Climate change and antimicrobial resistance: A combination driving disease spread in Africa

In early 2023, an exceptionally powerful tropical cyclone formed over the Indian Ocean, sweeping over Madagascar and Mozambique before finally dissipating-after more than five weeks-over Malawi. Cyclone Freddy remains the longest-lasting tropical storm system on record, and the third deadliest in the Southern Hemisphere. Nearly 85 percent of the 1,434 fatalities directly caused by Freddy were in Malawi. But the deaths didn't stop there.

When the cyclone struck, Malawi was in the midst of a cholera outbreak that began in March 2022, coinciding with Tropical Cyclone Gombe, which followed Tropical Storm Ana by just two months. These disasters disrupted water and sanitation services and pushed displaced people into overcrowded camps, creating the perfect environment for cholera to spread like wildfire. Between March 2022 and May 2023, nearly 60,000 people contracted the disease and more than 1,700 people died as a result.

In response to the health crisis, the World Health Organization (WHO) and other partners monitoring the situation reported an increase in antibiotic consumption in the affected locations and adjacent areas. This was followed by an uptick in cases of the multi-drug-resistant Vibrio cholerae strain of cholera, "indicating a direct exacerbation of AMR (antimicrobial resistance) due to a climate-related disaster," according to Ali Yahaya, a doctor who leads a team focused on antimicrobial resistance at WHO's regional office for Africa.

AMR occurs when disease-causing pathogens-whether bacteria, viruses, parasites, or fungi-develop resistance to drugs meant to treat the disease. In 2019, AMR was directly responsible for 1.27 million deaths and contributed to another 4.95 million deaths globally, according to the WHO, making it one of the top worldwide threats to public health.

Africa is particularly vulnerable. In sub-Saharan Africa alone, AMR was directly responsible for over 250,000 deaths in 2019 and contributed to more than 816,000 additional deaths over the same period. It also causes an estimated 5 percent loss to gross domestic product (GDP) annually per country across the continent.

"[AMR] is one of the most pressing health challenges facing Africa today, surpassing other major diseases in its impact," says Robert Onsare, a doctor who heads the Enteric Pathogens & Antimicrobial Resistance Research at Kenya Medical Research Institute.

"This makes AMR a greater killer than HIV/AIDS and malaria in many regions in Africa," he adds.

The cholera outbreak in Malawi illustrates how natural disasters and climate change can create or exacerbate public health crises. But researchers are only beginning to understand the relationship between climate change and AMR specifically. "For the last five years, a lot of new work has gone into how climate change and AMR are relating to one another," says Arshnee Moodley, the team lead for AMR at the International Livestock Research Institute (ILRI) in Nairobi.

Given that the UN's Interagency Coordination Group on Antimicrobial Resistance expects AMR to cause 10 million deaths annually by 2050, the need for more research and better understanding couldn't be more pressing. Tackling the gargantuan challenge of AMR in Africa will require increasing disease surveillance and improving the public health response, as well as studying the conditions-like antibiotic use in livestock systems-that allows AMR to develop. The challenge has become all the more daunting as the United States and the United Kingdom have drastically reduced their funding for public health programs and research in Africa.

"That which bends up"

In Africa, where public health infrastructure is already strained, authorities are watching out for imminent outbreaks of dengue and rift valley fevers, leishmaniasis, cholera, and other diseases. The variety of diseases and a lack of testing capacity can mean sick people get the wrong medicines at a doctor's office or pharmacy-antibiotics, for example, for viral diseases.

In April, there was a chikungunya outbreak in the coastal city of Mombasa, Kenya's second largest city. The disease, whose name is derived from the language spoken by the Makonde people of Tanzania and means "that which bends up" or "stooped walk," was detected for the first time in the area more than seven years ago. There had been no other cases reported since 2018 until this year.

According to Hildergard Wasike, a public health officer in charge of preventive and promotive health at the Department of Health Services in Mombasa County, this year's outbreak began during the long rainy season, from March to May, when indoor water storage, a common practice in the water-scarce region, was high. The Aedes aegypti mosquito that spreads chikungunya prefers indoor environments and lays its eggs in clean water.

A lack of diagnostic capacity for chikungunya in the region has meant that treatment and care for patients is delayed, thereby accelerating the spread of infection. Individuals might seek out drugs meant for other diseases, which is a contributing factor in the spread of AMR. Indeed, in Uganda, Zambia, South Africa, and elsewhere, studies have documented antibiotics being dispensed over the counter-that is, potentially before a patient has been properly diagnosed.

