Tracking the superbugs

Surveillance of “superbugs” — microbes that have become resistant to common treatments — is needed to shed light on this growing global health threat.

Dr. Toby Leslie explains how the Fleming Fund program is enabling that and improving health outcomes for the world’s poorest people.

The $365 million (£265 million) Fleming Fund has a fundamentally important mission: to equip health professionals and policymakers the world over with the knowledge they require to avert what threatens to be a runaway health disaster: antimicrobial resistance.

For years, microbes responsible for many common illnesses (and lots of rarer ones) have been mutating and developing resistance to the drugs doctors use to control them, known as antimicrobials.

It is estimated that, by 2050, drug-resistant diseases will cause 10 million additional deaths per year globally. Higher mortality combined with more widespread and serious illness will have a cumulative global economic cost of $100 trillion. Unless antimicrobial resistance can be stopped.

That is why the UK government launched the Fleming Fund in 2015, to improve surveillance of antimicrobial resistance in low- and middle-income countries. We are the managing agent for the fund and have placed grants worth approximately $234 million (£170 million) to date, across 22 countries in Africa and Asia.

Shining a light on the problem

What does AMR surveillance require? Data – more of it, and of a higher quality – and the ability to use it to plan effective strategies for fighting back against AMR.

The Fleming Fund is helping countries to develop their national surveillance networks, by supporting laboratories and experts to gather and analyse AMR samples, share data, and use the insights it provides to inform action. It is also working with health service providers, governments, supranational organisations, academia and the livestock industry. In 2021, critical equipment was installed at national reference laboratories in most of the 22 countries currently supported by the fund. In all 22 countries, the fund is also building core surveillance skills, such as bacteriology, antibiotic testing, and epidemiology. International professional networks are being strengthened.

Each country has its own AMR coordination committee, which collects and processes data from local labs, turning it into valuable information that can inform policy and interventions.

Data serves local and global purposes. For example, the fund has invested in equipment that can perform automated blood culture, drug sensitivity testing and species identification, trained staff to use it and organised long-term support and service contracts with the equipment providers. In Bhutan, this has increased national blood culturing capacity five-fold. When a doctor suspects a patient has a bacterial infection, they can now take a blood sample and send it off for laboratory analysis. Culturing the sample enables lab-based experts to perform drug susceptibility tests. Information about which drug will be most effective against the infection is sent back to the doctor, improving the patient’s chances of a speedy recovery and reducing the risk that the bacterial strain will be further strengthened by contact with an ineffective treatment.

As well as helping doctors, data gathered from many samples reveals local, regional and national patterns in what is causing infections and drug resistance. This enables local healthcare providers and health departments to select the most effective drugs. Data is also fed into the Global Antimicrobial Resistance Surveillance System, which is run by the World Health Organization (WHO) to provide a global picture of how the AMR threat is developing.

AMR is an inter-species problem. The US National Institutes of Health attributes almost 16% of all deaths worldwide to infectious diseases. Historically, about 60% of those diseases have been spread from animals to humans (zoonoses). But currently, about 75% of emerging infectious diseases are zoonotic. It is why the fund has supported development of poultry surveillance plans for most of the 22 countries. Antimicrobials are often used in raising chickens and other livestock because they are seen as helping improve production efficiency. AMR is a byproduct. Grants have helped complete one round of poultry sampling in Ghana, Laos, Pakistan, Uganda, Vietnam and Zambia with more planned in other countries. Data gathered is revealing trends in the use of antimicrobials and the incidence of AMR, which will be used to inform livestock rearing practices.

Investing in the future

About 75% of the funding is in the form of country grants. These support governments to develop the surveillance capacity needed to accomplish their AMR national action plans (NAPs), developed with the WHO.

We review the NAPs with governments, then craft terms of reference for a grant to improve the surveillance system. We then oversee procurement of the right delivery partner, through an open tender process, to put the NAP into practice. As grant managers, we check that value for money is being achieved, watch for risks, and monitor for technical excellence.

Remaining funding is equally split between fellowships and regional grants.

Fellowships are awarded to 12-15 people in each country who receive up to 18 months’ training via an international university or public health department. This includes mentoring and career development to build in-country expertise. There are more than 150 Fleming Fund fellows to date.

Regional grants are awarded for multi-country projects, where economies of scale can be achieved. These are focused in four main areas:

Quality assurance: The WHO’s global network of collaborating centres provides quality control for national and local centres, and our grants provide funding to further develop the network(s).

Advanced training: Training in advanced techniques is more cost-effective when done at a regional level – this approach also brings together practitioners from multiple countries and improves information and knowledge sharing.

Standardisation: Developing consistent high quality across and compatibility between datasets required for international collaboration and a holistic understanding of AMR.

Genome sequencing: Examining the origins and similarities between drug-resistant bacteria.

Infrastructure for success

In each country, within the first three years we typically have 10 laboratories fully up and running, contributing valuable data for local and international use.

The programme has been running for four years and in that time we have bolstered surveillance capacity at more than 250 labs. More than 1000 people have received training. Senior practitioners involved in the programme – Fleming Fund fellows – have published papers on their findings and recommendations in scientific journals, spreading knowledge and providing a valuable, lasting resource.

Insights into the origin and spread of AMR is already being used to adjust healthcare provision at hospitals and change farmers’ approaches to animal husbandry. In hospitals, on farms and in doctors’ and vets’ surgeries alike, antimicrobial drugs are being more carefully prescribed. The ultimate goal is that they will only go to people, or animals, in need.

Ultimately the battle against superbugs will only be won if there is sustained effort to understand the causes, evolution and spread of AMR, and identify the drugs and strategies that are most effective against it. Continued support and collaboration from countries we’re working in is crucial. The Fleming Fund’s legacy will live on: the surveillance data the programme is generating is already translating into tangible healthcare benefits – better-targeted treatments for citizens. As surveillance generates more data over the coming years, the benefits will become greater still. With robust national infrastructure and effective international networks, the Fleming Fund’s work will continue to provide evidence and data to address this growing global threat.

Dr Toby Leslie is a health specialist in the International Health practice. He is an infectious disease epidemiologist specialising in surveillance and health system development in developing countries.

Tracking the superbugs

This is the future