Search

We present the results of our technical validation process in establishing the analysis of circulating tumor DNA (ctDNA) as a diagnostic tool. Like most cells in our body, tumor cells shed DNA in the blood flow. Analysis of ctDNA mutational content can provide invaluable information on the genetic makeup of a tumor, and assist oncologists in deciding on therapy, or in following residual disease. However, low absolute amounts of circulating DNA and low tumor fraction constitute formidable analytical challenges. A key step is to avoid contamination with genomic DNA from cell lysis. Several brands of specialized blood collection tubes are available to prevent leukocyte lysis. We show that they are not equally efficient, depending on storage temperature and time before plasma preparation. We report our analysis of preanalytical factors pertaining to ctDNA analysis (tubes, transportation time, temperature) and our conclusions in terms of instructions to prescribing physicians. We also stress the importance of proper DNA quality control and compare several methods, including a differential amplicon length PCR technique which allows determination of multiple QC parameters from minimal amounts of DNA. Altogether, these data provide useful practical information to diagnostic laboratories wishing to implement the assay of ctDNA in clinical practice.

Objectives: The objective of this study was to explore the effect of gamma irradiation on the haematological and biochemical parameters of the allogeneic red blood cells units at different storage duration. Methods: A prospective comparative study was conducted at the Blood Bank unit, Department of Diagnostic Laboratory Services of Universiti Kebangsaan Malaysia Medical Centre (UKMMC) in year 2013. Total 36 allogeneic red blood cell units were selected by simple random sampling method and divided into two groups, 18 units in each group based on the storage period into i) up to 14 days and ii) >14 days to expiry. Pre and post irradiation samples were taken immediately before and after irradiation of the units to analyse for the haematological parameters such as plasma Hb level, percent red cell haemolysis, haemoglobin per unit blood (Hb/unit), haematocrit (HCT), red cell indices such as mean corpuscular volume (MCV), mean corpuscular haemoglobin (MCH), mean corpuscular haemoglobin concentration (MCHC) and biochemical parameters such as plasma sodium (Na + ), potassium (K + ) and LDH levels. Data was collected and statistical analysis was done. Results: Statistically significant changes were observed between red cell units of up to 14 days and > 14 days old and pre irradiated samples in terms of plasma haemoglobin level, percent red cell haemolysis and plasma Na + , K + and LDH levels. However, pre and post irradiation samples in each group of 14 days and >14 days showed significant changes in the plasma Hb and % haemolysis, Hb/unit, HCT, MCV and MCH in 14 days group while only in plasma Hb, MCV and MCH in >14 days group without any effect on plasma Na + , K + and LDH levels in both group. Conclusion : Comparison at two different red cells storage groups i.e. period of up to 14 days and >14 days, showed significant changes in haematological and biochemical parameters. In the pre irradiation group this reflects the gradual storage changes over time even without going through the irradiation process. On the other hand, the changes between pre and post–irradiation for both the groups of storage showed significant haematological changes indicating irradiation itself also causes significant changes. In view of all these findings, we recommend to irradiate the allogeneic red cell units within 14 days of collection to reduce the adverse effects resulted from irradiation on the cellular products. Bangladesh Journal of Medical Science Vol.17(1) 2018 p.30-35

Background and Objectives: Discovered in 1983, Extended spectrum beta-lactamase (ESBL) producers are still the leading cause of infections in India. Its prompt detection is crucial to the clinical management. The Clinical Laboratory Standards Institute (CLSI) recommends phenotypic screening and confirmatory tests to identify the ESBL producer making it cost and time consuming for the diagnostic laboratory. We compare here the screening and confirmatory tests offering a solution to the CLSI recommendation. Methods: Nosocomial isolates E. coli (71) and K. pneumoniae (25) resistant to cefotaxime and ceftazidime were included. CLSI recommended testing with cefotaxime, ceftazidime and in combination with clavulanic acid by disk diffusion and agar dilution methods were performed. E-test was performed on discrepant results. To determine the genetic relatedness of the organisms, 22 Medical and Surgical ICU isolates were genotyped by PFGE. Dendrogram was constructed using dice co-efficient, UPGMA method with diversity database software. Results and Conclusions: Phenotypic screening disk diffusion test versus the confirmatory agar dilution MIC tests with cefotaxime and ceftazidime correlated well with the final ESBL status (kappa 0.852 and 0.905 P < 0.001) and (kappa 0.911 and 0.822 P < 0.001). The tests show 99-100% sensitivity, 75-83.3% specificity, and positive likelihood ratios between 4.0 -5.9. E-test confirmed 6 of 12 discordant results as ESBLs. Of the 96 nosocomial isolates screened as possible ESBL producers by the Kirby-Bauer disk diffusion test, 86.5% were confirmed ESBL producers. Genotyping on the ICU isolates by PFGE revealed a genetically diverse population suggesting no transmission of phenotypically similar ESBL strains within the ICUs.

Nontuberculous mycobacteria (NTM) respiratory infections represent a growing public health problem in many countries. However, there are limited published epidemiologic studies for the Western Pacific region. We reviewed respiratory specimens submitted to Diagnostic Laboratory Services in Hawaii, USA, for culture of Mycobacterium tuberculosis during August 2007-December 2011 to determine the NTM isolation rate. We observed a statistically significant increase in the rate of specimens with NTM isolated in respiratory culture (adjusted rate ratio per year 1.65, 95% CI 1.54-1.77; p

Background Dogs seized by law enforcement agencies during dogfighting investigations are at increased risk of Babesia gibsoni infection. A rapid and cost‐effective diagnostic test would increase the feasibility of mass screening of dogs for infection and monitoring treatment efficacy in B. gibsoni‐infected dogs. Objective To determine the performance of a point‐of‐need insulated isothermal PCR (iiPCR) test for diagnosis of B. gibsoni in dogs rescued in dogfighting investigations. Animals Two hundred and thirty‐three dogs seized in dogfighting investigations. Methods Cross‐sectional study. Whole blood samples were tested for B. gibsoni and Babesia spp. by iiPCR. Results were compared to a reference standard comprised of concordant results from real‐time PCR in a commercial diagnostic laboratory and antibody titers. Results The iiPCR system was quick to learn, portable, and had a short processing time of

The procedures necessary to perform testing in a veterinary diagnostic laboratory have inherent associated risks to personnel in regard to exposure to infectious agents. In research institutions animals can be experimentally infected, acquire naturally occurring infections and can also be exposed to other hazards such as toxic chemicals or radiologic entities. A critical component of the use of animals in a research environment is the collaboration between the responsible researcher and the veterinary diagnostic laboratory with the institutional health and safety professionals to ensure that the proper engineering controls, personal protective equipment, laboratory procedures and training are in place for personnel working with the animals or their specimens. Unlike the typical researcher, the veterinary diagnostic laboratory generally has to be equipped to safely process and work with a wide range of potential hazards where the communication of pertinent information from the researcher to the diagnostic laboratory regarding the identity of the potential hazard is paramount. Diagnostic laboratory design, safety equipment, personal protective equipment, laboratory procedures, occupational health program and personnel training must be sufficient to address hazards based on a risk assessment performed in conjunction with safety professionals. This article will summarize safety considerations with the various areas of concern in the operation of a diagnostic laboratory for research animal specimens.

