scholarly journals Molecular Study of Norovirus in Pediatric Patients with Gastroenteritis

2019 ◽  
Vol 13 (1) ◽  
pp. 324-329
Author(s):  
Maysaa El Sayed Zaki ◽  
Abdel-Rahaman Eid ◽  
Amany Y. El Ashry ◽  
Nashwa M. Al-Kasaby

Aim: The aim of the present study was to detect the prevalence of norovirus and genotypes determination by real-time PCR among children below 18 years as an etiology of acute gastroenteritis and to compare rapid detection of norovirus by Enzyme-Linked Immunoassay (ELISA) to virus detection by real-time PCR. Methods: The research was a cross-sectional study conducted on children below 18 years complaining of community-acquired acute gastroenteritis. A stool sample was subjected to direct-antigen detection by ELISA for norovirus and molecular study by real-time polymerase chain reaction. Results: The study included 200 children with acute gastroenteritis with a mean age of 6.7±3.8 years. Norovirus antigen was detected by EIA in 34.5% and by real-time PCR in 30.5% of studied children with genotype GII, the predominant detected genotype (80.97%). Both real-time PCR and antigen detection of norovirus were positive in 43 (70.5%) of the children and negative in 113(81.3%) of the studied children. The sensitivity, specificity, positive predictive value, negative predictive value and accuracy for antigen detection by ELISA were 70.5%, 81.3%, 62.3%, 86.3% and 78%, respectively. Comparison between patients positive for norovirus and those negative for norovirus by real-time PCR revealed non-significant difference as regards age, sex, the season of occurrence and residence. Conclusion: The present study highlights that norovirus prevalence is common among pediatric patients with gastroenteritis above 5 years with GII genotype as the prevalent genotype. There was a significant correlation between positive and negative results of antigen detection of norovirus by ELISA and detection of RNA of norovirus by real-time PCR in stool samples. However, the screening for norovirus by ELISA has limited sensitivity and needs to be associated with a molecular method for accurate diagnosis of sporadic cases of gastroenteritis.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 343-343
Author(s):  
Christine Landlinger ◽  
Lenka Baskova ◽  
Sandra Preuner ◽  
Martine Van Grotel ◽  
Nico G. Hartwig ◽  
...  

Abstract Abstract 343 Invasive fungal infections are life threatening events in severely immunocompromised patients, and there is urgent need for reliable screening methods facilitating rapid and broad detection of pathogenic fungi. We have established a two-reaction real-time PCR assay permitting highly sensitive detection and quantitative monitoring of more than 80 fungal pathogens, covering a large spectrum of moulds, yeasts and Zygomycetes (European patent No. 06817468.9). To assess the clinical potential of the panfungal real-time PCR assay, more than 600 consecutive specimens from 126 pediatric patients carrying a high risk of invasive fungal infections were analyzed. The results revealed an excellent correlation between PCR positivity and the presence of proven, probable or possible fungal infection according to the criteria of the European Organization for Research and Treatment of Cancer (EORTC), indicating a sensitivity of the assay of 96% (95%CI: 81-99.3%). Hence, the negative predictive value of the panfungal PCR assay presented is very high, and our current data indicate that molecular screening of patients during febrile neutropenic episodes by the assay can help prevent unnecessary toxicity resulting from empirical antifungal treatment in individuals who may not be at risk of imminent fungal disease. The specificity of the assay in the test cohort of patients was in the range of 76% (95%CI:62-87%), and the observations indicate that rapid species identification may be required to assess the positive predictive value for impending fungus-related disease. The availabel data provide a basis for appropriately designed clinical studies addressing the full diagnostic potential of fungal screening by highly sensitive, broad- spectrum molecular assays in severely immunocompromised patients. Disclosures: No relevant conflicts of interest to declare.


2017 ◽  
Vol 63 (4) ◽  
pp. 296-302 ◽  
Author(s):  
Massimiliano Bergallo ◽  
Ilaria Galliano ◽  
Paola Montanari ◽  
Martina Rosa Brusin ◽  
Serena Finotti ◽  
...  

