On 12 October 2020, a group of public, private and non-profit organizations, led by the African Union Commission through the Africa Centres for Disease Control and Prevention (Africa CDC), launched the Africa Pathogen Genomics Initiative (Africa PGI(external link)) in a US$100 million, four-year partnership to expand access to next-generation genomic sequencing tools and expertise designed to strengthen public health surveillance and laboratory networks across Africa.
Africa PGI will be part of the Institute of Pathogen Genomics, launched by Africa CDC in 2019, with a vision to integrate pathogen genomics and bioinformatics into public health surveillance, outbreak investigations, and improved disease control and prevention in Africa. The institute’s capacity will be strengthened to manage and provide technical oversight for Africa PGI. This new initiative will build a continent-wide disease surveillance and laboratory network based on pathogen genomic sequencing. This network will not only help identify and inform research and public health responses to COVID-19 and other epidemic threats, but also for endemic diseases such as AIDS, tuberculosis, malaria, cholera, and other infectious diseases.
PulseNet International has recently implemented whole-genome sequencing analysis of pathogens as its primary laboratory method for surveillance and investigation of foodborne and waterborne diseases. Therefore, the vision of PulseNet International aligns well with the vision of Africa PGI, to integrate pathogen genomics into public health surveillance, outbreak investigations and improved disease control and prevention.
On 11-12 August 2010, a consultation was held at the National Institute for Communicable Diseases (NICD) www.nicd.ac.za(external link), Johannesburg, South Africa to explore the development of a regional network for Africa, namely PulseNet Africa. Participants included representatives from: PulseNet International; Centers for Disease Control and Prevention, USA; Health Protection Agency, United Kingdom; World Health Organization; Southern African Centre for Infectious Disease Surveillance (SACIDS); and 11 African Countries (South Africa, Kenya, The Gambia, Senegal, Cameroon, Malawi, Tanzania, Cote d´Ivoire, Ghana, Uganda and Mozambique).
Outcomes of the meeting, action plans and the way forward included the following. There was consensus to move forward with the development of PulseNet Africa. Participants agreed to spread the news of PulseNet Africa in their country and neighbouring countries. The Enteric Diseases Reference Unit (EDRU) of the NICD will be the coordinator for PulseNet Africa. Pulsed-field gel electrophoresis (PFGE) analysis is the primary subtyping technique used by PulseNet, which requires molecular capabilities including PFGE equipment, agarose gel documentation equipment and BioNumerics Software for analysis of PFGE patterns.
Of the 11 African countries represented at the meeting, 4 countries (Cote d´Ivoire, Ghana, Uganda and Mozambique) are lacking in molecular capabilities and have no PFGE equipment. So, for these 4 countries, a priority for them would be acquiring PFGE capabilities. Nonetheless, all African participants have committed to initiate PFGE analysis of enteric pathogens of priority and interest in their regions. Importantly, participants need to be self-sustaining particularly with regards to funding.
As coordinator for PulseNet Africa, the EDRU will be the 1st laboratory to be PulseNet-certified as competent in PFGE analysis techniques, of which we aim to have this certification process completed by December 2010. The EDRU then proposes to run a training course in PFGE analysis techniques by May 2011, to be followed by certification of the first group of African participating laboratories by September 2011. By December 2011, we hope to have started some PFGE analysis and creation of some databases of patterns.
In early 2012, a 2nd PulseNet Africa consultation is planned.
For further information please contact:
Dr Anthony Smith, NICD, South Africa
PulseNet Africa group photo, 2010
Contact details for member countries in PulseNet Africa
Dr Anthony Smith, Centre for Enteric Diseases , National Institute for Communicable Diseases, Johannesburg, South Africa.
Jane Muyodi, Kenya Medical Research Institute, Nairobi, Kenya. Tel:+254-722-371397
Dr Martin Antonio, Medical Research Council Laboratories, Benjul, The Gambia.
Dr Antoinette Ngandjio, Laboratoire de Bacteriologie, Centre Pasteur du Cameroun, Cameroon, Tel: +23722231015/99867321.
Dr Amy Gassama Sow, Institut Pasteur de Dakar, Dakar, Senegal, Tel: (221) 8399235.
Dr Kalpy Julien Coulibaly, Bacteriology and Virus Department, Food Disease Unit, Pasteur Institut of Cote d'Ivoire, Abidjan, Cote d'Ivoire.
Dr Fausta Mosha, National Health Laboratory, Ministry of Health and Social Welfare, Dar-es-salaam, Tanzania.
Dr Patrick Feglo, School of Medical Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
Dr Daniel Banda, Medical Laboratory Sciences Programme, University of Malawi-College of Medicine, Chichiri, Blantyre, Malawi.
Stephen Ndibowa, Clinical Laboratory, Lubaga Hospital, Kampala, Uganda.
Dr Inacio Mandomando, Manhica Health Research Centre, Maputo, Mozambique.
PFGE Training Course 2-4 June 2011
The first PulseNet Africa PFGE training course was held on 2-4th June 2011 at the National Institute for Communicable Diseases (NICD) (www.nicd.ac.za)(external link), Johannesburg, South Africa. The course was kindly sponsored by the WHO Global Foodbourne Infectious Network (GFN) and CDC global Disease Detection Program (GDD). Trainers included staff from the EDRU, NICD and a staff member (Molly Freeman) from PulseNet USA. Trainees included 9 persons made up of a representative from each of the following countries: Kenya, Senegal, Cameroon, Malawi, Cote d'Ivoire, Ghana, Uganda, The Gambia and Mozambique.