Background: Antibodies directed against dsDNA are a highly specific diagnostic marker for the presence of systemic lupus erythematosus and of particular importance in its diagnosis. To assess anti-dsDNA antibodies, the Crithidia luciliae-based indirect immunofluorescence test (CLIFT) is one of the assays considered to be the best choice. To overcome the drawback of subjective result interpretation that inheres indirect immunofluorescence assays in general, automated systems have been introduced into the market during the last years. Among these systems is the EUROPattern Suite, an advanced automated fluorescence microscope equipped with different software packages, capable of automated pattern interpretation and result suggestion for ANA, ANCA and CLIFT analysis. Methods: We analyzed the performance of the EUROPattern Suite with its automated fluorescence interpretation for CLIFT in a routine setting, reflecting the everyday life of a diagnostic laboratory. Three hundred and twelve consecutive samples were collected, sent to the Central Diagnostic Laboratory of the Maastricht University Medical Centre with a request for anti-dsDNA analysis over a period of 7 months. Results: Agreement between EUROPattern assay analysis and the visual read was 93.3%. Sensitivity and specificity were 94.1% and 93.2%, respectively. The EUROPattern Suite performed reliably and greatly supported result interpretation. Conclusions: Automated image acquisition is readily performed and automated image classification gives a reliable recommendation for assay evaluation to the operator. The EUROPattern Suite optimizes workflow and contributes to standardization between different operators or laboratories.

Background: Osteoporosis is a major public health problem and should be a priority for healthcare providers and policymakers as it is an important reason of morbidity, mortality, and high-cost incurred in the management of its complications such as hip fractures. This study is designed to assess the bone mineral density (BMD) variation with age, site, and sex. Study is based on diagnostic laboratory data of BMD. Methods: A retrospective analysis was conducted on a sample population of 935 persons (73.5% women, 26.4% men), who underwent dual-energy X-ray absorptiometry scan between 2015 and 2017 in a National Accreditation Board for Testing and Calibration Laboratories accredited Mumbai (Maharashtra, India) based diagnostic laboratory. Lumbar spine, right and left total femur, BMD were analyzed across age, sex, and sites. The prevalence of low BMD and osteoporosis at these sites has been estimated as per the World Health Organization criteria of osteoporosis diagnosis using T scores. Results: Overall the prevalence of osteoporosis was found to be 6.4%, 5.5%, and 16.4%, while the prevalence of low BMD was 32.6%, 32.8%, and 31.2% at right total femur, left total femur, and lumbar spine, respectively. The decline in BMD at lumbar spine is more among women and it was a consistent decline with age, while among men' decline rate was less at all three sites. Conclusion: Our study highlighted the variation of BMD at different sites of body and higher vulnerability of spine for fragility fractures. Our study has shown a sharp decline in BMD among women during transition from 5th to 6th decade which signifies association of menopause with osteoporosis. Major limitation of the study is unavailability of clinical profiles of the subjects because of which it is difficult to ascertain whether BMD estimation was a diagnostic or screening procedure. In addition, study is conducted in diagnostic lab settings, due to which it is possible to overestimate prevalence of low BMD and osteoporosis by extrapolating these findings to the community.

Introduction: A state and local Public clinical diagnostic laboratory quality improvement usually monitored by laboratory improvement strategies. The Institute of Medicine (IOM) in 1999 delivered a report on medical errors, which later focus on patient safety. Aim: The study was undertaken to find out the effect of quality improvement programme for the prevention of laboratory diagnostic errors. Materials and Methods: Diagnostic bias is called as any error from placing order of tests to analysis of results. The diagnostic process in the laboratory mainly divided in to three stages such as, pre-analytical, analytical and post analytical phase. Results: Out of 14,047 specimens, 14.01% requisition form found without any signature of clinicians and 6.88% with no brief clinical history and provisional diagnosis. Conclusion: The concluded quality improvement implementation program for deficient of out of TAT in clinical chemistry laboratory is mandatory to achieve the patient safety goal. The last step of the PDCA cycle “ACT” to maintain constant continuous improvement as ever ending program is the responsibility of the unit team work. Keywords: Laboratory diagnostic bias, Pre analytical phase, Analytical phase, Post analytical phase, Quality assurance and quality control.

Since the beginning of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) virus pandemic, several highly effective and safe vaccines have been produced at remarkable speed. Following global implementation of vaccination programmes, cases of thrombosis with thrombocytopenia following administration of adenoviral vector-based vaccines started being reported. In this review we discuss the known pathogenesis and epidemiology of so-called vaccine induced thrombocytopenia and thrombosis (VITT). We consider the available guidelines, diagnostic laboratory tests and management options for these patients. Finally, we discuss important unanswered questions and areas for future research in this novel pathoclinical entity.

Flow cytometry is used in cell-based diagnostic evaluation for blood-borne malignancies including leukemia and lymphoma. The current practice for cytometry data analysis relies on manual gating to identify cell subsets in complex mixtures, which is subjective, labor-intensive, and poorly reproducible. This article reviews recent efforts to develop, validate, and disseminate automated computational methods and pipelines for cytometry data analysis that could help overcome the limitations of manual analysis and provide for efficient and data-driven diagnostic applications. It demonstrates the performance of an optimized computational pipeline in a pilot study of chronic lymphocytic leukemia data from the authors' clinical diagnostic laboratory.

Carbapenemase-producing organisms (CPOs) represent an increasing threat in healthcare facilities and detection of these organisms in the diagnostic laboratory can be challenging. The EntericBio CPE (EBCPE) real-time PCR assay (Serosep Ltd) was evaluated for the detection of NDM, KPC, OXA-48-like, VIM, IMP and GES carbapenemase genes from a panel of 145 multidrug-resistant organisms (29 NDM, 35 OXA-48, 21 VIM, 4 OXA-23, 3 KPC, 5 NDM+OXA-48, 3 GES-5, 1 OXA-23+NDM, 1 IMI, 2 IMP-1 and 41 multidrug-resistant carbapenemase-negative isolates). The EBCPE assay performed well, with 100 % sensitivity and specificity for the detection of all genotypes included in the assay. Turnaround time and laboratory workflow were improved compared to culture-based assays. Users must remain aware of the limitations of molecular assays for CPO detection to ensure implementation of the most suitable CPO diagnostic pathways.

Comparison of first and second waves of Coronavirus disease (COVID-19) showed varied differences including the peak and time distribution. Contrary to published reports of comparing two waves in India wherein the younger age group was affected more in the second wave in India; a secondary data analysis of around 0.5 million real-time reverse transcription-polymerase chain reaction tests conducted in COVID-19 diagnostic laboratory in eastern Uttar Pradesh, India showed an increase in positivity rate in older age groups in the second wave. The positivity rate among symptomatic cases was found to be three times higher in second wave compare to the first wave. Higher positivity rates were seen across older age groups, with a shift of 11 years in the mean age of positivity in the second wave compared to the first.

