Poor waste management making bacteria harder to kill

Garbage dumped on the roadside in Kibera, Nairobi County.

Birds perched on trees eye piles of uncollected mounds of garbage, the playgrounds of rats scampering in and out of the dirt. To the naked eye, this is the routine of life, several parts of the ecosystem co-existing. However, beneath the surface is the constant war between bacteria, fighting to occupy space and depose each other. And this battle has implications on health, as people interact with the elements in that battle.

Eric Fevre, an infectious diseases expert and researcher at the International Livestock Research Institute (ILRI) spends his days getting to the bottom of that battle (how the interaction between the environment, animals and people affect human health) by researching anti-microbial resistance – the scientific term describing how disease-causing pathogens such as bacteria, are evolving to become too strong to be killed by antibiotics.
“If I were a micro-organism that causes disease, how would I mover from where I live – say, the gut of an animal – to the plate of food at a home to make the eater sick?” – such are the preoccupations of Prof Fevre's mind, making observations on a seemingly banal subject with far-reaching consequences. He and his colleagues from ILRI, the University of Liverpool, University of Nairobi, Kenya Medical Research Institute (KEMRI) and others have some of the answers. They recently published a paper which showed that animals such as rodents and birds – that hover around homes – carry a high burden of disease causing Escherichia coli (E.coli) that is resistant to recently developed drugs the World Health Organisation deems very important to human medicine. These medicines include third-generation cephalosporins, and synthetic fluoroquinolones which are used against tuberculosis and HIV-related infections.

E. coli lives in the environment – in the water, soil, sewer, garbage, abattoirs – as well as on food (meat, fruit and vegetables), and in human intestines and animal guts. Most strains are harmless, living in the body without causing problems, but some cause disease like diarrhoea or food poisoning, urinary tract infections or even pneumonia. People become infected with E. coli, when they eat meat that wasn’t cooked well enough to kill the bacteria on it, or if they drink unpasteurised milk or from contaminated fruits and vegetables or water or from poor hand hygiene (not washing hands after using the toilet or changing a baby’s diaper).
The researchers took samples from food, the environment, from rats and other rodents, bats and livestock, and tested them for bacteria. They found that more than half (52 per cent) of the 485 samples from rodents and birds carried E. coli, that was resistant to more than three drugs. Prof Fevre told HealthyNation that the battery of tests that were run on waste and other samples from 99 households from Nairobi found a higher diversity of anti-microbial resistance in livestock and humans, meaning that resistance was being created in humans and livestock, put out into the environment with waste and then being collected by rodents and birds for transfer.
The researchers wrote that rodents and birds were significantly more likely to carry resistance to multiple drugs when exposed to human and livestock waste through poor management practices, a common feature of poorer neighbourhoods. In Nairobi, where the study was done, the population has grown from 137,456 people in 1950 to the current 4.6 million, yet social amenities have not grown in tandem and sanitation has been a challenge. It is not uncommon to see broken sewers and in the wastewater and garbage mounds, E. coli thrives and morphs into a resistant bug.
“Rodents, bats and birds pick up these resistant bugs when they interact with particular aspects of the environment that humans create.
“A bird or rodent feeding on a pile of manure or waste will pick it,” said Prof Fevre, adding that while these animals are not the source of resistant bugs, they are agents of dispersal.


Samuel Kariuki, a professor of microbiology at the Kenya Medical Research Institute, who was also part of the study, describes how the fears of Alexander Fleming – who discovered penicillin, but warned that under-dosing would expose microbes to non-lethal quantities of the drug and make them resistant – are manifest in 2019.
The bacterium, a sly and cunning creature, existed way before mankind, but as humans bow to the pressures of changing climate and other threats, the microscopic creature has survived, and over time, recorded the knowledge of what is happening around it in its DNA, and marshalled this knowledge to withstand attack. This is what helps it develop resistance to the drugs that are supposed to kill it, as Prof Kariuki explains.
“When you expose bacteria to subtle doses of drugs and the dose is not strong enough to kill them, they learn the attacking style of that drug and change themselves for the next attack.”
For instance, some antibiotics work by breaking down the cell walls of bacteria to kill the microbes, so if the dose is not strong enough to kill them, the bacteria change their cell walls to overcome that or produce enzymes to disable antibiotics.
“The bacteria may develop ‘pumps’ to flush out the drugs or grow a thicker layer against the drug, such that the next time you take medicine to fight illness, the bacteria will just scoff at the drug,” said Prof Kariuki.