Gastroenteritis is a common disease in children. It is characterized by diarrhea, vomiting, abdominal pain, and fever. Sapovirus (SaV) is a causative agent of acute gastroenteritis, but it causes milder illness than do rotavirus and norovirus. There is high variability in the analytical performance of quantitative PCR-based assays among clinical laboratories. This study developed a reverse transcription real-time PCR method to detect SaV in fecal specimens collected from children under 5-years-old with acute gastroenteritis. Of 137 episodes of acute gastroenteritis, 15 (10.9%) were associated with SaV genomic detection, with a median viral load of 6.6(log10) ± 7.1(log10) genomes/mg fecal specimens. There was a significant difference in detection rate between males and females (9.48% (13/15) vs. 1.46% (2/15), p = 0.0232). Among the 15 SaV-positive cases, 6 were also positive for rotavirus. Viral RNA recovery rate ranged from 46% to 77% in the manual RNAzol protocol and from 31% to 90% in the automated Maxwell protocol. We also studied whether human genomic DNA influences the sensitivity of the assay: its presence caused a decrease in PCR sensitivity. The development of a laboratory-designed real-time PCR TaqMan assay for quantitative detection of SaV and the optimization and standardization of this assay, using stools of children with acute gastroenteritis, are described.


2017 ◽  
Vol 61 (3) ◽  
pp. 173-178 ◽  
Author(s):  
Vivek Gupta ◽  
Arvind Bhake

Objectives: The diagnosis of peripheral tubercular lymphadenopathy (TBLN) in pediatric patients is often a challenge because features evident on fine-needle aspiration cytology (FNAC) or tissue biopsy can be deceptive for the reason that they result from an immunological response. This study aimed to evaluate polymerase chain reaction (PCR) for Mycobacterium tuberculosis complex (MTBC) in pediatric patients under clinical suspicion for TBLN and to assess its role in the evaluation of cases cytodiagnosed as reactive lymphoid hyperplasia. Methods: This was a cross-sectional study conducted on 45 pediatric patients clinically suspected and unsuspected for TBLN. FNAC, culture on Löwenstein-Jensen medium, and real-time PCR were performed. Comparative values with reference to the culture were calculated. Results: Cytology had a sensitivity and specificity of 38.5 and 87.5%, respectively. Real-time PCR had a sensitivity and specificity of 84.6 and 81.3%, respectively. Of the 32 cases with a cytodiagnosis of reactive lymphoid hyperplasia, 53% were positive both on PCR and culture for M. tuberculosis; the φ value of 0.93 demonstrated a strong association between these 2 methods. Conclusion: Real-time PCR is useful in detecting MTBC in pediatric patients, and it also helps in the diagnosis of cases missed on FNAC.


2016 ◽  
Vol 5 (3) ◽  
Author(s):  
Eka Kurniawan ◽  
Raveinal Raveinal ◽  
Fauzar Fauzar ◽  
Zulkarnain Arsyad