Background: Kikuchi-Fujimoto Disease (KFD)11 KFD: Kikuchi-Fujimoto Disease. is a rare, benign, idiopathic, and self-limiting lymphadenitis typically affecting head and neck regions. It was first reported in 1972 in Japan, and seldomly reported in children. KFD may mimic diseases like lymphoma, autoimmune conditions, tuberculosis, and other diseases. There are no available specific diagnostic laboratory tests for diagnosing KFD. Histopathologic and immunohistochemistry study is the only tool to establish definite diagnosis. So, diagnosing KFD can be a challenge, especially in pediatric population. Case presentation: Here we describe three cases of KFD presenting to our hospital in Indonesia within 5 years. The first case demonstrated a rare case of KFD complicated with Systemic Lupus Erythematosus; the second case with relapsed pulmonary Tuberculosis; and the third case with multiple lymphadenopathies without any other symptoms. All three cases presented with specific immunochemistry results for KFD. Conclusion: Kikuchi-Fujimoto disease remains a challenge for clinicians and pathologists to diagnose. There are no clear diagnostic criteria. Clinicians must be aware of KFD in patients with prolonged fever and lymphadenopathy. Pathologist should be familiar with KFD morphology to avoid misdiagnosis and unnecessary treatments. Other differential diagnoses should be ruled out, especially tuberculosis where it is highly prevalent in Indonesia.

Dear Editor in Chief Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a pandemic (1). Early diagnosis and testing of symptomatic individuals and asymptomatic carriers (2) remain essential since the latter group can transmit the virus (3,4). Current assays for SARS-CoV-2 detection are mostly based on quantitative real-time PCR (RT-qPCR)(5). However, cross-contamination remains a challenge in RT-qPCR assays. Here, we would like to share the most interesting route of sample contamination in SARS-CoV-2 molecular diagnosis laboratories and the necessity of personnel testing. We set up our molecular diagnosis laboratory three months ago using RT-qPCR. We strictly adhered to biosafety guidelines to ensure personnel safety and avoid cross-contamination of samples. We use (i) two extraction negative controls (EXNC), (ii) one no template control for every 10 samples, and (iii) one negative control. Note that to minimize the probability of contamination, the positive control was prepared last, after each patient’s sample was added to the corresponding tube. After one month and a half, we noticed a slightly positive signal (Cq = 38) in one of the EXNC. Upon repeating the run, both EXNC showed a Cq = 38. We narrowed down the cause to the personnel. Thus, all the personnel were tested for SARS-CoV-2 by the reference laboratory of the Pasteur Institute of Iran. We were astonished when we found that the person who was in charge of extractions tested positive for SARS-nCoV-2. This same person also handled the extraction kits. Thus, a SARS-CoV-2 PCR-negative technician was assigned to perform viral RNA extraction. The results were perfectly satisfactory. How is it possible when the RNA extraction technologist used all necessary personal protective equipment and level 2 biosafety guidelines? Since the SARS-CoV-2 PCR-positive person handled the extraction kits, she contaminated all the buffers and solutions probably by inadvertent touching of her mask or face. What we observed is the trickiest route of cross-contamination in a molecular diagnostic laboratory even when the most experienced user is working. When molecular diagnostic laboratory personnel do not use shields, it is probable that they touch their masks or faces inadvertently. Especially when they work long hours, and the mask becomes wet because of the exhalation, the outer surface of the mask is certainly contaminated. We strongly recommend that all the personnel working in SARS-CoV-2 molecular diagnostic laboratories have to be tested. In fact, personnel of every molecular diagnosis laboratory should be tested especially for respiratory diseases that can be transmitted through exhalation of infected individuals. Ethical considerations Ethical issues (Including plagiarism, informed consent, misconduct, data fabrication and/or falsification, double publication and/or submission, redundancy, etc.) have been completely observed by the authors. Conflict of Interest Authors declared no conflict of interest.

O objetivo do presente trabalho foi relatar um caso de timoma epitelial em um felino, encaminhado para diagnóstico no Laboratório Regional de Diagnóstico, da Faculdade de Veterinária, da Universidade Federal de Pelotas (LRD/FV/UFPel). Segundo o médico veterinário clínico responsável o animal apresentou histórico de vômito e hiporexia, evoluindo rapidamente para o óbito, sendo o cadáver encaminhado ao LRD/FV/UFPel. Na necropsia observou-se uma massa pardo-clara, lobulada e aparentemente encapsulada no mediastino anterior. Fragmentos da massa mediastínica e dos órgãos das cavidades abdominal e torácica, bem como, o encéfalo foram coletados e fixados em formalina 10% tamponada. Após 48 horas as amostras de tecido foram clivadas, processadas rotineiramente e coradas pela técnica de hematoxilina e eosina. Cortes selecionados da massa mediastínica foram colhidos em lâmina positivada para realização da técnica de imuno-histoquímica (IHQ). Os anticorpos utilizados na IHQ foram o anti-citoqueratina, CD3 e CD79a. Na avaliação histopatológica da massa mediastínica observou-se proliferação de células epiteliais do timo em meio a linfócitos não neoplásicos. Na técnica de IHQ as células neoplásicas foram positivas para citoqueratina. O diagnóstico de timoma epitelial, neste caso, foi baseado nos achados macroscópicos, microscópicos e confirmado pela imuno-histoquímica.

Cutibacterium acnes (C. acnes), a Gram-positive biofilm-forming rod implicated in acne vulgaris, is increasingly recognized for its role in implant-associated infections. The diagnosis of C. acnes implant-associated infections remains challenging. The optimal treatment is a combination of both surgical intervention and antibiotic therapy. Areas covered: In this review, we discuss the different types of implant-associated infections caused by C. acnes. We also highlight the clinical manifestations pertaining to the various sites of infection, and identify several risk factors previously reported in the literature. We then cover the diagnostic laboratory markers, such as IL-6 and AD-1, optimizing C. acnes recovery in culture, and the specific molecular techniques. Finally, we examine the various effective antibiotic regimens and identify some preventive methods against C. acnes infections. Expert commentary: Biomarkers such as IL-6 and AD-1 should be further investigated for the diagnosis of C. acnes implant-associated infections. The use of 16S rRNA gene sequencing and other molecular techniques should be further explored in this setting. Longer incubation periods should be requested whenever C. acnes infection is suspected. If the clinical suspicion is high, sonication of the excised implant should be encouraged. Research should focus on developing effective anti-biofilm agents. Finally, preventive methods such as hair removal prior to surgery should be further explored.

Background: Hepatitis B infection is an alarming public health problem. Almost two billion people of the population alive today, would have been infected at some time in their lives by hepatitis B. Hepatitis C virus is another life threatening condition, and about 425,000 deaths occur each year due to its complications. The current study was carried out to provide care givers and health planners basic epidemiological data regarding the frequency and distribution of HBV and HCV based on age and sex during a time period of more than 5 years. Result: A total of 2109 different patients were found to be infected by HBV during the study period; 1641 (77.81%) were males and 468 (22.19%) were females with the age group of 20-39 years predominating (64%). In addition,16% of patients tested for HBeAg were found reactive. Conclusion: There were significant correlations observed between the levels of HBV DNA and ALT, AST and AFP. Regarding HCV, 70 males (54.9%) and 63 females (45.1%) were found to be infected, with preponderance of the age group 41 - 60 years and the genotype 4. Designing knowledge raising campaigns is appreciated as well as repetition of similar studies among larger populations in the following few years will help track a way to improvement.

