Evaluation of PCR Positive Cases in the Pediatric Emergency Department

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A rapid, high-volume cervical screening project using self-sampling and isothermal PCR HPV testing

 

Objective: Rapid, high-volume screening programs are needed as part of cervical cancer prevention in China.
Methods: In a 5-day screening project in Inner Mongolia, 3345 women volunteered following a community awareness campaign, and self-swabbed to permit rapid HPV testing. Two AmpFire™ HPV detection systems (Atila Biosystems) were sufficient to provide pooled 15-HPV type data within an hour. HPV+ patients had same-day digital colposcopy (DC) performed by 1 of 6 physicians, using the EVA™ system (MobileODT). Digital images were obtained and, after biopsy of suspected lesions for later confirmatory diagnosis, women were treated immediately based on colposcopic impression. Suspected low- grade lesions were offered treatment with thermal ablation (Wisap), and suspected high-grade lesions were treated with LLETZ.
Results: Of 3345 women screened, 624 (18.7%) were HPV+. Of these, 88.5% HPV+ women underwent same-day colposcopy and 78 were treated. Later consensus histology results obtained on 197 women indicated 20 CIN2+, of whom 15 were detected and treated/referred at screening (10 by thermal ablation, 4 by LLETZ, 1 by referral).
Conclusions: Global control of cervical cancer will require both vaccination and screening of a huge number of women. This study illustrates a cervical screening strategy that can be used to screen-and-treat large numbers of women. HPV self-sampling facilitates high-volume screening. Specimens can be tested rapidly, promoting minimal loss-to-follow-up.
Specifically, the AmpFire™ system used in this study is highly portable, simple, rapid (92 specimens per 65 min per unit), and economical. Visual triage can be performed on HPV+ women with a portable digital colposcope that provides magnification, lighting, and a recorded image. Diagnosis and appropriate treatment remain the most subjective elements. The digital image is under study for deep-learning based automated evaluation that could assist the management decision, either by itself or combined with HPV typing.

[The Identification of Acinetobacter baumannii Blood Isolates by MALDI-TOF MS, ARDRA and blaOXA-51-like Gene-Specific Real-Time PCR]

The Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) complex consists of phenotypically very similar nosocomial species; A.baumannii, Acinetobacter nosocomialis, Acinetobacter pittii, Acinetobacter seifertii and Acinetobacter djikshoorniae and one environmental species A.calcoaceticus. The rapid and accurate identification of the members of Acb complex is critical as these nosocomial pathogens can show differences in antimicrobial susceptibility and clinical outcomes.
The conventional phenotypic methods are slow, unreliable and less efficient for the differentiation of Acb complex species, including the A.baumannii species within the Acb complex. Although various molecular methods are available, such as amplified ribosomal DNA restriction analysis (ARDRA) and blaOXA-51-like gene specific PCR, they are usually inconvenient for the routine diagnostic laboratories. Recently, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) offers an opportunity for rapid, cost-effective and convenient bacterial identification in routine diagnostic procedures conducted in clinical laboratory. In this study, we aimed to evaluate the diagnosis performance of MALDI-TOF MS system to identify blood isolates of A.baumannii. A total of 180 nonduplicate carbapenem resistant Acb complex (strain numbers; TR1-TR60) and A.baumannii (TR61-TR180) blood isolates were collected from the intensive care units of the three university hospitals in Turkey from January 2016 to December 2016.
All isolates were evaluated by using blaOXA-51-like gene specific real time (Rt-PCR) analysis, ARDRA (restriction enzymes-AluI, CfoI, MboI, MspI, RsaI) method and MALDI-TOF MS (VITEK® MS, bioMérieux, France) system. All the strains except TR10, TR31, TR35 and TR52 were identified as A.baumannii by ARDRA method. Out of 177 of all the isolates, presence of blaOXA-51-like gene was found except for TR10, TR31 and TR52 isolates. However, TR31 without the presence of blaOXA-51-like gene was identified as A.pittii using the ARDRA. Totally 176 isolates which were identified as A.baumannii by both of the methods, ARDRA and Rt-PCR- blaOXA-51-like, were accepted as a reference for the evaluation of the diagnosis performance capacity of the MALDI-TOF MS. Overall, for all 176 isolates tested, the sensitivity obtained with the MALDI-TOF MS were 99.4% with 75% specificity.
The accuracy value of the method was determined as 98.9% for the identification of A.baumannii to the species level. MALDI-TOF MS is increasingly used in diagnostic microbiology for the routine identification of bacteria to the genus, species or subspecies level with high rates of sensitivity and specificity. In future, by expanding the database, MALDI-TOF MS system would possibly become the ideal method for routine diagnostic laboratories that could potentially identify more species and even determine some characteristics of antimicrobial resistance and virulence determinants.

Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data

 

SARS-CoV-2 antibody tests are available in various formats, detecting different viral target proteins and antibody subclasses. The specificity and sensitivity of SARS-CoV-2 antibody tests are known to vary and very few studies have addressed the performance of these tests in COVID-19 patient groups at different time points. We here compared the sensitivity and specificity of seven commercial (SNIBE, Epitope, Euroimmun, Roche, Abbott, DiaSorin, Biosensor) and two in-house LIPS assays (LIPS N and LIPS S-RBD) IgG/total Ab tests in serum samples from 97 COVID-19 patients and 100 controls, and correlated the results with the patients’ clinical data and the time-point the test was performed. We found a remarkable variation in the sensitivity of antibody tests with the following performance: LIPS N (91.8%), Epitope (85.6%), Abbott and in-house LIPS S-RBD (both 84.5%), Roche (83.5%), Euroimmun (82.5%), DiaSorin (81.4%), SNIBE (70.1%), and Biosensor (64.9%).
The overall agreement between the tests was between 71-95%, whereas the specificity of all tests was within 98-100%. The correlation with patients’ clinical symptoms score ranged from strongest in LIPS N (ρ = 0.41; p<0.001) to nonsignificant in LIPS S-RBD. Furthermore, the time of testing since symptom onset had an impact on the sensitivity of some tests. Our study highlights the importance to consider clinical symptoms, time of testing, and using more than one viral antigen in SARS-CoV-2 antibody testing. Our results suggest that some antibody tests are more sensitive for the detection of antibodies in early stage and asymptomatic patients, which may explain the contradictory results of previous studies and should be taken into consideration in clinical practice and epidemiological studies.
ALV Real-Time PCR Kit
PD65-15 96t
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Description: Please check the datasheet of ALV Real-Time PCR Kit before using the test.
hsa-mir-521 Real-time RT-PCR Detection Kit
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Novel Coronavirus COVID-19 (2019-nCoV) Real Time RT-PCR Kit
RR-0478-02 25 tests/kit
EUR 991.00
  • For use with PE5700, MJ-Opticon & other single color systems, ABI7000, ABI7300, ABI7500, ABI7900, ABI StepOne, StepOne plus, MJ-Opticon2, MJ-chromo4, MX3000P, MX3005P, Smart Cycler II, Rotor-Gene 6000, LightCycler 480, CFX 96, Life 96, Slan 96, iCycl
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Description: Novel Coronavirus (2019-nCoV) Real Time RT-PCR Kit is used for the qualitative detection of a novel coronavirus, which was identified in 2019 at Wuhan City, Hubei Province, China, in upper respiratory tract specimens (nasopharyngeal extracts, deep cough sputum, etc.) and lower respiratory tract specimens (alveoli irrigation fluid, etc.) by real time PCR systems.
dsGreen for Real-Time PCR, 100×, 2 mL
61010 2 mL
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0,1ML THIN WALL TUBES 8 PER STRIP. CLEAR & REAL TIME STRIP CAPS
PCR-0108-LP-RT-C 125/pk
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Description: PCR Plates & Tubes; PCR Strip Tubes and Strip Caps - Axygen
0,1ML THIN WALL TUBES 8 PER STRIP. WHITE & REAL TIME STRIP CAPS
PCR-0108-LP-RT-W 125/pk
EUR 770.00
Description: PCR Plates & Tubes; PCR Strip Tubes and Strip Caps - Axygen
dsGreen for Real-Time PCR, 100×, 50 mL
91010 50 mL
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dsGreen for Real-Time PCR, 100×, 10 mL
81010 10 mL
EUR 869.00
dsGreen for Real-Time PCR, 100×, 5 mL
71010 5 mL
EUR 625.00
dsGreen for Real-Time PCR, 100×, 1.5 mL
51010 1.5 mL
EUR 331.00
dsGreen for Real-Time PCR, 100×, 1 mL
41010 1 mL
EUR 249.00
dsGreen for Real-Time PCR, 100×, 100 uL
11010 100 uL
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hsa-mir-99b Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-101 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-105 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-124 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-129 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-130a Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-130b Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-132 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-133b Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-134 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-138 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-139 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-143 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-145 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-182 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-183 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-184 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-185 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-190a Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-190b Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-192 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-193a Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-193b Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-194 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-195 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-197 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
20-abx097738
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hsa-mir-198 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-199a Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-199b Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
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hsa-mir-200a Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
20-abx097742
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hsa-mir-200b Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
20-abx097743
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hsa-mir-202 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
20-abx097745
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hsa-mir-203 Real-Time RT-PCR Detection and cel-mir-39-3p Calibration Kit
20-abx097746
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20-abx097751
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20-abx097753
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[Evaluation of SARS-CoV-2 PCR Positive Cases in the Pediatric Emergency Department]

