Evaluation of PCR Positive Cases in the Pediatric Emergency Department

November 12, 2020
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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.

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Description: Novel Coronavirus (2019-nCoV) Real Time Multiplex 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. It detects N gene, E gene and RdRp gene of 2019-nCoV. RR-0479-02 has been also approverd by CFDA for emergency use and is WHO standard.

Azura PureView 1 Kb DNA Ladder - 100 Lanes
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AzuraView GreenFast qPCR Blue Mix Lo Rox - 200 Rxn
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AzuraView GreenFast qPCR Blue Mix Lo Rox - 500 Rxn
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AzuraView GreenFast qPCR Blue Mix Hi Rox - 200 Rxn
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AzuraView GreenFast qPCR Blue Mix Hi Rox - 500 Rxn
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Mouse Gdnf Signaling Primer Library
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Mouse Glucose Metabolism Primer Library
MGLM-I 1 set
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Mouse Hippo Signaling Primer Library
MHPO-I 1 set
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Mouse Hypoxia Signaling Primer Library
MHYP-I 1 set
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Mouse Notch Signaling Primer Library
MNOT-I 1 set
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Mouse Neurotransmitter Signaling Primer Library
MNTS-I 1 set
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Mouse Integrin Signaling Primer Library
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Mouse Oxidative Stress Primer Library
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Mouse Oncogene Primer Library
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Mouse Apoptosis Primer Library
MPA-I 1 set
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Mouse Ras Signaling Primer Library
MRAS-I 1 set
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Mouse T-Cell Receptor Signaling Primer Library
MTCR-I 1 set
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Mouse TGF Beta Signaling Primer Library
MTGFB-I 1 set
EUR 657.6

Mouse Tumor Invasion/Metastasis Primer Library
MTIM-I 1 set
EUR 540

Mouse Tumor Immunity Primer Library
MTIMU-I 1 set
EUR 657.6

Mouse p53 Signaling Primer Library
MTPS-I 1 set
EUR 540

Mouse WNT Signaling Primer Library
MWNT-I 1 set
EUR 657.6

Mouse Toll-like Receptor Signaling Primer Library
newitem 1 set
EUR 657.6

Mouse PI3K-AKT Signaling Primer Library
MAKT-I 1 set
EUR 657.6

Mouse Angiogenesis Primer Library
MAPL-I 1 set
EUR 540

Mouse Adherin - Tight Junction Primer Library
MATJ-I 1 set
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Mouse Autophagy Primer Library
MATPL-I 1 set
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Mouse Bdnf Signaling Primer Library
MBDNF-I 1 set
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Mouse BMP Signaling Primer Library
MBMP-I 1 set
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Mouse Cytokine Primer Library I
MCA-I 1 set
EUR 540

Mouse Cytokine Primer Library II
MCA-II 1 set
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Mouse Cell Cycle Primer Library
MCC-I 1 set
EUR 540

Mouse Cytokine and Chemokine Receptor Primer Library
MCCR-I 1 set
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Mouse CREB Signaling Primer Library
MCREB-I 1 set
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Mouse DNA Damage Signaling Primer Library
MDDS-I 1 set
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Mouse DNA Repair Primer Library I
MDRL-I 1 set
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Mouse DNA Repair Primer Library II
MDRL-II 1 set
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Mouse Adipogenesis Primer Library
MADG-I 1 set
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Mouse EGFR Signaling Primer Library
MEGFR-I 1 set
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Mouse Epithelial-Mesenchymal Transition Primer Library
MEMT-I 1 set
EUR 657.6

Mouse Estrogen Receptor Signaling Library
MESR-I 1 set
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Mouse Fatty Liver Signaling Primer Library
MFTL-I 1 set
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Mouse Jak/Stat Signaling Primer Library
MJAK-I 1 set
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Mouse MAP Kinase Signaling Primer Library
MMAP-I 1 set
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Mouse Myeloid Derived Suppressor Cell Primer Library
MMDSC-I 1 set
EUR 657.6

Mouse NFKappaB Primer Library
MNFKB-I 1 set
EUR 540

Human DNA Repair Primer Library I
HDRL-I 1 set
EUR 657.6

Human DNA Repair Primer Library II
HDRL-II 1 set
EUR 657.6

Human Drug Transporter I Primer Library
HDTP-I 1 set
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Human Drug Detoxication I
HDTX-I 1 set
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Human Drug Detoxication II
HDTX-II 1 set
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Human EGFR Signaling Primer Library
HEGFR-I 1 set
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Human Epithelial Mesenchymal Transition Primer Library
HEMT-I 1 set
EUR 657.6

Human Endothelial Cell Primer Library
HEND-I 1 set
EUR 657.6

Human ERBB Signaling Primer Library
HERBB-I 1 set
EUR 657.6

Human Estrogen Signaling Primer Library
HESR-I 1 set
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Human Focal Adhesion Signaling Primer Library
HFCA-I 1 set
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Human FGF Receptor Signaling Primer Library
HFGF-I 1 set
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Human Fatty Acid and Lipid Metabolism Primer Library
HFLM-I 1 set
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Human Gastric Cancer Primer Library
HGCPL-I 1 set
EUR 657.6

Human GDNF Signaling Primer Library
HGDNF-I 1 set
EUR 657.6

Human Glucose Metabolism Primer Library
HGLM-I 1 set
EUR 540

Human G-Protein Coupled Receptor Signaling Primer Library
HGPCR-I 1 set
EUR 657.6

Human Hedgehog Signaling Primer Library
HHOG-I 1 set
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Human Homeobox Gene Primer Library
HHOX-I 1 set
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Human Hippo Signaling Primer Pathway
HHPO-I 1 set
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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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100G AquaPor 3:1
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25G Bis (Methylene Bis-Acrylamide)
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250G Glycine
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