Objectives: Pre-analytic errors during diagnostic laboratory investigations can lead to increased patient morbidity and mortality. This study aimed to ascertain the effect of educational nursing activities on the incidence of pre-analytical errors resulting in non-conforming blood samples. Methods: This study was conducted between January 2008 and December 2015. All specimens received at the Haematology Laboratory of the Sultan Qaboos University Hospital, Muscat, Oman, during this period were prospectively collected and analysed. Similar data from 2007 were collected retrospectively and used as a baseline for comparison. Non-conforming samples were defined as either clotted samples, haemolysed samples, use of the wrong anticoagulant, insufficient quantities of blood collected, incorrect/lack of labelling on a sample or lack of delivery of a sample in spite of a sample request. From 2008 onwards, multiple educational training activities directed at the hospital nursing staff and nursing students primarily responsible for blood collection were implemented on a regular basis. Results: After initiating corrective measures in 2008, a progressive reduction in the percentage of non-conforming samples was observed from 2009 onwards. Despite a 127.84% increase in the total number of specimens received, there was a significant reduction in non-conforming samples from 0.29% in 2007 to 0.07% in 2015, resulting in an improvement of 75.86% (P

Background Expanded carrier screening (ECS), which can identify carriers of a large number of recessive disorders in the general population, has grown in popularity and is now widely accessible to prospective parents. This article presents a comprehensive overview of the characteristics of currently available ECS tests. Methods To identify relevant ECS providers, we employed a multi-step approach, which included online searching, review of the recent literature, and consultations with researchers familiar with the current landscape of ECS. Results As of January 2017, there were sixteen providers of ECS tests: 13 commercial companies, two medical hospitals and one academic diagnostic laboratory. We observed drastic differences in the characteristics of ECS tests, with the number of conditions ranging from 41 to 1700. Only three conditions (Cystic fibrosis, Maple syrup urine disease 1b, and Niemann-Pick disease) were screened for by all providers. Where the same disease gene was included by multiple providers, substantial differences existed in the mutations screened and/or variant interpretation/reporting strategies. Conclusion Given the importance of carrier screening results in reproductive decision-making, the observed heterogeneity across ECS panels is concerning. Efforts should be made to ensure that clear and concrete criteria are in place to guide the development of ECS panels.

The inherited bleeding disorder von Willebrand disease (VWD) is challenging to diagnose owing to disease heterogeneity, lack of a definitive laboratory test and variations in diagnostic criteria. We evaluated the impact of diagnosis and diagnostic delay on patient outcomes. The PharMetrics Plus Database was interrogated for medical claims for VWD (ICD-9 286.4) and bleeding events between 1 January 2006 and 30 June 2015. Longitudinal analysis was performed of patients newly diagnosed with VWD (≥9 months' continuous enrolment before first VWD claim) through 24 months following diagnosis. In total, 32 028 diagnosed, including 18 182 newly diagnosed, patients were identified. Most patients (72%) were female. Prediagnosis, bleeding symptoms were most commonly managed by a hospitalist/emergency room physician. Misrecognition of VWD was common, with 25% of patients visiting the same specialist type at least twice for an episodic bleed before diagnosis. Thirty-seven percentage of patients had no diagnostic laboratory test within 24 months of their initial diagnostic claim. Bleed claims reduced following diagnosis: 41% and 26% of female and male patients, respectively, had claims in the year prediagnosis, falling to 21% and 9% of patients at 1-2 years postdiagnosis. The proportion of patients with multiple bleed claims also decreased, from 17% to 6% (females) and 7% to 3% (males). Serially misrecognized patients continued to have more bleeding episodes than other patients, although bleed frequency was lower than before diagnosis. There is a need for improved patient management from bleeding presentation onward to reduce the time to VWD diagnosis and to enhance patient outcomes.

Haiti has the highest burden of rabies in the Western hemisphere, with 130 estimated annual deaths. We present the cost-effectiveness evaluation of an integrated bite case management program combining community bite investigations and passive animal rabies surveillance, using a governmental perspective. The Haiti Animal Rabies Surveillance Program (HARSP) was first implemented in three communes of the West Department, Haiti. Our evaluation encompassed all individuals exposed to rabies in the study area (N = 2,289) in 2014-2015. Costs (2014 U.S. dollars) included diagnostic laboratory development, training of surveillance officers, operational costs, and postexposure prophylaxis (PEP). We used estimated deaths averted and years of life gained (YLG) from prevented rabies as health outcomes. HARSP had higher overall costs (range: $39,568-$80,290) than the no-bite-case-management (NBCM) scenario ($15,988-$26,976), partly from an increased number of bite victims receiving PEP. But HARSP had better health outcomes than NBCM, with estimated 11 additional annual averted deaths in 2014 and nine in 2015, and 654 additional YLG in 2014 and 535 in 2015. Overall, HARSP was more cost-effective (US$ per death averted) than NBCM (2014, HARSP: $2,891-$4,735, NBCM: $5,980-$8,453; 2015, HARSP: $3,534-$7,171, NBCM: $7,298-$12,284). HARSP offers an effective human rabies prevention solution for countries transitioning from reactive to preventive strategies, such as comprehensive dog vaccination.

The updated RIDA® QUICK (N1402) immunochromatographic assay (R-Biopharm) for detection of norovirus was evaluated during a prospective, multicenter study using 771 stool samples from patients with gastroenteritis. Compared to real-time reverse transcriptase polymerase chain reaction (RT-rtPCR) as gold standard, the RIDA® QUICK had an overall sensitivity of 72.8% (91/125) and a specificity of 99.5% (640/643). Genotype analysis of the polymerase (ORF1) and capsid (ORF2) region of the genome indicated that the RIDA® QUICK assay could detect a broad range of genotypes including new variants (15 of 125 positive samples) which were detected by an in-house SYBR®Green RT-rtPCR, but not by the RIDA® GENE PCR PG1415 (R-Biopharm) and mostly not by the RIDA® GENE PCR PG1405 and the Xpert® Norovirus assay (Cepheid). The RIDA® QUICK can be used to reliably confirm norovirus in stool samples, but a negative result does not definitively exclude the presence of norovirus.

Clinical diagnostic laboratories are producing next-generation sequencing-based test results that are becoming increasingly incorporated into patient care. Whole genome and exome sequencing on fetal material derived from amniocytes, chorionic villi, or products of conception is starting to be offered clinically in specialized centers, but it has not yet become routine practice. The technical, interpretation, and ethical challenges are greatest in the area of prenatal medicine because the fetus has a limited health history, and the physical examination is only indirectly available via prenatal sonography. Here, we provide an overview of these challenges and highlight the clinical utility, reporting, and counseling issues associated with prenatal DNA sequencing. Future considerations are also discussed. © 2017 John Wiley & Sons, Ltd.

