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Purpose Artificial intelligence (AI) and variant prioritization tools for genomic variant analysis are being rapidly developed for use in clinical diagnostic testing. However, their clinical utility and reliability are currently limited. Therefore, we performed a validation of a commercial AI tool (Moon) and a comprehensive reanalysis of previously collected clinical exome sequencing cases using an open-source variant prioritization tool (Exomiser) and the now-validated AI tool to test their feasibility in clinical diagnostics. Methods A validation study of Moon was performed with 29 positive cases determined by previous manual analysis. After validation, reanalysis was performed on 80 previously manually analyzed nondiagnostic exome cases using Moon. Finally, a comparison between Moon and Exomiser was completed regarding their ability to identify previously completed positive cases and to identify new positive cases. Results Moon correctly selected the causal variant(s) in 97% of manually analyzed positive cases and identified 7 new positive cases. Exomiser correctly identified the causal gene in 85% of positive cases and agreed with Moon by ranking the new gene in its top 10 list 43% of the time. Conclusion The use of AI in diagnostic laboratories greatly enhances exome sequencing analysis by reducing analysis time and increasing the diagnostic rate.

Background: Commensal microflora such as Escherichia coli and Enterococcus spp. are representative indicators of antimicrobial resistance (AMR) as they are part of the normal intestinal microflora and can acquire and disseminate AMR to pathogenic or zoonotic bacteria like Salmonella spp. Objective: To investigate the state of AMR among E. coli and Salmonella spp., potential pathogens in humans, isolated from cecal contents of pigs submitted to a veterinary diagnostic laboratory in Colombia from 2016 to 2019. Methods: Susceptibility testing was conducted using the Kirby-Bauer disk diffusion method according to the Clinical and Laboratory Standards Institute guidelines for antimicrobial zone diameter breakpoints. An E. coli strain (ATCC 25922) was used as the quality control organism. Isolates showing resistance to three or more antimicrobial classes were classified as multidrug-resistant (MDR) as defined by a joint group of the European Centre for Disease prevention and Control and the Center for Disease Control and Prevention of the USA. Results: A total of 112 E. coli and 192 Salmonella spp. colonies were isolated from 557 samples received between 2016 and 2019. In order of decreasing frequency, E. coli was resistant to tetracycline (100%), sulfamethoxazol-trimethoprim (97.5%), amoxicillin (86.4%), enrofloxacin (82.6%), tylosin (82.1%), doxycycline (59%), neomycin (50%), ciprofloxacin (45.5%), ceftiofur (35%), gentamicin (30%), tilmicosin (29%), and fosfomycin (12.5%). When compared with E. coli, Salmonella spp. was generally resistant to the same agents with slightly less resistance (between 10-30%) to eight of the antimicrobials tested. Salmonella spp. showed

The Kenney–Doig scale is a histopathology categorization (grading) system often used as the standard for assessing endometrial disease and communicating prognostic fertility information for equine breeding prospects. We investigated how Kenney–Doig categories compared within the same institution and across different institutions to determine if observer variability may contribute to category frequencies. We conducted a retrospective analysis of all equine endometrial submission records between 1998 and 2018 at the Western College of Veterinary Medicine (WCVM) and Prairie Diagnostic Services (PDS). Of 726 biopsies, we found the following category distribution: 46 of 726 (6.3%) I, 307 of 726 (42.3%) IIA, 326 of 726 (44.9%) IIB, and 47 of 726 (6.5%) III. We also conducted a review of the literature and included 6 studies reporting Kenney–Doig category distributions. Chi-square analysis showed significant differences between the category distribution found at WCVM and PDS and the category distribution reported in the 6 studies. To account for differences in mare populations, individual category distributions were generated for 5 pathologists at the WCVM and PDS. The Fisher exact test among these 5 Kenney–Doig categories revealed significant differences in category tendencies, suggesting that observer variation affects the use of the scale. Our results suggest that there is a need for prospective inter-rater and intra-rater agreement studies of the repeatability of the Kenney–Doig scale.

