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Analyzing sewage poop in Nairobi averted a polio crisis and is now providing answers for antibiotic resistance

Dr. Sylvia Omulo and a colleague analyzing samples in the lab
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In 2018, the Kenyan ministry of health discovered a vaccine-derived polio outbreak when studying sewage samples in Nairobi. They immediately launched a renewed polio campaign targeting 2.8 million children in high risk areas. Kenya had, from 1988 to 2017, reduced the number of children suffering from polio-related paralysis from 350,000 a year to 22 and is close to eradicating polio.

Now, poop has come again to the rescue. This time in helping cash strapped scientists understand the extent and state of antimicrobial resistance (AMR) in different slums in Nairobi. AMR refers to the phenomenon of disease-causing microorganisms such as bacteria evolving to withstand attacks from medicine meant to eradicate them and is a deadly threat to human survival.

It is inexpensive, fast and adaptable.

An exhaustive two-year study commissioned by the UK government in 2016 concluded that AMR causes 700,000 deaths each year. There is little national data on the deaths caused by AMR in Kenya, but the country’s ministry of health reported more than 600,000 drug resistance tuberculosis cases in 2016.

Dr Sylvia Omulo, a PhD in the study of the immune system and infectious diseases, studies how medications for treating infections that kill hundreds of people in Kenya are slowly losing potency. To study this, she and her colleagues at Washington State University often take tissue from wounds, blood or urine and then expose those to particular drugs.

Dr Omulo has added an unlikely sample to this arsenal of study tools: sewage from pit latrines in Kenyan slums.  Between November 2015 and January 2016, she collected samples from Kibera, a slum in Kenya’s capital Nairobi. The analysis of the samples returned answers that could change how the country studies medicine use in the community.

Over the counter prescriptions for antibiotics are the norm for a majority or urban dwellers

In a paper under review for publication in the journal Pathogens, Dr Omulo and her colleagues wrote that there were high resistance levels in antibiotics that the public could access over the counter, such as Amoxycillin, but lower for harder-to-get but more effective antibiotics.  This points to excessive use of over the counter antibiotics for treating illnesses that require different antibiotics.

The most intriguing finding from the study is how close the results of the samples picked from the toilet were to those from samples collected from households. Often, standard studies researching antimicrobial resistance pick samples from households, and until now, no researcher had demonstrated that the samples picked from the toilet could return the same results.

Another researcher, Dr Eric Ng’eno a medical microbiologist, tested this same method from Kibera slums and found two life-saving nuggets of information: which pathogens were in abundance in certain areas and what antibiotics the pathogens were resistant to. Dr Ng’eno says that after testing the study on a large scale, he and his colleagues will make a case for “hotspot maps.”

“When a clinician knows what is circulating in what area, and which antibiotics the pathogens are resistant to in those areas, they will use the already scarce resources prudently by not prescribing drugs that would not work for patients in that area,” Dr Ng’eno told Quartz.

According to the 2019 Census, Nairobi has 4.4 million people, and 60% of them live in the slums such as Kibera, Mukuru, and Mathari. People in slums do not have social services such as healthcare. This drives improper use of antibiotics such as taking half doses or counterfeit ones, habits that lead to resistance. They also lack proper sanitation, making them vulnerable to outbreaks of waterborne related diseases such as cholera.

Surveillance involves the cost of getting ethical approvals, printing papers for the interviews, hiring staff trained to conduct interviews, collect the samples and transport them. We do not need most of this when studying latrines and sewage.

Between 2008-2011, the World Health Organization got reports from certain countries that Vibrio Cholera—the bacteria that causes cholera—was resistant to Cotrimoxazole, and studies have pointed to the increasing resistance of the antibiotic in other countries too. Cotrimoxazole, known by the generic name Septrin, is a broad-spectrum antibiotic that clinicians prescribe to people living with HIV to protect their compromised immunities. However, the bacterium acquired plasmids, genetic material from other bacteria capable of transferring resistance genes. Dr. Omulo is keen to understand how resistance comes about and is what she is studying in the slums.

“They are a huge part of the population we cannot ignore,” she told Quartz.

Studying sewage samples is a more affordable method of analyzing antimicrobial resistance

In the first meeting that the World Health Organisation (WHO) held to address the AMR menace, the global health body listed surveillance—what doctors Omulo and Ng’eno is doing—among four other means to tackle the problem. However, for countries in the developing world like Kenya, proper surveillance systems are expensive and out of reach.

Since Kenya is in the process of building its national system for tracking drug resistance, the results have encouraged scientists like Dr Omulo to consider including analyzing sewage as part of the system for tracking the use of medicines for public health response.

“It is inexpensive, fast and adaptable,” Dr Omulo said.

Dr Omulo says that it is precisely because of the cost that studying sewage waste is the easiest way.  Viruses and bacteria are ever-present in treated and raw sewage. Some studies estimate that an infected person can shed as many as 10 trillion bits and pieces of the pathogens in a teaspoon of feces. Dr Omulo said that in most cases, these microorganisms are harmless in the sewage but become deadly when they move to other places.

“Take the bacteria E. coli for instance; it could be in the gut or sewage, but when it gets to the urinary tract, it causes disease,” Dr Omulo says.

Sam Kariuki, a professor of microbiology and the director-general of Kenya’s premier medical research institute KEMRI, told Quartz that traditional surveillance would need technology for work such as sequencing that many African countries do not have.

When donors such as the UK government stepped in through projects such as the multimillion-dollar Fleming Fund, Prof Kariuki said, they prioritized collecting samples and data from hospitals and building the laboratory systems.

Prof Kariuki told Quartz “It is just Kenya, but many countries cannot truly implement the steps to making a surveillance system for AMR at a go; they phase the process.”

However, the national strategy included another component, the environment. Scientists like Dr Omulo have borrowed a leaf from it, especially given how people live in Nairobi and how it makes the city a cesspit of antimicrobial resistance. Thus, the fecal matter is free “data” that scientists are harvesting to study to guide clinical decisions at a meager cost.

Dr Omulo said: “Surveillance involves the cost of getting ethical approvals, printing papers for the interviews, hiring staff trained to conduct interviews, collect the samples and transport them. We do not need most of this when studying latrines and sewage.”

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