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Christine’s Trek to Kenya

Meet Christine Markwalter! She is one of the postdocs working with the O’Meara Lab and has been a member of the greater malaria research community at Duke for 3 years. Christine came to Duke after completing her doctoral studies at Vanderbilt University in chemistry. She is currently focused on a project analyzing haplotypes from mosquitos and humans that are a part of the Once Bitten cohort study, as well as some haplotype data from our Turkana project.

So how did Christine end up studying malaria in Kenya with a PhD in chemistry, you might ask?

Well, by way of bioanalytical chemistry, actually. For her doctoral work, Christine was investigating how to make rapid diagnostic tests (RDTs) more sensitive in order to detect lower density infections, specifically for malaria and schistosomiasis. After she finished her PhD studies in the lab, she decided she wanted to gain more epidemiology and field work experience, which is what ultimately landed her in the Malaria Collaboratory at Duke.

This past summer, Christine was able to spend 3 weeks in Kenya. This was her first trip visiting the field site there, and her trip started off with the ever-eventful loss of luggage by the airline. Normally this wouldn’t have been a huge deal for a seasoned traveler like Christine, but this time she was traveling with her husband Daniel, an Emergency Medicine fellow at UNC, and their baby daughter Ellis. Thankfully they had packed most of baby Ellis’ items in their carry-on’s, but the first day or two in Eldoret were spent going back and forth to the local mall to get spare clothes and supplies.

The ExactDx team, in true harambee fashion, did their best to help Christine and her family settle in sans luggage. On the way from the airport to retrieve their suitcases a few days later, Edna and Julius thought it would be fun to give Christine and Daniel a taste of traditional Kenyan cuisine. They stopped off and treated them to some nyama choma (grilled goat meat) and ugali. The meal remains a favorite from their visit, and Christine and Daniel cannot wait for their next opportunity to enjoy delicious Kenyan cuisine.

After a week of orientation in Eldoret, meeting with different team members in person, including some collaborators at Moi University, Christine and baby Ellis headed out to Webuye to experience a day of “ento.” “Ento” is short for “entomology” and refers to the days when field researchers (FRs) strap on their prokopacks and visit each of the households enrolled in the Once Bitten study to collect mosquitoes. The days begin early, usually around 6 am. This is the optimal time for catching mosquitoes in the households where they have potentially bitten members during the night. Household members are asked to keep windows and doors closed until team members arrive for mosquito collection.

“I was blown away with how generous the study participants are, letting the study team into their homes to collect the mosquitoes so early in the mornings. To me that is typical of the Kenyan hospitality I experienced throughout my trip,” recalled Christine.

Christine enjoyed getting to use the prokopack and helping collect some of the mosquitoes whose bloodmeals she’ll ultimately end up analyzing in the US. She was able to spend the afternoon with the FRs back at PEARL where she observed them sort species, rear, sacrifice and dissect the mosquitoes. The team places the mosquito parts (head, wing, and abdomen) in pre-labeled eppendorf tubes and package them by household and village before shipping them to the Taylor lab in the US. Once in Durham, members of the Taylor lab receive the mosquito parts (heads, wings, and abdomens) and processes the mosquitoes further, extracting and sequencing parasite DNA for analyses. This field visit provided Christine with knowledge and insight about the context and environment from which samples are collected, and will give her a richer understanding as she conducts her analyses and thinks about the team’s scientific questions.

In addition to gaining invaluable field experience, Christine volunteered some of her laboratory expertise at PEARL to help get a mosquito PCR speciation assay up and running. One difference she noticed between the lab set up in rural Webuye compared to Durham was the impressive amount of planning and forethought required to keep things running smoothly in the lab. At Duke, if a reagent runs out or if she runs into a problem with an instrument, she can just make an online order for next day delivery or take advantage of the many resources and experts available on campus. When challenges arise in the lab in Webuye, the team approaches them with creativity and careful planning, keeping a detailed inventory log so that orders can be placed months in advance. Christine was impressed by the  molecular assays and techniques the PEARL team performs, and she is excited by the lab’s potential to do more as the program continues to grow there.

Christine leads a CME course via Zoom.