Purpose Making a diagnosis from clinical genomic sequencing requires well-structured phenotypic data to guide genotype interpretation. A patient's phenotypic features can be documented using the Human Phenotype Ontology (HPO), generating terms used to prioritize genes potentially causing the patient's disease. We have developed GenomeDiver to provide a user interface for clinicians that allows more effective collaboration with the clinical diagnostic laboratory, with the goal of improving the success of the diagnostic process. Methods GenomeDiver uses genomic data to prompt reverse phenotyping of patients undergoing genetic testing, enriching the amount and quality of structured phenotype data for the diagnostic laboratory, and helping clinicians to explore and flag diseases potentially causing their patient's presentation. Results We show how GenomeDiver communicates the clinician's informed insights to the diagnostic lab in the form of HPO terms for interpretation of genomic sequencing data. We describe our user-driven design process, the engineering of the software for efficiency, security and portability, and examples of the performance of GenomeDiver using genomic testing data. Conclusion GenomeDiver is a first step in a new approach to genomic diagnostics that enhances laboratory–clinician interactions, with the goal of directly engaging clinicians to improve the outcome of genomic diagnostic testing. Graphical Abstract Unlabelled Image

Purpose of review Sympathetic ophthalmia is a bilateral granulomatous uveitis that occurs following unilateral trauma or surgery and is sight-threatening in the contralateral eye. Despite significant potential morbidity, disease remains poorly understood. Variable presentations and clinical courses, as well as a lack of definitive diagnostic laboratory tests can complicate the diagnosis and result in delayed treatment, which can beget permanent vision loss. This review focuses on recent advances in areas of pathophysiology, classification, diagnosis and treatment. Recent findings Sympathetic ophthalmia is thought to involve a cell-mediated immune response to retinal and uveal antigens exposed through trauma or surgery. Multiple mechanisms have been implicated, including activation of the interleukin-23/IL-17 pathway. Ongoing emphasis is placed on early disease recognition and prompt treatment with multimodal imaging. Multiple authors advocate for the routine use of optical coherence tomography (OCT) for screening and disease monitoring. Systemic steroids and steroids sparing-immunosuppressive agents remain the mainstay of treatment. Summary Understanding pathophysiology may provide useful targets for drug development, as well as allow for identification of patients at risk. OCT is a useful tool in early diagnosis and management of sympathetic ophthalmia, as OCT changes may precede clinical symptoms and signs, allowing for early disease detection and better visual outcomes.

In vivo confocal microscopy (IVCM) is a relatively new ocular imaging technique that permits morphological and quantitative assessment of the living cornea on the cellular level. The applications for IVCM in clinical ophthalmology are numerous and diverse. There are several advantages inherent to IVCM over standard diagnostic techniques currently used to confirm a diagnosis of infectious keratitis in veterinary ophthalmology. With IVCM, images can be viewed in real-time providing immediate diagnostic information. Traumatic corneal sampling techniques are avoided, and the procedure can be repeated as frequently as is clinically indicated without risk of corneal tissue damage. Both superficial and deep corneal lesions can be evaluated by IVCM in an atraumatic fashion. Microorganism viability is not required for their detection and specialized diagnostic laboratory assay procedures are not necessary. Many larger infectious agents can be directly identified within corneal lesions by IVCM, including fungi and parasites such as Acanthamoeba spp. In other situations, such as bacterial infectious crystalline keratopathy, the biological systems associated with the microorganism can be detected within the cornea. The current resolution of IVCM is inadequate to directly visualize some corneal infectious agents, such as herpesviruses, but host responses and virus-infected epithelial cells can be identified. This review summarizes the current knowledge and applications of IVCM in the management of infectious keratitis in veterinary ophthalmology, including its use in animals with bacterial, fungal, parasitic, and viral keratitis.

Background The uncertainty of how neurosyphilis is diagnosed and treated in clinical settings led us to investigate whether this serious manifestation of syphilis infection is properly managed in China. Methods: This national cross-sectional study of the diagnosis and treatment of neurosyphilis included 1392 clinicians at 398 hospitals located in 116 cities in China. Results: Of 398 hospitals, 244 (61.3%) failed to perform diagnostic laboratory tests and 181 (45.5%) failed to provide recommended treatment for neurosyphilis. Of 1392 clinicians, 536 (38.5%) had previously diagnosed patients with neurosyphilis, but 419 (78.2%) of the latter provided diagnoses that did not meet the criteria set by national guidelines. Of the 485 clinicians who had previously treated patients with neurosyphilis, 280 (57.7%) failed to follow national guidelines for treatment. Analysis indicated that clinicians working in North China (adjusted odds ratio (aOR), 4.24; 95% confidence interval (CI), 1.65–10.88), tertiary hospitals (aOR, 3.23; 95% CI, 1.63–6.41), and hospitals specialising in sexually transmitted infections (aOR, 2.49; 95% CI, 1.24–4.99) were more likely to follow national guidelines for neurosyphilis treatment. Conclusion: Lack of knowledge in disease management poses a great obstacle to prevent the serious consequences of neurosyphilis in Chinese patients. More effective measures are urgently needed to improve this suboptimal situation.

