiry-led nature of the practical. The quality of the laboratory reports submitted by teams were substantially improved over the individual reports submitted in previous years. (Students previously worked in teams, but simply followed a list of prescribed experiments and wrote individual reports.) Although, in conversation, teams of students had an improved understanding of the regulation of gut motility by the parasympathetic and sympathetic divisions of the autonomic nervous system and could readily distinguish between pharmacological and functional antagonism, no attempt was made to evaluate learning because the revision was triggered by the observed effect of a technical error and was not otherwise planned. It is likely that laboratory practicals, in general, would benefit from inclusion of inquiry.

Quo Vadis Point-of-Care Diagnostics? Report II of the SWISS SYMPOSIUM in Point-of-Care Diagnostics 2017.

U.S. studies show that the global point-of-care (POC) diagnostics market will reach $40.5 bn by 2022, with a compound annual growth rate (CAGR) of 10%. This is one of the reasons why HES-SO Valais-Wallis and CSEM, acting on behalf of the NTN Swiss Biotech thematic platform in vitro Diagnostics (TP IVD), invited interested parties on October 26, 2017 to the SWISS SYMPOSIUM in Point-of-Care Diagnostics (see CHIMIA No. 12/2017). We now bring the second report on the future prospects of POC diagnostics.

Discrepancies in central review re-testing of patients with ER-positive and HER2-negative breast cancer in the OPTIMA prelim randomised clinical trial.

BACKGROUND: There is limited data on results of central re-testing of samples from patients with invasive breast cancer categorised in their local hospital laboratories as oestrogen receptor (ER) positive and human epidermal growth factor receptor homologue 2 (HER2) negative. METHODS: The Optimal Personalised Treatment of early breast cancer usIng Multiparameter Analysis preliminary study (OPTIMA prelim) was the feasibility phase of a randomised controlled trial to validate the use of multiparameter assay-directed chemotherapy decisions in the UK National Health Service (NHS). Eligibility criteria included ER positivity and HER2 negativity. Central re-testing of receptor status was mandatory. RESULTS: Of the 431 patients tested centrally, discrepant results between central and local laboratory results were identified in only 19 (4.4%; 95% confidence interval 2.5-6.3%) patients (with 21 tumours). On central review, seven patients had cancers that were ER-negative (1.6%) and 13 (3.0%) patients with 15 tumours had HER2-positive disease, including one tumour discrepant for both biomarkers. CONCLUSIONS: Central re-testing of receptor status of invasive breast cancers in the UK NHS setting shows a high level of reproducibility in categorising tumours as ER-positive and HER2-negative, and raises questions regarding the cost effectiveness and clinical value of central re-testing in this sub-group of breast cancers in this setting.

Implementing Non-Invasive Prenatal Diagnosis (NIPD) in a National Health Service Laboratory; From Dominant to Recessive Disorders.

Our UK National Health Service regional genetics laboratory offers NIPD for autosomal dominant and de novo conditions (achondroplasia, thanataphoric dysplasia, Apert syndrome), paternal mutation exclusion for cystic fibrosis and a range of bespoke tests. NIPD avoids the risks associated with invasive testing, making prenatal diagnosis more accessible to families at high genetic risk. However, the challenge remains in offering definitive diagnosis for autosomal recessive diseases, which is complicated by the predominance of the maternal mutant allele in the cell-free DNA sample and thus requires a variety of different approaches. Validation and diagnostic implementation for NIPD of congenital adrenal hyperplasia (CAH) is further complicated by presence of a pseudogene that requires a different approach. We have used an assay targeting approximately 6700 heterozygous SNPs around the CAH gene (CYP21A2) to construct the high-risk parental haplotypes and tested this approach in five cases, showing that inheritance of the parental alleles can be correctly identified using NIPD. We are evaluating various measures of the fetal fraction to help determine inheritance of parental mutations. We are currently exploring the utility of an NIPD multi-disorder panel for autosomal recessive disease, to make testing more widely applicable to families with a variety of serious genetic conditions.

[Liquid Biopsy: Challenges and Possibilities Regarding Its Clinical Application.]

Cell-free DNA is "Fragmented DNA found in circulation in the Cell-free component of whole blood". Cell-free DNA derived from tumors is expressed as circulating tumor DNA. Examination of circulating tu- mor DNA for genetic alterations present in the tumor tissue is defined as liquid biopsy. Currently in the cancer field, Cell-free DNA or CTC (Circulating tumor cells) is the main target of "Liquid Biopsy". Acquir- ing Cell-free DNA or CTC presents little challenge because of the recent technological developments. However, we need to improve the efficiency of CTC retrieval, and we also need to establish how to culture the retrieved CTCs. For clinical applications, PGx (Pharmacogenomics) and PGt (Pharmacogenetics) fol- lowing NGS (Next Generation Sequencing) are attractive areas for new and future applications. The intro- duction of "Liquid Biopsy" to the area of clinical trials is already in progress. As an expert group, members of the JSLM (Japanese Society of Laboratory Medicine) need to indicate the presence of quality control or quality management in the area of "Liquid Biopsy". Besides these quality issues, we, as clinical pathologists, need to think about harmonizing our expertise with surgical pathologists, who have historically handled clas- sical biopsies of solid samples. The field of "Liquid Biopsy" has marked potential; however, we need to overcome various obstacles to realize this.