 AbstrakTuberkulosis (TB) paru adalah penyakit menular yang disebabkan oleh kuman Mycobacterium tuberkulosis. TB masih tetap menjadi masalah kesehatan dunia karena lebih kurang 1/3 penduduk dunia terinfeksi oleh kuman ini dan sumber penularannya berasal dari Basil Tahan Asam (BTA) positif maupun negatif. TB paru BTA negatif didiagnosis berdasarkan gambaran klinis dan rontgen torak yang sesuai TB serta pertimbangan dokter sehingga hal ini dapat menimbulkan under atau over diagnosis TB. GeneXpert merupakan pemeriksaan molekuler dengan metode “real time“ PCR dan merupakan penemuan terobosan untuk mendiagnosis TB secara cepat. Tujuan penelitiian ini adalah melakukan penilaian validitas GeneXpert pada TB paru BTA negatif dibandingkan dengan kultur Loweinstein Jensen. Desain penelitian uji diagnostik ini adalah cross sectional study. Penelitian dilakukan terhadap 40 orang pasien TB paru BTA negatif di Puskesmas sekitar kota Padang dan pasien yang dirawat di Bagian Penyakit Dalam RS dr. M. Djamil Padang. Dilakukan pemeriksaan sputum dengan GeneXpert dan dibandingkan dengan kultur Loweinstein Jensen. Hasil uji diagnostik dengan GeneXpert untuk mendiagnosis TB paru BTA negatif didapatkan sensitivitas 83.33%, spesifisitas 95.46%, nilai prediksi positif 93.75%, nilai prediksi negatif 87.5% dan akurasi 90% serta hasil uji kappa didapatkan 0.796. Disimpulkan GeneXpert memiliki sensitivitas, spesifisitas, nilai prediksi positif, nilai prediksi negatif dan akurasi yang tinggi pada TB paru BTA negatif.Kata kunci: nilai diagnostik, TB paru BTA negatif, GeneXpert AbstractPulmonary tuberculosis is an infectious disease caused by Mycobacterium tuberculosis. TB is still a global health problem. Approximately one third of the world population is infected by Mycobacterium tuberculosis and the source of infection came from smear positive and negative patient. Smear negative pulmonary TB can be considered based on clinical symptom and chest x-ray as well as description of TB and it’s depend on doctor's decision, so this can lead to under or over-diagnosis. Molecular examination with real time PCR method of GeneXpert is a breakthrough invention to diagnose TB quickly. The objective of this study was to assess the validity of GeneXpert in smear negative pulmonary TB and it’s compared with Loweinstein Jensen culture. Study design was diagnostic test with cross sectional study. Research conducted on 40 patients with smear negative pulmonary TB in public health centers around the city of Padang and the patients who were treated at the Internal Medicine department of dr. M. Djamil hospital Padang. Sputum examination conducted by GeneXpert compared with Loweinstein Jensen culture. Diagnostic value of GeneXpert for diagnosing smear negative pulmonary tuberculosis are sensitivity 83.33%, specificity 95.46%, positive predictive value 93.75%, negative predictive value 87.5% and accuracy 90%. Kappa value is 0.796. GeneXpert has a high sensitivity, specificity, positive predictive value, negative predictive value and accuracy on smear negative pulmonary tuberculosis.Keywords: diagnostic value, smear negative pulmonary tuberculosis, GeneXpert


2021 ◽  
Vol 7 (1) ◽  
pp. 88-93
Author(s):  
Silvani Permatasari ◽  
Vani Vrenika ◽  
Florence Felicia ◽  
Malasinta Malasinta ◽  
Ria Eriani ◽  
...  

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis. Indonesia is one of the developing countries with high TB patients in the world. The most common detection used for TB diagnosis is sputum smear examination. Smear negative pulmonary TB still have a risk of infection and can develop into active. The GeneXpert molecular examination is a rapid diagnosis of TB by the real-time PCR method. The purpose of this study was to assess the validity of GeneXpert in smear-negative pulmonary TB compared to Lowenstein Jensen's culture. The design of this diagnostic test study is a cross-sectional study. The study was conducted on 40 people with smear-negative pulmonary TB suspect patients in Dr. Doris Sylvanus Regional Hospital. Sputum examination was performed with GeneXpert and compared with Lowenstein Jensen culture. The results of GeneXpert validity for diagnosing smear-negative pulmonary TB suspect are sensitivity 81.8%, specificity 96.5%, positive predictive value 90%, negative predictive value 93.3%, and accuracy 92.5%. It was concluded that GeneXpert has sensitivity, specificity, positive predictive value, negative predictive value, and high accuracy as a diagnostic tool in smear-negative pulmonary TB suspects.


2020 ◽  
Vol 18 ◽  
Author(s):  
Pegah Shakib ◽  
Mohammad Reza Zolfaghari

Background: Conventional laboratory culture-based methods for diagnosis of Streptococcus pneumoniae are time-consuming and yield false negative results. Molecular methods including real-time (RT)-PCR rapid methods and conventional PCR due to higher sensitivity and accuracy have been replaced instead traditional culture assay. The aim of the current study was to evaluate lytA gene for detection of Streptococcus pneumoniae in the cerebrospinal fluid of human patients with meningitis using real-time PCR assay. Material and Methods: In this cross-sectional study, a total of 30 clinical specimens were collected from patients in a period from September to December 2018. In order to evaluate the presence of lytA gene, conventional and real-time PCR methods were used without culture. Results: From 30 sputum samples five (16.66%) isolates were identified as S. pneumoniae by lytA PCR and sequencing. Discussion: In this research, an accurate and rapid real-time PCR method was used, which is based on lytA gene for diagnosis of bacteria so that it can be diagnosed. Based on the sequencing results, the sensitivity for detection of lytA gene was 100% (5/5).