Salmonella organisms are widely distributed in nature and survive well in a variety of food and contamination and can occur at multiple steps along the food chain. The study was conducted at the Central Diagnostic Laboratory of the National Veterinary Research Institute (N.V.R.I) located in Vom Jos South Local Government Area of Plateau State Nigeria. Information was obtained via postmortem records and laboratory results that isolated Salmonella species were retrieved and analyzed retrospectively in the study area for five years. Descriptive statistics were used to analyze data while tables were used for result proportions presented in percentages. A total of 2512 cases of poultry diseases were documented for a period of five years from 2015 to 2019 with an average of 502.4 cases annually. A total of 436 of salmonellosis was documented during the period under review and an average of 87.2 cases annually. 24.4% prevalence was recorded in 2018 and 12.4% in 2015. 2019 had the highest prevalence of 28.4 with an average avian salmonellosis prevalence of 19%. 24.6% avian salmonellosis was recorded in the age bracket of 5 to 8 weeks, 29.5% was documented in the age bracket of 9 to 12 weeks which was the second highest and 33.3% in the age bracket of 0 to 4 which was the highest. Avian salmonellosis affects all types of birds. Out of 436 positive avian salmonellosis cases recorded in the period under review, 251 were layers while 156 were broilers with 29 being local birds and cockerels. This study does explicitly indicate that avian salmonellosis is highly prevalence in the study area and this could play a great role in lowering poultry productivity in the study area, thereby highlighting the need for effective health programs like good biosecurity practices and vaccination in order to boost poultry production.

Background Rates of detecting ≥1 potential enteric pathogens (PEP) or toxins (PEP-T) in feces, blood, or both of horses ≥6 months of age with enteric disease and impact of multiple detections on outcome of horses with colitis has not been reported. Objective To determine detection rates of PEP/PEP-T in feces, blood, or both of horses with enteric disease and effect of detecting multiple agents on outcome of horses with colitis. Animals Thirty-seven hundred fifty-three fecal samples submitted to IDEXX Laboratories and 239 fecal and blood samples submitted to Michigan State University's Veterinary Diagnostic Laboratory (MSUVDL). Methods Retrospective evaluation of PEP/PEP-T testing results was performed to determine rates of detection of 1 or more PEP/PEP-T. Impact of detecting multiple agents on outcome was assessed in 239 horses hospitalized for colitis. Results One or more PEP/PEP-T was detected in 1175/3753 (31.3%) and 145/239 (60.7%) of samples submitted to IDEXX Laboratories and MSUVDL, respectively. In a hospitalized cohort, survival to discharge was lower (76%) in horses with 1 agent, compared to horses with either no (88%) or multiple (89%) agents. There was no difference (P = .78) in days of hospitalization between horses with 0 (1-17), 1 (1-33), and > 1 positive (1-20) result. There was no difference in cost of hospitalization (P = .25) between horses with 0 ($2357, $1110-15 553), 1 ($2742, $788-11 005), and >1 positive ($2560, $1091-10 895) result. Conclusions and clinical importance Detection rates of PEP/PEP-T in horses with colitis vary with cohorts and tests performed. Detection of more than 1 PEP or PEP-T did not affect outcome.

In 2017, a single adult Triatoma sanguisuga (LeConte) (Hemiptera: Reduviidae) was identified from Indian Cave State Park in Nemaha County, NE. The following summer, a single adult specimen was found in a 4-H insect collection at the Nebraska State Fair from Richardson County. A subsequent investigation found that these were collected from a residence in Richardson County and three more adults were collected in 2019. In 2020, the latter three kissing bugs were submitted to Public Health Command-Central’s DoD Food Analysis and Diagnostic Laboratory (DOD FADL) for confirmatory species identification and diagnostic testing for Trypanosoma cruzi, the causative agent of Chagas disease. One specimen tested positive for T. cruzi using a real-time dual-target PCR screen followed by confirmatory dual-target traditional PCR. Based on these findings, a survey plan was developed for Richardson and surrounding counties in southeast Nebraska. In July of 2020, two adult and seven nymphs (multiple instars) of T. sanguisuga were collected in Richardson County, one of which tested positive for T. cruzi. This is the first record of an established population of T. sanguisuga and T. cruzi-infected kissing bugs in Nebraska.

