Protocols

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https://rscarchive.kuhes.ac.mw/handle/20.500.12988/331

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Browsing Protocols by Subject "Research Subject Categories::MEDICINE::Microbiology, immunology, infectious diseases"

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    Environmental Surveillance of Pathogens
    (Kamuzu University of Health Sciences, 2020-10-08) Feasey, Nick
    Type of Study Environmental Surveillance, unrelated to clinical cases or carriers. This protocol is therefore submitted as a waiver request. Broad Objective To develop spatial, field sampling and laboratory testing methods to identify environmental reservoirs of S. Typhi, Rotavirus, Enterovirus and SARS-CoV-2 as well as other key bacteria and viruses and use these findings to inform targeted intervention strategies through spatial modelling 1.4 Specific Objectives 1. Optimize strategy for detecting pathogens from food (fruit and vegetables available at the market), water and the environment in the laboratory 2. Optimize field sampling and sample concentration methods to support laboratory identification of pathogens 3. Use spatial modelling based on available data such as the physical geography or population density of Blantyre to develop our sampling strategy 1.5 Methods Optimize strategy for detecting pathogens from food, water and the environment in the laboratory will include: 1)concentration of field samples respecting staff safety and without rendering the pathogen of interest undetectable, 2)avoiding out-competition by other microorganisms (i.e. S. Typhi being outcompeted by E. coli), 3) quantitating the pathogens of interest and 4) multiplexing detection methods to make them cost effective. 2. Optimize field sampling and sample concentration methods to support laboratory identification of pathogens will include: 1)“Grabbing” enough sample that the pathogen of interest is present in and thus detected in the laboratory, 2) maintaining staff safety, 3) protecting equipment deployed overnight, and 4) developing methods that are cost effective. 3 Use spatial modelling based on available data such as the physical geography or population density of Blantyre to develop our sampling strategy will 1) enables a field sampling team to capture samples that the pathogen of interest is present in and 2) determine if this is economically feasible to roll-out at the level of field sampling necessary to reliably detect it. 1.6 Expected findings We aim to develop transferrable and translatable methods for the isolation or detection of pathogens from environmental sources, including S. Typhi, Rotavirus, enterovirus and SARS-CoV-2. This will be used to identify both reservoirs and transmission pathways. This information will be used to create a predictive model for where to locate high pathogen burden areas in an urban African context and this model can be validated and used in a variety of settings to support both future intervention studies. 1.7 Dissemination of study findings The study findings will be proactively disseminated through national and international scientific meetings, to key public health bodies in Malawi and through peerreviewed publications. Specifically, we will disseminate findings to COMREC, CoM and the Blantyre DHO. Any significant research findings will be shared to the Malawi government’s Ministry of Health who are already collaborating on on-going Typhoid and rotavirus vaccine surveillance studies and to support the national effort with regard to the COVID-19 pandemic.
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    Phenotypic and genotypic characterization of invasive bacterial isolates collected through MLW diagnostic activities from 1996 – 2030
    (Kamuzu University of Health Sciences, 2020-11-24) Cornick, Jennifer
    This protocol is a minimally updated version of Protocol P.08/14/1614 which expired on 15/12/2018. Due to increasing rates of drug-resistant infections being observed at Queen Elizabeth Central Hospital in Blantyre, it is important that we resume our phenotypic and genotypic characterization of invasive bacterial isolates collected through Malawi-Liverpool-Wellcome (MLW) Trust diagnostic activities. This audit will allow us to access archived bacterial isolates obtained from routine blood and CSF cultures over a period of more than three decades (1996– 2030). Invasive bacterial infections caused by typhoidal and nontyphoidal Salmonella, Streptococcus pneumoniae, Staphylococcus aureus, Escherichia coli and, Klebsiella amongst others, account for high rates of morbidity and mortality in both Malawian children and adults at Queen Elizabeth Central Hospital (QECH). Treatment of bacteraemia and meningitis caused by these bacterial species is made difficult because of increased levels of multiple antibiotic resistant strains. Bacterial surveillance at QECH and MLW in Blantyre began in 1996 and has thus far provided a rich collection of strains that allows phenotypic and genotypic investigations with a historical perspective, data which is used by the Ministry of Health to support its surveillance programmes. Whole genome sequencing has given us novel insights into the epidemiology and mechanisms of antibiotic resistance (AMR) of diverse bacteria that are regionally relevant. For example, WGS gave deep insights into the genetic diversity of S. pneumoniae strains in the era before the introduction of the pneumococcal conjugate vaccine in Malawi, which has been invaluable to support vaccine implementation and to the study of vaccine effectiveness. We have been able to describe increasing antimicrobial resistance rates over the last twenty years amongst key enteric pathogens, with some now locally impossible to treat using first line antibiotics. This audit aims to expand on these achievements by investigating the phenotype and genotype of all the major invasive bacterial isolates at QECH over time. From past experience with stored, frozen samples, it is anticipated that >95% of isolates will be recoverable and the impact on the validity of results obtained would therefore be very limited. Specifically, the audit aims to characterize the type and nature of isolates causing severe bacterial disease in Malawi making use of advanced genotyping and phenotyping techniques, some of which are not yet possible in Malawi. The audit has five main objectives: 1. To perform antimicrobial susceptibility testing to assess AMR rates over time; 2. To perform genotypic characterisation to identify genetic markers of AMR and virulence over time; 3. To employ whole genome sequencing to detect epidemic outbreaks; 4. To perform phenotypic characterization of bacterial isolates to identify the biological mechanisms driving AMR and virulence and to evaluate the efficacy of novel antimicrobials; 5. To build upon existing or develop novel bioinformatic pipelines to analyse bacterial genomic data. The findings will be disseminated among collaborating partners and manuscripts will be prepared for publication in international peer-reviewed journals. A copy of any published paper(s) of the research findings will also be submitted to the College of Medicine Research and Ethics Committee (COMREC), the College of Medicine Research Dissemination Conference, College of Medicine Library, the National Health Sciences Research Committee and the University Research and Publication Committee (URPC) (the latter two through the COMREC Secretariat). As with all our work, with collaborators at the Wellcome Trust Sanger Institute, sequencing will be undertaken free of charge. The number of isolates that can be sequenced each year will be dictated by the Wellcome Trust Sanger Institute sequencing budget. In addition to this, we will actively pursue research funding from national and international funders to prospectively address the objectives outlined in the proposal. At this moment in time, it is however impossible to predict how many samples we will process in total. COMREC overhead costs will therefore be retrospectively calculated based on the number of bacterial isolates