Chikungunya symptoms include fever, exhaustion, swollen joints, dehydration, rash, and joint pains. There is no cure for chikungunya, but with proper management using analgesics (pain killers) and fluids, the virus can clear from the patient's system within a week of seeking medical attention. But the symptoms can be easily mistaken for either malaria or dengue fever or both. This makes it even more difficult for public health officials to track its spread. "The health seeking behavior of people here is very poor, because they will self-medicate with over-the-counter drugs, at the first sign of an onset fever," observes Wasike.

Of the 45 blood samples taken for testing in Mombasa, 25 were confirmed to be chikungunya while one was positive for dengue fever.

Could climate change have been a factor in the outbreak? Fatma Ali, the Manager for Emergency Operation Centre at the Health Department of Mombasa County, says that the coastal region has been experiencing "hotter episodes" in the recent past, in addition to unexplained or unpredictable weather conditions, especially during the rainy season.

This is why, she explains, the National Disease Surveillance Unit is now investigating whether climate has any bearing on vector populations. The unit will also study whether the virus has evolved as a result.

A growing problem

Yahaya, the AMR team lead for WHO-AFRO, says that his group's analysis shows over half of Africa's public health emergencies from 2001 to 2021 were climate-related, "particularly water-borne and vector-borne diseases such as malaria, dengue, cholera, and Lassa fever." Those diseases have increased in frequency and geographical spread due to altered rainfall, temperatures, and flooding, he says.

Bridget Kimani, a senior research scientist at the Kenya Medical Research Institute, concurred, citing the case of malaria as one of the most climate sensitive diseases globally.

In Kenya, for example, a warming climate has expanded the range of mosquito breeding areas into highland regions, which were previously malaria-free zones. The WHO has also documented climate-related malaria shifts in other regions on the continent.

"This has led to increased transmission rates in populations with low immunity," Kimani says.

Similar trends have also been observed in Asia. Dengue fever, which is a mosquito-borne infection, was first reported in Nepal in the early 2000s. "Now it is a major threat even in the high-altitude region," Professor Amir Sapkota, chair of epidemiology at the School of Public Health, University of Maryland, says.

Cholera outbreaks in many African countries have also been linked to seasonal rains and floods. Between 2015 and 2020 multiple cholera outbreaks took place in Kenya with the drug-resistant Vibrio cholerae strains reported in some cases.

Cyclone Idai in 2019 and Cyclone Chido in 2024 ravaged Malawi, Mozambique, and Zimbabwe in southern Africa. The damage to health infrastructure in these countries led to cholera and other diarrheal epidemics.

An issue of equity

Although it contributes less than 4 percent of global greenhouse gas emissions, Africa is the most exposed region to climate change and its impact. According to WHO-AFRO, Africa faces higher projected increases in mortality rates due to climate change than other parts of the world "highlighting the continent's exceptional vulnerability," Yahaya says. A group of African countries known as Small Island Developing States (SIDS) are particularly vulnerable to the vagaries of fluctuating weather patterns.

"These islands often have fragile health systems, limited financial and human resources, and geographic isolation, which reduces their ability to adapt quickly or recover from climate shocks," Yahaya says.

Storms interfere with power supplies much the same way droughts reduce hydroelectricity generation. Unstable energy supplies further impair health care services, including vaccine storage and diagnostics.

When transport and communication infrastructure are damaged by flash floods, for example, health services find it more difficult to respond. More severe and frequent droughts degrade soils over time, interfering with food production, leading to malnutrition and a weakened resistance to infection.

Extreme weather events such as floods and droughts also can disrupt sanitation systems leading to increased infections. This is especially the case in informal urban settlements where the population density is extremely high, but without the corresponding sanitation infrastructure.

Warming temperatures promote the growth of pathogens that cause diarrheal disease, while extreme precipitation helps to spread these pathogens in the environment. This is particularly true in resource-limited settings, where people still practice open defecation and lack access to clean drinking water. Runoffs during extreme precipitation leads to contamination of unprotected wells, rivers, boreholes, and water pans.

"This increases the fecal-oral route of exposure to bacterial pathogens, making people sick," says Sapkota, whose research team is developing an early warning system for diarrheal disease for the Asia-Pacific region.

Widespread disease outbreaks lead to larger populations of disease-spreading pathogens and more opportunities for AMR pathogens to emerge through genetic mutations and natural selection. Disease outbreaks also encourage the misuse or overuse of antimicrobial agents, which is one of the primary ways that human activity accelerates and spreads AMR.

