Search

Introduction The rapid increase of extended-spectrum beta-lactamase (ESBL)-producing pathogens makes it difficult to choose appropriate antimicrobials in patients with Gram-negative bacterial infection. The Cica-beta reagent (Kanto Chemical, Tokyo, Japan) is a chromogenic test that detects ESBLs from bacterial colonies. This study aimed to reveal whether Cica-beta reagent could detect ESBLs directly from urine samples to facilitate rapid diagnosis of antibiotic susceptibility. Methods A prospective study was conducted from July 2019 to November 2019. Patients in whom urine culture tests were performed were eligible. Each urine sample was centrifuged, and the pellet was mixed with Cica-beta reagent. The test was considered positive when the enzymatic reaction turned from yellow to red or orange. Results In total, 350 urine samples were analysed. Urinary tract infection (UTI) was diagnosed in 214 patients. ESBL-producing Enterobacterales were isolated from 79 samples. The Cica-beta test showed sensitivity of 79.8% and specificity of 99.3% in patients with Gram-negative bacteriuria. Sensitivity and specificity improved to 90.2% and 100%, respectively, in patients with UTI. Conclusion The Cica-beta test could be an efficient test for the detection of ESBL-producing pathogens in urine. By providing immediate information about ESBLs, it might be a useful point-of-care test to guide appropriate antimicrobial use in patients with UTI.

BACKGROUND Mycobacterium mucogenicum (M. mucogenicum) belongs to the group of rapidly growing Nontuberculous mycobacteria. This microorganism is associated with a wide spectrum of infectious diseases. Due to a low detection rate or the time required for conventional culture methodology, a rapid and broad-spectrum method is necessary to identify rare pathogens. CASE SUMMARY A 12-year-old immunocompetent girl presented with painful masses for five months. The first mass was found in the right upper quadrant of the abdomen, and was about 1 cm × 1.5 cm in size, tough but pliable in texture, with an irregular margin and tenderness. An abscess gradually formed and ulcerated with suppuration of the mass. Three new masses appeared on the back one by one. Chest computed tomography showed patchy and streaky cloudy opacities in both lungs. Needle aspiration of the abscess was performed, but the smear and conventional culture were negative, and the pathological examination showed no pathogens. We then performed next-generation sequencing using a formalin-fixed, paraffin-embedded specimen to identify the pathogen. A significantly high abundance of M. mucogenicum was detected. The patient’s abscesses gradually decreased in size, while inflammation in both lungs improved following 12-wk of treatment. No recurrence was observed four months after the end of the one-year treatment period. CONCLUSION Next-generation sequencing is a promising tool for the rapid and accurate diagnosis of rare pathogens, even when using a formalin-fixed, paraffin-embedded specimen.

BackgroundProbe electrospray ionization-mass spectrometry (PESI-MS) can rapidly visualize mass spectra of small, surgically obtained tissue samples, and is a promising novel diagnostic tool when combined with machine learning which discriminates malignant spectrum patterns from others. The present study was performed to evaluate the utility of this device for rapid diagnosis of colorectal liver metastasis (CRLM).MethodsA prospectively planned study using retrospectively obtained tissues was performed. In total, 103 CRLM samples and 80 non-cancer liver tissues cut from surgically extracted specimens were analyzed using PESI-MS. Mass spectra obtained by PESI-MS were classified into cancer or non-cancer groups by using logistic regression, a kind of machine learning. Next, to identify the exact molecules responsible for the difference between CRLM and non-cancerous tissues, we performed liquid chromatography-electrospray ionization-MS (LC-ESI-MS), which visualizes sample molecular composition in more detail.ResultsThis diagnostic system distinguished CRLM from non-cancer liver parenchyma with an accuracy rate of 99.5%. The area under the receiver operating characteristic curve reached 0.9999. LC-ESI-MS analysis showed higher ion intensities of phosphatidylcholine and phosphatidylethanolamine in CRLM than in non-cancer liver parenchyma (P P ConclusionThe combination of PESI-MS and machine learning distinguished CRLM from non-cancer tissue with high accuracy. Phospholipids categorized as monounsaturated fatty acids contributed to the difference between CRLM and normal parenchyma and might also be a useful diagnostic biomarker and therapeutic target for CRLM.

Objective The aim of this study was to assess the clinical utility of metagenomic next-generation sequencing (mNGS) on smear-negative extrapulmonary specimens collected in China. Methods Specimens were tested by mNGS and other routine tests for tuberculosis (TB). The diagnostic accuracy of mNGS was calculated and compared with the final clinical diagnosis. Results The sensitivity of mNGS was found to be significantly higher than the sensitivities of the other routine TB tests. Receiver operating characteristic curve analysis showed that mNGS achieved the highest area under the curve (AUC) value of 0.79. The mNGS positive rate was highest for tuberculous meningitis. All non-tuberculous extrapulmonary pathogens were directly and simultaneously detected. Conclusions mNGS appeared to be superior to all previous etiological tests for TB on smear-negative extrapulmonary specimens and could identify all possible pathogens at once within 48 h.

Background: Typhoid fever is a serious public health problem. It causes severe systemic infection in lesser developed areas of the world. Although blood culture is regarded as the gold standard for diagnosis, it is a time taking procedure. An early and accurate diagnosis is necessary for an effective treatment. Aims: The present study was done to comparatively evaluate rapid card and Widal slide agglutination tests for rapid diagnosis of typhoid cases. Settings and Design: The study design was a cross-sectional descriptive study done over a period of 6 months from January to June 2018. Materials and Methods: A total of 265 patients suspected of typhoid fever who gave their consent were included in the study whose blood samples were tested by both rapid card and Widal slide agglutination tests. Statistical Analysis Used: The collected data were analyzed using SPSS Data Editor Software version 20. Percentage of variables was calculated. Results: Of 265 patients, 97 patients were positive by the Widal slide test, whereas 113 patients were positive by the rapid card test, with 96.9% sensitivity and 88.7% specificity. Of 113 positives, 83 cases were positive for immunoglobulin M (IgM) only, whereas 30 cases were positive for both IgM and IgG. Conclusion: Rapid card test is a simple and easy to perform the diagnostic test for rapid detection of typhoid cases with an additional advantage of separate determination of IgM and IgG antibody, thereby aiding in identification of current infection and previous exposure so that appropriate and timely treatment could be given to the patients.

Objective Metagenomic Next-Generation Sequencing (mNGS) has been applied as a novel method of detection pathogens for infectious diseases, but its value in the rapid diagnosis of tuberculous meningitis(TBM)has not been clarified based on large samples. Methods A retrospective analysis was conducted on 51 inpatients with suspected TBM who underwent mNGS and four other tests in cerebrospinal fluid (CSF). Results Among 51 included patients, 45 cases were diagnosed as TBM (38 definite, 5 probable, 2 possible) and 6 cases as non-TBM. Using final diagnosis as reference standard, the sensitivity, specificity, PPV (positive predictive value), and NPV (negative predictive value) of mNGS in CSF for TBM were 84.44%(38/45, 69.94%–93.01%), 100%(6/6, 51.68%–100%), 100%(40/40, 88.57%–100%) and 46.15%(6/13, 20.40%–73.88%). The diagnostic sensitivity of mNGS(84.4%)was significantly higher than that of AFB (0%, P = 0.000), MGIT960 culture(22.2%, P = 0.000), MTB PCR(24.4%, P = 0.000) and Xpert MTB/RIF(40%, P = 0.000). The ROC curve showed that CSF protein quantification and CSF cell count might be valuable in the prediction of NGS positive detection of MTB (Mycobacterium tuberculosis). Conclusion CSF mNGS had high sensitivity, specificity and PPV in the diagnosis of TBM. Patients with a significant increase in CSF cell number and protein quantification might have a higher likelihood of positive MTB detection of NGS.

Tuberculosis (TB) is major health concern and reason of deaths from decades to current date. Even though with a lot of advancements, diagnostic techniques, and discovery of standard antibiotics TB remains crucial challenge and can create worst scenario for human health in near future. Nanoparticles play emerging role in diagnosis and treatment of TB. In this study, we developed mesoporous silica nanoparticles containing gold (MSNs@GNPs) for rapid diagnosis and treatment of TB. The physicochemical characterization revealed effective surface morphology and particles diameter, that is applicable for in vitro applications. The in vitro antimicrobial analysis revealed that the designed MSNs@GNPs has retained significantly lower minimal inhibitory concentration (MIC) values and can effectively demolish mycobacterium tuberculosis (Mtb). Furthermore, the diagnosis efficiency of the MSNs@GNPs was evaluated by calorimetric analysis. Which demonstrates that MSNs@GNPs can be used for rapid diagnosis of the tuberculosis when applied on in vitro culture of the Mtb. The current study needs further verification on human’s clinical samples from tuberculosis patients. However, MSNs@GNPs can be a versatile clinical approach for the rapid diagnosis and clinical treatment of the tuberculosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-021-03451-7.

