Student field work: STH diagnostics in Bungoma

Liya Assefa and Tom Crellen in Bungoma, Kenya

Tom Crellen and Liya Assefa are completing their MSc studies at the London School of Hygiene & Tropical Medicine. For their summer projects they evaluated techniques for diagnosing STH infection in western Kenya and here they document their experience.

17 September 2013

Tom Crellen and Liya Assefa are completing their MSc studies at the London School of Hygiene & Tropical Medicine. For their summer projects they evaluated techniques for diagnosing soil-transmitted helminth (STH) infection in Bungoma, western Kenya, and in this blog post they document their experience.

Tom’s Project

The main aim of my study was to compare diagnostic tests for soil-transmitted helminth (STH) infection. Having sensitive and accurate diagnostic tools is an essential part of STH surveillance programs, as the WHO recommends mass drug administration in areas where the prevalence exceeds 25% of the population. In this study the comparison was made between the current WHO recommended technique (Kato-Katz) and mini-FLOTAC, a newly developed test. As mini-FLOTAC is manufactured in Naples, Italy, I was lucky enough to spend a week there at the Federico II University where I was instructed in its use before we flew to Kenya.

Liya’s Project

My project was a cost-effectiveness study of surveillance methods for detection of STH. I was interested in the costs that go into the WHO standard method of STH surveillance—school-based sampling paired with Kato-Katz diagnosis—and also the costs of alternative surveillance methods. These alternatives were household sampling and the new diagnostic technique mini-FLOTAC. My project consisted of modelling the cost-effectiveness of four different surveillance combinations using the different sampling and diagnostic pairings. The main outcome of interest was positive detection of STH infection. I was also curious to see which surveillance scenario would provide the lowest costs for cost per case detected. Additionally, I was able to calculate how much it cost our team to test one child. These costing measures were all collected with hopes of informing surveillance practices for STH.

The study site

Bungoma is a tropical region of Western Kenya that borders Uganda. The landscape was lush and fertile—homes were surrounded by green fields of sugar cane and maize. Other crops such as peas and sweet potato were also abundant. The rust red dirt paths were starkly contrasted against the green fields and surrounding hills. It was calming to walk for hours each morning to collect stool samples in the villages. We wound our way through the maze of dirt paths leading from household to household, often having to part sugar cane to clear our way.

Children walk through sugarcane plantations around the villages.


We set up our laboratory in an unused hospital ward at the local clinic. There was a pump nearby, but no running water, and occasional power outages. Our project benefitted greatly from the links established by Stella Kepha, a PhD student working with the Kenya Medical Research Institute (KEMRI).  Stella assembled her team of lab technicians from the Ministry of Health and health workers from the community. The team was invaluable in both field collection and when processing samples in the lab.

Setting up

The first hurdle we faced was a teacher’s strike. As so many infectious disease control programmes are conducted in primary schools, it is a challenge if schools are closed. Therefore, sampling had to initially take place in the community. This involved a targeted sampling approach where we went to village homes in order to track down the school children.

Days in the field

Our days were divided into two parts. The mornings were devoted to sample collection, whether household or school-based, and the afternoons were spent diagnosing samples in the Bumula clinic.

After picking us up at 6:30am, the group would divide into two teams with each team working in a separate village until midday. Walking in the villages from household to household provided a window into the daily life of locals. As Bungoma is dependent on agriculture, it was common for children to be working in the fields helping their parents during the day. The children would be harvesting barefoot in the fields and as very few families had formal toilets, it was easy to see how the cycle of STH infection was perpetuated.

Children walk through sugarcane plantations around the villages.


Our lunch each day took place at a small restaurant named Fwebe’s, down the road from the clinic. We quickly grew accustomed to the menu, which consisted of local food such as ugali with chicken or beef, beans and chapati, scuma and white rice.

Our stomachs full, we would all head to the lab. There the health workers and technicians would prepare samples, with Tom leading the mini-FLOTAC preparations. Liya would observe, noting the materials, quantities, and time that went into sample preparations and diagnostics. Work in the lab became more fluid as the days went on and we established a routine. There was the occasional power outage but the team was quite impressive in their ability to adapt—the lab technicians were able to tape mirrors to their microscopes, face them toward the sun and continue their diagnostic work unfazed.

Community health workers prepare mini-FLOTAC apparatus to diagnose STH.



A comparison of the diagnostic efficacy between mini-FLOTAC and Kato-Katz revealed the methods were similar in their sensitivity to detect STH infection. The results confirmed mini-FLOTAC as a promising new technique that should be tested in a range of settings before coming to an overall conclusion on its effectiveness.

The costing data revealed the school-based sampling paired with the Kato-Katz diagnostic was the cheapest in terms of cost per child tested. This supports the standard acceptance of those methods for STH testing. Cost-effectiveness results for cost per case detected indicated that community sampling with the Kato-Katz diagnostics was the cheapest surveillance scenario. This was largely due to the role that prevalence played in the surveillance scenarios of this specific setting and would not necessarily be the case in other settings or cost evaluations for STH.

Final thoughts

We both had very valuable experiences while working on our projects.We were able to explore a region of new tastes and sights, observing and participating in life in Bungoma. We were able to see how fieldwork is typically conducted and the amount of time and effort that go into conducting STH survey activities. The conditions we saw in Bungoma, particularly in the basic laboratory, were representative of what one may see in rural settings where STH is endemic.  It was extremely insightful for us to have this experience, especially because we both would like to continue working in the area of neglected tropical diseases (NTDs). We are very thankful for the support and assistance of those at the Kenya Medical Research Institute (KEMRI) and Prof. Simon Brooker of GAHI at LSHTM, all of whom contributed to making our project possible.

Liya prepares the stool containers as children line up expectantly.