 

In December 2019, a previously unknown type of coronavirus was detected in China and named as “severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)”. The World Health Organization has named the SARS-CoV-2 related as coronavirus disease-2019 (COVID-19) and declared it as a pandemic. There is a limited data about the COVID-19 disease for the pediatric patients. In this study, it was aimed to evaluate the epidemiological, clinical, laboratory and radiologic findings, treatment and clinical outcomes of patients admitted to the pediatric emergency department with the suspicion of COVID-19. Between March 11 and June 16, 2020, patients aged between 1 month-18 years admitted to the pediatric emergency department and who have an indication for sampling for the polymerase chain reaction (PCR) method with the suspicion of COVID-19 according to the current guidelines published by the Ministry of Health were included in the study. The demographic characteristics, symptoms, durations and the history of contact with the suspected/definite COVID-19 cases were questioned in the patients with positive results. Physical examination, laboratory and imaging data of the patients were recorded. According to clinical severity, patients were divided into five groups.
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Treatment methods, ward/intensive care unit admission, length of stay at hospital, and prognosis were recorded. Of the 237 patients included in the study, 45 (18.9%) of the samples were positive and 192 (81.1%) were negative. There was a history of contact with COVID-19 positive case in 38 (85.6%) of COVID-19 PCR positive patients. The mean time for onset of symptoms after contact was 3.5 ± 1.7 days. Twenty-one of the patients (46.6%) were asymptomatic and the most common symptom was fever (34.1%) and cough (27.3%). Of the patients whose laboratory tests were requested, lymphopenia wasdetected in 50% and 52.3% of procalcitonin, 23.5% of C-reactive protein and 64.7% of D-dimer values were found to be high.
Chest radiography was obtained from 45.4% of the patients; 90.0% were evaluated as normal, bronchovascular change, pleural effusion and consolidation were detected in one of each (5.0%) patient. Thorax computed tomography (CT) was obtained from 4 (9.0%) patients. One patient had normal CT findings, two patients had consolidation, one patient had peripheral ground-glass appearance and one patient had pleural effusion. Antibiotics were started in 38.6% of the patients and the most commonly used antibiotic was azithromycin (34.1%). Oseltamivir was started in one (2.3%) patient, and 10 (24.7%) patients were treated with hydroxychloroquine.
There were no serious and critical cases according to the clinical severity. Pediatric patients constitute a small part of COVID-19 individuals in the community, and a significant part of them are asymptomatic, and patients who are symptomatic present with a mild clinic. In our study, most of the patients had a history of contact with COVID-19 positive cases, therefore, it should be questioned when evaluating a pediatric patient. There were no specific findings for COVID-19 positive patients in terms of laboratory and radiology.
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