Christine also facilitated the monthly CME course for July, which is part of the many training activities that are conducted out of PEARL. Her topic was diagnostic technologies and she went over the advantages/disadvantages of different formats (rapid tests, PCR, antibody detection, etc.). The topic was very timely given the recent discussion globally around COVID-19 diagnostic methods and was attended by clinicians and researchers at PEARL and virtually.

She wrapped up her trip in Eldoret working with some other expat collaborators who were fortuitously visiting our office at the same time (a rarity during pandemic times!). She and her family are so grateful to have met the ExactDx team in person and for their genuine hospitality and care. They are already looking forward to returning! Karibu!

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Welcome Zena!

“My brother thought I’d like to code but I didn’t want to listen to him,” says Zena Lapp, our newest computational postdoctoral research associate. Famous last words!

Zena joins us from the University of Michigan where she finished up her studies in Bioinformatics and Statistics. Even though she just got to Durham this past August, it seems like she’s been a part of the team for ages. She jumped right into the Once Bitten project and has started sharing some of her initial analyses at group meetings. Listening to her present her colorful, well-thought out figures, you would never guess that she didn’t always know that she wanted to pursue a career in malaria genomics research.

Zena grew up in Pittsburgh. Her father was a doctor and throughout her childhood, her entire family packed their bags and accompanied him on medical trips to South and Central America. These experiences were incredibly formative for Zena, whose family members all speak Spanish to varying degrees as a result. So it was only natural when she graduated from undergrad that she decided to take a gap year in Bolivia working with Nuestros Pequeños Hermanos, the same organization her father had volunteered for. As is requisite while taking a gap year, Zena was using the year to think about what she wanted to do for the rest of her life. In the meantime, she was volunteering at a children’s home, coordinating volunteers and managing the organization’s donation website. But as the year went on, she felt like she needed a little more intellectual stimulation. It was then that she realized that maybe she should have listened to her little brother’s advice after all.

“I had a computer and internet access.” And so, she started to teach herself how to code.

She started learning Python with Codecademy. Upon her return to the US, she sat in on some computational biology and bioinformatics classes at the University of Pittsburgh. It was then that she found her calling! She combined her undergrad experience in biochemistry and molecular biology and coding, and decided to apply to PhD programs in bioinformatics. She never lost her passion for global health, and after completing her PhD where she worked in an infectious disease lab, she decided to pursue a postdoc in global infectious disease epidemiology, focused on using genetics/genomics to study transmission of ID. This ultimately brought her to the Malaria Collaboratory at Duke. But the rest is not history.

While Zena was studying for her PhD at Michigan, she and her friend Brooke Wolford decided to co-found a Girls Who Code chapter. During her undergraduate studies, Zena had avoided programming classes because she just had the idea in her mind that she would hate computers. Now, she was working with young girls to help inspire them to pursue careers in computer science by not only teaching them how to code, but also by exposing them to women working in the field. Every meeting started with a guest speaker who talked about her own career trajectory, many of them Zena’s fellow grad student friends as well as some women working in industry at places like Google. Her favorite part of Girls Who Code was seeing the girls become more confident and excited about their coding skills and projects, and she is super happy to see the next generation of board members continuing to inspire young women to code.

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Updates from Turkana

Over the last few months, we have worked on setting up community-based malaria surveillance in Turkana with the help of the County Health Leadership. Here are a few highlights:

We trained 100 community health workers from five communities to follow malaria cases identified in the health facility to their home and test household members for malaria

No power in the training hall so all of our ‘slides’ had to be drawn by hand

We also initiated surveillance of travelers coming into Turkana via the road and the airstrip. We offer free malaria diagnostic testing and treatment following a positive test. We have screened hundreds of passengers and found several malaria cases among them.

Entomological surveillance for both larvae and adult vectors is now beginning.

Hand-dug canals leading from the Turkwel river into the fields are a potential source of mosquitoes if the water is not moving or if stagnant pools form.

Along the dry riverbed, people dig shallow pits where water seeps up from below. Water is scooped out for household use. The pits are excellent mosquito breeding sites

We also tested light traps for catching blood-seeking mosquitoes inside homes

We had the good fortune to sleep outside at the Turkana Basin Institute and see the sunrise over the river.

