Environmental Surveillance of Pathogens
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Date
2020-10-08
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Kamuzu University of Health Sciences
Abstract
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.
Description
1.2 The problem has some comments
Keywords
Research Subject Categories::MEDICINE::Microbiology, immunology, infectious diseases