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Africa Against Antimicrobial Resistance

Antimicrobial Resistance (AMR) is the resistance of microbes such as bacteria to our antibiotics. It is an emerging phenomenon across the globe, and not well tracked. This online and local community is creating challenges, grants and programmes to counteract this phenomenon and track it in Africa.

Over the past decade, Antimicrobial Resistance (AMR) has become a major global development issue, threatening environmental, veterinary, and human health. Antibiotics are potent tools against bacterial infections, however microorganisms previously known to be sensitive to some antimicrobial agents are developing partial to complete resistance against them. This can be combated using traditional academic techniques and is already being researched by many labs across the world, however global health and research capacity is not uniform. Development of systems, more open to medical labs and community labs, where universities are less concentrated is essential. This capacity can be granted through proper application of open science, and connection of these communities online, such as that of our project. We aim to develop open and taught materials and a database for tracking of AMR by the international community sustainably. Then use this model to scale up community lab capacity and independence.

Open science is a global movement that aims to make scientific research and its findings accessible to the general public. Its collaborative and participatory ethos presents an opportunity for a bottom-up approach to research and development that is beneficial to the public. It embraces digital technologies to build communities, work processes, and tools, while embracing frugal innovation achieving significant results with minimal resources. We have already achieved this, through a global program to great effect with minimal funding during the COVID19 pandemic with OpenCOVID19, we can repeat this on AMR to create a grass roots AMR surveillance community.


Fig 1. A grassroots means of AMR data sharing through local training and project facilitation.

We are a collection of local laboratories, academics and developers. We plan to use the existing collaborative framework established on JOGL, to create an open community centred towards AMR in the African region. From July 2021, we will start a 4 month project to create an AI powered laboratory companion for bacterial isolate and AST pattern determination to create an AMR database, with UX/UI already designed and to locally, and through online support train new communities, clinicians and volunteers with prior or no experience in AMR to test for newly emergent strains, and educate them on how to upload this data to a central open database. The database we have created uses AI to identify isolate types, using a series of classical tests already available in Ghana and Tanzania. Additional resources will be used to create a de novo community, using open grant review as a technique to connect communities on the JOGL platform. (Figure 1).



Activities


AMR in Africa Grant Challenge

A microgrant round to win 1500 euros for projects counteracting microbial resistance in Africa.


Online MOOC for learning AMR screening and theory

Our Online resources for teaching AMR screening online for free globally, targeted and physically taught in Ghana and Tanzania 


Mapping AMR in Ghana and Tanzania 

Our challenge to build the Microbis app, and gather AMR data in Ghana and Tanzania to build a map of AMR. This method will then be used to create further maps as time goes on.


Overall Aims/ Objectives

1. Knowledge transfer, and online database formationThe main project aim is to improve knowledge and surveillance on existing, and new antimicrobial resistance in Ghana and Tanzania through online collaboration.

This aim will be achieved through the following objectives;

○ We will develop a curriculum that will be openly documented and made open access.

○ Train students, researchers and veterinarians in AMR testing within Africa by Hive Biolab.

○ Create an online data visualization tool to visualize AMR in Ghana and Tanzania

○ Document learning to build a replicable model

○ Build a global community on the JOGL platform

○ Panel of Volunteer AMR experts to assess and peer review this system

○ Contact already existing AMR networks to create a map using existing AMR data


2. Open Science development in Ghana and TanzaniaThe secondary aim of the project is to establish a new method of grassroots project funding and grant distribution in AMR. This will consist of a single locally allocated grant from the consortium, hosted by JOGL and Chris’s peer review methods, to enable local communities to decide the best use of AMR funding in their area.

This aim will be achieved through the following objectives:

○ We will customise Chris’s peer reviewing technique currently in use by the NGO JOGL for COVID project funding, to that of AMR.

○ Local laboratories will be invited by the Harry, Gamelis and Lindas contacts locally, to encourage grassroot project startups and methods, relevant to the area.

