USAMRU-K HIV Program Briefing

Clinical Microbiology Laboratory
Capacity Building in Kenya
CPT Brett E Swierczewski, PhD
Director, Microbiology Hub Kericho
US Army Medical Research Unit – Kenya
(USAMRU-K)

Disclaimer: The views expressed in this
presentation are those of the author and not
necessarily of those of the US Army
or the DoD.

Outline
• USAMRU – K and Kericho Field Station Overview
• Microbiology Hub Kericho (MHK)
– Overview
– Current studies
– Laboratory capabilities
• Local microbiology capacity building
– Challenges
– Interventions
• Future outlook

USAMRU-K Overview
• Established in 1972
• Overseas laboratory
– WRAIR
• Partnership: KEMRI
• Three Sites
– Nairobi: HQ, viral
hemorraghic fever labs
– Kisumu: Malaria and
entomology
– Kericho: HIV and enterics

Kericho Field Station Overview
• Clinical Research Center
• Primary mission
– HIV operational and
interventional research
– Diagnostics,therapeutics,
and evaluation of vaccine
candidates
– Co-infections: TB
• PEPFAR Program
• Staff
– 200 Kenyan
– 3 US Personnel
• 2009: Microbiology Hub
Kericho operational

• Personnel
Microbiology Hub Kericho
– 1 Army microbiologist
– 7 Lab technologists
• Sections: CRC, Enterics

Why does the US Army Study Diarrhea?
• Disease non-battle injury
• Operations in Middle East and Africa
– Desert Storm/Shield: 57%
– Somalia: 20%
• AFRICOM
– Deployment of US personnel likely to increase
• Future enterics vaccine development

Current MHK Diagnostic
Capabilities: Enterics
• Enteric bacteria identification and antibiotic
susceptibility
– Conventional methodologies, conventional PCR
– Microscan (automated AST)
• Microscopy for parasites (helminths and protozoans)
– Phase contrast and immunofluorescence
• Rotavirus and norovirus identification
– Real time PCR
• Enrolled in external Quality assurance/Quality control
(QA/QC) proficiency panels

Microbiology Hub Kericho

MHK Current Studies: Enterics
• Surveillance of enteric pathogens of
Kenya
– 5 yr Case-Control study: Acute diarrhea
– District hospitals in western and central Kenya
– Central hospitals and clinics from Kenyan tea
plantations
• 11total surveillance sites
• Demographic information
• Age, water source, rural/urban living area

• Bacteria
Enteric Pathogens Captured
– Shigella spp, Campylobacter spp, Salmonella spp, ETEC,
EAEC, Vibrio cholerae (outbreaks)
– Multidrug resistant
• Parasites
– Giardia lamblia, Entamoeba histolytica/dispar,
Cryptosporidium parvum, Schistosoma mansoni, Ascaris
lumbricoides, Strongyloides stercoralis, hookworm,
Entamoeba spp
• Viruses
– Rotaviruses and noroviruses

Surveillance Site Activation
• Meeting with site staff
– Protocol and ethics training
– Assess laboratory’s capabilities/limitations
• Meeting medical superintendent
• First step: Building local laboratory
capacity
• “What can we do to improve the lab?”

“Dr Brett, can you please help us get
running water in our lab?” (17 May 2011)

Capabilities
Enterics Microbiology Assessment:
Surveillance Sites Laboratories
• Essential media and
stains
– MacConkey, Blood agar
– Gram and trichrome stains
• Equipment
– Autoclave, incubator,
microscope, refrigerator
• Subject matter experts
– Enteric pathogens are
highly endemic
• Biochemical tests
Limitations
• Variable range of
equipment
– e.g. Microscopes
• Lack of some media and
reagents
• Variable staffing levels
• Antibiotic susceptibility
• Biochemical tests
• Sterility, EQA
• Medical maintenance

Microbiology Laboratories (1)

Microbiology Laboratories (2)

Microbiology Laboratories (3)

Microbiology Laboratories (4)

Equipment
• Microscope
• Bunsen burner
• Safety cabinet
• pH meter
• Balance
• Incubator
• Autoclave
“Could you help us get these
reagents and equipment?”
Supplies
• Stool cups
• Media:
– XLD, Sheep blood
• Biochemical tests
– Indole
– Oxidase
– TSI
• Gloves, petri dishes
• Drugs for treatment

• Equipment
MHK Interventions: Laboratory
2 nd Step
– Donated equipment: Microscopes, autoclave, incubator
• Reagents
– About to expire media, API strips, and biochemical
reagents
• Monthly results reports
– Common enteric pathogens at site
– Gear media and reagents to those that are most common
• Outbreaks: Supplies, collection materials, and testing
– Cholera, typhoid fever

New Equipment

• QA/QC
MHK Interventions:
MHK to Laboratory Partnerships
– Positive controls for media preparation
– Temperature monitoring of equipment
– Backup power sources
• External quality control
– Exchange of bacterial isolates between labs
– Permanent stains of protozoans
• Training
– Laboratory staff rotations in the MHK
– Learn new techniques, QA/QC (College of American
Pathologists)

• Infrastructure issues
– Water
Short term outlook
– Renovations of clinic
reception/sample
collection rooms
• Equipment
– Microscopes
– Incubators
– Autoclaves
• QA/QC

Long term outlook
Final Step
• Kericho Field Station: CRC PEPFAR
– 15 laboratory sites: HIV diagnosis
– Viral loads, CD4 counts, Hepatitis B and C
– Follow this example for local micro labs
• Continued MHK integration/collaboration
– Kenyan Ministry of Health
– Studies expand: Sites expand
– Civil Affairs units (AFRICOM)
• MEDCAPs

USAMRU-K
COL Thomas Logan
Dr Douglas Shaffer
Dr Fred Sawe
MHK Staff
Elizabeth Odundo
AFRIMS
COL Robert Bowden
COL Carl Mason
Acknowledgements
WRAIR
Dr Edwin Oaks
MAJ Max Wu
Kenya
CDC- Kisumu Enterics Lab
Kenyan Staff at Sites

Asante Sana