2021 ◽  
Author(s):  
Zhuo Liu ◽  
Feng He ◽  
Jing Liu ◽  
Shengrong OuYang ◽  
Zexi Li ◽  
...  

Abstract Background Wilms’ tumor, also called nephroblastoma, is the most common pediatric renal malignancy. The pathogenesis of Wilms’ tumor has been attributed to several genetic and epigenetic factors. However, the most pervasive internal mRNA modification that affects almost every process of RNA metabolism, RNA N6-Methyladenosine (m6A) methylation, has not been characterized in Wilms’ tumor. Methods Wilms’ tumor (WT) and adjacent non-cancerous (NC) tissue samples were obtained from 23 children with nephroblastoma, and the global m6A levels were measured by mass spectrometry. Analyses by m6A-mRNA epitranscriptomic microarray and mRNA microarray were performed, and m6A-related mRNAs were validated by quantitative real-time PCR for input and m6A-immunoprecipitated RNA samples from WT and NC tissues. Gene ontology analysis and KEGG pathway analysis were performed for differentially expressed genes, and expression of RNA methylation-related factors was measured by quantitative real-time PCR. Results The total m6A methylation levels in total RNA of WT samples and NC samples were (0.21 ± 0.01)% and (0.22 ± 0.01)%, respectively, with no statistically significant difference. Fifty-nine transcripts were differentially m6A-methylated between the WT and NC groups, which showed distinct m6A modification patterns. Gene ontology analysis indicated that m6A-modified genes were enriched in cancer-associated pathways, including the mTOR pathway, and conjoint analysis of the unique methylation and gene expression patterns in WT samples suggested an association with metabolic pathways.The mRNA levels of the m6A-related “reader” genes, YTHDF1, YTHDF2 and IGF2BP3, were statistically higher in WT samples than in NC samples. Conclusion This is the first study to determine the m6A modification profiles in Wilms’ tumor. Our data provide novel information regarding patterns of m6A modification that correlate with carcinogenesis in Wilms’ tumor.


2019 ◽  
Vol 263 ◽  
pp. 101-104 ◽  
Author(s):  
Nikolay Yu. Saushkin ◽  
Jeanne V. Samsonova ◽  
Alexander P. Osipov ◽  
Sergey E. Kondakov

2021 ◽  
Vol 8 (4) ◽  
pp. 325-332
Author(s):  
Kate Deepali Rajesh ◽  
Puranam Vatsalaswamy ◽  
Manvikar Purshotam Rao

To study the relevance of sperm telomere length and infertility in men. : Our case-control study included twenty-five males in couple with sub-fertility/infertility (test group) and twenty five healthy males (control group) with proven paternity in the age group 25 to 35 years. The Absolute Sperm Telomere length (aSTL) was measured by real-time PCR. We investigated whether any significant difference in the aSTL value existed between the groups and analysed the relationship between aSTL and other sperm parameters.The mean (SE) aSTL recorded in the infertile cases was significantly shorter than for the control group being 140.60 (6.66) Kb/genome and 239.63 (12.32) Kb/genome respectively (p <0.001) A weak correlation was eminent between aSTL kb/genome and the total sperm count mil/ml (rho= 0.04, p - 0.86), progressive sperm motility (rho= - 0.02, p=0.934) and sperm viability (rho= - 0.07 p=0.741) in the infertile group. The measurement of aSTL by real-time PCR is a simple and rapid method that offers further paramount information with respective to the quality of sperm. It is befitted for epidemiological studies, hence opening new perspectives in the evaluation of male infertility. Limitations - Our study was confined to men aged between 25 and 35 years. Further comparative studies are needed to explore the significance of STL and infertility in older males. Additional studies will help illumine the significance of aSTL as a prognostic biomarker in assisted reproduction.