Background Timely and accurate identification of uropathogens and determination of their antimicrobial susceptibility is paramount to the management of urinary tract infections (UTIs). The main objective of this study was to develop an assay using LAMP (Loop mediated isothermal amplification) technology for simple, rapid and sensitive detection of the most common bacteria responsible for UTIs, as well as for the detection of the most prevalent genes (encoding cefotaximases from CTX-M group 1) responsible for resistance to 3rd generation of cephalosporins. Method We designed primers targeting Proteus mirabilis, while those targeting Escherichia coli, Klebsiella pneumoniae and Enterococcus faecalis and the CTX-M group 1 resistance gene were benchmarked from previous studies. The amplification reaction was carried out in a warm water bath for 60 min at 63 ± 0.5 °C. The amplicons were revealed by staining with Sybr Green I. Specificity and sensitivity were determined using reference DNA extracts spiked in sterile urine samples. The analytical performance of the assays was evaluated directly on pellets of urine samples from patients suspected of UTI and compared with culture. Results We found a high specificity (100%) for LAMP assays targeting the selected bacteria (P. mirabilis, E. coli, K. pneumoniae, E. faecalis) and the CTX-M group 1 when using DNA extracts spiked in urine samples. The sensitivities of the assays were around 1.5 103 Colony Forming Units (CFU) /mL corresponding to the cut-off value used to define bacteriuria or UTIs in patients with symptoms. Out of 161 urine samples tested, using culture as gold standard, we found a sensitivity of the LAMP techniques ranging from 96 to 100% and specificity from 95 to 100%. Conclusion We showed that the LAMP assays were simple and fast. The tests showed high sensitivity and specificity using a simple procedure for DNA extraction. In addition, the assays could be performed without the need of an expensive device such as a thermal cycler. These LAMP assays could be useful as an alternative or a complementary tool to culture reducing the time to diagnosis and guiding for more effective treatment of UTIs but also as a powerful diagnostic tool in resource-limited countries where culture is not available in primary health care structures.

Background Testing individuals suspected of severe acute respiratory syndrome–like coronavirus 2 (SARS-CoV-2) infection is essential to reduce the spread of disease. The purpose of this retrospective study was to determine the false negativity rate of the LumiraDx SARS-CoV-2 Ag Test when utilized for testing individuals suspected of SARS-CoV-2 infection. Methods Concurrent swab samples were collected from patients suspected of SARS-CoV-2 infection by their healthcare provider within two different urgent care centers located in Easton, MA, USA and East Bridgewater, MA, USA. One swab was tested using the LumiraDx SARS-CoV-2 Ag Test. Negative results in patients considered at moderate to high risk of SARS-CoV-2 infection were confirmed at a regional reference laboratory by polymerase chain reaction (PCR) using the additional swab sample. The data included in this study was collected retrospectively as an analysis of routine clinical practice. Results From October 19, 2020 to January 3, 2021, a total of 2241 tests were performed using the LumiraDx SARS-CoV-2 Ag Test, with 549 (24.5%) testing positive and 1692 (75.5%) testing negative. A subset (800) of the samples rendering a negative LumiraDx SARS-CoV-2 Ag Test was also tested using a PCR-based test for SARS-CoV-2. Of this subset, 770 (96.3%) tested negative, and 30 (3.8%) tested positive. Negative results obtained with the LumiraDx SARS-CoV-2 Ag test demonstrated 96.3% agreement with PCR-based tests (CI 95%, 94.7–97.4%). A cycle threshold (CT) was available for 17 of the 30 specimens that yielded discordant results, with an average CT value of 31.2, an SD of 3.0, and a range of 25.2–36.3. CT was > 30.0 in 11/17 specimens (64.7%). Conclusions This study demonstrates that the LumiraDx SARS-CoV-2 Ag Test had a low false-negative rate of 3.8% when used in a community-based setting.

BackgroundThe coronavirus disease 2019 (COVID-19) continues to spread around the world. Therefore, rapid, simpler, and more accurate diagnostic tests are urgently needed to diagnose the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. The purpose of this study was to evaluate the SARS-CoV-2 IgM/ IgG rapid antibody test results in symptomatic patients with COVID-19 and their chest computed tomography (CT) data.MethodsA total of 320 patients admitted to our hospital for different durations due to COVID-19 were included in the study. Serum samples were obtained within 0 to 7 days from COVID-19 patients confirmed by RT-PCR and chest CT scan. According to the SARS-CoV-2 RT-PCR results, the patients included in the study were divided into two groups: PCR positive group (n=46), and PCR negative group (n=274).ResultsOf the 320 COVID-19 serum samples, IgM, IgG, and IgM/IgG were detected in 9.4%, 3.1%, and 17.8% within one week respectively. IgG/IgM antibodies were not detected in 69.7% of the patients. In the study, it was determined that 249 (77.8%) of 320 patients had positive chest CT scans. Four (5.6%) of 100 patients with negative chest CT scan had IgM positive and 2 (2.8%) had both IgM/ IgG positive. IgM was detected in 23 (9.2%), IgG in 1 (0.4%) and IgM/IgG in 35 (14%) of chest CT scan positive patients. The rate of CT findings in patients with antibody positivity (n=97) was found to be significantly higher than those with antibody negativity.ConclusionsThe results of the present study show the accurate and equivalent performance of serological antibody assays and chest CT in detecting SARS-CoV-2 0 to 7 days from the onset of COVID19 symptoms. When the RT-PCR is not available, we believe that the combination of immunochromatographic test and chest CT scan can increase diagnostic sensitivity for COVID-19.

Background Sepsis remains a major challenge in intensive care units, causing unacceptably high mortality rates due to the lack of rapid diagnostic tools with sufficient sensitivity. Therefore, there is an urgent need to replace time-consuming blood cultures with a new method. Ideally, such a method also provides comprehensive profiling of pathogenic bacteria to facilitate the treatment decision. Methods We developed a Random Forest with balanced subsampling to screen for pathogenic bacteria and diagnose sepsis based on cell-free DNA (cfDNA) sequencing data in a small blood sample. In addition, we constructed a bacterial co-occurrence network, based on a set of normal and sepsis samples, to infer unobserved bacteria. Results Based solely on cfDNA sequencing information from three independent datasets of sepsis, we distinguish sepsis from healthy samples with a satisfactory performance. This strategy also provides comprehensive bacteria profiling, permitting doctors to choose the best treatment strategy for a sepsis case. Conclusions The combination of sepsis identification and bacteria-inferring strategies is a success for noninvasive cfDNA-based diagnosis, which has the potential to greatly enhance efficiency in disease detection and provide a comprehensive understanding of pathogens. For comparison, where a culture-based analysis of pathogens takes up to 5 days and is effective for only a third to a half of patients, cfDNA sequencing can be completed in just 1 day and our method can identify the majority of pathogens in all patients.

The features of economic diagnostics of power engineering enterprises in the Republic of Belarus are considered. Accounting and analysis of the activities of enterprises of the power system in the emerging energy market requires improving approaches of economic monitoring. This can be achieved through a comprehensive system of economic diagnostics of the enterprise. The structure of economic diagnostics is represented by three elements, viz.: rapid diagnostics, diagnostics of bankruptcy and complex diagnostics of the economic condition, each of which has its own purpose and objectives of the study, as well as its own content of the reports to be analyzed reporting and of analytical procedures to be fulfilled. The choice of methods of economic diagnostics also depends on the stage of the life cycle of the enterprise. But it is the specificity of the type of economic activity that has a major impact on the diagnosis. The article describes the specific features of using methods of express-diagnostics, diagnostics of bankruptcy based on multivariate models as well as of integrated diagnosis of power utilities (by example of “Oblenergo” enterprises). The study demonstrated that the use of universal financial ratios in rapid assessment and models for assessing the risk of bankruptcy for domestic energy enterprises is not quite suitable, since these methods do not take into account the existing specifics of the structure of the capital of the organizations of power engineering system. The authors came to the conclusion that each of the approaches to diagnosis makes it possible to evaluate only individual criteria of the state of the economy of the organization. To improve the efficiency of analytical work at the enterprises of the power system, it is necessary to improve diagnostic procedures taking into account the technological features of production and the influence of factors of the external and internal environment. Only a comprehensive diagnosis can give a comprehensive unbiased assessment of the enterprise at all stages of its life cycle.

