Progress Report - December

The past quarter of my time here in Eldoret has been marked by the major transition from the planning to the on-the-ground implementation of the project I have been given the responsibility of managing this year.  My work here in the TB Care and Research Projects Office at AMPATH is focused on the roll out of new GeneXpert MTB/Rif machines at three district-level hospitals, in Western, Nyzana, and Rift Valley provinces in the western part of this country.  

Morning coffee and emails at Hotel Rowcena in Busia over looking the local track and football field.

My high class Kshs 1,000/night room in Busia

Thus, I’ve been traveling a good deal in recent months. I have been involved in the design and management of this project at all levels: from hiring new staff, developing site- and personnel-specific standard operating procedures, memoranda of understanding with partnering institutions, designing data and outcome collection methods, submitting payment request for purchasing of all equipment, developing and conducting week-long training on the project aims and the GeneXpert machine, and building relationship with clinical and laboratory staff at all levels.

My role in our office has been slowly evolving as I become more independently functional within the AMPATH system and in the field.  I have been enjoying being on the other end of my initial learning curve as it allows me to plan and prepare much more effectively for each step along the way.  Although I have been feeling much more comfortable at being an effective project manager here, there are times when I feel overwhelmed when I think about the large-scale goals of this project for the year.  Specifically, the largest challenge that I believe this project will face is to develop a regional referral and transport network of cooperating clinics surrounding each of our GeneXpert sites to marshal patient samples eligible for Xpert evaluation.  The project goal is to create a huge catchment region so as to reach as many patients as possible with this new rapid TB diagnostic assay.  The logistical challenges of creating this network are many; this will be further complicated by the requirement that samples processed on this assay are to be less than 3 days old in settings without an established cold chain.  This will likely be an issue even at our Xpert sites, let alone out in the periphery.  I digress.

All you need for the GeneXpert: cartridge, lysis buffer, and sputum.

That will be the primary challenges we will need to tackle next quarter.  This past quarter we have been successful in the hiring and training of our GeneXpert lab techs and have installed one of our machines at a district hospital in Busia, a fast growing dusty border town.  This site should be poised to begin in the first week of January, during which month I will spend on the road working to establish this equipment and gain some traction for our program at our two other sites.

I could go on and on regarding this project, but do not want to get caught in the weeds.  I really believe in this work and, even in the face of the myriad of challenges that lay ahead, I remain optimistic about our project.  It is good work for me to be involved with this year, as it has really challenged me to develop my skills as a project manager and as a person able to work effectively in a different culture and in this setting that is vastly different in terms of the overall system of how-things-happen as well as the resource availability.  Moreover, I have grown as a clinical researcher.  Every day when I am making decisions regarding this or that my thoughts are always grounded both with the known academic literature regarding a specific issue and balancing that with the on-the-ground clinical relevance to our patients here in this unique setting.  I believe that it is our role as physician-researchers to continually conduct this higher-order analytical integration of academically derived knowledge and its on-the-ground impact on people’s lives.

Our new Xpert Lab Tech, Maurice, processing his first sample.  

In the case of implementing this new technology, there are so many context-specific decisions to make.  There simply is not a lot known about clinical and community health impact of GeneXpert implementation; much of what we know about its performance is based off of one large-scale multi-centered trial [1].  There are so many fascinating questions that have yet to be asked.
When designing case definitions for eligibility we had to integrate the imperfect offerings of the literature to the realities of this unique health system to best figure out how we can apply our finite resources for TB screening with the GeneXpert for this granting cycle.  We are specifically targeting new smear negative patients who meet the criteria for a clinical diagnosis for TB.  Thus, we are not screening all patients who are evaluated for TB in this region (that would be nearly ten thousand for the regions surrounding our sites), we are limiting our screening to those who are clinically suspect for TB but do not have a laboratory diagnosis of TB.  Here, many patients treated for TB are clinically diagnosed.  We are applying the GeneXpert to provide the clinicians with an additional diagnostic tool to assist in their evaluation.