○ Expertise provided by Chris, Linda and Harry will enable us to host a grant review decided by applicants, and online collaboration, through already established methods

○ The success and establishment of the community of applicants will be used to seed future projects, and provide a pilot for a scaled up version with more than one grant available, across multiple countries, led by local peoples.



Methodology

Training of volunteers in Tanzania and Ghana: Linda and Harry are part of large existing community science labs. As part of their organisations’ structure, they often take part in large teaching symposiums, recruiting and inspiring new scientists in their region. Their expertise will be used to create a series of online seminars, advertised using the power of JOGL, and their own connections to train health professionals, volunteers and clinicians in AMR surveillance. These seminars will make collection and submission of data to the newly created database of great importance.


Establishing new grass roots AMR projects: Chris within JOGL and Helpful Engineering has been successful in connecting volunteers online through powerful open peer review methods. Using £1000 as an initial pilot grant, and encouraging applicants across Tanzania and Ghana community labs to apply, a community of unconnected individuals can be connected online. The best of the projects proposed will be established by the new and existing communities on JOGL and go on to help develop independence of communities and AMR testing in the regions. It is known this method of grant allocation can be used as a community builder and to share other communications, as it has been tested in Helpful Engineering and JOGL previously during the COVID pandemic. This is in combination with seminars on the topic.


● Grants are advertised and proposal templates shared with communities affected online and locally by Harry, Linda and their network

● Applicants enter a community of applicants, whom after submission attend a seminar on grant review.

● Community collection is used to increase reach of projects by the team, and test a new grassroots funding method.

● Review is performed through use of an online form, and open dissemination of projects online, allowing new collaborators worldwide to help.

● Successful projects tend to favour the grant awarding body, and introduce new communities, initiating a growth pattern if multiple grant rounds are created.


Creation of a new database and tool for AMR identification and tracking: A database has already been designed, but must be finished by local developers to allow for submission of AMR data. This data can be easily translated into a visual of AMR strains by location, to advise governments and consolidation of unused local data.


● Database is shared across network of collaborators, and applicants

● Community leaders share new database

● Governments, NGOs and relevant universities are contacted by PR lead Gameli, to share the database and one health vision, established by locally empowered labs in Ghana and Tanzania


Timeline

● July 2021

Finish development of AMR platform and its launch.

Develop curriculum for AMR training

Launch Program page for AMR resistance internationally on JOGL, for community coordination

● August 2021

  • ○ Invite community labs in Ghana and Tanzania, along with medical professionals
  • to take part in AMR training
  • ○ Commence AMR training, and international seminars
  • ○ Start Open Grant Review community building technique,

○ Open Grant proposal submission for AMR related projects in Ghana and

  • Tanzania.

● September 2021

○ Continue training of local communities, and facilitate further use of the platform, rewarded by association with local grant decisions.

○ Use community to review grant applications, and focus their effort on local project chosen

● October 2021

○ Coordinate data on AMR platform, and volunteers established to build large community based paper on emerging AMR in Ghana and Tanzania regions.

○ Apply for funding based on outputs, and projects, continue with training with leftover materials, and international collaboration on JOGL platform

○ Release and widely publicise new AMR platform internationally.



Expected Research Outcomes


The project ultimately will develop a curriculum, educational resources for training AMR stakeholders and a web-based laboratory assistant for aiding in bacterial isolate determination. The database proposed will serve as an open microbiological information system for collecting data on identified bacterial isolates and antimicrobial susceptibility test results. This data will go towards extended surveillance on AMR in Ghana and Tanzania. In addition to development of a new open science model specifically tailored to these countries.

The knowledge produced will be in several areas.

Grass roots One Health via online means : We will write a paper, to emphasize the new One Health establishment through grassroot means. This paper will be used as a model for future One Health projects by our team, JOGL and promoted across social media/conferences hosted by Gameli.