Background Talaromyces marneffei is a thermally dimorphic fungus endemic in south-east Asia. It predominantly occurs in both immunocompromised and immunosuppressed patients and can be fatal if diagnosis and treatment are delayed. The clinical manifestations of T. marneffei infection are nonspecific and rapid diagnosis of T. marneffei infection remains challenging. Case presentation A 24-year-old man came to our outpatient department with the sign of common skin lesions. The lesions were cuticolor follicular papules with or without central umbilication, nodules and acne-like lesions, which are common in syringoma, steatocystoma multiplex and trichoepithelioma. A dermatoscopy examination was performed to differentiate these skin lesions. The dermatoscopic images revealed circular or quasi-circular whitish amorphous structure with a central brownish keratin plug, providing the diagnostic clues of T. marneffei infection. Therefore, a skin scrapings culture, skin biopsy and serological detection for human immunodeficiency virus (HIV) were performed. The final diagnosis of this patient was T. marneffei and HIV co-infection. Conclusion Rapid diagnosis of T. marneffei infection is clinically challenging since presenting clinical manifestations are nonspecific with significant overlap with other common conditions. This case highlights that dermatoscopy is a promising tool for the rapid diagnosis of T. marneffei infection in patients with nonspecific skin lesions, assisting clinicians to avoid delayed diagnosis or misdiagnosis.

As demonstrated with the novel coronavirus pandemic, rapid and accurate diagnosis is key to determine the clinical characteristic of a disease and to improve vaccine development. Once the infected person is identified, hematological findings may be used to predict disease outcome and offer the correct treatment. Rapid and accurate diagnosis and clinical parameters are pivotal to track infections during clinical trials and set protection status. This is also applicable for re-emerging diseases like dengue fever, which causes outbreaks in Asia and Latin America every 4 to 5 years. Some areas in the US are also endemic for the transmission of dengue virus (DENV), the causal agent of dengue fever. However, significant number of DENV infections in rural areas are diagnosed solely by clinical and hematological findings because of the lack of availability of ELISA or PCR-based tests or the infrastructure to implement them in the near future. Rapid diagnostic tests (RDT) are a less sensitive, yet they represent a timely way of detecting DENV infections. The purpose of this study was to determine whether there is an association between hematological findings and the probability for an NS1-based DENV RDT to detect the DENV NS1 antigen. We also aimed to describe the hematological parameters that are associated with the diagnosis through each test.

Introduction: Rapid antigen testing can help in early diagnosis of Influenza in resource limited settings in patients presenting with Influenza Like Illness (ILI). Aim: To evaluate the usefulness of Rapid Influenza Direct antigen Testing (RIDT) in comparison to Real Time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) for diagnosis of Influenza virus infection in clinically suspected patients with ILI in a tertiary care hospital. Material and Methods: A prospective observational independent study was done to evaluate RIDT for Influenza virus infection, considering RT-PCR as gold standard. Throat swabs and nasal swabs from patients meeting Category 3 definition of ILI by Ministry Of Health and Family Welfare (MOHFW) were collected from July 20th, 2019 to October 20th, 2019 from hospitals in and around the study area. Onsite Rapid test (Biogenix, China) was used as per manufactures instructions for rapid detection of Influenza antigen. RNA extraction was done using Qiagen kit followed by RT-PCR using primer, probes recommended by National Institute of Virology (NIV, Pune) as per their protocols. Data was recorded on a predesigned proforma and managed using Microsoft Excel 2018 (Microsoft Corp, Redmond, WA). The Statistical software MedCalc version 9.1 for Windows was used for data analysis. Results: The overall sensitivity of the RIDT was 37.9% and specificity was 94.4%. The Positive Predictive Value (PPV) and Negative Predictive Value (NPV) were 73.3% and 78.8%, respectively. Kappa was calculated to be 0.37 that suggested a fair agreement between RIDT and RT-PCR. When the Cycle threshold (Ct) values were compared to the results of RIDT, there were more false positives at low Ct value and more false negatives at high Ct values. Conclusion: The RIDT is not useful in screening during an outbreak in acute care settings. The negative result of RIDT should be followed up with RT-PCR. With a strong clinical suspicion, it is better to start antivirals than wait for laboratory report in severely ill patients with ILI.

Background Rapid diagnostic tests (RDTs) for infectious diseases, with a turnaround time of less than 2 hours, are promising tools that could improve patient care, antimicrobial stewardship and infection prevention in the emergency department (ED) setting. Numerous RDTs have been developed, although not necessarily for the ED environment. Their successful implementation in the ED relies on their performance and impact on patient management. Objectives The aim of this narrative review was to provide an overview of currently available RDTs for infectious diseases in the ED. Sources PubMed was searched through August 2019 for available studies on RDTs for infectious diseases. Inclusion criteria included: commercial tests approved by the US Food and Drug Administration (FDA) or Conformite Europeenne (CE) in vitro diagnostic devices with data on clinical samples, ability to run on fully automated systems and result delivery within 2 hours. Content A nonexhaustive list of representative commercially available FDA- or CE-approved assays was categorized by clinical syndrome: pharyngitis and upper respiratory tract infection, lower respiratory tract infection, gastrointestinal infection, meningitis and encephalitis, fever in returning travellers and sexually transmitted infection, including HIV. The performance of tests was described on the basis of clinical validation studies. Further, their impact on clinical outcomes and anti-infective use was discussed with a focus on ED-based studies. Implications Clinicians should be familiar with the distinctive features of each RDT and individual performance characteristics for each target. Their integration into ED work flow should be preplanned considering local constraints of given settings. Additional clinical studies are needed to further evaluate their clinical effectiveness and cost-effectiveness.

Coronavirus disease 2019 (COVID-19), declared a pandemic by the WHO on March 11th, 2020 (1), requires an early diagnosis to optimize patient management and limit further transmission.….

Background Diagnostic testing for respiratory tract infections is a tool to manage the current COVID-19 pandemic, as well as the rising incidence of antimicrobial resistance. At the same time, new European regulations for market entry of in vitro diagnostics, in the form of the in vitro diagnostic regulation, may lead to more clinical evidence supporting health-economic analyses. Objective The objective of this systematic review was to review the methods used in economic evaluations of applied diagnostic techniques, for all patients seeking care for infectious diseases of the respiratory tract (such as pneumonia, pulmonary tuberculosis, influenza, sinusitis, pharyngitis, sore throats and general respiratory tract infections). Methods Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, articles from three large databases of scientific literature were included (Scopus, Web of Science and PubMed) for the period January 2000 to May 2020. Results A total of 70 economic analyses are included, most of which use decision tree modelling for diagnostic testing for respiratory tract infections in the community-care setting. Many studies do not incorporate a generally comparable clinical outcome in their cost-effectiveness analysis: fewer than half the studies (33/70) used generalisable outcomes such as quality-adjusted life-years. Other papers consider outcomes related to the accuracy of the test or outcomes related to the prescribed treatment. The time horizons of the studies generally are limited. Conclusions The methods to economically assess diagnostic tests for respiratory tract infections vary and would benefit from clear recommendations from policy makers on the assessed time horizon and outcomes used. Supplementary Information The online version contains supplementary material available at 10.1007/s40273-021-01054-1.

While influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure., While influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure. From October 2019 to March 2020, we conducted a home-based cross-sectional study in the greater Seattle, WA, area, utilizing electronic consent and data collection instruments. Participants received nasal swab collection kits via rapid delivery within 24 hours of self-reporting respiratory symptoms. Samples were returned to the laboratory and were screened for 26 respiratory pathogens and a housekeeping gene. Participant data were recorded via online survey at the time of sample collection and 1 week later. Of the 4,572 consented participants, 4,359 (95.3%) received a home swab kit and 3,648 (83.7%) returned a nasal specimen for respiratory pathogen screening. The 3,638 testable samples had a mean RNase P relative cycle threshold (Crt) value of 19.0 (SD, 3.4), and 1,232 (33.9%) samples had positive results for one or more pathogens, including 645 (17.7%) influenza-positive specimens. Among the testable samples, the median time between shipment of the home swab kit and completion of laboratory testing was 8.0 days (interquartile range [IQR], 7.0 to 14.0). A single adverse event occurred and did not cause long-term effects or require medical attention. Home-based surveillance using online participant enrollment and specimen self-collection is a safe and feasible method for community-level monitoring of influenza and other respiratory pathogens, which can readily be adapted for use during pandemics.