The recent spread of novel and highly variant pathogenic viruses, including the coronavirus (SARS-CoV-2), has increased the demand for diagnostic testing for rapid confirmation. This has resulted in investigating the functional capability of each space, and preparing facility guidelines to secure the safety of medical technologists. During viral evaluations, there is a requirement of negative pressure facilities along with thread separation, during pre-treatment of samples and before nucleic acid amplification. Space composition therefore needs to be planned by considering unidirectional air flow. This classification of safety management facilities is designated as biosafety level 2, and personal protective equipment is placed accordingly. In case of handling dangerous materials, they need to be carried out of the biosafety cabinet, and sterilizers are required for suitable disposal of infectious agents. A common feature of domestic laboratories is maintenance of the sample pre-treatment space at a negative pressure of −2.5 Pa or less, and arranging separate pre-treatment and reagent preparation spaces during the test process. We believe that the data generated in this study is meaningful, and offers an efficient direction and detailed flow for separation of the inspection process and space functions. Moreover, this study introduces construction of the laboratory by applying the safety management standards.

Background Mild to moderate bleeding disorders are a diagnostic challenge. Many patients remain undiagnosed despite thorough and repeated laboratory testing. Thrombin generation (TG) is an overall assay measuring the functionality of the hemostatic system and may be a useful tool in diagnosing patients with bleeding tendency. Objectives We examined the added value of TG in patients with mild bleeding tendency with and without diagnosis after classical laboratory testing. Further, we investigated the role of different expressions of results, between-method variation, and reference ranges. Methods TG of patients and controls was measured in parallel by two TG platforms (ST Genesia and calibrated automated thrombogram [CAT]). All TG parameters in patient and control groups were compared by statistical analysis (Mann-Whitney U tests) including visual representation with box-and-whisker plots. Results were expressed as normalized ratios (ST Genesia and CAT) or corrected values (ST Genesia). Reference intervals were calculated to which patient results were compared. We studied lot-to-lot reagent variability for both platforms. Results In 62.7% (ST Genesia) to 69.5% (CAT) of patients undiagnosed with a traditional laboratory work-up, abnormal TG parameters (lag time and endogenous thrombin potential expressed as normalized ratio and/or corrected value) were detected. In the group of previously diagnosed patients, abnormal parameters were found in 58.1% of patients for both TG assays. No relevant lot-to-lot reagent variability was observed. Conclusions Adding TG helps with diagnosing patients with mild bleeding disorder. TG seems a promising tool in diagnosis of bleeding tendency, but further evaluation is necessary before application in diagnostic laboratory testing.

Precise molecular diagnosis of pathogenic bacterial infections decreases the spread of the disease and facilitates to make suitable disease management strategies. Advanced molecular diagnostics has taken a noticeable place and has revealed advantageous in diagnostic laboratory for routine detection, fingerprinting and epidemiologic analysis of infectious microorganisms. Molecular tests reduce the exposure to infectious agents and decreases the health risk for the consumers. This review aims to discuss our most recent of state-of-the-art molecular diagnostic techniques enabling fast and accurate detection and identification of plant and food borne pathogens based on well-developed genotyping techniques like polymerase chain reaction, Multiplex PCR, RT PCR, LAMP, LSSP PCR and SSCP PCR assay.