2013 ◽  
Author(s):  
Δήμητρα-Τζιμούλα Κοτρώτσιου

Εισαγωγή: Το U.urealyticum spp. είναι ένας μικροοργανισμός πολύ διαδεδομένος στον άνθρωπο, που αποικίζει διάφορες περιοχές του σώματός του και συχνά προκαλεί οξείες ή χρόνιες λοιμώξεις. Καθώς ο μικροοργανισμός στερείται κυτταρικού τοιχώματος, η αντιμετώπιση των λοιμώξεων που προκαλεί περιορίζεται κυρίως στις κινολόνες, τις μακρολίδες και τις τετρακυκλίνες. Η περιορισμένη πλέον παραγωγή νέων αντιμικροβιακών καθιστά επιτακτική την ανάγκη ορθής και αποτελεσματικής χορήγησης αυτών που υπάρχουν. Η παγκόσμια επιστημονική κοινότητα είναι ήδη ευαισθητοποιημένη, καθώς τα ουρεαπλάσματα έχουν ήδη από ετών αποκτήσει ικανά επίπεδα ανθεκτικότητας σε ορισμένα από τα χορηγούμενα αντιμικροβιακά. Σκοπός: Σκοπός αυτής της έρευνας ήταν να ελέγξει την ανθεκτικότητα των στελεχών του U.urealyticum spp., που κυκλοφορούν στη Βόρεια Ελλάδα, στα χρησιμοποιούμενα αντιμικροβιακά φάρμακα, σε φαινοτυπικό όσο και σε γονιδιακό επίπεδο.Υλικό και μέθοδος: Επρόκειτο για συγχρονική μελέτη (cross-sectional study) χρονικής στιγμής σε σχέση με τον επιπολασμό, η οποία περιλαμβάνει έλεγχο της ανθεκτικότητας του U.urealyticum spp. στα χρησιμοποιούμενα αντιμικροβιακά με συμβατικές και μοριακές τεχνικές. Το υλικό της εργασίας αποτέλεσαν 100 θετικά δείγματα για U.urealyticum spp. που προήλθαν από νοσοκομεία της Θεσσαλονίκης, το διάστημα 2010-2011. Τα κλινικά δείγματα ήταν τραχηλικά επιχρίσματα γυναικών και ουρηθρικά εκκρίματα ανδρών, στα οποία ο μικροοργανισμός απομονώθηκε με καλλιέργεια σε άγαρ Α7. Και τα 100 θετικά δείγματα για U.urealyticum spp. που επιλέχθηκαν είχαν συγκέντρωση μικροβίου >104 CFU/ml και δεν υπήρχε συλλοίμωξη του γεννητικού συστήματος των ασθενών με άλλο γεννητικό μυκόπλασμα. Ακολούθησε φαινοτυπικός έλεγχος ανθεκτικότητας του μικροοργανισμού με προτυποποιημένη μέθοδο. Επιβεβαιωτικά έγινε ανίχνευση του γονιδίου της ουρεάσης με real-time PCR στα δείγματα με θετική καλλιέργεια. Πραγματοποιήθηκε μοριακός διαχωρισμός του U.urealyticum spp. στα είδη του και μοριακός διαχωρισμός στελεχών U.parvum στους γονοτύπους τους. Για την ανίχνευση πιθανών μεταλλάξεων στις υπομονάδες-στόχους των χρησιμοποιούμενων αντιμικροβιακών, έγινε ενίσχυση όλων των υπομονάδων-στόχων των κινολονών σε όλα τα στελέχη, όλων των υπομονάδων-στόχων των μακρολιδών στα μη ευαίσθητα στελέχη και του γονιδίου tetM για τις τετρακυκλίνες σε όλα τα στελέχη. Η ανίχνευση των γονιδίων ουρεάσης και tetM πραγματοποιήθηκε για πρώτη φορά βιβλιογραφικά με εφαρμογή τεχνικών Real Time PCR. Ακολούθησε αλληλούχηση των προϊόντων ενίσχυσης για τις κινολόνες και τις μακρολίδες σε επιλεγμένα στελέχη και έγινε σύγκριση των αλληλουχιών με αυτές των αντίστοιχων πρότυπων στελεχών. Για τη στατιστική ανάλυση χρησιμοποιήθηκε η μέθοδος χ2 και οι παραλλαγές της