Infection with Helicobacter pylori is a global health issue, and rapid and accurate testing is a key to diagnosis. We aimed to assess the performance of two novel enzyme immunoassays (EIA), the H. PYLORI QUIK CHEK™ and the H. PYLORI CHEK™ assays, for the detection of H. pylori antigen in stool. Patients from five geographically diverse sites across the USA, Germany, and in Bangladesh were tested for infection with Helicobacter pylori with the two novel stool antigen tests and two commercially available stool antigen assays. All patients provided a stool sample and underwent esophagogastroduodenoscopy for biopsy. Results were compared to a clinical diagnosis using a composite reference method consisting of histological analysis and rapid urease testing of the biopsy. A total of 271 patients, 68.2% female and mean age of 46 years, were included. The overall prevalence of H. pylori infection was 24.1%. The sensitivity of the H. PYLORI QUIK CHEK™ and H. PYLORI CHEK™ was 92% and 91%, respectively. The specificity of H. PYLORI QUIK CHEK™ and H. PYLORI CHEK™ was 91% and 100%, respectively. No significant cross-reactivity against other gut pathogens was observed. The H. PYLORI QUIK CHEK™ and H. PYLORI CHEK™ assays demonstrate excellent clinical performance compared the composite reference method.

The FilmArray® Pneumonia plus Panel (FAPP) is a new multiplex molecular test for hospital-acquired pneumonia (HAP), which can rapidly detect 18 bacteria, 9 viruses, and 7 resistance genes. We aimed to compare the diagnosis performance of FAPP with conventional testing in 100 intensive care unit (ICU) patients who required mechanical ventilation, with clinically suspected HAP. A total of 237 samples [76 bronchoalveolar lavages (BALDS) and 82 endotracheal aspirates (ETADS) obtained at HAP diagnosis, and 79 ETA obtained during follow-up (ETATT)], were analyzed independently by routine microbiology testing and FAPP. 58 patients had paired BALDS and ETADS. The positivity thresholds of semi-quantified bacteria were 103-104 CFUs/mL or 104 copies/mL for BAL, and 105 CFUs/mL or copies/mL for ETA. Respiratory commensals (H. influenzae, S. aureus, E. coli, S. pneumoniae) were the most common pathogens. Discordant results for bacterial identification were observed in 33/76 (43.4%) BALDS and 36/82 (43.9%) ETADS, and in most cases, FAPP identified one supplemental bacteria (23/33 BALDS and 21/36 ETADS). An absence of growth, or polybacterial cultures, explained almost equally the majority of the non-detections in culture. No linear relationship was observed between bin and CFUs/mL variables. Concordant results between paired BALDS and ETADS were obtained in 46/58 (79.3%) patients with FAPP. One of the 17 resistance genes detected with FAPP (mecA/C and MREJ) was not confirmed by conventional testing. Overall, FAPP enhanced the positivity rate of diagnostic testing, with increased recognition of coinfections. Implementing this strategy may allow clinicians to make more timely and informed decisions.

Since its 2013 emergence in the Americas, Chikungunya virus (CHIKV) has posed a serious threat to public health. Early and accurate diagnosis of the disease, though currently lacking in clinics, is integral to enable timely care and epidemiological response. We developed a dual detection system: a CHIKV antigen E1/E2-based enzyme-linked immunosorbent assay (ELISA) and a lateral flow test using high-affinity anti-CHIKV antibodies. The ELISA was validated with 100 PCR-tested acute Chikungunya fever samples from Honduras. The assay had an overall sensitivity and specificity of 51% and 96.67%, respectively, with accuracy reaching 95.45% sensitivity and 92.03% specificity at a cycle threshold (Ct) cutoff of 22. As the Ct value decreased from 35 to 22, the ELISA sensitivity increased. We then developed and validated two lateral flow tests using independent antibody pairs. The sensitivity and specificity reached 100% for both lateral flow tests using 39 samples from Colombia and Honduras at Ct cutoffs of 20 and 27, respectively. For both lateral flow tests, sensitivity decreased as the Ct increased after 27. Because CHIKV E1/E2 are exposed in the virion surfaces in serum during the acute infection phase, these sensitive and specific assays demonstrate opportunities for early detection of this emerging human pathogen.

Background: The COVID-19 Ag (Antigen) Respi-Strip assay is a new immunochromatographic diagnostic tool recently available for antigenic diagnosis of SARS-CoV-2. The proposed sensitivity is not higher than 60 %, but its high specificity allows both quick decisions for the management of patients and confirmation by molecular diagnosis for only negative tests. However, from the first tests performed, we suspected that the sensitivity observed with routine use was much lower than that announced by the manufacturer. Materials and methods: Over a period of one month, we compared the negative results obtained with the COVID-19 Ag Respi-Strip kit with those obtained from qRT-PCR performed in a laboratory qualified for the molecular diagnosis of SARS-CoV-2. All samples tested were naso-pharyngeal smears from UTM-RT medium. Results: Of 774 patients tested, 714 negative samples were sent for confirmation, and 159 were found to be positive by qRT-PCR. The median positive percentage agreement was 23.9 % (95 % CI: 14.2 %–38.2 %). The Cohen's kappa score was 0.35. Conclusion: Using this immunochromatographic assay as a triage test did not significantly reduce the number of samples outsourced for COVID-19 confirmation by qRT-PCR. In addition, even if the turn-around time is short, the assay is completely manual, which is not suitable for large volumes of routine samples. The sensitivity of this rapid test is poor, and improvements are needed to enhance its performance., SCOPUS: ar.j, info:eu-repo/semantics/published

Granulomatous amoebic encephalitis (GAE) caused by Balamuthia mandrillaris is a rare subacute infection with exceptionally high mortality. Diagnosis is typically made by brain biopsy or at autopsy. Detection of Balamuthia mandrillaris cell-free DNA by next-generation sequencing of plasma enabled rapid, noninvasive diagnosis in a case of amoebic encephalitis.

Laboratory tests are necessary for diagnosis of scrub typhus (ST) especially in the absence of the distinctive eschar. Performance of an ELISA and ICT (immunochromatography) to detect IgM antibodies to scrub typhus was assessed using a panel of 346 sera chosen from healthy individuals, those with scrub typhus and scrub-typhus like illness. A sensitivity of 98.7% for ST IgM ICT and 97.4% for ST IgM ELISA was observed while specificity was 96.3% for ICT and 95.9% for ELISA. As excellent concordance (98.8%) was noted between the two assays, IgM ICT can be used for rapid diagnosis of scrub typhus. Abbreviations: ST IgM ELISA: Scrub typhus IgM ELISA; ST IgM ICT: Scrub Typhus IgM Immunochromatography, Rapid diagnostic test: RDT.

This paper investigates opportunities to rapidly detect defects in photovoltaic (PV) panels. It is worth noting that a defect in a single PV cell can significantly reduce the output power of a PV panel and, thereby, of an entire PV array. Hence, it is crucial to detect faults in PV panels and replace them within PV power plants. In this paper, we utilise synchronized thermography (ST) to obtain infrared (IR) images under outdoor environmental conditions. We illustrate how IR-images obtained under changing irradiation and different angles can be analysed to rapidly detect defects in PV panels. Our technique allows maintenance staff to quickly identify PV panels with defects on the site of a PV power plant.

Current molecular PCR-based techniques used for detecting Streptococcus pneumoniae, the causative pathogen of invasive pneumococcal disease (IPD), are accurate but have a run time of several hours. We aimed to develop and validate a novel real-time loop mediated amplification (LAMP) assay for rapid detection of pneumococcus in normally sterile samples with accuracy comparable to a gold standard real-time PCR. Conserved regions of lytA were used for the design of the LAMP test. Analytical validation included assessment of linearity, limit of detection (LOD), intra-assay and inter-assay precision and analytical specificity, which was evaluated by using reference strain S. pneumoniae R6 and a quality control panel. Clinical performance was assessed on all samples collected from children with suspicion of IPD attended in Hospital Sant Joan de Deu (Barcelona, Spain) during the period April-September 2015. Fresh samples were analyzed after DNA extraction. The following values of analytical parameters were determined: linearity within the range 108-104 copies/mL; limit of detection, 5·103 copies/mL; intra- and inter-assay precision measured by mean coefficient of variance, 3.61 and 6.59%; analytical specificity, 9/9 pathogens similar to S. pneumoniae and 14/14 strains of different S. pneumoniae serotypes correctly identified as negative and positive results, respectively. Diagnostic sensitivity and specificity values were 100.0 and 99.3%. Median time of DNA amplification was 15 min. The new LAMP assay showed to have similar accuracy as PCR while being 5-fold faster and could become a useful diagnostic tool for early diagnosis of IPD. info:eu-repo/semantics/publishedVersion

Background: Automated molecular panels are attractive tools for improving early meningitis diagnosis. This study assessed the Eazyplex® CSF direct M panel (EP), a multiplex real-time Loop-Mediated Isothermal Amplification assay. Methods: From December 2016 to December 2019, cerebrospinal fluid (CSF) samples were routinely tested with the EP V1.0. CSF parameters and microbiological and clinical data were retrospectively collected. Results: Out of 230 CSF samples, the EP yielded positive, negative, and invalid results for 32 (13.9%) (16 N. meningitidis, nine S. pneumoniae, two S. agalactiae, two E. coli, two H. influenzae, one L. monocytogenes), 182 (79.1%), and 16 (7%) samples, respectively. Among the positive samples, 14 (44%) remained negative in culture (antibiotic therapy before lumbar puncture (n = 11), meningococcal meningitis (n = 3)). High CSF protein concentrations and cellularity were associated with LAMP inhibition, counteracted by centrifugation. The automated software yielded 13 false positive and five false negative results. Amplification curve analysis was necessary and enabled the attainment of positive (PPA) and negative percentage agreement and positive and negative predictive values of 91.4%, 100%, 100%, and 98.3%. Three false negative results remained (two E. coli and one N. meningitidis). E. coli presented the poorest PPA (50%). Conclusion: This work confirms the strong performance of the EP, of particular interest in cases of antibiotic therapy before lumbar puncture.

