Update: 99 Household study update
Well, time has flown since we sampled the first household in the 99 households study. On 7th June we visited our 66th household, meaning that after 8 months we are now two thirds of the way through. The project is taking us to all parts of Nairobi, as the maps illustrate. The field teams normally spend Monday to Wednesday collecting data, then use Thursdays and Fridays to recruit new households to the study, meet with local chiefs and county officials, give feedback to participants and keep on top of all the other jobs, such as vehicle maintenance, stock-keeping, accounting and paperwork. The wildlife team regularly go out on evenings and weekends to set and check traps for rodents and bats (who inconveniently refuse to venture out during normal working hours!) In some areas it has occasionally been necessary to conduct the study interviews in the evening, when participants return from work. Having to be flexible to fit around our human and animal participants’ needs, plus the perennial problem of Nairobi traffic, means early starts and long days.
The laboratory teams also come in for their share of hard work. Even with motorbike couriers, samples normally do not arrive at the labs until the afternoon, especially when large households are sampled. To process all these samples takes time. Each sample is first incubated in an enrichment broth, then undergoes two rounds of purification on a special type of agar which selects for E. coli, before being cultured on a more general agar prior to freezing the bacteria for storage. As you may imagine, this is several days’ work – each step takes at least 24 hours – and of course the bacteria don’t stop growing at weekends! Timing of steps is crucial, to ensure that pure colonies can be selected for storage. Later on, batches of isolates are revived and a number of biochemical tests are performed, to check that the bacteria we send to the UK for sequencing really are the E. coli that we are interested in. Once we are reasonably sure that what we have is an E. coli, they have to be regrown once more so that they can be sent to ILRI, where the DNA is extracted to send to the sequencing facility at Oxford.
So as you might imagine, it is extremely gratifying to finally start to see some of the results of all this hard work. Dr. Melissa Ward recently visited the teams in Nairobi and brought with her some of the first outputs of the sequencing to show us. In return, we took her along to see the sampling in action, in one of the slum sites. Melissa said, “It really brings the project to life, to see exactly how all the data and the samples are collected. Now, when I sit at my computer, I can really understand where it’s all coming from.” For us, it was equally exciting to get some tantalising glimpses of what the final dataset might look like and what kind of patterns we may be able to identify from the phylogenetic structure and genomic data. We’re not giving anything away at this stage – but we can tell you that we definitely have E. coli – and lots of it!
Article by Judy Bettridge
This blog entry is an article on our quarterly Urban Zoo Newsletter Volume 3 Issue 3 which can be accessed by clicking here.