A challenging subject to research

Inadequate surveillance and laboratory capacity; overuse and misuse of antibiotics; and poor infection, prevention, and control strategies have contributed to the spread of antimicrobial resistance in Africa. As a result, the continent's share of the global burden of AMR is the highest in the world, standing at approximately 21 percent and projected to account for 40 percent of AMR-related deaths wordwide by 2050.

Given that seven out of 10 countries most vulnerable to climate change are in Africa, understanding how the changing climate influences AMR should be a priority. But there are many logistical hurdles that make this area of study difficult. 

"One of the challenges we have in Africa is that we lack very strong surveillance systems, making it very difficult to quantify the scale of the problem, or to monitor trends," the livestock institute's Moodley says.

Without this data, she explains, it is difficult for governments to respond effectively, or to assess priority areas for intervention, given the finite nature of resources required to invest in data collection.

Progress on AMR surveillance has been hampered by a lack of data, which is crucial to informing policies that ultimately lead to healthcare strategies against antimicrobial resistance. A 2022 study conducted by the Africa Centres for Disease Control (CDC) and Prevention, in collaboration with the African Society for Laboratory Medicine and other partners, made the dearth of data glaringly clear.

The study sought to identify obstacles faced by 14 African countries in generating data around the subject. The results were not encouraging; a mere 1.3 percent of laboratories had the capacity to test for AMR to the required standard.

"This is crucial evidence showing that we do not have enough laboratory capacity and funding to implement national [AMR] action plans," observes Yewande Alimi, a doctor who leads AMR efforts at the Africa Centres for Disease Control and Prevention. What's more, only a handful of countries in Africa consistently submit AMR data to the WHO's Global Antimicrobial Resistance Surveillance System (GLASS). Only 23 of the 54 African countries were participating in the system.

Alimi maintains that generating continental evidence on the link between climate change and AMR will help design programs tailor-made for specific public health interventions in different countries. 

"We need to understand where the needs are and create a context-specific solution," she says.

There was a six-year long program funded by the US Agency for International Development-the Infectious Disease Detection and Surveillance project-which helped detect, track, and rapidly respond to infectious diseases and drug-resistant infections across 20 countries in Africa and Asia. But it ended in May 2024.

Retrospective analyses and clinical reports show that AMR has been a growing problem in Africa for years. A 2012 systematic review of antibiotic resistance in East Africa showed resistance in common pathogens like E. coli, Klebsiella pneumoniae, and Salmonella began to emerge as early as the 1980s. "Historically, Africa has been reporting AMR and we have been talking about multi-drug-resistant TB and malaria for decades now," Alimi says.

Onsare at the Kenya Medical Research Institute concurs that Africa is not alien to drug-resistant pathogens. He cites examples in the 1950s and 1960s when the use of such antibiotics as penicillin and tetracycline became widespread. Even though these antibiotics were effective against a wide range of bacterial infections, some bacteria began developing resistance. For example, reports of penicillin-resistant Neisseria gonorrhoeae began to emerge in a number of African countries in the 1970s.

Multi-drug-resistant tuberculosis became an enormous health issue in the 1990s with the rapid spread of HIV in many African countries. The co-infections of HIV and TB created just the right conditions-including misdiagnosis and delayed diagnosis-for drug resistance to take hold.

Perhaps no one case of AMR has received as much attention and scientific inquiry as the emergence of drug-resistant malaria. Resistance to chloroquine, a long-time treatment, by the malaria parasite Plasmodium falciparum was first detected in Southeast Asia in the 1950s before spreading to Africa in the late 1970s.

The spread of treatment resistant malaria prompted a partial success story: the development of artemisinin-based combination therapies (ACTs) at the beginning of the 21st century that became the standard treatment for the disease. This treatment combined drugs derived from the artemisia plant species, which clear the malaria parasite very quickly, with secondary antimalarial drugs that target different stages of the parasite's development. The two-punch combination makes it difficult for the Plasmodium falciparum parasite to develop resistance.

However, where ACTs are unavailable or prohibitively expensive, people have begun using herbal medicines made from artemisia plant material, like teas and capsules, which are less effective against the malaria parasites. This has led the WHO to warn against this practice, in part because it could lead to the widespread artemisinin resistance, potentially undermining the effectiveness of the current best available treatment.

Preventing spillover events

The role climate change will play in either exacerbating or fostering the emergence of treatment-resistant microbes will complicate efforts to combat this longstanding problem. The thawing of permafrost due to rising temperatures could release long-frozen pathogens into the environment. Changes in water temperature and salinity can directly affect the propagation of AMR via the abundance, richness, and diversity of antimicrobial resistance genes in natural aquatic environments. Severe droughts in Africa may cause goatherds to drive their livestock into game reserves and national parks looking for pasture, creating opportunities for spillover events.