AFB Smear microscopy slide: the most common screening method for TB

It is exciting in that no one has used these machines for active, community-based, case finding of TB; we simple have no one else to compare ourselves to (there are two other GeneXpert machines in Kenya, one in Mombasa and one at the CDC/KEMRI in Kisusm, however, they are solely using it for multi-drug resistant TB screening on re-treatment cases).  As such, each day brings us into new territory with so many unexpected challenges.  I really cannot predict the project outcomes for this work, there are times when I believe that it will be a total failure and other times I am very confident in the future success of this important new technology, not only for our sites but for the whole country.  We’ll likely end up somewhere in between.

A view of Busia

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My goals within medicine are being influenced and solidified during this year.  Working at AMPATH within a community of academic clinical researchers has provided me with an excellent perspective of what clinic research is and its impact on the health communities in places like western Kenya.  My experience last year with MetroPAP which allowed me to spend my third year of medical school working in the urban-underserved community of North Minneapolis has been an important backdrop for me to view my time working here in Kenya in terms of both my career goals and what I believe is possible within medicine.  I had excellent mentorship last year with MetroPAP during which time the primacy of community-base care became clear to me.  It is fascinating for me now to be working in an environment where there is essential no primary care, and only a handful of family medicine physicians.  I am excited about bridging my interests in primary care, urban health, and development, and figuring out exactly what this will look like in the years to come.  

Kabarnet District Hospital

I have been fortunate to be working on an implementation project that has the goal of expanding and improve TB care to communities here (our funding in from the WHO/Stop TB Partnership that is all about implementation, which is different than most projects that are funded by, say the NIH, which are more focused on scientific/clinical practice advancement).  I find great meaning within my work this year; I am not sure I would be as satisfied had I been working on one of the more research-minded project here is not either translational or implementation/operational based.  Although I find much of the clinical research going here fascinating and necessary, I enjoy my work because it brings me into the field and keeps me on the ground.  

My intellectual development has been very academic and research oriented during the past six years.  This has provided me with an important foundation for my work within medicine as it has enhanced my capacity for diverse engagement within the biomedical/public health field and provided me with research-oriented skill set.  However, at the end of the day my passion lies outside of the literature and within addressing the immediate health challenges facing communities.  The more I learn about health and wellness, disease and illness, here, the more crystallized my enthusiasm for primary care becomes.  I believe that much of the success of academic medicine has seen in recent years has been at the expense of overlooking the foundations of our health systems both in the US and in places such as Kenya.  Disease prevention through universal primary care access should be our common goal within medicine and should be emphasized in the global health community much more than it is.  We already know so much (i.e. how to cure TB!), let's start learning about how we can now use this information effectively and sustainably.

School in Kabarnet, one of our three GeneXpert sites.

I do not believe that I will commit my life’s work to addressing issues specific to only one disease, like I am this year.  However, the skills and perspective that I am gaining working in this field this year has brought me in contact with many issues I will face in my future role as a physician working towards health care innovation and development to improve care and access.  At the present time, medicine has a way of corralling academic talent into specific silos: the HIV/AIDS silo, the TB silo (which, by comparison is incredibly empty), the NTDs silo, the catch-all Infectious Disease silo etcetera.  I do not believe I fit into any of these silos as I do not I believe diseases and their impact on people's health and lives fit into these silos.  


Many believe that a holistically integrated view and approach to the health on an individual or a community is idealistic and, within the academic community, there is a subtext that such an approach is irresponsible (that is, if you try to understand everything that is going on with a patient your ability to address any one concern is diluted).  I believe that this reflects the compounding priorities of the western biomedical establishment that has created the health system that we find ourselves in today.  It is all a matter of perspective: you can either pay attention to the context of illness and have those external influences effect your therapeutic approach to how to best address disease, or you can ignore it completely and focus solely on the mechanism of disease itself.  I worked at the National Human Genome Research Institute at the NIH for a year and found much of their rhetoric to be equally as idealist and irresponsible (i.e. gene therapy?  and let's spend tens of millions of dollars on creating a therapy that will take a century for its cost to amortize).  Thus, it is all a matter of perspective and priorities.

