One of the primary objectives of the Urban Zoo project is to quantify and understand microbial diversity in an urban setting and to try and link that to urban livestock keeping. In so doing we aim to elucidate the possible role of livestock as a risk factor in the emergence of disease in cities.
To give us a handle on microbial diversity we have chosen commensal Escherichia coli as an indicator species, which we have isolated from samples taken from a diversity of sources across the city of Nairobi. These comprise people and their living spaces, including the food they eat; their immediate environments, including water sources, waste and wildlife; and the livestock that they keep either for their own consumption or for sale. From these samples we isolate and culture E. coli, extract their DNA, and perform whole genome sequencing, enabling us to compare isolates from different compartments and to determine how closely related they are, and thus how microorganisms might pass from one to another.
The collection of these samples has been guided by a highly structured sampling frame, which I described in Urban Zoo newsletter number 7. Essentially, we have selected 33 sub-locations in Nairobi representing a range of social strata and, within each, have chosen 3 households to sample: one with no livestock; one with only monogastric species (pigs or chickens); and one with ruminant livestock (sheep, goats or cattle); You can view the spatial maps at our earlier post by clicking here .
The collection of such comprehensive data from these 99 households was an enormous undertaking and has been a considerable logistical feat of coordination between the field and the laboratory. The good news is that the sampling is now complete, thanks to the heroic efforts of the field team, led by Judy Bettridge and James Akoko, and of our colleagues in the laboratories.
Overall, 2,351 samples have been collected and we managed to culture E. coli from 80% of these (1,850). Once the last few have been done this will give us 1,809 whole genome sequences to analyse. 327 of these are from people; 58 from the places where they prepare food; 64 from animal source foods (milk meat and eggs); 644 from 12 different species of livestock; 239 from the environment around the home-stead including water sources; and 477 from a wide diversity of wildlife in the vicinity of the household.
But it is not over yet. We will very soon have finalised the sequencing and now comes the equally challenging task of deciphering all of this genetic data to unveil the pattern of microbial diversity across Nairobi. Over to you Melissa!
On that note, I would like once again to congratulate the field and laboratory teams, and to wish everyone a great year ahead, 2017.
This article was authored by Dr. Timothy Robinson who is a co-principal investigator in the Urban Zoo project and also a principal scientist with ILRI’s Livestock Systems and Environment research group.