The use of molecular diagnostic methods to improve the detection of the common bacterial and viral causes of community acquired meningitis in children in South Africa

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dc.contributor.advisorBamford, Colleenen_ZA
dc.contributor.advisorDu Toit, Elloiseen_ZA
dc.contributor.authorKhumalo, Jermaineen_ZA
dc.date.accessioned2015-12-03T14:10:44Z
dc.date.available2015-12-03T14:10:44Z
dc.date.issued2015en_ZA
dc.description.abstractWith conventional methods of diagnosis, substantial overlaps are common due to an absence of the expected CSF findings clearly aligning to bacterial or viral infection. Reduced sensitivity is commonly observed chiefly due to empiric antibiotic treatment leading to bacterial culture negative results. This leads to costly hospital admissions and unnecessarily prolonged treatment for the unexplained aetiology, further compounded by routine viral diagnostics not being commonly implemented for meningitis diagnosis. We developed and validated in-house quantitative real-time (qPCR) multiplex assays to test for bacterial causes namely: Neisseria meningitidis (ctrA gene), Haemophilus influenzae (hpd gene) and Streptococcus pneumoniae (lytA gene) and viral causes namely: enterovirus (5' UTR), herpes simplex (UL30 gene) and mumps virus (Fusion protein gene). The qPCR assays were carried out on the Biorad CFX 96 real-time instrument. These validated assays were used to screen a cohort of suspected meningitis cases. The retrospective study included 300 paediatric patients aged from 60 days-12 years, over a 1-year period (November1, 2012 to November 30, 2013) with suspected meningitis presented to the outpatient departments of the Red Cross War Memorial Children‟s Hospital (RCCH) in Cape Town. Cerebrospinal fluid with abnormal chemistry and cell counts was selected and total nucleic acid was extracted with the QIAsymphony virus/bacterial DSP kit (QIAGEN, Valencia, CA). The median age of children was 19 months (IQR: 6-65 months). Among the screened 291 CSF samples, 7 (2.4%) cases Gram stain results were obtained along with relatively few cases with positive bacterial culture growth 4/291 (1.4%). Based on bacterial qPCR results, 8 (2.7%), 3 (1%) and 1 (0.3%) were positive for S. pneumoniae, N. meningitidis and H. influenzae respectively. A majority of cases were viral positives with enteroviruses being the dominant at 91/291 (31.3%) and mumps virus 3/291 (1%). No herpes simplex DNA was detected. The bacterial qPCR showed a sensitivity and specificity of 85.7% and 97.7% respectively when compared against a composite reference standard (CRS). We report an improvement with additional detected causes of bacterial meningitis and highlight the burden of the common viral causes. However, a large proportion of cases (63.6 %) have aetiology still unknown. PCR shows valuable in concluding viral aetiology in routine diagnosis.en_ZA
dc.identifier.apacitationKhumalo, J. (2015). <i>The use of molecular diagnostic methods to improve the detection of the common bacterial and viral causes of community acquired meningitis in children in South Africa</i>. (Thesis). University of Cape Town ,Faculty of Health Sciences ,Division of Medical Biochemistry. Retrieved from http://hdl.handle.net/11427/15539en_ZA
dc.identifier.chicagocitationKhumalo, Jermaine. <i>"The use of molecular diagnostic methods to improve the detection of the common bacterial and viral causes of community acquired meningitis in children in South Africa."</i> Thesis., University of Cape Town ,Faculty of Health Sciences ,Division of Medical Biochemistry, 2015. http://hdl.handle.net/11427/15539en_ZA
dc.identifier.citationKhumalo, J. 2015. The use of molecular diagnostic methods to improve the detection of the common bacterial and viral causes of community acquired meningitis in children in South Africa. University of Cape Town.en_ZA
dc.identifier.ris TY - Thesis / Dissertation AU - Khumalo, Jermaine AB - With conventional methods of diagnosis, substantial overlaps are common due to an absence of the expected CSF findings clearly aligning to bacterial or viral infection. Reduced sensitivity is commonly observed chiefly due to empiric antibiotic treatment leading to bacterial culture negative results. This leads to costly hospital admissions and unnecessarily prolonged treatment for the unexplained aetiology, further compounded by routine viral diagnostics not being commonly implemented for meningitis diagnosis. We developed and validated in-house quantitative real-time (qPCR) multiplex assays to test for bacterial causes namely: Neisseria meningitidis (ctrA gene), Haemophilus influenzae (hpd gene) and Streptococcus pneumoniae (lytA gene) and viral causes namely: enterovirus (5' UTR), herpes simplex (UL30 gene) and mumps virus (Fusion protein gene). The qPCR assays were carried out on the Biorad CFX 96 real-time instrument. These validated assays were used to screen a cohort of suspected meningitis cases. The retrospective study included 300 paediatric patients aged from 60 days-12 years, over a 1-year period (November1, 2012 to November 30, 2013) with suspected meningitis presented to the outpatient departments of the Red Cross War Memorial Children‟s Hospital (RCCH) in Cape Town. Cerebrospinal fluid with abnormal chemistry and cell counts was selected and total nucleic acid was extracted with the QIAsymphony virus/bacterial DSP kit (QIAGEN, Valencia, CA). The median age of children was 19 months (IQR: 6-65 months). Among the screened 291 CSF samples, 7 (2.4%) cases Gram stain results were obtained along with relatively few cases with positive bacterial culture growth 4/291 (1.4%). Based on bacterial qPCR results, 8 (2.7%), 3 (1%) and 1 (0.3%) were positive for S. pneumoniae, N. meningitidis and H. influenzae respectively. A majority of cases were viral positives with enteroviruses being the dominant at 91/291 (31.3%) and mumps virus 3/291 (1%). No herpes simplex DNA was detected. The bacterial qPCR showed a sensitivity and specificity of 85.7% and 97.7% respectively when compared against a composite reference standard (CRS). We report an improvement with additional detected causes of bacterial meningitis and highlight the burden of the common viral causes. However, a large proportion of cases (63.6 %) have aetiology still unknown. PCR shows valuable in concluding viral aetiology in routine diagnosis. DA - 2015 DB - OpenUCT DP - University of Cape Town LK - https://open.uct.ac.za PB - University of Cape Town PY - 2015 T1 - The use of molecular diagnostic methods to improve the detection of the common bacterial and viral causes of community acquired meningitis in children in South Africa TI - The use of molecular diagnostic methods to improve the detection of the common bacterial and viral causes of community acquired meningitis in children in South Africa UR - http://hdl.handle.net/11427/15539 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/15539
dc.identifier.vancouvercitationKhumalo J. The use of molecular diagnostic methods to improve the detection of the common bacterial and viral causes of community acquired meningitis in children in South Africa. [Thesis]. University of Cape Town ,Faculty of Health Sciences ,Division of Medical Biochemistry, 2015 [cited yyyy month dd]. Available from: http://hdl.handle.net/11427/15539en_ZA
dc.language.isoengen_ZA
dc.publisher.departmentDivision of Medical Biochemistryen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.subject.otherMedical Microbiologyen_ZA
dc.titleThe use of molecular diagnostic methods to improve the detection of the common bacterial and viral causes of community acquired meningitis in children in South Africaen_ZA
dc.typeMaster Thesis
dc.type.qualificationlevelMasters
dc.type.qualificationnameMSc (Med)en_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceThesisen_ZA
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