In this article relevance of timely carrying out the financial analysis of the enterprises in the conditions of an economic crisis is considered; standard methods of the financial analysis of an i obosnovan expediency of use of ways of the factorial analysis of a financial productive performance at the initial stages of evaluating a financial condition of the enterprises for the purpose of timely identification of the negative moments and undesirable tendencies of their development are listed. Much attention in article is paid to definition of a concept of the determined factorial models, allocation of their features and the existing types. Importance of specification of complex factors of the first order on factors of the second and following level is considered; requirements to creation of the combined factorial models; algorithm of calculation of influence on a financial productive performance of factors of the second order in the way of proportional division. In article practical examples of use of a way of proportional division when evaluating influence of articles of current assets on coefficient of the current liquidity and an assessment of influence of main types of expenses on usual kinds of activity for profitability of production are also given; necessary formulas and calculations on the example of the concrete enterprises are given; results of the factorial analysis are generalized.

The purpose of the study is determined by the need for further development and improvement of methodology of economic diagnostics. The study of theoretical issues and practical implementation of diagnostic studies and crisis management showed that the methodological basis of economic diagnostics needs work and updating, can extend practical approaches to research. Research complement and deepen the complex scientific and theoretical developments in the methodology of economic substantiation of diagnosis. The author presents a methodological approach to the classification of types of diagnostic studies on various grounds. The main emphasis in the developed classification of types is made on a thorough and complete rationale for each attribute, put with the basis of the classification of economic diagnostics, and describe the direction of the diagnostic study.

The present multi-centre study aimed at assessing the performance of air sampling as a novel method for monitoring Campylobacter in biosecured poultry farms. We compared, using a harmonized procedure, the bacteriological isolation protocol (ISO 10272-1:2017), and a real-time PCR method on air filter samples. Air samples and boot swabs were collected from 62 biosecured flocks from five European countries during the summer of 2019. For air filters, the frequency of PCR-positive findings was significantly higher (n=36; 58%) compared to the cultivation methods (PPn=23; 37%), followed by direct plating after homogenization in Preston (n=21; 34%) or Bolton (n=20; 32%). It is noteworthy that the Norwegian flocks, a country known to have low Campylobacter prevalence in biosecured chicken flocks, tested negative for Campylobacter using the new sensitive approach. In conclusion, air sampling combined with real-time PCR is proposed as a multi-purpose, low-cost and convenient screening method that can be up to four times faster and four times more sensitive than the current boot-swab testing scheme used for screening biosecured chicken production.Importance: Campylobacter bacteria are the cause of the vast majority of registered cases of foodborne illness in the industrialized world. In fact, the bacteria caused 246,571 registered cases of foodborne illness in 2018, which equates to 70% of all registered cases in Europe that year. An important tool to prevent campylobacter from making people sick is good data on where in the food chain the bacterium is present. The present study reports a new test method that quadruples the likelihood of identifying campylobacter-positive chicken flocks. It is important to identify campylobacter-positive flocks before they arrive at the slaughterhouse. This is because negative flocks may be slaughtered first in the morning in order to avoid cross-contamination along the production line.

Bloodstream infection (BSI) is defined by positive blood cultures in a patient with systemic signs of infection and may be either secondary to a documented source or primary—that is, without identified origin. Community-acquired BSIs in immunocompetent adults usually involve drug-susceptible bacteria, while healthcare-associated BSIs are frequently due to multidrug-resistant (MDR) strains. Early adequate antimicrobial therapy is a key to improve patient outcomes, especially in those with criteria for sepsis or septic shock, and should be based on guidelines and direct examination of available samples. Local epidemiology, suspected source, immune status, previous antimicrobial exposure, and documented colonization with MDR bacteria must be considered for the choice of first-line antimicrobials in healthcare-associated and hospital-acquired BSIs. Early genotypic or phenotypic tests are now available for bacterial identification and early detection of resistance mechanisms and may help, though their clinical impact warrants further investigations. Initial antimicrobial dosing should take into account the pharmacokinetic alterations commonly observed in ICU patients, with a loading dose in case of sepsis or septic shock. Initial antimicrobial combination attempting to increase the antimicrobial spectrum should be discussed when MDR bacteria are suspected and/or in the most severely ill patients. Source identification and control should be performed as soon as the hemodynamic status is stabilized. De-escalation from a broad-spectrum to a narrow-spectrum antimicrobial may reduce antibiotic selection pressure without negative impact on mortality. The duration of therapy is usually 5–8 days though longer durations may be discussed depending on the underlying illness and the source of infection. This narrative review covers the epidemiology, diagnostic workflow and therapeutic aspects of BSI in ICU patients and proposed up-to-date expert statements.

Prompt and targeted antifungal treatment has a positive impact on the clinical outcome of mucormycosis; however, current diagnostic tools used in histopathology laboratories often fail to provide rapid results. Rapid culture-based strategies for early diagnosis of Mucorales infections, which may influence treatment decisions, are urgently needed. Herein, we evaluated a microculture assay for the early diagnosis of mucormycosis in an immunocompetent murine model of disseminated infection, by comparing it with traditional diagnostic methods. The assay specificity was assessed using blood (n = 90) and tissue (n = 90) specimens obtained from mice infected with Rhizopus arrhizus using different inoculum sizes [1 × 104, 1 × 105, and 1 × 106 colony forming units (CFUs)/mouse] and blood (n = 15) and tissue specimens (n = 15) from uninfected mice. Surprisingly, 26 of 90 (28.9%) blood samples revealed positive results by microculture, whereas all blood samples were negative when assayed by conventional culture. The overall positive conventional culture rate for the mouse tissue (kidney) samples was 31.1% (28/90). The calculated sensitivity for kidney microculture was 98.8% [95% confidence interval (CI) 96.6–100], with an assay specificity of 100%. Hence, the microculture assay may be useful for rapid culturing and diagnosis of mucormycosis caused by R. arrhizus directly in blood and tissue samples. Hence, this method may allow for the timely administration of an appropriate treatment.

A rapid clinical diagnosis may efficiently improve the survival rate and prognosis of patients with ischemic heart disease (IHD). Therefore, a one-step, rapid and inexpensive analysis for the quick diagnosis of IHD was investigated in the present study. Consecutive patients who were subjected to myoglobin, cardiac troponin I and creatine kinase-MB isoenzyme assessment at the Emergency Department of Shenzhen Second People's Hospital (Shenzhen, China) between December 2017 and March 2018 prior to treatment were screened. Clinically applicable disposable strips were employed for quantification of the cardiac biomarkers. The analytical performance of the strips was evaluated by receiver operating characteristic (ROC) curves and compared with the traditional chemiluminescence immunoassay (CLIA) method. The data of 391 participants were collected. At the baseline, 57 patients were diagnosed with IHD and 334 patients were diagnosed with other diseases. The area under the ROC curve (AUC) of the CLIA model was 0.787 (95% CI, 0.709-0.865) with a specificity of 76.7% and a sensitivity of 71.9%. At the optimal cutoff value of -1.867, the negative and the positive predictive value were 94.1 and 34.5%, respectively. The AUC of the disposable strip model was 0.792 (95% CI, 0.729-0.855). At the cutoff value of -1.820 or below, the negative predictive value was 94.9%, the positive predictive value was 28.9%, the specificity was 66.8% and the sensitivity was 79.0%. The P-value of the ROCs was 0.858, indicating no statistically significant difference between the two assay methods. The cost of the disposable strip was 50% of that of the CLIA method and it took only 25% of the time that was required for the quantification of the three cardiac markers by CLIA. In conclusion, the disposable strip provides a platform for point-of-care testing and may be an easy, rapid, reliable and cost-saving method for the diagnosis of IHD.