I am curious about the future and believe that we won't be able to rely on traditional approaches to global health to address emerging realities that are unfolding as we speak.  Here, I see a need for a shift in priorities away from academic research towards a focus on implementation and operational work that has an ethos founded in care delivery.  I am certainly not advocating against clinical research; I truly believe that we need to continue with the research that has the highest potential for the greatest impact.  I take issue with the conservatism of traditional granting mechanisms and the expensive incremental changes that such work yields.  The state of our global health emergency merit taking greater risks with what type of projects and initiatives are funded.  (For an excellent discussion on this very topic see Tim Harford's new book Adapt: why success always starts with failure).


At present, I believe that I am not alone in feeling that there is too heavy of an emphasis on basic science and clinical research in developing countries.  As such, perhaps the changes that I am envisioning for the future of global health will begin to expand beyond the realm of academic or governmental institutions.  If academic institutions cannot provide the supportive innovation that the present realities require, then we need to confidently look elsewhere. There needs to be a domain within our idea of ‘global health’ in the medical community that focused on improving access to care and professional avenues to achieve this goal.  AMPATH is an excellent model for academic partnerships that prioritize providing care first, sustainability second, and research third.  Their motto is, Leading With Care.   

There has never been a better time for us to focus on primary care expansion in the developing world.  Specifically, I believe the next big step in improving the health communities in LMICs such as Kenya is to take advantage of the vast outpatient clinic network that has been built over the past 20 years in response to the HIV/AIDS epidemic.  We need to maintain the relevancy and viability of this critical community health resource.  The overwhelming majority of these clinics are still disease-specific in their focus but have the capacity to integrate a diversity of clinical services that are emergently (and immediately) relevant to the communities that they serve.  HIV/AIDS remains a critical issue and more resources are required for traditional outreach, screening, treatment and prevention.  However, hundreds of thousands of people here in East Africa, are living healthy lives with HIV and their health needs are shifting to include diabetes and cardiovascular disease prevention/management, TB screening, chronic pulmonary disease etc., and they have no where to go to address these needs.  I am very excited to see the transition towards primary care integration in developing countries; from my perspective, it is one of the most exciting potentials in the field of medicine and is where I believe we could have tremendous impact. 

However, this idea is a relatively new concept and is only slowly building momentum.  I had the opportunity to have lunch with Dr. Joe Mamlin, the director of AMPATH and all around amazing person (I was told he was considered for nomination for the Nobel peace prize last year… that sort of amazing).  I expressed to him my interest and optimistic view about family medicine and the importance, yet scarcity of primary care services here.  He answered, “family medicine is the most important thing, and is the most difficult thing.”  I have no reason to doubt Dr. Mamlin; his words are both an incredible endorsement but also an intimation to the challenges that lay ahead, not only for my own professional path, but for the field of primary care itself.

A woman at the strange hot springs near Lake Bogoria

I have almost reached the halfway point on my FlexMD year and have thus far found it to be an incredibly enriching experience for me on a personal level, but also rewarding in that it has provided me with the opportunity to do real work.  There are times when I am out in the field going to meetings and making things happen that I reflect to myself, ‘finally, at 27, you are actually doing something.’  There is such satisfaction and heavy joy to be found working in medicine beyond the walls of the hospital or classroom.  It is a heavy joy because it finds it foundations within the rhythms of life and within the entire spectrum of our shared reality where neither all is bad, nor where are most things good.  Life simply is, everywhere.  Medicine has brought me closer to people living within the confines of the joys and sorrows constructed by our society and expressed through the body.  Its my daily ambition to continue to broaden this perspective and understanding as well as to work hard to ease the burden a little day by day through making sure this project is as successful as it can be.  I am looking forward to beginning my second half of my time here.  Now the real work begins.