Background: Diarrhoea is a major cause of morbidity in Cape Town, South Africa, and mortality is attributed to a failure to recognize the severity of the condition. Cryptosporidium and Giardia are increasingly recognized as important causes of diarrhoea in Africa however, suboptimal diagnostic techniques may lead to underappreciation of their significance. Our objectives are to compare the diagnostic yield of direct immunofluorescent antigen (DFA) microscopy on concentrated stool samples for Cryptosporidium and Giardia, with the current approach of wet mount microscopy for Giardia and auramine fluorescent stain for Cryptosporidium on unconcentrated stool.Methodology: Stool specimens (n=104) received at our hospital laboratory for routine microbiological investigations were used for the study. Direct wet-mount auramine-phenol fluorescent microscopy (auramine) detection of Cryptosporidium oocysts and wet mount iodine microscopy for Giardia detection, were performed on unconcentrated stool samples, while DFA stain for simultaneous detection of Cryptosporidium and Giardia was performed on sodium-acetate formalin concentrated stool samples. The diagnostic yields of the tests were compared using the MEDCALC® version 18.0Results: Of the 104 stool specimens received for microbiological analysis, only 66 (63.5%) had specific Cryptosporidium requests while 38 (36.5%) had no Cryptosporidium specific requests. Of the 66 specimens, 9 (13.6%) were positive for Cryptosporidium oocysts with DFA while only 1 (1.5%) was positive with auramine staining (p=0.013). The one auramine-positive specimen was also positive by DFA. Auramine stain microscopy gave a sensitivity of 11.1% (95%CI: 0.28-48.25%) and specificity of 100% (95%CI: 93.7%-100%) when compared to DFA. Of the 38 stool specimens without specific Cryptosporidium request, DFA yielded 5 (13.2%) additional positive results. Taken together, Cryptosporidium was detected in 14/104 (13.5%; 95%CI: 8.36–21.7%) specimens and only 1 of 14 (7.1%) specimens with the current routine laboratory testing approach. Giardia was detected by DFA in 3/104 (0.9%) specimens, while direct iodine wet mount microscopy did not yield any positive results (0%). All 3 Giardia-positive specimens had Cryptosporidium oocysts detected by DFA.Conclusion: These data suggest that a large proportion of Cryptosporidium cases remain undetected by the laboratory due to suboptimal testing methods, and failure by clinicians to specifically request for Cryptosporidium detection. There is need to periodically assess the effectiveness of diagnostic microbiology laboratory approaches to diarrhoea, and access to improved diagnostic laboratory techniques will contribute to more accurate differential diagnosis and a broadened understanding of local aetiology of diarrhoea diseases in Africa. Keywords: Cryptosporidium, Giardia, diarrhoea, stool concentration, DFA, microscopy French Title: Amélioration des découvertes de cas de Cryptosporidium à l'aide de la microscopie immunofluorescente sur des selles concentrées Contexte: La diarrhée est une cause majeure de morbidité au Cap, en Afrique du Sud, et la mortalité est attribuée à l'incapacité de reconnaître la gravité de la maladie. Cryptosporidium et Giardia sont de plus en plus reconnus comme des causes importantes de diarrhée en Afrique, cependant, des techniques de diagnostic sous-optimales peuvent conduire à une sous-estimation de leur importance. Nos objectifs sont de comparer le rendement diagnostique de la microscopie à antigène immunofluorescent direct (DFA) sur des échantillons de selles concentrées pour Cryptosporidium et Giardia, avec l'approche actuelle de la microscopie à montage humide pour Giardia et la coloration fluorescente auramine pour Cryptosporidium sur des selles non concentrées.Méthodologie: Des échantillons de selles (n=104) reçus au laboratoire de notre hôpital pour des examens microbiologiques de routine ont été utilisés pour l'étude. La détection directe par microscopie fluorescente auramine-phénol à montage humide (auramine) des oocystes de Cryptosporidium et la microscopie à l'iode à montage humide pour la détection de Giardia, ont été effectuées sur des échantillons de selles non concentrées, tandis que la coloration DFA pour la détection simultanée de Cryptosporidium et de Giardia a été réalisée sur de l'acétate de sodium formaline concentré échantillons de selles. Les rendements diagnostiques des tests ont étécomparés à l'aide de MEDCALC® version 18.0Résultats: Sur les 104 échantillons de selles reçus pour l'analyse microbiologique, seuls 66 (63,5%) avaient des demandes spécifiques de Cryptosporidium tandis que 38 (36,5%) n'avaient pas de demandes spécifiques de Cryptosporidium. Sur les 66 échantillons, 9 (13,6%) étaient positifs pour les oocystes de Cryptosporidium avec DFA tandis que seulement 1 (1,5%) était positif avec coloration à l'auramine (p=0,013). Le seul échantillon positif à l'auramine était également positif au DFA. La microscopie à l'auramine a donné une sensibilité de 11,1% (IC 95%: 0,28-48,25%) et une spécificité de 100% (IC 95%: 93,7% -100%) par rapport au DFA. Sur les 38 échantillons de selles sans demande spécifique de Cryptosporidium, le DFA a donné 5 (13,2%) résultats positifs supplémentaires. Pris ensemble, Cryptosporidium a été détecté dans 14/104 (13,5%; IC à 95%: 8,36–21,7%) et seulement 1 des 14 échantillons (7,1%) avec l'approche actuelle des tests de routine en laboratoire. Giardia a été détecté par DFA dans 3/104 (0,9%) échantillons, tandis que la microscopie directe à l'iode sur monture humide n'a donné aucun résultat positif (0%). Les 3 échantillons positifs à Giardia avaient des oocystes deCryptosporidium détectés par DFA.Conclusion: Ces données suggèrent qu'une grande proportion des cas de Cryptosporidium ne sont pas détectés par le laboratoire en raison de méthodes de test sous-optimales et de l'échec des cliniciens à demander spécifiquement la détection de Cryptosporidium. Il est nécessaire d'évaluer périodiquement l'efficacité des approches de laboratoire de microbiologie diagnostique pour la diarrhée, et l'accès à des techniques de laboratoire de diagnostic améliorées contribuera à un diagnostic différentiel plus précis et à une compréhension élargie de l'étiologie locale des maladies diarrhéiques en Afrique. Mots clés: Cryptosporidium, Giardia, diarrhée, concentration des selles, DFA, microscopie