Usually, 18-48 h are needed for the identification of microbial pathogens causing urinary tract infections (UTIs) by urine culture. Moreover, antimicrobial susceptibility testing (AST) takes an additional 18-24 h. Rapid identification and AST of the pathogens allow fast and precise treatment. The objective of this study was to shorten the time of diagnosis of UTIs by combining pathogen screening through flow cytometry, microbial identification by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS), and AST using the VITEK 2 system for the direct analysis of urine samples. We analyzed 1,638 urine samples from patients with suspected UTIs submitted to the microbiology laboratory for culture. Each urine sample had an approximate volume of 30 mL and was divided into three aliquots. Urine processing included differential centrifugation and two washes to enrich the bacterial fraction for direct MALDI-TOF MS and direct AST. From a total of 1,638 urine samples, 307 were found to be positive through UF-1000i screening. Among them, 265 had significant growth of a single-microorganism. Direct identification was obtained in 229 (86.42%) out of these 265 samples, and no pathogens were misidentified. Moreover, species-level identification was obtained in 163 (88.59%) out of the 184 samples with Gram-negative bacteria, and 27 (38.03%) out of the 71 samples with Gram-positive bacteria. VITEK 2 AST was performed for 117 samples with a single-microorganism. Enterobacteriaceae data showed an agreement rate of antimicrobial categories of 94.83% (1,229/1,296), with minor, major, and very major error rates of 4.17% (54/1,296), 0.92% (12/1,296), and 0.08% (1/1,296), respectively. For Enterococcus spp., the overall categorical agreement was 92.94% (158/170), with a minor error rate of 2.94% (5/170) and major error rate of 4.12% (7/170). The turnaround time of this combined protocol to diagnose UTIs was 1 h for pathogen identification and 6-24 h for AST; noteworthily, only 6-8 h are needed for AST of Enterobacteriaceae using the VITEK 2 system. Overall, our findings show that the combination of flow cytometry, MALDI-TOF MS, and VITEK 2 provided a direct, rapid, and reliable identification and AST method for assessing urine samples, especially for Gram-negative bacterial infections.

BackgroundIn patients with suspected ventilator-associated pneumonia, a rapid etiological diagnosis is crucial as incorrect or delayed treatment in the first few hours leads to a worse prognosis and a higher mortality rate. This study examines the efficacy of a rapid antibiogram on bronchial aspirates in patients with suspected ventilator-associated pneumonia (VAP).MethodsThe direct gradient diffusion susceptibility testing method (GDM) on respiratory samples was compared with a standard broth microdilution method (BMD) after quantitative cultures in patients with suspicion of VAP. Samples were preselected by Gram staining (for good quality microbiological samples with a predominant single bacterial morphotype). The antibiotics tested were ceftazidime, ceftobiprole, ceftolozane-tazobactam, meropenem, doripenem, and tedizolid.ResultsOver a 16-month study period, 445 bronchial aspirate samples were selected from 1376 samples received at our laboratory from 672 adult patients. By direct plating on Mueller-Hinton agar, we recovered 504 (95.5%) of the 528 microorganisms identified by the standard semiquantitative method. Antimicrobial susceptibility testing by GDM was compared with the BMD method in 472 strains (216Enterobacteriaceae, 138P. aeruginosaand 118 S. aureus.) and 1652 individual microorganism-antimicrobial agent combinations. There was total agreement between both methods in 98% of combinations. The Kappa index between both techniques was excellent (over 80%). There was only one potential major error forP. aeruginosasusceptibility to ceftazidime.ConclusionsThe six GDM strips directly placed on plated bronchial aspirates obtained from patients with a suspicion of VAP provided accurate and reliable susceptibility results within 24 h.

Background Mycoplasma pneumoniae (M pneumoniae) is a common human etiology of respiratory infections. Nuclear acid sequence-based amplification (NASBA) shows good value for the detection of M pneumoniae that surpasses PCR. However, the optimal detection technology still remains to be identified. The purpose of this meta-analysis was to systematically evaluate the overall accuracy of NASBA for diagnosing M pneumoniae infections. Methods The databases PubMed, Cochrane Library, Google Scholar, CNKI, Wang Fang, and Baidu Scholar were comprehensively searched from their initiation date to December 2017 for NASBA in the diagnosis of M pneumoniae infection. Meta-DiSc 1.4 statistical software was used to evaluate the sensitivity (SEN), specificity (SPE), negative likelihood ratio (-LR), positive likelihood ratio (+LR), diagnostic odds ratio (DOR), and summary receiver operating characteristic (SROC). RevMan 5.2 statistical software was used for quality evaluation of the included articles. Publication bias was evaluated by funnel plot. Results Six articles with high quality, including 10 studies, were finally included in this meta-analysis. The combined statistics results for the diagnosis of M pneumoniae infection by NASBA were 0.77 (SEN, 95% CI: 0.71 to 0.82); 0.98 (SPE, 95% CI: 0.98 to 0.99); 0.22 (-LR, 95% CI: 0.13 to 0.39); 50.38 (+ LR, 95% CI: 21.85 to 116.17); 292.72 (DOR, 95% CI: 95.02 to 901.75); and 0.9875 (the area under the curve of SROC). Conclusion Nuclear acid sequence-based amplification is a reliable technique to diagnose M pneumoniae infection. However, whether it can replace PCR and serology need to be further studied.

Objectives To test our hypothesis that routine year-round testing of specimens from multiple body sites and genotyping of detected virus would describe seasonal changes, increase diagnostic yield, and provide a better definition of clinical manifestations of human parechovirus (PeV-A) infections in young febrile infants. Study design PeV-A reverse-transcriptase polymerase chain reaction (RT-PCR) analysis was incorporated in routine evaluation of infants aged ≤60 days hospitalized at Nationwide Children's Hospital for fever and/or suspected sepsis-like syndrome beginning in July 2013. We reviewed electronic medical records of infants who tested positive for PeV-A between July 2013 and September 2016. Genotyping was performed with specific type 3 RT-PCR and sequencing. Results Of 1475 infants evaluated, 130 (9%) tested positive for PeV-A in 1 or more sites: 100 (77%) in blood, 84 (65%) in a nonsterile site, and 53 (41%) in cerebrospinal fluid (CSF). Five infants (4%) were CSF-only positive, 31 (24%) were blood-only positive, and 20 (15%) were nonsterile site–only positive. PeV-A3 was the most common type (85%) and the only type detected in CSF. Although the majority (79%) of infections were diagnosed between July and December, PeV-A was detected year-round. The median age at detection was 29 days. Fever (96%), fussiness (75%), and lymphopenia (56%) were common. Among infants with PeV-A–positive CSF, 77% had no CSF pleocytosis. The median duration of hospitalization was 41 hours. Four infants had bacterial coinfections diagnosed within 24 hours of admission; 40 infants had viral coinfections. Conclusions Although most frequent in summer and fall, PeV-A infections were encountered in every calendar month within the 3-year period of study. More than one-half of patients had PeV-A detected at more than 1 body site. Coinfections were common. PeV-A3 was the most common type identified and the only type detected in the CSF.

The aim of the study was to conduct clinical testing of the rapid diagnostic test system «Streptatest» (Dectra Pharm, France) and to evaluate its performance in accordance with its purpose in solving the functional problems of express diagnostics of Group A streptococci. In the work the evaluation of the performance characteristics of the test systems «Streptatest» with an assessment of the feasibility and acceptability of its use in the interests of practical public health have been studied. Materials and methods: Clinical approbation was carried out by examining 200 military personnel contracted for outpatient admission to a medical service with suspected acute tonsillitis for the carriage of Group A beta-hemolytic streptococcus using this test system. The following results were obtained during the study. Of 200 examined patients, the number of people with a positive test was 31 (15,5%), negative – 169 (84,5%), which corresponds to the literature data on the prevalence of acute tonsillitis caused by GAS. Before the application of «Streptatest» antibiotic therapy was prescribed in 80-90% of cases, after the start of the use of the test system, the number of antibiotic prescriptions was reduced to 16%, which led to a reduction in the costs of treatment of acute tonsillitis. Test system «Streptatest» is a highly effective and sufficiently reliable medical device, the ease of using test strips and a simple evaluation of the results of the study are its advantages. The indication for the application of the rapid diagnostic test system is the request for medical care of a patient with clinical signs of acute tonsillitis, tonsillopharyngitis, pharyngitis. The social significance lies in obtaining a reliable result with the simplicity and ease of working with the test system. Conclusions. Estimating the prevalence of streptococcal group A infections in organized groups, providing rapid differential diagnosis, primarily of tonsillitis and viral streptococcal etiology, allows timely and adequate appointment of the necessary treatment, reduce the risk of complications and reduce the severity of the disease, reduce the economic costs of medical care .