AMR tracking: We will write a further paper on the AMR database creation, and the initial map of AMR in Ghana and Tanzania made possible by the project. Enabling further improvement and international scale up in AMR control measures.

Both these aims will be continued by an ongoing collaboration, with a focus on improving the AMR tracking and one health system synergistically, dependent on further funding. One health funding streams will be the primary means of future funding.

A new teaching resource for AMR. We will develop a new curriculum for AMR management in Africa. Evaluation Measures


The success of the project will be measured using the milestones below;

● Successful documentation of an open AMR training curriculum and educational materials made open access.

● Train 100 participants (students, researchers, diagnosticians and veterinarians) on AMR and how to perform tests for AMR.

● A developed web-based data capturing and visualization platform for supporting the continuous data collection for AMR surveillance.

● The successful creation and seeding of new open science communities locally.


Benefits to Research

The project will develop teaching resources and tools for tracking AMR in the community which will serve as a learning tool kit for launching the project in other interested communities.

The project will also provide preliminary materials and pilot studies for a much larger grant to tackle AMR and to build AMR tracing capability in Ghana, Tanzania and neighbouring countries, through development and seeding of further projects.



Sustainability and legacy

The project will develop an AMR data collection tool which will continue past the project completion and will be integrated into laboratory testing workflows to guide continuous data collection and subsequent sequencing using the minion platform for extended genetic mapping of emerging AMR strains. Suitable funding opportunities will be sought to scale the project across other countries in Africa through the JoGL Africa program and platform.



Knowledge of personnel

Chris LB Graham MSci: A PhD student funded by the BBSRC at the University of Warwick BB/M01116X/1 2097310 (2018-2022) and head of peer review at “Just One Giant Lab'' for 2 years. Chris has 6 years experience in AMR, having worked in various labs on the topic since part way through his undergraduate studies. In 2020, he was co-founder of Helpful Engineering, an international charity for COVID relief now numbering 19,000 volunteers and responsible for a great deal of volunteer efforts in PPE relief, and design of open ventilators. He created a new adhoc system with Helpful to direct efforts of its crowd, and went on to pioneer the world's first “open grant review” funded by AXA with Just One Giant Lab, which has funded 33 projects grants of up to 3000 euros each, which he continues to work on and iterate as a model for new grass root project incubation. Currently his focus is on his PhD, and the balance of interactions between the inner membrane, peptidoglycan and outer membranes in E. coli . He has won the “MITACS global link Canada 2020 grant NE/T014717/1 ”(2020-2021) from NERC and Mitacs for his theories on the interaction of peptidoglycan and outer membrane, and previously a grant on the insertion mechanism of the BAM apparatus in Gram Negatives 202374/Z/16/Z (2015-2016) from Wellcome Trust. He oversees and advises on grant applicants to the JOGL grant system he co-created in April 2020, with a focus on COVID relief efforts, and 3 publications to date and large in field impacts have been created by DIY biology applicants since the grant round initiation. His expertise extends from social systems in peer reviewing with JOGL to antimicrobial resistance mechanisms in E. coli and predatory bacteria such as Bdellovibrio.sp as his PhD focus. These skills in building large international communities, in new peer review systems and background AMR knowledge match the grant aims in connecting International

communities on AMR topics uniquely well. Role: Peer review engineer, international community creation, UK AMR advise, developer and project lead.


Harry Akligoh: Trained as a medical laboratory scientist and has two years experience in diagnostic medical microbiology and a final year MPhil student in molecular medicine at the Kwame Nkrumah University of Science and Technology. Currently, Harry is also co-founder of the Hive Biolab at Kumasi Hive where he leads his team to design and implement research projects some of which include developing a digital platform for managing microbiological data towards fighting Antimicrobial Resistance in his community in Ghana. Harry co-developed several educational materials and helped trained students, researchers and lecturers in microbiology topics including microbial genetics and how they apply to protein production and also AMR. Harry’s current research focus is on enabling efficient data management of bacterial isolates and their antimicrobial susceptibility test results for extended surveillance towards highlighting their molecular distribution through further research in order to fight AMR while using the information gathered to develop educational resources to teach stakeholders within the diagnostics-antibiotics prescription value chain in Ghana. Role: Ghana coordinator and database creation lead.


