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Grogan J.A.,Our Ladys Childrens Hospital | Grogan J.A.,The Coombe Women and Infants University Hospital | Logan C.,Our Ladys Childrens Hospital | Logan C.,The Coombe Women and Infants University Hospital | And 5 more authors.
Journal of Medical Microbiology | Year: 2011

Novel real-time PCR assays targeting the Bordetella pertussis insertion sequence IS481, the toxin promoter region and Bordetella parapertussis insertion sequence IS1001 were designed. PCR assays were capable of detecting ¡10 copies of target DNA per reaction, with an amplification efficiency of ¢90%. From September 2003 to December 2009, per-nasal swabs and nasopharyngeal aspirates submitted for B. pertussis culture from patients ¡1 month to.15 years of age were examined by real-time PCR. Among 1324 patients, 76 (5.7%) were B. pertussis culture positive and 145 (10.95%) were B. pertussis PCR positive. Of the B. pertussis PCR-positive patients, 117 (81%) were aged 6 months or less. A total of 1548 samples were examined, of which 87 (5.6%) were culture positive for B. pertussis and 169 (10.92%) were B. pertussis PCR positive. All culture-positive samples were PCR positive. Seven specimens (0.5%) were B. parapertussis culture positive and 10 (0.8%) were B. parapertussis PCR positive, with all culture-positive samples yielding PCR-positive results. A review of patient laboratory records showed that of the 1324 patients tested for pertussis 555 (42%) had samples referred for respiratory syncytial virus (RSV) testing and 165 (30%) were positive, as compared to 19.4% of the total 5719 patients tested for RSV in this period. Analysis of the age distribution of RSV-positive patients identified that 129 (78%) were aged 6 months or less, similar to the incidence observed for pertussis in that patient age group. In conclusion, the introduction of the real-time PCR assays for the routine detection of B. pertussis resulted in a 91% increase in the detection of the organism as compared to microbiological culture. The incidence of infection with B. parapertussis is low while the incidence of RSV infection in infants suspected of having pertussis is high, with a similar age distribution to B. pertussis infection. Source


Carcopino X.,Hopital NORD | Carcopino X.,University of Medicine of Marseille | Carcopino X.,Institute Paoli Calmettes | Bolger N.,The Coombe Women and Infants University Hospital | And 7 more authors.
Journal of Medical Virology | Year: 2011

The persistence of high-risk HPV (HR-HPV) infection is necessary for the development of cervical intraepithelial neoplasia. The aim of this study was to evaluate if HR-HPV typing and HPV16, 18, 31, and 33 quantitation are predictive for type-specific infection persistence and/or the development of CIN in women under 30 with normal cervical cytology. Young women (under 30) attending a family planning clinic who were HPV positive with normal cervical cytology were included. HPV genotyping was assessed by MY09/MY11 PCR, sequencing, phylogenetic analysis, and cloning when necessary. HR-HPV viral load was quantified using duplex real-time PCR. Study patients were offered for a second smear and HR-HPV detection and quantitation after 12 months. HR-HPV was identified in 43 (21.9%) of the 199 included women. Of these, 39 patients had a second cervical sample taken within a mean interval of 11.7 months (8.8-18.3 months). The mean HR-HPV 16, 18, 31, and 33 initial viral load was 1.9×106copies/million cells. The level of viral load did not reveal any significant association with type-specific HR-HPV persistence or the subsequent development of cervical intraepithelial neoplasia. Only HPV16 infection was significantly more likely to persist (91.7% vs. 33.1%, P=0.001) and to develop CIN (33.3% vs. 3.7%, P=0.025). In women under 30 with normal cytology, HR-HPV viral load is common and is not predictive of HPV persistence or the development of cervical intraepithelial neoplasia. HPV16 positive women are significantly more likely to have persistent infection and to develop cervical intraepithelial neoplasia. © 2011 Wiley-Liss, Inc. Source


Vencken S.F.,St Jamess Hospital | Vencken S.F.,The Coombe Women and Infants University Hospital | Sethupathy P.,University of North Carolina at Chapel Hill | Blackshields G.,St Jamess Hospital | And 11 more authors.
BMC Genomics | Year: 2014

Background: SOX2 is a core component of the transcriptional network responsible for maintaining embryonal carcinoma cells (ECCs) in a pluripotent, undifferentiated state of self-renewal. As such, SOX2 is an oncogenic transcription factor and crucial cancer stem cell (CSC) biomarker in embryonal carcinoma and, as more recently found, in the stem-like cancer cell component of many other malignancies. SOX2 is furthermore a crucial factor in the maintenance of adult stem cell phenotypes and has additional roles in cell fate determination. The SOX2-linked microRNA (miRNA) transcriptome and regulome has not yet been fully defined in human pluripotent cells or CSCs. To improve our understanding of the SOX2-linked miRNA regulatory network as a contribution to the phenotype of these cell types, we used high-throughput differential miRNA and gene expression analysis combined with existing genome-wide SOX2 chromatin immunoprecipitation (ChIP) data to map the SOX2 miRNA transcriptome in two human embryonal carcinoma cell (hECC) lines.Results: Whole-microRNAome and genome analysis of SOX2-silenced hECCs revealed many miRNAs regulated by SOX2, including several with highly characterised functions in both cancer and embryonic stem cell (ESC) biology. We subsequently performed genome-wide differential expression analysis and applied a Monte Carlo simulation algorithm and target prediction to identify a SOX2-linked miRNA regulome, which was strongly enriched with epithelial-to-mesenchymal transition (EMT) markers. Additionally, several deregulated miRNAs important to EMT processes had SOX2 binding sites in their promoter regions.Conclusion: In ESC-like CSCs, SOX2 regulates a large miRNA network that regulates and interlinks the expression of crucial genes involved in EMT. © 2014 Vencken et al.; licensee BioMed Central Ltd. Source

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