Acacia tree

[1] Boehme CC, et al. Rapid molecular detection of tuberculosis and rifampin resistance. N Engl J Med. 2010 Sep 9;363(11):1005-15. Epub 2010 Sep 1. PubMed PMID: 20825313; PubMed Central PMCID: PMC2947799. 

Roll Out (TBusiness)

Roll out!  Roll out! Roll out! Roll out!


I got my quad-module Xperts with that anti-hack
me and my Xpert homies, so drop that
we rollin in Landcruisers with a top rack
So much grant money, you can't stop that


Now where'd you get that GeneXpert with them cartridges in it?
Where'd you get that mataching barcode scanner, all newly mint'd?
Who them patients you be with when they not smearin positive?
Breaking the rules, I get that diagnosis even tho smear negative.
Tell me who's your doc, how do you cough so good?
You's a TB suspect, why you still up in the hood?
What in the world is in that BAL? what you got in that BAL?
A couple cans of whoopin' cough; TB in micro amounts we good at eyein' it spyin' it.


Roll out

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Today.  Busia.  GeneXpert on the ground.  We begin the roll out.

That TB still ravages is ludicrous, so, above, a few lines inspired by Ludacris. 

Quad-module GeneXpeter MTB/Rif with laptop, scanner, and box of 10 cartridges.  The future of TB diagnostics?

Hibiscus in bloom, everywhere.  This one is in front of my house. 

This machine can run up to 20 smear negative samples per workday. 90 minutes later, violá.

Mountain View Hotel, Eldoret town... no mountain in site.  Nairobi-Uganda Rd.

All you need for the GeneXpert: 2 ml of sputum, cartridge, sample buffer & transfer pipette

On the road to Busia - World AIDS Day

"Take Care: Speed Kills, HIV/AIDS Kills, both can be prevented". 

                                                                              -Kopsi the Tiger.  

A very on-point sign for today's journey to Busia... 

Today is World AIDS Day. I was three years old when this global campaign of awareness was started by two PR managers at the WHO.  In 1984, when the 'AIDS' became a diagnosis (& the year I was born), there were 26 confirm cases of AIDS in Kenya.  The following year, 59 cases.  The following year was pivotal; both in terms of the impact of this disease on Kenya & the rest of Sub-Saharan Africa, but for its advocacy.  By January of  1987, there were 286 cases and 36 deaths.  With 11 months when the first World AIDS Day was recognized, it was estimated that between 1-2% of the entire population of Kenya was infected with HIV.  Prevalence peaked in 2000 at 13.4%, and latest figures reports 6.3%.

Sunset on Lake Victoria

I spent nearly my entire day in a SUV with two colleagues from AMPATH bumping along the paved and pot-holed roads between Eldoret and the Uganda boarder enjoying the scenery and listening to local radio.  We were traveling to Busia & Chulaimbo in the far western edge of Kenya to conduct a series of job interviews.  My relationship with driving here is mixed and highly dependent on the mode.  

A view of a forest between Nakuru and Eldoret

Today, we had a very nice car that could handle the terrain that was navigated by a very competent driver.  It was one of those rare trips where I spent the majority of time truly enjoying the landscape in contemplative thought and the minority of my time on edge fearing the worse with my mind alternating between going over CPR & trauma response triage protocols, meditative mantras & focusing on other non-embarrassing thoughts that would seem noble to count as my last.

Rainstorm sweeping through the valley

The radio was full of HIV/AIDS related stories today: from factual reports proclaiming that we have made great strides, yet 80% of people with HIV here do not know their status and that only 48% of people who know they have HIV are on appropriate therapy [amazing], to moving personal stories about people living HIV.  One such story was by a 20 year-old college student here at Moi University who was born with the virus and has lived a very healthy, successful, and productive life who is committed to spreading awareness and advocating for HIV prevention and treatment.  Incredible.

As we drove on and as the radio played, I thought a lot about how I was personally connected to this day and to this disease.  Today is one in which our global community builds consensus around understanding the structural social, economic, and political issues that perpetuate this epidemic and call for action against these forces.  I think that for many, when we recognize World AIDS Day it is one that we understand how this disease, like so many others, are proxy battles that we fight as physicians, public health and social workers, artists, activists, policy makers and advocates against these greater injustices.  