The subtle doses are introduced to the body in several ways: one, patients do not complete the prescribed dosage or because of poverty, they can only afford to buy half of it. Two, without any prescription, the public buys antibiotics and use them for viral problems such as a cold. Three, and perhaps the most unregulated is in animals.
The Global Antibiotic Resistance Partnership, a project of the Center for Disease Dynamics Economics and Policy, states that 70 per cent of the antibiotics that are imported for use in the country are given to chickens, pigs, cows and other animals that eventually end up on dinner tables with traces of these antibiotics. In 2016 alone, Kenya imported 5.2 million kilogrammes of antibiotics for use in veterinary practice, almost thrice what is used in human medicine.
Robert Onsare, a researcher at KEMRI told HealthyNation that farmers give antibiotics for prophylaxis — to prevent their livestock from getting sick — as well as to treat the animals when they get sick, and often without any prescription. In 2016, this paper’s investigations reported that local farmers in Kiambu, Thika and Gatundu said that they give antibiotics to animals, “just in case they fall sick when it is cold.”
Data from the Veterinary Medicine Directorate shows that in 2018, small scale farmers used 65,653 kilogrammes of antibiotics on animals to enhance their growth – not for treating any sickness; just to fatten them.
Naphtali Mwanziki, the chief executive of the directorate lamented about the ease with which people can sell veterinary medicine. He gave examples and a spot check in Kariobangi revealed people hawking veterinary products from the back of their vehicles.


The antibiotics used in livestock also appear in milk. In Nakuru, Peter Lamuka, a lecturer at the University of Nairobi, tested milk samples in Ndundori and Olenguruone, some of the county’s major suppliers of the commodity. He found that 47 per cent of the milk had antibiotic residues higher than the recommended levels. When he visited the farmers, he found that they were not withdrawing their livestock from drugs before either milking or slaughtering them, yet experts advise that farmers should not sell or consume milk from a cow that has been under medication for at least three days. When the animals excrete, they leave these traces of antibiotics and bacteria that have developed resistance to the drugs in the garbage which could end up in water sources and also which livestock, rodents, bats and birds interact with.
It is not just drug resistant E. coli that is a problem in Kenya. In 1998, 50 per cent of typhoid fever strains were found to be resistant to the recommended antibiotics — ampicillin, chloramphenicol, tetracycline, streptomycin and cotrimoxazole — and that figure rose to 82 in certain parts of Thika, Embu and Nairobi by 2002.
Another survey in Kilifi in 2016 showed that Staphylococcus aureus which causes pneumonia, meningitis and boils was 92 per cent resistant to penicillin and other medicines such as erythromycin.
During a series of cholera outbreaks in 2017, research scientist John Kiiru raised the alarm that the strain responsible had “acquired a resistant characteristic, an extended-spectrum beta-lactamases or just ESBL, which makes it able to break down stronger antibiotics and therefore more difficult to treat.”
Moreover, according to the Ministry of Health, an estimated 1,400 cases of tuberculosis that is resistant to treatment are recorded every year, straining the health system as one case of drug-resistant tuberculosis costs more than Sh1.5 million to treat.
Decades after Fleming’s warning, bacteria that have evolved to scoff at antibiotics kill 700,000 people each year around the world, and ever more powerful strains are spreading. For instance, at the annual American Society for Microbiology, scientists from the Centers for Disease Control and Prevention and the Chicago Department of Public Health confirmed what scientists have feared all along: patients in hospitals with the fungal superbug Candida auris shed copious amount of it from their skin, contaminating the environment in the hospitals and manage to infect others with it.