Context Implementation of quality management system (QMS) which encompasses various quality indicators (QIs), can serve as a stepping stone for continuous improvement & help in achieving globally accepted quality standards in a diagnostic laboratory. Aims To generate preliminary data on trends of post-analytical QIs in Bacteriology section. Settings and design A pilot study was conducted at a tertiary care teaching hospital located in Rishikesh, Uttarakhand. Methods and material Data of the following four quality indicators pertaining to aerobic culture and sensitivity testing of various clinical samples received in Clinical Bacteriology laboratory was compiled and retrospectively analysed: (i) Rate of reporting errors; (ii) Rate of re-dos; (iii) Percentage of reports correlating with clinical diagnosis; (iv) Percentage of adherence to safety precautions by employees working in diagnostics. Statistical analysis used Descriptive statistics like mean and frequency distribution plots. Results The mean reporting error rate was 0.12 per 1000 tests. It was consistently low from July 2018 to May 2019, after which an overall increasing trend was observed. The mean rate of re-dos was 2.79 per 1000 tests. An overall decreasing trend was observed with maximum rates during the months of December 2017 and January 2018. On an average only 7.86% of the reports co-related with clinical diagnosis. Almost 100% adherence to safety precautions was observed with the exception of two instances of needle stick injuries (NSIs). Conclusions Commitment of laboratory personnel in adopting, maintaining and analysing QMS data will lead to further strengthening of our existing healthcare system.

BackgroundSince the emergence of the COVID-19, health officials have struggled to devise strategies to counteract the speed of the pandemic’s spread across the globe. It became imperative to implement accurate diagnostic tests for the detection of SARS-CoV-2 RNA on respiratory samples. In many places, however, besides the limited availability of test reagents, laboratory personnel face the challenge of adapting their working routines to manipulate highly infective clinical samples. Here, we proposed the use of a virus-inactivating solution as part of a sample collection kit to decrease the infectious potential of the collected material without affecting the integrity of RNA samples used in diagnostic tests based on RT-qPCR.MethodsNasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. RNA extracted from all samples was tested by RT-qPCR using probes for viral and human genes. Exposure of laboratory personnel to infective viruses was also accessed using ELISA tests.FindingsThe use of the DS did not interfere with the detection of viral genome or the endogenous human mRNA, since similar results were obtained from samples collected with VTM or DS. In addition, all tests of laboratory personnel for the presence of viral RNA and IgG antibodies against SARS-CoV-2 were negative.InterpretationThe methodology described here provides a strategy that allow high diagnostic accuracy as well as safe manipulation of clinical samples by those involved with diagnostic procedures.FundingCAPES, FAPEMIG, CNPq, MCTIC, FIOCRUZ and the UK Global Challenges Research Fund (GCRF).