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Opening of the Partnership for Education and Academic Research Laboratory in Webuye, Kenya!

Wendy OMeara and Eric Nalianya demonstrate for Governor Wangamati and Dean Atwoli the telemedicine capacity being developed at PEARL

On Thursday, the Governor of Bungoma County, the Vice Chancellor of Moi University, the Dean of Medicine and Dean of Public Health of Moi University joined Dr. O’Meara, Dr.

Laktabai and Dr. Kisaka to official open the PEARL laboratory in Webuye, Kenya. 

PEARL is the latest development in a longstanding partnership between Moi University in Eldoret, Kenya, Webuye County Hospital and Duke University. The lab is being established under the leadership of Jeremiah Laktabai, chair of the Department of Family Medicine at Moi University, and Wendy Prudhomme-O’Meara, an associate professor of medicine and global health at Duke University who’s based full-time in Eldoret.

Housed in two forty-foot refurbished shipping containers with a state-of-the-art multi-head teaching microscope, the lab will initially focus on building clinical microscopy skills among technicians across 224 facilities in the region. Microscopes are a cost-effective and versatile tool for examining patient specimens and making accurate diagnoses, and nearly every rural health center in Kenya has a microscope. However, with the exception of malaria smears, these diagnostic tests are rarely performed due primarily to lack of expertise.

“There are so many different ways you can improve patient care with a microscope if you have the training to use it,” said Prudhomme-O’Meara. “We’re developing programs to help technicians in rural facilities learn how to better support clinical care with their microscope, which in many cases is the only piece of diagnostic equipment they have.”

Another goal of the lab is to support ongoing research efforts in Bungoma County, including studies on and interventions for HIV, hypertension, diabetes, fevers in children and malaria transmission, led by local and international faculty and trainees.

“Through our collaborative research projects, we’ve been able to improve care and prevention for illness in Bungoma County and beyond,” said Prudhomme-O’Meara. “We expect that PEARL will help us expand this work and impact, as access to a research laboratory will allow Moi University faculty and their partners to tackle critical research questions affecting clinical care and community health.”

Here’s a link to a story in the Kenyan national news:

Moi University to put up a research laboratory for Webuye Sub County Hospital

The lab building and infrastructure were made possible by support from Webuye County Hospital, Duke University and The Bill & Melinda Gates Foundation.

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New grant to improve targeting of subsidized antimalarials sold over-the-counter

This month, we received a new award from the National Institute of Allergy and Infectious Diseases (NIH) to study interventional approaches to improve the targeting of artemisinin combination therapy to individuals with confirmed malaria infection. This new project builds on our previous work to target antimalarials through a partnership between community health workers and private medicine retailers.

In 2016, the WHO estimated that 216 million cases of malaria occurred worldwide, yet more than 400 million treatment courses of first-line antimalarials (artemisinin combination therapy or ACT) were consumed.  This substantial overuse of ACTs is driven in large part by the private retail sector. More than half of families in sub-Saharan Africa seek treatment for febrile illness in retail medicine outlets where ACT is available over-the-counter, but malaria diagnostic testing is virtually absent and presumptive treatment of fever as malaria is the norm. Availability of inexpensive, donor-subsidized ACTs and the absence of diagnostic testing lead to very poor targeting of ACTs to people who need them. Individuals without malaria consume between 65-90% of ACTs distributed through retail outlets. Unnecessary consumption of ACTs is a drain on scarce public health resources and threatens the future sustainability of publicly-funded subsidies.

Although accurate point of care diagnostics are available for malaria (called rapid diagnostic tests or RDTs), they are uncommon in the retail sector and, where they have been tried, their impact on appropriate ACT use is often poor. We hypothesize that both providers and clients’ decisions about testing and treatment are strongly influenced by price (or profit). In response to this, we will test a scalable, policy-relevant strategy that integrates testing and treatment subsidies for the client, with incentives to the provider to test for malaria. ACT subsidies will be available only to customers with a positive malaria test (conditional ACT subsidy). Differential ACT pricing for clients based on the results of the diagnostic test, combined with provider rewards for testing, will align both consumers and providers incentives (price and profit) with testing and appropriate ACT use. Our approach will ensure that public subsidies are directed to confirmed malaria cases thereby enhancing the sustainability of such programs. By allocating subsidy dollars across both testing and conditional treatment (rather than universal, treatment-only subsidies), we can reduce the cost of subsidizing malaria treatment and improve targeting of ACTs without compromising access.