Dr. Courage Kosi Setsoafia Saba is a Senior Lecturer of Microbiology at the University of Development Studies (UDS) where he has been teaching since 2006. He is the Acting Director of International Relations and Advancement (DIRA) in the same university and has participated in several international projects. He has won several competitive grants such as the WHO-AGISAR country grant (2014-2015) project and the International Foundation for Science research grant (2015-2017). He is currently part of the global sewage consortium that is looking for antibiotic resistant genes in sewage from over 70 countries. He is part of the Network of European and African Researchers on Antimicrobial Resistance. He is currently serving on the Expert roster for the WHO/FAO Joint Committee on Microbiological Assessment of Food (JEMRA) from 2018 to 2022. Role: AMR advisor and academic mentor/facilitator of Harry in Ghana.


Dr. Linda Salekwa is an early career scientist in biomedical sciences and currently a lecturer and researcher at Mbeya University of science and Technology in Tanzania. She has conducted research in microbiology particularly in vector borne infectious diseases in Tanzania. Currently she aims to work further on AMR in Tanzania including strengthening the infrastructure on AMR research works in the country. As well, Linda aims to work on AMR development and transmission as a result of the increased consumption of antibiotics due to the current Covid 19 pandemic. Linda has a seven years experience in international projects including a WHO- funded Project at the Nelson Mandela African Institution of Science and Technology in “Predicting Vulnerability and Improving resilience of Maasai communities to vector borne infections: An ecohealth approach” and recently in a USAID funded project Collaborative project between University of Texas at El-Passo (UTEP) and Sokoine University of Agriculture (SUA) on “Feed the Future Innovation Lab for Rift Valley Fever Control in Agriculture”.Out of these works she has published more than 8 publications in peered reviewed journals as well as presenting her findings in regional and international conferences. Role: AMR advisor and Tanzania teachings and collaborative lead


Gameli Adzaho: Gameli is an Environment and Human Health professional, researcher, educator, and community leader passionate about sustainable change through social innovation. He has experience across public health, technology, education, and the civic sector. Gameli is the Africa Regional Program Manager at Just One Giant Lab (JOGL). In Ghana, he leads Global Lab Network, a community of STEM students and professionals interested in applying science and technology for social impact. He was Steering Committee Member of Africa Open Science & Hardware, a platform dedicated to enabling sustainable development on the continent through grassroots research & innovation. He is fascinated by community science as a tool to tackle environmental health challenges.

Role: JOGL Coordinator and Community Lead.


Collaborators

Just One Giant Lab (JOGL) [Gameli and Chris Graham] already use the open science and collaboration approach to further global development. We have galvanised a global community of scientific experts, activists, innovators, entrepreneurs, and students to create participatory research programs for understanding and solving complex health, environmental, social and humanitarian issues related to COVID-19, and vaccine hesitancy. JOGL is uniquely placed to connect talent with need, and foster networks and interactions that can deliver research and innovation projects at a fraction of the cost of traditional institutions.

JOGL accomplished this through the targeted funding of 33+ community-driven projects through a new “open peer review” process and the facilitation and invigoration of “do it yourself” communities and individuals. The OpenCovid19 Program has led to ~276 new COVID-19 related projects (some of which are now international NGOs), 5000+ people on our new online platform for catalyzing collaborative science and over 20,000 people mobilised within those projects created within and outside our platform . In this light JOGL project’s account for half of all voluntary science in the fight against COVID-19. As part of this success JOGL’s efforts have led to 1 of the top 10 COVID-19 tests of the international X-Prize $6M Rapid Test competition, open source designs for syringe pumps, ventilator designs, masks produced across the world and far more.


Funding status: Funded by the Microbiology Society.


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