WOS: 000398529000002, PubMed ID: 27898418, Background/Aim: The aim of this study was to use targeted next-generation sequencing (TNGS) including all known genes associated with 46,XY disorders of sex development (DSD) for a fast molecular genetic diagnosis. Methods: Twenty pediatric patients were recruited, and 56 genes related to 46,XY DSD were sequenced using TNGS. The time elapsed between initial appointment and final diagnosis as well as the mean expenditure was determined. Results: A total of 9 (45%) mutations in 4 different genes were identified. Mutations in the HSD17B3 gene were observed in 6 (30%) patients. A heterozygous mutation in WT1 gene and a hemizygous mutation in SRY gene were detected in patients with gonadal dysgenesis. One patient had a homozygous mutation in LHCGR gene. Prior to the molecular diagnosis, the mean number of clinical visits, time elapsed until diagnosis, and expenditure were 27.4 +/- 14.6 visits, 5.9 +/- 4.1 years per patient, and USD 2,142 +/- 1,038, respectively. With TNGS, time elapsed until diagnosis was significantly reduced (3 days), and expenditure per patient was only one third of the conventional approach (USD 761). Conclusions: TNGS is an efficient, rapid, and cost-effective technique for mutation detection in 46,XY DSD. (C) 2016 S. Karger AG, Basel, Ege University Scientific Research Projects (EGEBAP)Ege University [2015-TIP-044], This project was supported by Ege University Scientific Research Projects (EGEBAP) with grant No. 2015-TIP-044.

Resumen Las infecciones respiratorias bajas siguen siendo una de las causas más frecuentes de mortalidad en todo el mundo, de ahí que el diagnóstico precoz sea fundamental. Tradicionalmente, el diagnóstico microbiológico de este tipo de infecciones se ha basado en métodos convencionales que incluyen cultivos en medios artificiales para aislamiento de bacterias y hongos y cultivos celulares para virus, así como en la detección antigénica o de anticuerpos mediante reacciones antígeno-anticuerpo. El principal inconveniente de las metodologías anteriormente citadas es el tiempo necesario para obtener un diagnóstico etiológico de la infección. Las técnicas basadas en la biología molecular han irrumpido con fuerza en las últimas décadas como herramientas de diagnóstico rápido de las infecciones. Algunas de estas técnicas —sobre todo aquellas que pueden detectar diversos microorganismos en la misma reacción— acostumbran a ser caras, por lo que la cuestión que se plantea es si el gasto de tales ensayos se ve justificado por la información obtenida y por el impacto clínico que su implementación determina. En este artículo se pretende hacer una revisión de las diversas técnicas de biología molecular aplicadas al diagnóstico de las infecciones respiratorias, centrándose fundamentalmente en la neumonía, y analizar el impacto que pueden tener en el manejo del paciente con infección respiratoria aguda.

Context: Early diagnosis is the mainstay in the management of severe cutaneous adverse reactions (SCARs) to drugs. Aims: To study the role of frozen section in the rapid diagnosis of SCARs and the impact on outcome of the affected patients. Settings and Design: A single-blind, hospital-based study was conducted from December 2014-July 2016. Methods and Material: We biopsied 32 adults with SCARs diagnosed by clinical features and standard criteria. The histopathological features seen on frozen sections were compared to that of paraffin blocks. The impact of rapid diagnosis on the clinical outcome was studied in toxic epidermal necrolysis (TEN), Stevens-Johnson syndrome (SJS), drug rash with eosinophilia and systemic symptoms (DRESS) and acute generalized exanthematous pustulosis (AGEP). Statistical Analysis: Z test was used to compare two proportions. Kappa statistic, sensitivity, specificity, positive predictive value, and negative predictive value of the frozen section diagnosis were calculated in TEN/SJS and DRESS using MedCalc software. Results: Frozen and paraffin sections were done in TEN/SJS spectrum (13), DRESS (17), and AGEP (2). The sensitivity, specificity and kappa values for frozen section diagnosis in SJS/TEN and DRESS were 91.7%, 95%, 0.867 and 94.4%, 100%, 0.937 respectively. The concordance between frozen and paraffin section diagnosis was 100% in TEN, SJS, DRESS and AGEP. All the 6 patients with TEN and 2 with AGEP survived. Taking the worst-case scenario, the mortality in SJS was 28.6%. The mortality among patients with DRESS was 11.8%. Conclusions: Frozen section helps in the rapid diagnosis and early treatment of SCARs and differentiates it from diseases that mimic it.

Coronavirus disease (COVID-19), caused by SARS-CoV-2, evolved into a global pandemic in 2020, and the outbreak has taken an enormous toll on individuals, families, communities and societies around the world. One practical and effective strategy is to implement rapid case identification based on a rapid testing to respond to this public health crisis. Currently, the available technologies used for rapid diagnostics include RT-PCR, RT-LAMP, ELISA and NGS. Still, due to their different limitations, they are not well suited for rapid diagnosis in a variety of locations. Paper-based devices are alternative approaches to achieve rapid diagnosis, which are cost-effective, highly selective, sensitive, portable, and easy-to-use. In addition to individual virus screening, wastewater-based epidemiology has been emerged to be an effective way for early warning of outbreak within the population, which tests genomic viral sequence to reflect information on the spread and distribution of the virus because SARS-CoV-2 can be shed into wastewater through the feces and urine from infected population. In this paper, we describe paper-based device as a low-cost and rapid sensor for testing of virus for both diagnosis and early warning of outbreak for wastewater-based epidemiology. Most importantly, the device has great potential for real-time detection in the field, without any advanced facilities and well-trained skilled personnel, and provides early warning or timely intervention of an outbreak of pandemic.

Rapid point-of-care testing is a megatrend in infectious disease diagnosis. We have introduced a homogeneous immunoassay concept, which is based on the simultaneous binding of antigen and protein L to a given immunoglobulin molecule. The complex formation is detected utilizing time-resolved F&ouml, rster resonance energy transfer between antigen-attached donor and acceptor-labeled protein L, hence the name LFRET. Here, we demonstrate that urine can be used as a sample matrix in LFRET-based serodiagnostics. We studied urine samples collected during the hospitalization and recovery of patients with acute Puumala orthohantavirus (PUUV) infection. We compared PUUV antibody-specific LFRET signals in urine to those in plasma, and found excellent correlation in the test outcomes The LFRET test from urine was positive in 40/40 patients with acute PUUV infection. PUUV causes a mild form of hemorrhagic fever with renal syndrome, characterized by acute kidney injury and proteinuria. Immunofluorescence and western blotting demonstrated PUUV-IgG and -IgA in urine, however, the presence of intact immunoglobulins did not fully explain the LFRET signals. We purified free light chains (FLCs) from both urine and serum of healthy volunteers and patients with acute PUUV infection, and verified the presence of antigen-specific FLCs. Antigen-specific FLCs provide a new means for non-invasive antibody detection and disease diagnosis.

Introduction: While fever is the main complaint among pediatric emergency services and high antibiotic prescription are observed, only a few studies have been published addressing this subject. Therefore this systematic review aims to summarize antibiotic prescriptions in febrile children at the ED and assess its determinants. Methods: We extracted studies published from 2000 to 2017 on antibiotic use in febrile children at the ED from different databases. Author, year, and country of publishing, study design, inclusion criteria, primary outcome, age, and number of children included in the study was extracted. To compare the risk-of-bias all articles were assessed using the MINORS criteria. For the final quality assessment we additionally used the sample size and the primary outcome. Results: We included 26 studies reporting on antibiotic prescription and 28 intervention studies on the effect on antibiotic prescription. In all 54 studies antibiotic prescriptions in the ED varied from 15 to 90.5%, pending on study populations and diagnosis. Respiratory tract infections were mostly studied. Pediatric emergency physicians prescribed significantly less antibiotics then general emergency physicians. Most frequent reported interventions to reduce antibiotics are delayed antibiotic prescription in acute otitis media, viral testing and guidelines. Conclusion: Evidence on antibiotic prescriptions in children with fever presenting to the ED remains inconclusive. Delayed antibiotic prescription in acute otitis media and guidelines for fever and respiratory infections can effectively reduce antibiotic prescription in the ED. The large heterogeneity of type of studies and included populations limits strict conclusions, such a gap in knowledge on the determining factors that influence antibiotic prescription in febrile children presenting to the ED remains.