Antemortem blood biochemical and blood gas analyses are routinely used in health screening and diagnosis of disease in domestic veterinary species. These testing modalities are not routinely performed in poultry, in part, due to the distance from the diagnostic laboratory. Portable blood analyzers such as the i-STAT and VetScan (VS2) can be used to obtain results on the farm without delay, potentially offering a more practical option for poultry practitioners. We investigated the time effect on blood chemistry values and compared the results obtained using the i-STAT and VS2 with those obtained using conventional laboratory analyzers (GEM Premier 3000 and Cobas c501, respectively). We tested blood from 60 healthy chickens. Each sample was tested in triplicate using each of the portable analyzers and once using conventional analyzers. All samples were analyzed within 60 minutes of collection. The concentrations of some analytes were outside the limit of detection of the portable analyzers (i.e., bile acids). Although statistically significant differences were found for some biochemical analytes over time, the actual mean or median differences were too small to be considered of clinical importance. As observed in mammals, significant time-dependent changes in blood gas analytes were observed in whole blood samples exposed to ambient air. Correlation coefficients between portable and conventional analyzers were moderate to high for most of the analytes. For the most part, there was an agreement between the portable and conventional analyzers. We identified constant and proportional biases in the measurement of multiple analytes by both the i-STAT and VS2. Future studies are warranted to establish analyzer-specific reference intervals for poultry.

Objective: To determine the vitamin D deficiency in pregnant women presented at tertiary care Hospital with gestational diabetes. Methodology: This case control study has been conducted at gynecology department of Liaquat University of Medical and health Sciences, during one year from 2018 to 2019. Women having diagnosed as gestational diabetes, age more than 18 years and equal quantity of non-diabetic pregnant women were included in the study. A 5ml blood sample was taken from each patient and sent to the Hospital diagnostic laboratory to assess the vitamin D level. All the data was collected via self-made proforma. Data was analyzed by using SPSS version 20. Results: Total 80 women with gestational diabetes and of non-gestational diabetes were studied. Mean age of the women was 34.23±12.3 years and mean gestational age was 29.34±5.7 weeks. Vitamin D deficiency was significantly high in women having gestational diabetes (P=0.0001). There was no difference in vitamin D deficiency according to occupation, residence, SES, booking status and parity. Conclusion: Vitamin D deficiency was significantly high in women having gestational diabetes as compared to normal women. By early assessment of vitamin D deficiency and its management can be reduce the risk of gestational diabetes.

The COVID-19 pandemic, associated with the new coronavirus SARS-CoV-2, has caused a surge in incidence worldwide, as well as a severe crisis in global health and economy. Therefore, fast and accurate diagnosis of infection is key to timely treatment and elimination of the spread of the virus. Currently, the standard method for detecting coronavirus is reverse transcription polymerase chain reaction (RT-PCR). However, this method requires expensive equipment and trained personnel, which limits the conduct of mass testing and lengthens the time to obtain a research result. Serological tests for antibodies against SARS-CoV-2 and the determination of protective immunity in various populations are used to retrospectively identify patients with asymptomatic and mild forms of infection, monitor the course of infection in hospitalized patients, and also track contacts and epidemiological surveillance. The use of standard methods for diagnosing COVID-19 in conditions of mass morbidity, especially in conditions of insufficient resources and lack of appropriate infrastructure, is associated with a number of limitations. Therefore, the search and development of new, fast, inexpensive, simple, device-free and no less sensitive and specific tests is an urgent task. Therefore, the search and development of new, fast, inexpensive, simple, device-free and no less sensitive and specific tests is an urgent task. The review examines new laboratory technologies for diagnosing a new infection - loop isothermal amplification (LAMP) and immunochromatographic analysis (ICA), which can become a real alternative to the used molecular and enzyme immunoassay methods. The dynamic development of these methods in recent years expands the prospects for their use both for diagnosing COVID-19 and monitoring a pandemic.

The first case of the coronavirus SARS-CoV-2 infection was confirmed in December 2019 in Wuhan, China, from whence the virus spread across the world within several weeks. Due to the alarming level of infections, the World Health Organisation (WHO) announced a SARS-CoV-2 pandemic on 12 March. This dynamic and unprecedented epidemiological situation created an urgent need to carry out SARS-CoV-2 tests in individuals meeting the criteria defined for COVID-19 suspect cases. According to the current WHO recommendations, active SARS-CoV-2 infection diagnostics is based on molecular method using a real-time reverse transcription – polymerase chain reaction (real-time RT-PCR). Highly specific and sensitive, this method makes it possible to detect even a small amount of RNA particles of the virus in the tested sample. Undoubtedly, the launch of new COVID laboratories and the implementation of adequate procedures increases the effectiveness of activities aimed at directly combatting the SARS-CoV-2 pandemic. The population of oncological patients is particularly exposed to the risk of complications and death resulting from the SARS-CoV-2 infection; therefore it is essential to ensure them the possibility of quick testing for COVID-19. This article presents the authors’ own experiences as well as technical and formal issues related to the launching of a SARS-CoV-2 laboratory.