The role of Streptococcus pneumoniae as a causative agent of skin and soft tissue infections (SSTI) is unusual and its clinical interpretation is difficult. We describe here three cases of SSTI due to S. pneumoniae in patients admitted to the Provincial Pediatric Hospital of Misiones, Argentina that were detected during 10 years of invasive disease (ID) surveillance documented in 2010, 2011 and 2015. These cases involved two girls aged 8 and 7 months old, and a two-year-old male child with diagnoses of gluteal abscess, preseptal cellulites and pyoderma respectively. All the patients were eutrophic and in good general condition on admission; one of them was seropositive for HIV. Antimicrobial susceptibility and serotypes were framed within the local epidemiology of invasive pneumococcal disease. Despite its low frequency, S. pneumoniae as an etiological agent of SSTI must be considered. Our findings revalue the role of the diagnostic laboratory and contribute to document the behavior of this pathogen.

Introduction Clinicians who treat nerve and muscle disorders may be asked to evaluate patients who have unilateral or bilateral scapular winging. Traditionally, this evaluation has relied upon a thorough history, physical examination, and electrodiagnostic testing to localize the cause of winging and detect the underlying neuromuscular pathology. Neuromuscular ultrasound has emerged as a non-invasive technique that can be used for structural evaluation of nerve and muscle abnormalities. Methods Previous studies of imaging in scapular winging and experiences from our diagnostic laboratory are reviewed. Results Four standard and 4 ancillary ultrasound views are described for evaluation of scapular winging. Conclusion Ultrasound is a non-invasive, painless, and radiation-free technology that can be used to evaluate scapular winging. Muscle Nerve 56: 7-14, 2017.

The incursion of highly pathogenic avian influenza (HPAI) into the United States during 2014 resulted in an unprecedented foreign animal disease (FAD) event; 232 outbreaks were reported from 21 states. The disease affected 49.6 million birds and resulted in economic losses of $950 million. Minnesota is the largest turkey-producing state, accounting for 18% of U.S. turkey production. Areas with concentrated numbers of turkeys in Minnesota were the epicenter of the outbreak. The first case was presumptively diagnosed in the last week of February 2015 at the Minnesota Veterinary Diagnostic Laboratory (MVDL) and confirmed as HPAI H5N2 at the National Veterinary Services Laboratories on March 4, 2015. A total of 110 farms were affected in Minnesota, and the MVDL tested >17,000 samples from March to July 2015. Normal service was maintained to other clients of the laboratory during this major FAD event, but challenges were encountered with communications, staff burnout and fatigue, training requirements of volunteer technical staff, test kit validation, and management of specific pathogen–free egg requirements.

The use of laboratory information systems (LIS) are now an important part of the activities of clinical diagnostic laboratory of modern hospitals. The results of the work on the creation in 2002 and implementation in practice of clinical diagnostic laboratory multi-departmental hospital LIS. Upgrading the system and add-ins carried out in 2005, 2008, 2010 and 2012. The system is designed for lab work thresholds from 200 to 1000 samples per day, which this LIS operates clinical laboratories in the normal mode, which confirmed the successful implementation of the LIS-1477 in the laboratories of hospitals years. Fokino, Spassk-Dal’niy, Dalnegorsk, outpatient department VMKG. Using the LIS-1477 changes the prin ciple of the clinical diagnostic laboratories to optimize all the effort, organize, standardize and simplify workflow. Promising areas for improvement of the system described in this section is to create a «quality control», as well as interfacing with automated laboratory analyzers. This will automatically transmit orders to the analyzers and obtain their research results without manual data entry.

// Kyle M. Schachtschneider 1, 2, 3 , Regina M. Schwind 3 , Kwame A. Darfour-Oduro 1 , Arun K. De 1 , Lauretta A. Rund 1 , Kuldeep Singh 4 , Daniel R. Principe 5 , Grace Guzman 6 , Charles E. Ray Jr. 3, 7 , Howard Ozer 7 , Ron C. Gaba 3 and Lawrence B. Schook 1, 3 1 Department of Animal Sciences, University of Illinois, Urbana, IL, USA 2 Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands 3 Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA 4 Veterinary Diagnostic Laboratory, University of Illinois, Urbana, IL, USA 5 College of Medicine, University of Illinois at Chicago, Chicago, IL, USA 6 Department of Pathology, University of Illinois at Chicago, Chicago, IL, USA 7 Department of Medicine, Division of Hematology/Oncology, University of Illinois at Chicago, Chicago, IL, USA Correspondence to: Lawrence B. Schook, email: schook@illinois.edu Keywords: hepatocellular carcinoma, human, porcine model, gene expression, interventional radiology Received: October 21, 2016 Accepted: June 05, 2017 Published: June 29, 2017 ABSTRACT Difficult questions are confronting clinicians attempting to improve hepatocellular carcinoma (HCC) outcomes. A large animal model with genetic, anatomical, and physiological similarities to humans is required to transition from mouse models to human clinical trials to address unmet clinical needs. To validate our previously reported inducible porcine cancer model (Oncopig) as a transitional HCC model, Oncopig hepatocyte cultures were transformed using Cre recombinase. The resulting porcine HCC cells (pHCC) expressed oncogenic TP53 R167H and KRAS G12D , and displayed nuclear pleomorphisms with pale to granular cytoplasm arranged in expanded plates similar to human HCC histopathology. Human HCC transcriptional hallmarks were detected in pHCC cells using RNA-seq, including TERT reactivation, apoptosis evasion, angiogenesis activation, and Wnt signaling activation. Master regulators of gene expression were conserved across Oncopig and 18 human HCC cell lines. pHCC injection into SCID mice resulted in tumors recapitulating human HCC characteristics, including thick trabeculae formation, pseudoacini patterning, and sheets of well-vascularized stroma. Finally, autologous injection of pHCC cells subcutaneously yielded a tumor histologically characterized as Edmondson Steiner (HCC nuclear grade assessment system) grade 2 HCC with trabecular patterning and T-lymphocyte infiltration. These data demonstrate the Oncopig HCC model’s utility for improving detection, treatment, and biomarker discovery relevant to human HCC.

Objective. To study the changes of impedance agregatometry indicators in patients with a history of stroke receiving antiplatelet therapy. Design and methods. We analyzed 324 medical records of patients with cerebrovascular events in past. Among them 252 patients (77,7 %) took aspirin, 53 patients (16,4 %) — clopidogrel and 19 patients (5,9 %) received in dual antiplatelet therapy. Simultaneously, all patients were treated with standarddose antihypertensives and statins for secondary prevention. In all patients the impedance agregatometry was performed (CHRONO-LOG, USA, Model 590). The platelet function in whole blood was evaluated with the use of adenosine diphosphate (ADP, final concentration — 10 pM/ml) and collagen (2 mg/ml) as inductors. The results were compared with the reference values intervals used in the diagnostic laboratory of urban advisory diagnostic center № 1 of St. Petersburg. Results. The patients treated with aspirin show an increase in time of the beginning of platelet aggregation up to 74,0 ± 1,1 (71,8–76,2) s and a platelet aggregation area under curve (AUC) decrease to 53,8 ± 1,1 (51,7–55,9) om × s when collagen is used as an inducer. The patients receiving clopidogrel 75 mg once daily demonstrate a decrease in amplitude of platelet aggregation to 8,8 ± 0,8 (7,1–10,5) om and AUC to 37,6 ± 3,5 (30,5–44,7) om × s when adenosindiphosphate (ADF) is used as the inductor. Also clopidogrel (75 mg/day) therapy is associated with the prolongation of time of aggregation onset (Lag Time) to 76,9 ± 5,3 (66,3–87,5) s, and with the decrease in AUC to 53,6 ± 2,9 (47,4–59,5) om × s when collagen is used as the inductor. Conclusions. The impedance agregatometry may be used to assess the impact of antiplatelet drugs on platelet aggregation in out-patients with a history of stroke.