Future demands for food will place agricultural systems under pressure to increase production. Poultry is accepted as a good source of protein and the poultry industry will be forced to intensify production in many countries, leading to greater numbers of farms that house birds at elevated densities. Increasing farmed poultry can facilitate enhanced transmission of infectious pathogens among birds, such as avian influenza virus among others, which have the potential to induce widespread mortality in poultry and cause considerable economic losses. Additionally, the capability of some emerging poultry pathogens to cause zoonotic human infection will be increased as greater numbers of poultry operations could increase human contact with poultry pathogens. In order to combat the increased risk of spread of infectious disease in poultry due to intensified systems of production, rapid detection and diagnosis is paramount. In this review, multiple technologies that can facilitate accurate and rapid detection and diagnosis of poultry diseases are highlighted from the literature, with a focus on technologies developed specifically for avian influenza virus diagnosis. Rapid detection and diagnostic technologies allow for responses to be made sooner when disease is detected, decreasing further bird transmission and associated costs. Additionally, systems of rapid disease detection produce data that can be utilized in decision support systems that can predict when and where disease is likely to emerge in poultry. Other sources of data can be included in predictive models, and in this review two highly relevant sources, internet based-data and environmental data, are discussed. Additionally, big data and big data analytics, which will be required in order to integrate voluminous and variable data into predictive models that function in near real-time are also highlighted. Implementing new technologies in the commercial setting will be faced with many challenges, as will designing and operating predictive models for poultry disease emergence. The associated challenges are summarized in this review. Intensified systems of poultry production will require new technologies for detection and diagnosis of infectious disease. This review sets out to summarize them, while providing advantages and limitations of different types of technologies being researched.

Burkholderia pseudomallei causes significant global morbidity and mortality, with the highest disease burden in parts of Asia where culture-based diagnosis is often not available. We prospectively evaluated the Active Melioidosis Detect (AMD; InBios International, USA) lateral flow immunoassay (LFI) for rapid detection of B. pseudomallei in turbid blood cultures, pus, sputum, sterile fluid, urine, and sera. The performance of this test was compared to that of B. pseudomallei detection using monoclonal antibody latex agglutination (LA) and immunofluorescence assays (IFA), with culture as the gold standard. AMD was 99% (99/100; 95% confidence interval, 94.6 to 100%) sensitive and 100% (308/308; 98.8 to 100%) specific on turbid blood culture bottles, with no difference from LA or IFA. AMD specificity was 100% on pus (122/122; 97.0 to 100%), sputum (20/20; 83.2 to 100%), and sterile fluid (44/44; 92 to 100%). Sensitivity on these samples was as follows: pus, 47.1% (8/17; 23.0 to 72.2%); sputum, 33.3% (1/3; 0.84 to 90.6%); and sterile fluid, 0% (0/2; 0 to 84.2%). For urine samples, AMD had a positive predictive value of 94% (32/34; 79.7 to 98.5%) for diagnosing melioidosis in our cohort. AMD sensitivity on stored sera, collected prospectively from melioidosis cases during this study, was 13.9% (5/36; 4.7% to 29.5%) compared to blood culture samples taken on the same day. In conclusion, AMD is an excellent tool for rapid diagnosis of melioidosis from turbid blood cultures and maintains specificity across all sample types. It is a promising tool for urinary antigen detection, which could revolutionize diagnosis of melioidosis in resource-limited settings. Further work is required to improve sensitivity on nonblood culture samples.

BackgroundRare genetic conditions are frequent risk factors for, or direct causes of, organ failure requiring paediatric intensive care unit (PICU) support. Such conditions are frequently suspected but unidentified at PICU admission. Compassionate and effective care is greatly assisted by definitive diagnostic information. There is therefore a need to provide a rapid genetic diagnosis to inform clinical management.To date, Whole Genome Sequencing (WGS) approaches have proved successful in diagnosing a proportion of children with rare diseases, but results may take months to report or require the use of equipment and practices not compatible with a clinical diagnostic setting. We describe an end-to-end workflow for the use of rapid WGS for diagnosis in critically ill children in a UK National Health Service (NHS) diagnostic setting.MethodsWe sought to establish a multidisciplinary Rapid Paediatric Sequencing (RaPS) team for case selection, trio WGS, a rapid bioinformatics pipeline for sequence analysis and a phased analysis and reporting system to prioritise genes with a high likelihood of being causal. Our workflow was iteratively developed prospectively during the analysis of the first 10 children and applied to the following 14 to assess its utility.FindingsTrio WGS in 24 critically ill children led to a molecular diagnosis in ten (42%) through the identification of causative genetic variants. In three of these ten individuals (30%) the diagnostic result had an immediate impact on the individual’s clinical management. For the last 14 trios, the shortest time taken to reach a provisional diagnosis was four days (median 7 days).InterpretationRapid WGS can be used to diagnose and inform management of critically ill children using widely available off the shelf products within the constraints of an NHS clinical diagnostic setting. We provide a robust workflow that will inform and facilitate the rollout of rapid genome sequencing in the NHS and other healthcare systems globally.FundingThe study was funded by NIHR GOSH/UCL BRC: ormbrc-2012-1

Background Parasitic diseases are one of the world's most devastating and prevalent infections, causing millions of morbidities and mortalities annually. In the past, many of these infections have been linked predominantly to tropical or subtropical areas. Nowadays, however, climatic and vector ecology changes, a significant increase in international travel, armed conflicts, and migration of humans and animals have influenced the transmission of some parasitic diseases from ‘book pages’ to reality in developed countries. It has also been noted that many patients who have never travelled to endemic areas suffer from blood-borne infections caused by protozoa. In the light of existing knowledge, this new trend can be explained by the fact that in the process of migration a large number of asymptomatic carriers become a part of the blood bank donor and transplant donor populations. Accurate and rapid diagnosis represents the crucial weapon in the fight against parasitic infections. Aims To review old and new approaches for rapid diagnosis of parasitic infections. Sources Data for this review were obtained through searches of PubMed using combinations of the following terms: parasitological diagnostics, microscopy, lateral flow assays, immunochromatographic assays, multiplex-PCR, and transplantation. Content In this review, we provide a brief account of the advantages and limitations of rapid methods for diagnosis of parasitic diseases and focus our attention on current and future research in this area. The approximate costs associated with the use of different techniques and their applicability in endemic and non-endemic areas are also discussed. Implications Microscopy remains the cornerstone of parasitological diagnostics, especially in the field and low-resource settings, and provides epidemiological assessment of parasite burden. However, increased use and availability of point-of-care tests and molecular assays in modern era allow more rapid and accurate diagnoses and increased sensitivity in the identification of parasitic infections.

The performance of the new ePlex Respiratory Pathogen (RP) panel (GenMark Diagnostics) for the simultaneous detection of 19 viruses (influenza A virus; influenza A H1 virus; influenza A 2009 H1 virus; influenza A H3 virus; influenza B virus; adenovirus; coronaviruses [HKU1, OC43, NL63, and 229E]; human rhinovirus/enterovirus; human metapneumovirus; parainfluenza viruses 1, 2, 3, and 4; and respiratory syncytial virus [RSV] [RSV subtype A and RSV subtype B]) and 2 bacteria ( Mycoplasma pneumoniae and Chlamydia pneumoniae ) was evaluated. Prospectively and retrospectively collected nasopharyngeal swab (NPS) specimens ( n = 2,908) were evaluated by using the ePlex RP panel, with the bioMérieux/BioFire FilmArray Respiratory Panel (BioFire RP) as the comparator method. Discordance analysis was performed by using target-specific PCRs and bidirectional sequencing. The reproducibility of the assay was evaluated by using reproducibility panels comprised of 6 pathogens. The overall agreement between the ePlex RP and BioFire RP results was >95% for all targets. Positive percent agreement with the BioFire RP result for viruses ranged from 85.1% (95% confidence interval [CI], 80.2% to 88.9%) to 95.1% (95% CI, 89.0% to 97.9%), while negative percent agreement values ranged from 99.5% (95% CI, 99.1% to 99.7%) to 99.8% (95% CI, 99.5% to 99.9%). Additional testing of discordant targets (12%; 349/2,908) confirmed the results of ePlex RP for 38% (131/349) of samples tested. Reproducibility was 100% for all targets tested, with the exception of adenovirus, for which reproducibilities were 91.6% at low virus concentrations and 100% at moderate virus concentrations. The ePlex RP panel offers a new, rapid, and sensitive “sample-to-answer” multiplex panel for the detection of the most common viral and bacterial respiratory pathogens.