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Africa bears the brunt of antimicrobial-resistant bacterial infections

Nearly 1.3m people die annually because of antimicrobial-resistant (AMR) bacterial infections, with Africa bearing the greatest burden of deaths. Collectively, these numbers suggest that the burden of AMR might be on the level of – or greater than – that of HIV-Aids or COVID-19.

Staphylococcus aureus is the source of a skin infection that can turn deadly if drug-resistant. Estimates regarding the most common resistant variation, methicillin-resistant Staphylococcus aureus (MRSA), exceeded 100 000 deaths globally in 2019.

But until recently, we did not have a solid grasp on how much of a problem MRSA – or any other antimicrobial-resistant pathogen – was in Africa. After testing 187 000 samples from 14 countries for antibiotic resistance, our colleagues found that 40% of all Staph infections were MRSA, write Dr Pascale Ondoa and DrYewande Alimi in the Daily Maverick.

Africa, like every other continent, has an AMR problem. But Africa stands out because we have not invested in the capacity and resources needed to determine the scope of the problem, or how to fix it. Take MRSA. We still don’t know what’s causing the bacteria to become resistant, nor do we know the full extent of the problem.

We are failing to take AMR seriously, perhaps because it is not glamorous and relatable. The technology we currently use to identify resistant pathogens is not fancy or futuristic looking. Combating AMR does not involve miracle drugs, expensive treatments, or fancy diagnostic tests.

Instead, we have bacteria and other pathogens that are commonplace and have learned how to shrug off the good old medicines that used to work.

The global health and pharmaceutical industries do not seem to consider solving this problem to be very profitable. Compare that to the urgency of solving COVID-19, which has been embraced – and interventions such as diagnostics subsidised – by governments eager to end the pandemic. The COVID-19 response has been characterised by innovations popping up literally every other week.

Why can’t we mobilise resources and passion for AMR? Are resistant pathogens too boring? Is it too difficult to solve through innovations? Does this make prospects for quick wins and fast return on investment too elusive for AMR, especially when compared to COVID-19 or other infectious disease outbreaks?

The World Health Organisation (WHO) has repeatedly stated that AMR is a global health priority, and is, in fact, one of the leading public health threats of the 21st century.

A recent study estimated that in 2019, nearly 1.3m people died because of antimicrobial-resistant bacterial infections, with Africa bearing the greatest burden of deaths. A high prevalence of AMR has also been identified in food-borne pathogens isolated from animals and animal products in Africa.

Collectively, these numbers suggest that the burden of AMR might be on the level of – or greater than – that of HIV-Aids or COVID-19. The growing threat of AMR is likely to take a heavy toll on Africa’s health systems and poses a major threat to progress made in attaining public health goals set by individual nations, the African Union and the United Nations.

And the paucity of accurate AMR information limits our ability to understand how well commonly used antimicrobials actually work. This also means we cannot determine the drivers of AMR infections and design effective interventions in response.

We have just wrapped up a project that gathered data on many of the scariest pathogens in 14 countries, revealing stark insights on the under-detected and under-reported depth of the AMR crisis across Africa. Fewer than 2% of the medical laboratories in the 14 countries examined can conduct bacteriology testing, even with conventional methods developed more than 30 years ago.

While providing national stakeholders with critical information to advance their policies on AMR, we have also trained and provided basic electronic tools to more than 300 health professionals to continue this important surveillance. While a strengthened workforce is critical, many health facilities on the continent are coping with interrupted access to electricity, poor connectivity, and serious, ongoing workforce shortages.

Our work has painted the dire reality of the AMR surveillance situation, informing concrete recommendations for improvement that align with the new continental public health ambition of the African Union and Africa Centre for Disease Control (CDC). The challenge is to find the funding to expand this initiative to cover the entire African continent.

AMR containment requires a long-term focus – especially in Africa, where health systems are chronically underfunded, while also being disproportionately challenged by infectious threats. More funding needs to be dedicated to the problem and this cannot only come from international aid.

We urge African governments to honour past commitments and allocate more domestic funding to their health systems in general, and to solving the crisis of AMR in particular. We also call upon bilateral funders and global stakeholders to focus their priorities on improving the health of African people.