The delivery of diagnostic laboratory services has undergone significant change in recent years. Specifically, clinical microbiology laboratories are being asked to become more efficient and to utilize health care dollars more effectively while still providing the highest level of care for patients and meeting the needs of health care providers. In some cases, this has led to the need to centralize and consolidate the clinical microbiology laboratory. Here, we discuss the key points to consider surrounding centralization and consolidation of microbiology services during these uncertain times, many of which we have encountered ourselves. We present a methodical approach to assess the factors associated with consolidation, including topics related to management of the microbiology laboratory and ensuring that quality patient care stays at the center of the decision-making process, all while maintaining efficiency and compliance with regulatory guidelines.

Food protein-induced enterocolitis syndrome is still a mysterious disease, pathogenically poorly characterized, although the first FPIES case has been described in 1967. Mainly, food protein-induced enterocolitis syndrome diagnosis is based on clinical history. The oral food challenge remains the gold standard to confirm the diagnosis, especially in particular situations. Although there are no diagnostic laboratory or imaging tests which are specific for diagnosis, they could, however, sometimes be helpful to rule out clinical conditions which are similar to food protein-induced enterocolitis syndrome reactions. The purpose of this review is to define the clinical features of FPIES and to summarize the current available tools for the diagnosis of FPIES. This review is intended to be a practical guide for the clinician facing a patient with food protein-induced enterocolitis syndrome avoiding delayed diagnosis with unnecessary laboratory tests and detrimental treatments. Moreover, it highlights the unmet needs in diagnosis that require urgent attention from the scientific community to improve the management of patients with FPIES.

The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) workshop on genomics and metagenomics was held in Lausanne from 9th to 12th September 2019. As many as 68 participants from 20 countries from all 5 continents participated to this postgraduate technical workshop. During 4 days, the participants shared their time between conferences on various topics related to the implementation of genomics and metagenomics in a clinical diagnostic laboratory. These included talks from the clinics and talks from bioinformatic experts. A significant time was also dedicated to practicals covering various aspects of the data analysis of NGS sequences (quality check, annotation of virulence and antibiotic resistance genes, taxonomic assignment of amplicons, strain typing, …). This ESCMID meeting co-organized by A Lebrand and G Greub, with the help of the European Study Group for Genomics ad Molecular Diagnostics (ESGMD) provided a unique opportunity to exchange knowledge and ideas on the most recent bioinformatic approaches, as well as how to report such NGS results in diagnostic laboratories. This meeting report summarizes the key messages of this meeting.

Objective Diagnosis of systemic lupus erythematosus (SLE) made by standard diagnostic laboratory tests (SDLTs) has sensitivity and specificity of 83% and 76%, respectively. A multivariate assay panel (MAP) combining complement C4d activation products on erythrocytes and B cells with SDLTs yields a sensitivity and specificity of 80% and 86%, respectively, presumably enabling earlier SLE diagnosis at lower severity, with associated lower health care costs compared with SDLT diagnoses. We compared the payer budget impact of diagnosing SLE using MAP (incremental cost of $108) versus SDLTs. Methods We modeled a health plan of 1 million enrollees. SLE diagnosis among suspected patients was 9.2%. The MAP arm assumed 80%/20% of patients were tested with MAP/SDLTs, versus 100% tested with SDLTs in the SDLT arm. Prediagnosis direct costs were estimated from claims data, and postdiagnosis costs were obtained from the literature. Based on improved MAP performance, the assumed hazard ratio for diagnosis rate compared with SDLTs was 1.74 (71%, 87%, 90%, and 91% of patients who develop SLE are diagnosed in years 1 to 4 compared with 53%, 75%, 84%, and 88% of patients diagnosed with SDLTs). Results Total 4-year pre- and postdiagnosis direct costs for patients with suspected SLE tested with MAP were $59 183 666 compared with $61 174 818 tested by SDLTs, with lower costs in the MAP arm due primarily to prediagnosis savings related to reduced hospital admissions. Conclusion Incorporating MAP into SLE diagnosis results in estimated 4-year direct cost savings of $1 991 152 ($0.04 per member per month). By facilitating earlier diagnosis of SLE, MAP may enhance patient outcomes.