For those of us who have worked in HIV clinics in developing countries we know that for families living each day with HIV, it is not the disease itself that we worry about but rather issues of job security, food safety, education, and primary health care access for the entire family.  Today is a day to recognize those living with HIV and its greater implications for communities and entire generations.

I like to understand this day of awareness as one that truly parallels, and has perhaps inspired, the growth of my generation's global consciousness of the complex nature of the origin & perpetuation of a disease.  Although our world has suffered from incredible health inequities forever (TB, for one, just think: here is a disease that is completely curable and has killed more people than any other disease and has a great economic burden on countries than AIDS & malaria combined, and it receives essentially no attention), it has never seen such a social movement around any other disease as it has with AIDS.  When you critically appraise this epidemic, you unmask very contemporary issues of globalization, foreign policy, and our collective priorities that has gotten so many of us to approach these issues in their education.  

World AIDS Day brings up many different issues for many different people.  I believe that we can all locate ourselves within this movement wherever and whoever we are.  We are all implicated, either passively or actively into this situation.  The fight against HIV/AIDS is a broadly encompassing movement and today is a day that we may again raise our voices in a call to action as well as an opportunity every year to reassess our relationship with the movement and to reflect on its impact on our career path, outlook, and lifestyle.

When we were driving through the countryside I understood my relationship with this movement has changed.  I realized that I was actually here, not the 'idea of here'.  Throughout college and into medical school my academic interests and experiences abroad gave me a sense of what 'here' would be like.  As such, in years pasts it has always been easy for me to pour my extracurricular energies in November helping organize for the event and spend time really diving into the literature about this topic.  However, now that I find myself here, my relationship with this previously-imaged situation has changed dramatically, so has my relationship with the very concepts so familiar to anyone in their early stages of medical school interested in global health.  Here, I feel more like just some dude, than a person with meaningful knowledge and opinions about how things should be.   

"The preoccupation with what should be is estimable only when the respect for what is has been exhausted" — Orega y Gasset

I have been so humbled and moved by what is here, that all my prior academic and idealist preoccupation of what should be has completely ceased.  I am left with 'what is.'  And here, I am just a dude, nobody special, who is taking steps to understand what it is like elsewhere, for everybody else.  Here, I find myself starting over in many ways; rebuilding and refining my perspective. 

This deconstruction of my ideas of and relationship with the issues and themes I have been interested in as I have been drawn towards 'global health' throughout my academic career has been a slow incremental process during the past three months and I am sure will continue.  I have come to believe that the idea of 'global health' is only a useful or sensible concept when you are very far away from it.  

With all of this in mind I kept giving this question of what World AIDS Day means for me a little more time and a new space to breathe that is now unfettered by the ideas and ideals I have freely adopted as my own and sourced my energy from in years pasts.  

I realized that one thing that I claim about my personal relationship to this day and to this devastating epidemic was that it truly began the year that I was born.  Although the origins of the HIV virus extend way back over a century (for an amazing story about the origins of HIV, you must check out this recent Radio Lab episode), the epidemic truly began during the years I was learning how to talk and play and explore my little world in St. Cloud.  The epidemic peaked (here in 2000) when I was a freshman in high school and just beginning to really develop an independent and critical view about the world beyond.  

I remember attending a lecture this summer at the NIH given by Dr Tony Fauci.  Usually datasets and figures of health issues on the global scale are perhaps the most impersonal representation of such a scale great incomprehensible humanity.  However, I remember seeing this one graph that started in 1984 and show a rising swell of color bars into the early 2000s then began to level off a bit.  Sometimes I like to just squint at a graph or at some data just to get a basic gestalt of its trends before I dive into the numbers, doing this here I couldn't help but superimpose my own growth and developmental curve and think, 'huh.'  The parallel was remarkable.  I found it impossible not to extrapolate. 

Patient charts at the Chulaimbo Distric Hospital / AMPATH clinics