This work will be carried out in Kenya and Nigeria in collaboration with Clinton Health Access Initiative.

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Improving antimalarial use at the community level

ExactDx  in PLoS Medicine! The primary results of our community-based cluster randomized trial in western Kenya. The main points:

  • In most malaria-endemic countries, first-line antimalarials called artemisinin combination therapies, or ACTs, are available over the counter in retail medicine outlets and can be purchased without a diagnostic test.
  • ACTs are heavily subsidized by government or international donors and are very inexpensive to the consumer. Approximately 40% of all subsidized ACTs are sold through the private sector, where it is estimated that 80% are taken by people without malaria.
  • Misuse and overconsumption of ACTs has serious consequences; it can lead to delayed treatment for the true cause of illness and may contribute to the spread of antimalarial resistance. It also wastes public subsidy funds for patients who don’t need antimalarials.
  • The use of a diagnostic test before treatment could improve the correct use of ACTs.
  • We tested an innovative approach that created a partnership between community health workers (CHWs) and retail medicine outlets. Our intervention was specifically designed to reach individuals purchasing drugs over the counter and to incorporate the retail sector, which delivers the majority of ACTs in Kenya.
  • The CHWs provided free malaria testing in the community using simple point-of-care malaria rapid diagnostic tests (RDTs) and issued a voucher to anyone with a positive test, which could be redeemed at a retail medicine outlet in exchange for a discounted ACT.
  • The voucher allowed the ACT subsidy to be targeted only to patients with a confirmed malaria infection and created an incentive for patients to be tested by a CHW before buying a drug. Individuals with a negative test or without a test had to pay a higher price for retail ACTs.
  • We tested the effect of this intervention on testing before treatment and correct use of ACTs in a cluster-randomized controlled trial. After 18 months, the intervention improved the proportion of fevers tested before treatment by 25% and improved the proportion of ACT dispensed to true malaria cases by 40% compared to the control arm.
  • Making ACT subsidies conditional on the diagnostic test result could help ensure that the information from the test informs treatment.
  • Community-based interventions that include the private sector can have an important impact on diagnostic testing and population-wide rational use of ACTs, as well as potentially improve care for the millions of suspected malaria cases seeking treatment in retail outlets.
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ExactDx at the Kenya National Malaria Forum!

This week, the Kenya National Malaria Control Programme hosted the 3rd Kenya Malaria Forum in Nairobi. ExactDx team presented in two session. Joseph Kipkoech (above) presented results from the Malaria Voucher Study to demonstrate how targeting of antimalarials could be improved for patients who buy drugs over-the-counter. Wendy O’Meara presented about malaria in Turkana (below) and our work on understanding the magnitude and source of the malaria problem in this unique ecosystem.

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DGHI Director Chris Plowe and Chancellor Eugene Washington visit Eldoret

We were delighted to host Chris Plowe (DGHI Director), Eugene Washington (Chancellor), Chris Tobias (DGHI Director of Finance and Operations) and Jamie Mills (Grants and Contracts Manager) to Eldoret this week! We were able to introduce them to the wide range of collaborations and initiatives in Eldoret and most importantly introduce them to our partners here at Moi University. They were able to visit the Cardiac Care Unit at Moi Teaching and Referral Hospital, a group of peer counsellors working with Eve Puffer’s team, and visit our community-based cohort in Webuye, Kenya.

Dr. Plowe trying his hand at catching mosquitoes by vacuum aspiration in one of our cohort households
His catch!
Dr. Washington examining some bloodfed female anopheles mosquitoes with Eric Nalianya, one of our field researchers

    Dr. Plowe and Dr. Washington learning the finer points of identifying mosquito species by microscope

Dr. Plowe and Dr. O’Meara inspecting a sticky barrier trap for mosquitoes

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