Co PI’s Letter: Microbiology Thread

On a dark and cold November afternoon, Edinburgh feels very far from Nairobi and the UrbanZoo project. But I like to think that we still have a useful contribution to make, not least by helping to put together different pieces of research together to reveal the “big picture”. It is going to be a very unusual picture though; we want to construct a kind of map of Nairobi from the point of view of a ubiquitous bacterium, Escherichia coli. We want to find out where different strains of E. coli live and how they move through the different compartments that make up Nairobi: healthy people  in the community, sick children in clinics, wildlife, food, water and waste and especially the livestock species that live in the city.

Those urban livestock are central to UrbanZoo: we want to know how they fit into the ecology of E. coli in Nairobi and, in doing so, we hope to illuminate a general theme of the entire ESEI programme (of which UrbanZoo is one of 3 funded projects). We will be testing the idea that urban livestock are a risk factor for outbreaks of emerging diseases (not just E. coli-related disease) in cities everywhere.

Though often stated, that hypothesis has rarely been tested. It might not even be true: we shall see. It all starts with the highly structured collection of samples by the field teams, who are systematically working their way around Nairobi as they conduct the 99 Household survey. The microbiology teams will then give us a first glimpse of the big picture by carefully typing the E. coli isolated from those samples.

That work is vital, but although standard typing methods can tell us whether two samples share similar kinds of E. coli, they often cannot tell us the direction of movement. For example, if samples from a child and a pig in the same household contain very similar E. coli, does it mean that the pig infected the child, the child infected the pig, or they were both infected from some other source? The state-of-the-art tool for answering those questions is kind of statistical analysis called phylodynamics. Our phylodynamic analyses will use two kinds of information: whole genome sequences of UrbanZoo E. coli; and the metadata – place, time and host
species in particular – that go with those sequences.

That is why everyone is working so hard to obtain the best possible set of isolates for sequencing and all the field and typing data that go with them, why we are spending so much money on whole genome sequencing, and why Melissa Ward is devoting so
much of her time to doing the phylodynamics analyses.

Over the next 12 months or so we hope to build up a collection of E. coli sequences that is by far the best of its kind in the world and that gives us completely new insights into the ecology of the bacterium within the extremely complex ecosystem that is Nairobi. We hope to reveal a picture that no one else has ever seen before. I can’t wait.