Lactate monitoring is an important issue in the food industry, in clinical diagnosis and sport medicine. Biosensors that can quantify lactic acid in biological samples are extremely attractive because of their advantages such as simplicity, ease of miniaturization, high sensitivity and low-cost. The proposed biosensor is based on a screen-printed electrode modified with Prussian Blue, that senses the hydrogen peroxide produced by the reaction catalysed by the lactate oxidase enzyme immobilized onto the electrode surface, coupled with a portable instrumentation. This biosensor showed a working range of 0.025–0.25 mM with a detection limit of 0.01 mM. After recovery studies, the biosensor was employed for the analysis of 12 saliva samples, taken from athletes, whose lactate levels were compared with the blood lactate content measured with a portable lactate analyser. The results showed a good correlation. The developed electrochemical biosensor could be a useful, alternative and non-invasive tool for a correct and rapid monitoring of lactate in saliva. This method is easy to use, cost effective, rapid, and suitable for analysis performed outside the classical diagnostic laboratory.

Rapid diagnostic tests for cystic echinococcosis (CE) are convenient to support ultrasound diagnosis in uncertain cases, especially in resource-limited settings. We found comparable diagnostic performances of the experimental Hyd Rapid Test and the commercial VIRapid HYDATIDOSIS Test, used in our diagnostic laboratory, using samples from well-characterized hepatic CE cases.

Over a 2-year period, samples of tomato suspected of being infected with bacterial spot were collected across Indiana and sent to the Purdue Plant and Pest Diagnostic Laboratory (PPDL). A total of 50 strains were collected over 2 years. An effort was made to collect from both fresh market and processing tomato fields (22 from fresh market, 25 from processing, and 3 unspecified). The PPDL screened samples for bacterial spot, and they isolated and confirmed the pathogen. The Xanthomonas isolates were then sent to Jeff Jones at the University of Florida to determine taxonomic identification, race determination, and sensitivity to copper at 50 ppm and streptomycin at 200 ppm. The majority of Xanthomonas strains collected (78%) were classified as X. perforans. The majority of the X. perforans strains were designated race T4. A total of 12% of strains were classified as X. gardneri, all of which were collected north of U.S. I-70, a route that bisects the state into approximately even halves. X. euvesicatoria was only observed on one sample. X. vesicatoria was not observed. Of all strains collected in Indiana, 84% were copper tolerant. In contrast, only 58% of the strains were insensitive to streptomycin.

Peripheral neuropathy is a common neurological disorder, with high prevalence especially in the aged population. The general evaluative approach is to first identify the type of peripheral neuropathy prior to investigating for a possible underlying etiology, which is an increasingly important endeavor, as many causes of peripheral neuropathy are now recognized as treatable. To this end, laboratory testing plays an important adjunctive role to a detailed history and examination. This review will discuss possible diagnostic laboratory testing pathways for different types of peripheral neuropathy, with the goal of minimizing costs and false-positive results while maximizing the likelihood of identifying a potentially reversible etiology.

Blood groups are inherited biological characteristics that do not change throughout life only in healthy people. Blood group antigens determine the adaptation of a human, as a biological species, to the surrounding environment. Our goal was to study the combination and frequency characteristics of three group systems (ABO, RH, KELL) in blood donors. The blood of 743 donors (aged ≥ 18 years) has been investigated on erythrocyte blood group antigens (521 male and 222 female). The sample has been provided from diagnostic laboratory of “Health Centre Medina Ltd” of Batumi. Research was agreed with hematology department of the clinic. Blood typing of the sample has been carried out on the basis of immunogenetic laboratory of Batumi Shota Rustaveli State University. The express method with universal mono-clone antibodies was used in order to reveal blood group system antigens. ABO blood group are distributed the following order: O > A > B > AB. We allocated 16 phenotypic groups. O, Rh+, K− (38.62 ± 1.7%) are represented with the highest percentage among donors and a rather large number of the investigated donors (287 donors) is the carrier of this phenotype. A frequency distribution of the A, Rh+, K− phenotype group 10% (28.93 ± 1.6) was less. 215 donors carry A, Rh+, K− phenotype combination. O, Rh+, K+ and A, Rh+, K+ variations of the phenotype are represented with an equal percentage (3.23 ± 0.4%). 7.94 ± 0.9% donors are characterized by features of the O, Rh−, K− Erythrocyte group. A frequency distribution of B, Rh+, K− phenotype is slightly less − 6.86 ± 0.9%. A, Rh−, K combination of phenotype occurs with a frequency of 4.97 ± 0.7%, and AB, Rh+, K− occurs with a frequency of 2.28 ± 0.5%. I n the donor population there were only single cases of B, Rh−, K+ (0.13 ± 0.01); AB, Rh+, K+ (0.13 ± 0.01); AB, Rh−, K− (0.40 ± 0.2); B, Rh+, K+ (0.26 ± 0.1); O, Rh−, K+ (0.40 ± 0.2); A, Rh−, K+ (0.67 ± 0.2) combination of phenotype. The phenotype AB, Rh−, K+ was not identified. The existence of this database will increase the safety level of transfusion, widen donors database and allow the clinics to find quickly the rare combination of blood group for transfusion and decrease of the risk of post-transfusion complications.

Pseudomonas aeruginosa is an opportunistic pathogen that has been associated with mastitis in dairy animals, including goats (Yuan et al, 2017). An outbreak of mastitis in dairy goats was investigated at the Utah Veterinary Diagnostic Laboratory (UVDL). Identification of the etiologic agent(s) and source of infection was the primary objective., American Association of Bovine Practitioners Proceedings of the Annual Conference, 2019

Respiratory disease negatively impacts growth, reproductive performance, milk production, and longevity of adult cattle. Most calves diagnosed with clinical respiratory disease on dairy farms are treated with antibiotics. Treatment failure is not uncommon and although management factors likely contribute to these treatment failures, the role of antimicrobial resistance cannot be ruled out. Therefore, the objective of this study was to describe pathogen prevalence and antimicrobial resistance patterns for pathogens associated with respiratory disease isolated from samples submitted to the Wisconsin Veterinary Diagnostic Laboratory between 2008-2017., American Association of Bovine Practitioners Proceedings of the Annual Conference, 2019