This might require more attention to locally relevant evidence to inform investments and less attention to profit-driven market interventions, as well as prioritising the scale-up of technologies and strategies proven to work, whether or not they are innovations.

Containing AMR means we have to fix African health systems. The work starts now.

Dr Pascale Ondoa is the director of science and new initiatives of the African Society for Laboratory Medicine (ASLM) and Dr Yewande Alimi is the Africa Center for Disease Control (CDC) antimicrobial resistance programme coordinator.

Study details

Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis

Antimicrobial Resistance Collaborators

Published in The Lancet 19 January 2022


Antimicrobial resistance (AMR) poses a major threat to human health around the world. Previous publications have estimated the effect of AMR on incidence, deaths, hospital length of stay, and health-care costs for specific pathogen–drug combinations in select locations. To our knowledge, this study presents the most comprehensive estimates of AMR burden to date.

We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with bacterial AMR for 23 pathogens and 88 pathogen–drug combinations in 204 countries and territories in 2019. We obtained data from systematic literature reviews, hospital systems, surveillance systems, and other sources, covering 471 million individual records or isolates and 7585 study-location-years. We used predictive statistical modelling to produce estimates of AMR burden for all locations, including for locations with no data. Our approach can be divided into five broad components: number of deaths where infection played a role, proportion of infectious deaths attributable to a given infectious syndrome, proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antibiotic of interest, and the excess risk of death or duration of an infection associated with this resistance. Using these components, we estimated disease burden based on two counterfactuals: deaths attributable to AMR (based on an alternative scenario in which all drug-resistant infections were replaced by drug-susceptible infections), and deaths associated with AMR (based on an alternative scenario in which all drug-resistant infections were replaced by no infection). We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. We present final estimates aggregated to the global and regional level.

On the basis of our predictive statistical models, there were an estimated 4·95 million (3·62–6·57) deaths associated with bacterial AMR in 2019, including 1·27 million (95% UI 0·911–1·71) deaths attributable to bacterial AMR. At the regional level, we estimated the all-age death rate attributable to resistance to be highest in western sub-Saharan Africa, at 27·3 deaths per 100 000 (20·9–35·3), and lowest in Australasia, at 6·5 deaths (4·3–9·4) per 100 000. Lower respiratory infections accounted for more than 1·5 million deaths associated with resistance in 2019, making it the most burdensome infectious syndrome. The six leading pathogens for deaths associated with resistance (Escherichia coli, followed by Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa) were responsible for 929 000 (660 000–1 270 000) deaths attributable to AMR and 3·57 million (2·62–4·78) deaths associated with AMR in 2019. One pathogen–drug combination, meticillin-resistant S aureus, caused more than 100 000 deaths attributable to AMR in 2019, while six more each caused 50 000–100 000 deaths: multidrug-resistant excluding extensively drug-resistant tuberculosis, third-generation cephalosporin-resistant E coli, carbapenem-resistant A baumannii, fluoroquinolone-resistant E coli, carbapenem-resistant K pneumoniae, and third-generation cephalosporin-resistant K pneumoniae.

To our knowledge, this study provides the first comprehensive assessment of the global burden of AMR, as well as an evaluation of the availability of data. AMR is a leading cause of death around the world, with the highest burdens in low-resource settings. Understanding the burden of AMR and the leading pathogen–drug combinations contributing to it is crucial to making informed and location-specific policy decisions, particularly about infection prevention and control programmes, access to essential antibiotics, and research and development of new vaccines and antibiotics. There are serious data gaps in many low-income settings, emphasising the need to expand microbiology laboratory capacity and data collection systems to improve our understanding of this important human health threat.


The Lancet article – Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis (Open access)


Daily Maverick article – Antimicrobial-resistant bacterial infections are a major public health threat for Africa (Open access)


See more from MedicalBrief archives:


Urgent need for more funds to fight AMR drug resistance


Stories from the frontlines of antimicrobial resistance during COVID-19


Pharma companies to share data on anti-microbial resistance


UK’s 5-year action plan to fight super-bug threat


Drug resistance linked to antibiotic use and patient transfers in hospitals




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