Where and How Does Cross

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A new study of emerging diseases in the fast-growing capital city of Nairobi, Kenya shows that pathogens may be more likely to jump from animals to humans in parts of the city with high densities of people, livestock and urban-adapted wildlife such as rats. These areas also tend to be lower income with a lack of adequate sanitation and waste management as well as lower levels of biodiversity.

The findings, published today in the Proceedings of the National Academy of Sciences, suggest places to prioritize disease surveillance, improve access to basic healthcare and explore targeted disease control measures.

The study is among the first to use concrete evidence to get at the questions of where and how disease transmission occurs in urban settings. Led by Dr. James Hassell, a wildlife veterinarian and epidemiologist for the Smithsonian’s National Zoo and Conservation Biology Institute (NZCBI)’s Global Health Program, in collaboration with Kenyan and United Kingdom partners, the study’s findings were based on genetic relationships between E. coli bacteria collected from a group of more than 2,000 people, livestock and urban wildlife from 33 locations across Nairobi.

E. coli bacteria have some genes, called mobile genetic elements, that carry traits like drug resistance and can be transferred to other E. coli nearby. This allowed Hassell and his colleagues to infer the same kind of close physical proximity between any E. coli that shared many of the same mobile genetic elements.

Comparing the E. coli bacteria collected from people, wildlife and livestock across Nairobi allowed the scientists to map parts of the city that featured the most overlap in these bacterial genes and, ultimately, identify these areas as key battlefronts for emerging diseases. The rationale is, if the bacteria from a person and a cow, for example, got close enough to develop significant genetic overlap, then their hosts could get close enough to swap pathogens.

Though the results apply directly to Nairobi, Hassell said the Kenyan city is emblematic of many cities in the tropics experiencing what researchers term rapid, unplanned urbanization. When cities grow extremely fast without meaningful urban planning they are often missing basic infrastructure such as adequate sanitation or waste management systems, especially in low-income neighborhoods.

Combine these conditions with high population densities and large numbers of residents still relying on livestock to support their families, and opportunities for diseases to jump from animals to humans abound. Additionally, while these neighborhoods tend to have reduced biodiversity overall, they provide a favorable environment for certain wildlife species, including rodents, certain bird species, and some bats, that have been shown to be particularly effective disease carriers.

As more and more people move to cities for economic opportunities and a host of other reasons globally, Hassell said the issue of emergent diseases in urban areas experiencing rapid, unplanned growth is only expected to grow.

To study this issue and to provide effective public health recommendations, it is essential to pinpoint, with hard evidence, the interfaces between people and animals in an urban environment that make disease transmission more likely to occur.

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To do this, Hassell and his co-authors set off on an ambitious data collection project in Nairobi in 2016 as part of the UrbanZoo project, led by Eric Fevre at the University of Liverpool in the United Kingdom. In 33 parts of Nairobi, selected to represent a full range of diversity with regard to household wealth, the researchers collected samples of E. coli from people, livestock and wildlife in and around 99 different households.

Next the researchers sequenced all these cultures of E. coli and constructed a network of genetic overlap between the bacteria from various hosts. By combining this network with the location within Nairobi associated with each E. coli sample, the team was able to identify the parts of the city with the most genetically similar bacteria.

“This genetic similarity is a good proxy for disease transmission potential between two hosts,” said Hassell. “We can’t know if the bacteria were transferred from human to animal or animal to human, but it tells us something important about the epidemiological connection between them.”

The final analysis revealed neighborhoods with the highest densities of people and livestock and the lowest levels of biodiversity featured the greatest degree of genetic overlap between the E. coli samples collected from humans and animals. Poor management of livestock manure, especially inside the household, in these communities was also implicated as a significant source of genetic overlap between wildlife and livestock.

“In these high population density areas, people and animals are really closely connected from a potential disease transmission standpoint,” said Hassell. In general, Hassell said these were lower-income neighborhoods that had poor sanitation or waste management.

“These are the places where the ingredients are there for emerging pathogens to jump from animals to humans, and places where it would be easy for those pathogens to multiply before being detected,” said Hassell. “This means these places are also where it makes sense to prioritize access to healthcare and disease surveillance.”

Other potential interventions based on these study results include improving sanitation and waste management, particularly the handling of manure from livestock. Hassell said this is another illustration of why it’s important to improve living conditions for people and their animals and to increase access to doctors and veterinarians from a public health perspective.

“We can’t really redesign urban environments to completely eliminate the risk of disease spillover,” said Hassell. “But we want to detect these diseases quickly and minimize their impact, and to do that, the focus needs to be on access to quality healthcare that can diagnose and identify new pathogens.”

Follow-up research is currently trying to gather even more information on the mechanisms of disease transmission in Nairobi by placing tracking devices on livestock, bats and birds from many of the same households surveyed in the current study. The study will use GPS tracking as well as devices called proximity loggers that record when two animals wearing the devices get closer than half-a-foot from one another to build contact networks.

“This is the next progression from using E. coli as a marker of how animals and people are connected to being able to see in time and space how they’re coming in contact,” said Hassell.

Reference: Hassell JM, Muloi DM, VanderWaal KL, et al. Epidemiological connectivity between humans and animals across an urban landscape. PNAS. 2023;120(29):e2218860120. doi:10.1073/pnas.2218860120

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