Сучасна клініко-діагностична лабораторія повинна вирішувати проблеми впровадження та забезпечення системи якості, заснованої на застосуванні принципів спеціалізованого стандарту ISO 15189:2015 «Лабораторії медичні. Окремі вимоги до якості та компетентності» як елементу забезпечення процедури оцінки відповідності результатів лабораторних досліджень. Ефективне вирішення цих питань стає однією з важливих умов при акредитації, а впровадження оцінювання придатності методів у повсякденну діяльність є свідченням компетентності сучасних клініко-діагностичних лабораторій.Мета. Дослідження підходів до забезпечення якості у Лабораторії клінічної діагностики Клініко-діагностичного центру НФаУ за допомогою проведення валідаційних процедур з оцінки придатності біохімічних методик визначення рівнів лактатдегідрогенази (ЛДГ) та глюкози у біологічних рідинах.Матеріали та методи. Об’єктами дослідження стали стандартизовані біохімічні методики визначення рівнів ЛДГ та глюкози. В якості контрольної сироватки був обраний «Хімічний контроль. Набір реагентів. Рівень 1», виробництва High Technology, Inc. (США) з відомою концентрацією аналітів. Вимірювання проводилися на автоматичному біохімічному аналізаторі Express Plus виробництва фірми «Bayer Corporation», Німеччина. При обробці результатів досліджень були використані показники описової статистики та проведено ряд статистичних оцінок.Результати. Процедура валідації методик складається з кількох етапів. На базі Лабораторії клінічної діагностики КДЦ НФаУ були розроблені протоколи та валідаційні звіти для оцінки придатності методик визначення ЛДГ та глюкози в біологічних рідинах фотометричним методом за допомогою біохімічного аналізатора Еxpress Рlus. Валідацію було проведено за допомогою реагентів виробництва High Technology, Inc.,USA та контрольних матеріалів (стандартних зразків). Були визначені валідаційні характеристики методик: специфічність, збіжність та відтворюваність, правильність, невизначеність вимірювань. Оцінка внутрішньо-лабораторної збіжності та відтворюваності методик визначення концентрації ЛДГ та глюкози при роботі аналізаторі, яка була проведена двома операторами-лаборантами однакової кваліфікації, вказує на відсутність грубих помилок у роботі аналізатора та статистично важливих відмінностей при проведенні вимірювань. Оцінка правильності методик, проведених за допомогою контрольної сироватки, довела, що систематична похибка не значима (по заданому критерію прийнятності). Отже, дані методики забезпечують правильність вимірів у межах лабораторії. Розрахунок розширеної невизначеності показав, що отримані значення рівнів ЛДГ та глюкози можна вважати точними та достовірними.Висновки. Валідація методик визначення лактатдегідрогенази та глюкози в крові людини фотометричним методом довела, що дані методики мають робочі характеристики, які відповідають регламентованим, задовольняють встановленим критеріям, а вимірювані за допомогою них параметри відповідають належним., A modern clinical and diagnostic laboratory should solve the problems of implementing and maintaining the quality system based on the application of the principles of the specialized standard ISO 15189: 2015 “Medical laboratories. Some requirements for quality and competence” as an element of providing the procedure for assessing the conformity of the laboratory research results. The effective solution of these issues becomes one of the important conditions for accreditation, and the introduction of the assessment of the suitability of methods in daily activities is evidence of the competence of modern clinical and diagnostic laboratories.Aim. To study the approaches to quality assurance in the Clinical Diagnostics Laboratory of the Clinical Diagnostic Center at the NUPh by carrying out validation procedures for assessing the suitability of biochemical methods for determining levels of lactate dehydrogenase (LDH) and glucose in biological fluids.Materials and methods. The objects of the study were standardized biochemical methods for determining levels of LDH and glucose. “Chemical control. Reagent kit. Level1” produced by High Technology, Inc. (USA) with the known concentration of analytes was selected as a control serum. The measurements were performed on an Express Express Plus automatic biochemical analyzer manufactured by Bayer Corporation,Germany. When processing the research results the indicators of descriptive statistics were used, and a number of statistical evaluations were carried out.Results. The procedure for validation of methods consisted of several stages. Protocols and validation reports were developed at the premises of the Clinical Diagnostics Laboratory of theClinicalDiagnosticCenter at the NUPh to assess the suitability of methods for determining LDH and glucose in biological fluids by the photometric method using an Еxpress Рlus biochemical analyzer. Validation was performed using reagents manufactured by High Technology, Inc. (USA) and control materials (standard samples). The following validation characteristics of the methods were determined: specificity, convergence and reproducibility, accuracy, measurement uncertainty. Assessment of the internal laboratory convergence and reproducibility of methods for determining the concentration of LDH and glucose during the operation of the analyzer, which was carried out by two laboratory operators of the same qualification, indicated the absence of gross errors in the operation of the analyzer and statistically important differences in the measurements. Assessment of the correctness of the methods performed using the control serum proved that the systematic error was not significant (according to the given acceptance criterion). Thus, these methods provided correct measurements within the laboratory. The calculation of the expanded uncertainty showed that the values of LDH and glucose levels obtained could be considered accurate and reliable.Conclusions. Validation of methods for determining lactate dehydrogenase and glucose in the human blood by the photometric method has proven that these methods have performance characteristics that meet the regulated and established criteria, and the parameters measured with their help correspond to the proper ones., Современная клинико-диагностическая лаборатория должна решать проблемы внедрения и обеспечения системы качества, основанной на применении принципов специализированного стандарта ISO 15189:2015 «Лаборатории медицинские. Отдельные требования к качеству и компетентности» как элемента обеспечения процедуры оценки соответствия результатов лабораторных исследований. Эффективное решение этих вопросов становится одним из важных условий при аккредитации, а внедрение оценки пригодности методов в повседневную деятельность является свидетельством компетентности современных клинико-диагностических лабораторий.Цель. Исследование подходов к обеспечению качества в Лаборатории клинической диагностики Клинико-диагностического центра НФаУ посредством проведения валидационных процедур по оценке пригодности биохимических методик определения уровней лактатдегидрогеназы (ЛДГ) и глюкозы в биологических жидкостях.Материалы и методы. Объектами исследования стали стандартизированные биохимические методики определения уровней ЛДГ и глюкозы. В качестве контрольной сыворотки был выбран «Химический контроль. Набор реагентов. Уровень 1» производства High Technology, Inc. (США) с известной концентрацией аналитов. Измерения проводились на автоматическом биохимическом анализаторе Express Plus производства фирмы «Bayer Corporation», Германия. При обработке результатов исследований были использованы показатели описательной статистики и проведен ряд статистических оценок.Результаты. Процедура валидации методик состоит из нескольких этапов. На базе Лаборатории клинической диагностики КДЦ НФаУ были разработаны протоколы и валидационные отчеты для оценки пригодности методик определения ЛДГ и глюкозы в биологических жидкостях фотометрическим методом с помощью биохимического анализатора Еxpress Рlus. Валидацию было проведено с помощью реагентов производства High Technology, Inc., USA и контрольных материалов (стандартных образцов). Были определены валидационные характеристики методик: специфичность, сходимость и воспроизводимость, правильность, неопределенность измерений. Оценка внутренне-лабораторной сходимости и воспроизводимости методик определения концентрации ЛДГ и глюкозы при работе анализатора, которая была проведена двумя операторами-лаборантами одинаковой квалификации, указывает на отсутствие грубых ошибок в работе анализатора и статистически важных различий при проведении измерений. Оценка правильности методик с использованием контрольной сыворотки доказала, что систематическая погрешность не значима (по заданному критерию приемлемости). Таким образом, данные методики обеспечивают правильность измерений в пределах лаборатории. Расчет расширенной неопределенности показал, что полученные значения уровней ЛДГ и глюкозы можно считать точными и достоверными.Выводы. Валидация методик определения лактатдегидрогеназы и глюкозы в крови человека фотометрическим методом доказала, что данные методики имеют рабочие характеристики, которые соответствуют регламентированным, удовлетворяют установленным критериям, а измеренные с их помощью параметры соответствуют надлежащим.