και το στατιστικό πρόγραμμα SPSS 17.0. Αποτελέσματα: Η συχνότητα ανεύρεσης του U.urealyticum spp. σε υγιείς ασυμπτωματικές γυναίκες ηλικίας 20-70 ετών στην Βόρεια Ελλάδα βρέθηκε σε ποσοστό 16,13%. Οι υγιείς φορείς του μικροοργανισμού σε υψηλές συγκεντρώσεις (≥104CFU/ml) είναι στην πλειοψηφία τους γυναίκες σε αναπαραγωγική ηλικία, ενώ το κυρίαρχο είδος στα στελέχη του μικροοργανισμού βρέθηκε το U.parvum. Η ομάδα των τετρακυκλινών προκρίνεται, ως η πιο αποτελεσματική φαινοτυπικώς θεραπευτική αγωγή (αντοχή 0%), ακολουθούμενη από τις μακρολίδες (αντοχή 4%), ενώ αντίθετα η ανθεκτικότητα του μικροοργανισμού στις κινολόνες είναι ιδιαίτερα υψηλή (>50%). Η οφλοξασίνη υπερέχει στατιστικά σημαντικά της σιπροφλοξασίνης ως προς την ευαισθησία στο σύνολο των θετικών δειγμάτων για U.urealyticum spp., και στα δύο είδη του μικροοργανισμού. Οι περισσότερες νουκλεοτιδικές/αμινοξικές αλλαγές που σχετίζονται με ανθεκτικότητα στις κινολόνες σημειώνονται στις πρωτεϊνικές υπομονάδες της τοποϊσομεράσης IV, ειδικότερα στην υπομονάδα ParC. Σε ότι αφορά τις μακρολίδες, στελέχη με χαμηλές MIC εμφανίζουν μεταλλάξεις στους γνωστούς στόχους των εν λόγω αντιβιοτικών. Σε περισσότερα από το ένα τρίτο των φαινοτυπικώς ευαίσθητων στελεχών του U.urealyticum spp. στις τετρακυκλίνες ανιχνεύθηκε το γονίδιο ανθεκτικότητας tetM. Ανιχνεύθηκαν 11 νέοι πολυμορφισμοί στην υπομονάδα ParC, 1 στην υπομονάδα ParE για τις κινολόνες και 1 στο γονίδιο της πρωτεΐνης L22 για τις μακρολίδες, που αναφέρονται για πρώτη φορά διεθνώς. Δεν υπάρχει συσχέτιση μεταξύ της κλινικής εικόνας και της παρουσίας ή όχι μεταλλάξεων και γονιδίων ανθεκτικότητας.Συμπεράσματα: Οι υγιείς φορείς του μικροοργανισμού υπολογίζονται σε περίπου μία στις 6 γυναίκες στη Βόρεια Ελλάδα, με το υψηλότερο ποσοστό στην αναπαραγωγική ηλικία. Οι κινολόνες θα πρέπει να χρησιμοποιούνται με περίσκεψη και αν υπάρχει η δυνατότητα επιλογής, συνιστάται η οφλοξασίνη. Τα στελέχη που απομονώθηκαν από ασθενείς και φορείς δεν διέφεραν στατιστικά ως προς την ευαισθησία στις κινολόνες. Ανιχνεύθηκαν νέοι πολυμορφισμοί που αναφέρονται για πρώτη φορά διεθνώς. Διαπιστώθηκε ότι στελέχη με την ίδια φαινοτυπική ευαισθησία παρουσιάζουν διαφορετικές μεταλλάξεις, που οδηγούν στην υπόθεση ότι όλες οι μεταλλάξεις δεν σχετίζονται ισχυρά με ανθεκτικότητα. Επίσης, η σημασία της παρουσίας του γονιδίου tetM αξιολογείται με περίσκεψη. Συμπερασματικά: α) η χορηγούμενη θεραπευτική αγωγή καλόν είναι να βασίζεται στον έλεγχο φαινοτυπικής ευαισθησίας του μικροοργανισμού, αντί της εμπειρικής θεραπείας που συνήθως δίνεται στην καθ’ημέρα κλινική πράξη β) για την επιδημιολογική επιτήρηση του U.urealyticum spp. έχει σημασία η συσχέτιση της φαινοτυπικής ανθεκτικότητας με το γονοτυπικό του προφίλ.


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