[Quality Management of Pre-Testing Step of POCT].

To maintain a trusting relationship between clinical and hospital laboratory staff, highly reliable reporting based on precise quality control of the test results is required. Testing work is divided into 3 steps: pre-testing, testing, and post-testing. Quality control (QC) of laboratory testing has been performed to improve the precision and accuracy of measurements after sample collection, mainly in the testing step. However, various factors influencing the measurement results are present in the process from requests for testing to the reporting of the test results, and it is necessary to make efforts to minimize these factors. The characteristics of POCT devices and reagents are their simple operation method, compact size, and use at sites other than laboratories, and most users are physicians and nurses. Sample measurement rooms have opened at sites other than medical institutions, and testing using POCT-compatible devices and reagents has been rapidly spreading. It is very important to clarify factors leading to false high and low values in the pre-testing step. The results of investigating reasons for predicted events were presented, and the necessity of quality management in the pre-testing step was clarified. If the pre-testing step is not properly performed, accuracy cannot be assured even though quality management of the testing and post-testing steps is optimal.

[Management of POCT Devices and Reagents].

In order to ensure the accuracy of POCT devices and reagents, it is necessary to appropriately manage and store them. There are various points to be considered for these items, such as management before and environments when using them; it is more complex than when using conventional analysis apparatuses in clinical laboratories. In addition, staff using such devices should be provided with opportunities to obtain sufficient knowledge and skills. These approaches are indispensable to ensure POCT accuracy and provide reliable data, and, in this respect, support for staff with expertise in clinical examination is crucial.

[Internal Quality Control and External Quality Assessment on POCT].

The quality management (QM) of POCT summarizes its internal quality control (IQC) and external quality assessment (EQA). For QM requirements in POCT, ISO 22870-Point-of-care testing (POCT) -Requirements for quality and competence and ISO 15189-Medical laboratories-Requirements for quality and competence, it is performed under the guidance of the QM committee. The role of the POC coordinator and/or medical technologist of the clinical laboratory is important. On measurement performance of POCT devices, it is necessary to confirm data on measurement performance from the manufacturer other than those in the inserted document. In the IQC program, the checking and control of measurement performance are the targets. On measurements of QC samples by the manufacturer, it is essential to check the function of devices. In addition, regarding the EQA program, in 2 neighboring facilities, there is an effect to confirm the current status of measurement and commutability assessment in these laboratories using whole blood along with residual blood samples from daily examinations in the clinical laboratory.

Impact of surface chemistry.

The applications of molecular surface chemistry in heterogeneous catalyst technology, semiconductor-based technology, medical technology, anticorrosion and lubricant technology, and nanotechnology are highlighted in this perspective. The evolution of surface chemistry at the molecular level is reviewed, and the key roles of surface instrumentation developments for in situ studies of the gas-solid, liquid-solid, and solid-solid interfaces under reaction conditions are emphasized.

Clinical utility of the erythrocyte sedimentation rate: a case study.

Erythrocyte Sedimentation Rate (ESR) is a laboratory test of historical significance and broad applicability. Its current role in medical diagnostics, however, is often debated due to a lack of specificity in the results and the emergence of more up-to-date alternatives. This case study, however, illustrates a clinical scenario where the ESR was utilized on more than one occasion to significantly aid the diagnostic process and ultimately, improve patient care.

[From laboratory to practice: counseling with clinicians].

The provision of medical laboratory services is a key element in diagnostic and treatment. The care of analytical quality remains in focus of attention. The interest to pre-analytical quality increased. However, alongside with it quality of post-analytical stage and such its significant element as support of timely and effective application of laboratory results in interest of patient has great importance. The purpose of study was to consider approaches to development of this aspect of medical laboratory practice and to demonstrate the modes which proved their effectiveness.

[The laboratory medicine as a foundation for personalized medicine. The application of biochips in medicine].