Background Capture sequencing (CS) is widely applied to detect small genetic variations such as single nucleotide variants or indels. Algorithms based on depth comparison are becoming available for detecting copy number variation (CNV) from CS data. However, a systematic evaluation with a large sample size has not been conducted to evaluate the efficacy of CS-based CNV detection in clinical diagnosis. Methods We retrospectively studied 3010 samples referred to our diagnostic laboratory for CS testing. We used 68 chromosomal microarray analysis–positive samples (true set [TS]) and 1520 reference samples to build a robust CS-CNV pipeline. The pipeline was used to detect candidate clinically relevant CNVs in 1422 undiagnosed samples (undiagnosed set [UDS]). The candidate CNVs were confirmed by an alternative method. Results The CS-CNV pipeline detected 78 of 79 clinically relevant CNVs in TS samples, with analytical sensitivity of 98.7% and positive predictive value of 49.4%. Candidate clinically relevant CNVs were identified in 106 UDS samples. CNVs were confirmed in 96 patients (90.6%). The diagnostic yield was 6.8%. The molecular etiology includes aneuploid (n = 7), microdeletion/microduplication syndrome (n = 40), and Mendelian disorders (n = 49). Conclusions These findings demonstrate the high yield of CS-based CNV. With further improvement of our CS-CNV pipeline, the method may have clinical utility for simultaneous evaluation of CNVs and small variations in samples referred for pre- or postnatal analysis.

BACKGROUND Acute-phase proteins (APPs) are considered biomarkers for diagnoses, prognoses, and treatment and health status monitoring. Reference intervals (RIs) are an integral part of diagnostic laboratory testing and clinical decision-making. The RIs for neonatal lambs are lacking. OBJECTIVE This study aimed to determine the RIs of serum amyloid A (SAA), haptoglobin (Hp), ceruloplasmin (Cp), and fibrinogen (Fb) concentrations in neonatal cross-bred Kivircik lambs. METHODS The study consisted of 42 neonatal cross-bred Kivircik lambs. Physical examinations were performed daily, and blood samples were collected at 0 (precolostrum), 1, 3, 7, 14, 21, and 28 days of age. The RIs of SAA, Hp, Cp, and Fb concentrations were calculated according to the recommendation of the American Society for Veterinary Clinical Pathology. Results were also evaluated for age- and sex-related effects. RESULTS The RI for serum Hp was 0-0.4 g/L, and no apparent effect of age or sex was noted. Because of significant age- and sex-related differences, the SAA (0.34-55.12 µg/mL), Cp (2.4-26.07 mg/mL), and Fb (218.86-527.82 mg/mL) results were given as minimum and maximum values. Serum SAA on the 1st, 3rd, and 7th days of life, and Cp and Fb concentrations on the 14th and 21st days of life, were significantly higher than those on other study days. CONCLUSIONS This study is the first to establish RIs for neonatal lambs, and the values obtained could be useful for making clinical decisions regarding cross-bred Kivircik lambs during this critical period.

BackgroundAntimicrobial resistance (AMR) poses a major threat to human health. Whole-genome sequencing holds great potential for AMR identification; however, there remain major gaps in comprehensively detecting AMR across the spectrum of AMR-conferring determinants and pathogens.MethodsUsing 16 wild-type Burkholderia pseudomallei and 25 with acquired AMR, we first assessed the performance of existing AMR software (ARIBA and CARD) for detecting clinically relevant AMR in this pathogen. B. pseudomallei was chosen due to limited treatment options, high fatality rate, and AMR caused exclusively by chromosomal mutation (i.e. single-nucleotide polymorphisms [SNPs], insertions-deletions [indels], copy-number variations [CNVs], and functional gene loss). Due to poor performance with existing tools, we developed ARDaP (Antimicrobial Resistance Detection and Prediction) to identify the spectrum of AMR-conferring determinants in B. pseudomallei.ResultsCARD failed to identify any clinically-relevant AMR in B. pseudomallei, ARIBA cannot differentiate AMR determinants from natural genetic variation, and neither CARD or ARIBA can identify CNV or gene loss determinants. In contrast, ARDaP accurately detected all SNP, indel, CNV, and gene loss AMR determinants described in B. pseudomallei (n≈50). Additionally, ARDaP accurately predicted three previously undescribed determinants. In mixed strain data, ARDaP identified AMR to as low as ~5% allelic frequency.ConclusionsWe demonstrate that existing AMR software are inadequate for comprehensive AMR detection; ARDaP overcomes the shortcomings of existing tools. Further, ARDaP enables AMR prediction from mixed sequence data down to 5% allelic frequency. ARDaP databases can be constructed for any microbial species of interest for comprehensive AMR detection.

The Choosing Wisely Initiative aims to collect statements from medical societies all over the world on medical interventions that result in no benefit to patients, with the potential to cause harm. In this article we present the views of the Diagnostic Laboratory Group at the Brazilian Society of Infectious Diseases (SBI). Ten experts from SBI were asked to list 10 diagnostic tests that were perceived as unnecessary in the field of infectious diseases. After voting for the more relevant topics, a questionnaire was sent to all SBI members, in order to select for the most important items. A total of 482 votes were obtained, and the top 10 results are shown in this manuscript. The Choosing Wisely statements of SBI should facilitate clinical practice by optimizing the use of diagnostic resources in the field of infectious diseases. Keywords: Choosing wisely, Quality, Safety, Infectious diseases, Microbiology, Diagnostic tests, Healthcare administration

Objectives: Given the relatively high prevalence and emphasis on the pathogenicity of Blastocystis sp., especially in immunocompromised patients and other at risked populations like military personnel, this study was carried out to investigate the prevalence of Blastocystis sp. in the city of Karaj during 2014 - 2015. Methods: In this descriptive study, 2500 stool samples were screened for Blastocystis sp. using microscopically examinations and iodine-stained, wet-mount preparations and formalin-ether as a sedimentation method. Demographic information such as age, gender, and symptoms of patients, were recorded in the questionnaire. Three stool samples were collected from each patient in disposable plastic containers. Data were analyzed using chi-square, ANOVA, and t-test SPSS V. 24 software. Results: From the total of 2500 cases, 345 (13.8%) cases were positive for Blastocystis sp., 56.5% of patients were male, and 43.5% were female. A total of 33.3% of patients had a clinical symptom and 66.7% of patient had no clinical symptoms. Anorexia was the most common symptom in patients with Blastocystis sp. Conclusions: The use of appropriate diagnostic laboratory procedures in hospitals and medical centers can provide an effective and accurate diagnosis that will play an important role in the promotion of community health; considering some unspecific signs could help the health professionals to have correct diagnose.