The aims of the course were to teach the technique of PFGE analysis of bacteria, describe how PFGE is the primary genotyping method for international foodborne disease surveillance, and teach the importance of standardized genotyping methods in order to perform inter-laboratory comparison of data and facilitate international investigations. The course focused on Salmonella bacteria and included hands-on practical laboratory training.
The course structure included:
PFGE YouTube Videos
PulseNet Latin America have produced a series of videos explaining PFGE. These have been uploaded to YouTube(external link) where they are accessible to all - but at this stage only in Spanish!
Proficiency Testing Program
A proficiency testing program for PFGE analysis of enteric pathogens will be launced in October 2011. The program will start with a Salmonella test panel. The program is aimed at laboratories in sub-Saharan Africa with capacity to perform PFGE. The program will be an assessment of the testing laboratory, so we will be assessing the laboratory's readiness and effectiveness to perform PFGE. A positive outcome of the testing program will indicate that the laboratory has everything in place (equipment, reagents, trained personnel, etc) to adequately perform PFGE analysis of Salmonella in order to produce results which meet the standards set by PulseNet International. There will be no cost involved to participate in the program. For further information, please contact Dr Anthony Smith.
PFGE & MLVA training course, 13-17 May 2013
The second PulseNet Africa training course was held on 13-17 May 2013 at the NCID, Johannesburg, South Africa. The course was sponsored by the CDC Global Disese Detection Program (GDD) and the WHO Global Foodbourne Infections Network (GFN). Trainers included the following staff from the Centre for Enteric Diseases (CED): Anthony Smith, Husna Ismail, Nomsa Tau, Alfred Mthanti and Kingdom Mncube. Trainees included 11 persons made up of a representative from each of the following countries: Cameroon, Senegal, Kenya, The Gambia, Ivory Coast, Ghana, Uganda, Ethiopia, Zimbabwe, Zambia and South Africa (Onderstepoort Veterinary Research Institute). The PulseNet training course was held in parallel with a GFN training course aimed at participants from countries in Southern Africa; GFN training focused on laboratory investigation (isolation and phenotypic characterization of aetiological agents) and epidemiological investigation of foodborne and waterborne diseases. For PulseNet training, the following genotyping techniques were taught: pulsed-field gel electrophoresis (PFGE) analysis of Salmonella and multiple-locus variable-number tandem-repeats analysis (MLVA) of Salmonella Typhimurium. Besides the hands-on laboratory training, the following topics were also covered: how to interpret genotypic data; how to troubleshoot genotypic data; to describe the importance of using standardized methodology, which allows for inter-laboratory comparison of laboratory data, which facilitates international investigations; to describe the importance of quality assurance activities; to give examples of how genotyping is used for surveillance activities and how it is used to assist in outbreak investigations. For further information on future training courses, please contact Dr Anthony Smith.
Proficiency Testing Program for PFGE , October 2013
The second PulseNet Africa PFGE proficiency testing (PT) program was launched in October 2013. The testing panel includes 4 Salmonella strains. Six African countries are registered for the program. The deadline for return of results is 28 February 2014. The program is aimed at laboratories in sub-Saharan Africa with capacity to perform PFGE. The program is an assessment of the testing laboratory, so we will be assessing the laboratory’s readiness and effectiveness to perform PFGE. A positive outcome of the testing program will indicate that the laboratory has everything in place (equipment, reagents, trained personnel, etc) to adequately perform PFGE analysis of Salmonella in order to produce results which meet the standards set by PulseNet International. There are no costs involved to participate in the program. For further information on future PT programs, please contact Dr Anthony Smith.
Listserv for PulseNet Africa, November 2013
A listserv for PulseNet Africa has been launched. To join the listserv, go to “http://lists.wits.ac.za/mailman/listinfo/pulsenetafrica(external link)” and complete the on-line form (with e-mail address and name) to request to join the listserv. This listserv will be the PulseNet Africa communication tool and most correspondence will go via this listserv, so you must stay subscribed, otherwise you will lose out on PulseNet Africa communications. Please spread the news of this listserv throughout Africa to anybody working in the field of enteric pathogens/diarrhoeal diseases. Once subscribed to the listserv, then you are able to post a message by sending an e-mail message to “firstname.lastname@example.org” - the listserv system then does the rest - it forwards the message to the e-mail in-box of all subscribers - to respond or comment, hit reply, and the reply message forwards on to all subscribers - so, we can get a discussion going on any topic and all can participate. Now, this discussion forum is not only for molecular subtyping issues, this forum can be used for discussion all any issue related to our work in the field of enteric pathogens/diarrhoeal diseases, so for example, you may want to post a message related to: sharing of information related to an outbreak investigation - request for information from others; request information related to phenotypic identification of pathogens - help with identification of pathogens, help with serotyping, help with susceptibility testing; request information related to molecular subtyping of pathogens; share information about research projects - request collaborators for projects; share information about funding opportunities; share information about training opportunities, etc. For further information about the listserv , please contact the listserv administrator Dr Anthony Smith.
PulseNet Africa Meeting, October 2017
On 4-5 October 2017, a PulseNet Africa meeting was held at the National Institute for Communicable Diseases (NICD), Johannesburg, South Africa to discuss ‘Molecular characterization of foodborne and waterborne pathogens, including whole-genome sequencing (WGS) analysis of pathogens’. The aims of the meeting were to review current WGS activities in sub-Saharan African countries, discuss the readiness for WGS implementation, plan the way forward for implementation of WGS and plan/discuss potential WGS projects. Meeting participants included representatives from 13 sub-Saharan African countries and representatives from institutions in the United Kingdom and India.