The development and application of biochips provide possibility to drastically transform laboratory medicine and to implement studies of arrays of biomarkers realizing approaches and concepts of personalized medicine. The main areas of application of microbiochips in laboratory medicine such as laboratory diagnostic, classification and prognosis of course of diseases, analysis of mechanisms of biologic processes are considered. The identification of inherent mutations in human genome is considered as perspective direction. These mutations cause various pathology and first of all oncologic diseases responsible for biotransformation of pharmaceuticals applied in chemotherapy of tumors in particular and also simultaneous identification of various infection agents (viruses, microorganisms, fungi, etc.) and their antibiotic-resistant forms. The role of biochips as a tool is demonstrated in genetic studies, technologies of genetic typing, large-scale international projects of studies of genome-wide screening of associations (GWAS).

Minor improvement of venous blood specimen collection practices in primary health care after a large-scale educational intervention.

BACKGROUND: Venous blood specimen collection is a common health care practice that has to follow strict guidelines, non-compliance among sampling staff may compromise patient safety. We evaluated a large-scale 2 h educational intervention that emphasised guideline adherence to assess possible improvements of venous blood specimen collection practices. METHODS: Blood specimen haemolysis is usually caused by inadequate venous blood specimen collection and handling, reflecting overall pre-analytical handling. We monitored haemolysis of serum samples with haemolysis index corresponding to ≥ 150 mg/L of free haemoglobin for specimens sent from 11 primary health care centres and analysed on a Vitros 5,1 clinical chemistry analyser before (2008, n = 6652 samples) and after (2010, n = 6121 samples) the intervention. RESULTS: The total percentage of haemolysed specimens was 11.8 % compared to 10.5 % (p = 0.022) before the intervention. As groups, rural primary health care centres demonstrated a significant reduction [Odds ratios (OR) = 0.744] of haemolysed specimens after intervention, whereas urban primary health care centres demonstrated a significant increase (OR = 1.451) of haemolysis. CONCLUSIONS: A large-scale 2 h educational intervention to make venous blood specimen collection staff comply with guideline practices had minor effects on collection practices. Educational interventions may be effective in wards/care centres demonstrating venous blood specimen collection practices with larger deviations from guidelines.

Laboratory diagnosis of tuberculosis in resource-poor countries: challenges and opportunities.

With an estimated 9.4 million new cases globally, tuberculosis (TB) continues to be a major public health concern. Eighty percent of all cases worldwide occur in 22 high-burden, mainly resource-poor settings. This devastating impact of tuberculosis on vulnerable populations is also driven by its deadly synergy with HIV. Therefore, building capacity and enhancing universal access to rapid and accurate laboratory diagnostics are necessary to control TB and HIV-TB coinfections in resource-limited countries. The present review describes several new and established methods as well as the issues and challenges associated with implementing quality tuberculosis laboratory services in such countries. Recently, the WHO has endorsed some of these novel methods, and they have been made available at discounted prices for procurement by the public health sector of high-burden countries. In addition, international and national laboratory partners and donors are currently evaluating other new diagnostics that will allow further and more rapid testing in point-of-care settings. While some techniques are simple, others have complex requirements, and therefore, it is important to carefully determine how to link these new tests and incorporate them within a country's national diagnostic algorithm. Finally, the successful implementation of these methods is dependent on key partnerships in the international laboratory community and ensuring that adequate quality assurance programs are inherent in each country's laboratory network.

[The metrological support of medical laboratory activity].

The article discusses the methodological approaches in implementing of regulations of the Federal law FZ-102 "On the support of unity of measurements in the area of laboratory medicine "from the positions of GOSTK ISO 9001-2008 "The systems of quality management. Requirements" and GOST K ISO 15189-2009 "medical laboratories. The particular requirements to quality and competence". The application of GOSTK ISO 18113.1-5 "The medicine items for diagnostic in vitro. Information provided by manufacturer (marking)" neatly assigns the responsibility for support of metrological correctness of laboratory measurements.

Laboratory medicine and sports: between Scylla and Charybdis.

Laboratory medicine is complex and contributes to the diagnosis, therapeutic monitoring and follow-up of acquired and inherited human disorders. The regular practice of physical exercise provides important benefits in heath and disease and sports medicine is thereby receiving growing focus from almost each and every clinical discipline, including laboratory medicine. Sport-laboratory medicine is a relatively innovative branch of laboratory science, which can provide valuable contributions to the diagnosis and follow-up of athletic injuries, and which is acquiring a growing clinical significance to support biomechanics and identify novel genomics and "exercisenomics" patterns that can help identify specific athlete's tendency towards certain types of sport traumas and injuries. Laboratory medicine can also provide sport physicians and coaches with valuable clues about personal inclination towards a certain sport, health status, fitness and nutritional deficiencies of professional, elite and recreational athletes in order to enable a better and earlier prediction of sport injuries, overreaching and overtraining. Finally, the wide armamentarium of laboratory tests represents the milestone for identifying cheating athletes in the strenuous fight against doping in sports.