PANGenS

The challenge

Drug resistance is an increasing challenge for both tuberculosis (TB) and malaria. Using antibiotics for TB and antimalarials such as artemisinin combination therapy (ACT) creates selection pressures that favour the spread of drug-resistant pathogens. A reduced response to drugs leads to poorer clinical outcomes for individuals and provides more opportunities for pathogens to spread through populations.

Genomic surveillance provides an opportunity to detect pathogens carrying genetic variants associated with drug resistance. This can provide policymakers with key information to shape disease control policies and treatment guidelines based on local patterns of drug resistance. 

However, genomic surveillance capabilities are currently limited in sub-Saharan Africa. In addition to applying sequencing technologies, countries need to manage and analyse the huge volumes of data generated and develop tools to communicate findings to policymakers to inform actions. Many countries face similar challenges, so coordinated development of genomic surveillance capabilities will deliver significant efficiency gains.

The project

The PANGenS project is bringing together policymakers and representatives from national public health institute from 12 African countries (Ghana, Nigeria, South Africa, Togo, Benin, Sierra Leone, The Gambia, Liberia, Tanzania, Namibia, Mozambique and Gabon), the Africa Centre for Disease Control and Prevention (Africa CDC), and genomics researchers from Europe to develop a common platform for detecting and tracking resistance to anti-TB drugs and antimalarials.

The project will apply a shared technological approach, adapting newly developed technologies to characterise drug-resistant strains of TB bacteria and malaria parasites. A comprehensive training programme will cover key areas such as the use of sequencing technologies, bioinformatics analysis, and data management. Infrastructure upgrades will enable countries to apply the latest sequencing technology. PANGenS will also develop integrated data platforms that collate genetic data with the associated epidemiological and clinical data.

For TB, the project will have a particular focus on the emergence and spread of resistance to newer drugs, bedaquiline and clofazimine. Surveillance will also help to identify new mutations associated with drug resistance. 

To maximise impact, national public health institutes, disease control programmes and the African Pathogen Genomics Initiative will be at the heart of project activities. An extensive programme of training activities will be undertaken, covering genomics, bioinformatics and data management, with hands-on workshops and the creation of a web portal for virtual bioinformatics training.  

Impact

The PANGenS project will enhance the ability of a large group of countries in sub-Saharan Africa to track the spread of resistance to anti-tuberculosis and antimalarial drugs. It will:

• Provide a deeper understanding of drug-resistant TB and malaria in the African region.
• Help to identify hotspots where drug resistance is a particular challenge, so control efforts can be targeted more effectively.
• Feed into improved diagnostic tools able to identify a wider range of isolates carrying drug-resistance genes.
• Support research into the mechanisms of drug resistance. 

These new insights will enable countries to adapt treatment policies as needed, better control the spread of resistance, and reduce the burden of disease associated with hard-to-treat, drug-resistant infections.