One of the biggest factors in the rise of AMR is the overuse and misuse of antibiotics in animal agriculture. Although most African countries use less antibiotics to raise livestock than many other parts of the world, that doesn't mean it isn't a problem on the continent.

The International Livestock Research Institute is part of a network of more than a dozen research centers around the world studying food security, known as CGIAR, formerly the Consultative Group on International Agricultural Research. An AMR hub under the CGIAR umbrella was established in 2019, using an approach that encompasses human, animal, and environmental health aspects, known as One Health.

The livestock institute is working with partners to look at the antibiotic use in livestock systems in Africa. A collaboration of this type is important, because the direct AMR burden on livestock and potential spillover effects on humans could cause a cumulative GDP loss of $5.2 trillion by 2050 globally.

At the end of the day, the volume of antimicrobial use in livestock systems is not as big of a concern as the manner and the reasons behind their use, the livestock institute's Moodley says. "The future concerns are the predictions that as livestock populations increase in Africa, we will see intensification of livestock farming increase as well as antibiotics use," she observes. This could pose a problem of resistance developing going forward, given the less-than-adequate veterinary health infrastructure on the continent.

Livestock farming in Africa includes systems that are extensive, peri-urban, and pastoral, unlike in developed countries which practice mainly intensive farming. Pastoral livestock systems present a different kind of challenge when it comes to antibiotics use. This practice takes place on sparsely populated vast expanses of land, which happens to be some of the remotest in the world. This means that accessing veterinary services is hard to do, and over the counter antibiotic access is therefore not uncommon.

In some instances, people live in close proximity to their livestock in Africa, something which leads to a different kind of risk, compared to, say, Europe. "The way I can acquire resistance from livestock in Europe is through contaminated food and water. But in Africa, transmission can be acquired through direct contact with livestock," Moodley says.

The livestock institute recently completed a study in Dagoretti, an area just outside Nairobi, that looked the risk of diarrhea for children under five in families that live close to the livestock they keep. 

"What we see is that the contact with manure is a risk factor for the acquisition of resistance," Moodley says.

Moving towards solutions

Africa CDC has established programs that address AMR and climate change within the One Health unit, according to Alimi. These programs also address zoonotic diseases, food safety, and related issues that require a one-health approach.

Only recently, Africa CDC launched an AMR international surveillance exchange program, where countries learn from each other. By using the resources at the National Institute for Communicable Diseases (NICD) in South Africa, this initiative aims to encourage other African countries to build their own capabilities in generating quality AMR data. Very soon, the center will launch a project that uses genomic sequencing to help in the surveillance of AMR pathogens across Africa.

Such programs have their work cut out for them, as cuts by the US and UK governments have left a gaping hole in Africa's public health infrastructure.

When the Trump administration dismantled USAID earlier this year, it cut billions in aid earmarked for Africa. US foreign aid was a crucial contributor to Africa's health system. Without it, former acting assistant administrator for global health at USAID Nicholas Enrich estimated, there will be up to 18 million more cases of malaria and more than 28,000 new cases of infectious diseases like Ebola and Marburg every year. It's not a stretch to see how this increase in disease spread could contribute to the rise of more antimicrobial resistant pathogens.

The dismantling of USAID also ended a longstanding public health program that collected information about maternal and child health and mortality, nutrition, reproductive health and HIV infections, among many other health indicators in 90 low- and middle-income nations. This will make it even harder to identify vulnerable communities and nip disease outbreaks in the bud.

And only this month, the UK government shut down the Fleming Fund, a program that helps tackle AMR in the developing world, due to shifting priorities by that government. The ₤265 million ($354 million) program was supporting efforts in building national surveillance systems in human, animal, and environmental health in two dozen countries in Africa and Asia.

On the other hand, it is encouraging to see various projects addressing this emerging challenge in an effort to arrest things before they get out of hand. For instance, the One Health Regional Network for the Horn of Africa project, funded by UK Research and Innovation, is supporting research on how livestock production, climate stressors, and antibiotic use intersect in African communities. And for its part, the Global Antibiotic Research and Development Partnership, a nonprofit focused specifically on AMR, is collaborating with the nonprofit Drugs for Neglected Diseases initiative on research and training efforts. Nurturing and expanding these nascent efforts to monitor, respond to, and mitigate antimicrobial resistant pathogens will be essential going forward, not just for Africa but also for an interconnected world in which-as the COVID-19 pandemic illustrated all too well-disease pays little attention to borders.