Baylor College of Medicine
Children’s Foundation - Uganda

Improving Health Security and building IHR Core Capacities in the Republic of Uganda (2020-2025)


AMR surveillance

The emergence and spread of drug-resistant pathogens that have acquired resistance to existing antimicrobial agents is a threat to human health and modern medicine and a risk to animal health and food production. Baylor Foundation Uganda supports the Ministry of Health to prevent and control the spread of AMR through strengthening AMR surveillance and ensuring the appropriate use of antimicrobials. This support is delivered through the provision of technical assistance to MOH in the AMR technical working groups, and building the capacity of hospitals to conduct AMR surveillance and implement antibiotic stewardship activities. The achievements included the following:

  • Built the capacity of two regional labs to conduct bacterial culture and susceptibility testing.
  • Conducted AMR diagnostic network capacity assessments at 12 hospitals and developed and implementation of site-specific quality improvement (QI)
  • Standardized AMR detection and reporting procedures and practices by adapting and disseminating technical AMR laboratory standard operating procedures (SOPs) and tools at two regional referral hospitals labs (hub) and 10 general hospitals (spokes).
  • Provided buffer Microbiology/AMR reagents to avert stockout and critical equipment (incubators).

Promoting optimal use of antibiotics:

  • Established Medicines and Therapeutics Committees (MTCs) and developed site-specific QCI plans at 10 hospitals. Operationalized QCI learning collaborative between the 10 hospitals to promote sharing of knowledge and best practice


COVID-19 Vaccination

The Ministry of Health (MoH) started to roll out COVID-19 vaccination in May 2021. Since then, Baylor Foundation Uganda has supported the Ministry of Health (MoH) through the Uganda National Expanded Program on Immunization (UNEPI) to implement routine/targeted COVID-19 vaccination and Accelerated Mass Vaccination Campaigns (AMVC) at the national and subnational level (17 districts and two cities in Bunyoro and Rwenzori regions). Our support includes capacity building for healthcare workers (HCWs) and community mobilizers, microplanning and coordination, supportive supervision and mentorship, vaccine supply chain management, data management, Advocacy, risk communication and community engagement. As of August 2022, 88% (2,625,739) and 61% (1,816,732) of the target population people from Rwenzori and Hoima regions had received the first dose and were fully vaccinated for COVID-19 respectively.

  • Micro-planning: Supported 17 districts and two cities in Bunyoro and Rwenzori regions to develop, implement and monitor COVID-19 vaccination micro-plans for 3 AMVCs; supported coordination of the campaigns.
  • Capacity building: Trained 7296 vaccinators (HCWs) and 18,573 mobilizers in Bunyoro and Rwenzori.
  • Advocacy, Risk Communication and Community Engagement: Supported the MoH to develop communication messages and materials; printed and distributed over 700, 000 COVID-19 IEC materials; Engaged over 200 political, religious and cultural leaders to advocate for COVID-19 vaccination; Conducted x radio shows and aired x spot messages.
  • Supply Chain Management: We supported stock reporting and monitoring, and last-mile delivery vaccines including re-distribution to ensure sufficient stocks and avert vaccine expiries. 1,105,743 COVID-19 vaccine doses were delivered to healthcare facilities. Improved COVID-19 vaccination reporting from 17.5% to 95% in 3 months.
  • Service delivery: Supported COVID-19 vaccination at 383 static sites, 99 community outreach vaccination sites, and 1525 AMVC sites.
  • Data management: Supported COVID-19 backlog data entry and reduced backlog from x % to x% in 3 months, and roll out of SMART paper technology for real vaccine data capture in 17 districts and 2 cities.
  • Monitoring of adverse events following immunization (AEFI): Established pharmacovigilance sub-committees in 10 hospitals supporting, supporting the detection, reporting and follow-up of AEFI.

Yellow Fever Preventive Mass Vaccination Campaign (YFPMVC): The Ministry of Health/UNEPI with support from GAVI transferred YFPMVC funds to Baylor-Uganda to provide technical and financial support to local governments. The campaign targeted populations aged 9 months – 60 years in Bunyoro and Rwenzori regions.

Life course vaccination


Lab systems strengthening

Since 2007, Baylor Foundation Uganda, with funding from CDC and USAID, has been supporting the Ministry of Health to build a laboratory network with the capacity to provide diagnostic and surveillance services. Baylor Foundation Uganda uses the Strengthening Laboratory Management Towards Accreditation (SLMTA) approach to train labs to implement the Laboratory Quality Management System (LQMS) and attain international accreditation status. Baylor Foundation Uganda also supports laboratory infrastructure refurbishment and equipment procurement, laboratory equipment management through subgrants to two regional laboratory equipment workshops, supply chain management, biosafety and biosecurity, and a robust specimen referral and transportation system. The laboratory capacity-building program is implemented through training, mentorships and quality assurance in collaboration with Uganda MOH’s National Health Laboratory System (UNHLS). Through this capacity, the laboratory network is able to deliver quality results to inform clinical decisions, early detection and response to disease outbreaks.

  • Public health laboratory leadership, coordination and communication: Supported 32 districts in Rwenzori, Bunyoro and Mbale regions to implement district-specific laboratory network plans and district-led diagnostic network improvements.
  • LQMS: Trained 1,394 Laboratory staff in LQMS and supported 15/21 lab hubs to attain and sustain international/ISO 15189 accreditation by the South African National Accreditation System. Additionally, one regional laboratory attained microbiology diagnostics accreditation and the Center of Excellence Laboratory at Baylor Foundation Uganda in Kampala attained and sustained the College of American Pathologists (CAP)
  • Laboratory infrastructure improvements: Upgraded/refurbished 25 laboratories in 21 districts to optimize testing workflow and enhance biosafety and biosecurity.
  • Capacity for the detection of priority diseases: Trained and mentored 2,231 Health care workers from 55 health facilities in 17 districts and 3 cities on COVID-19 RDT use, reporting using electronic laboratory investigation forms, supply chain management, and quality assurance. We further rolled out point of care EID/Viral load and Xpert/MTB Rif testing at 32 health facilities in 21 districts.
  • Biosafety and biosecurity: Trained and mentored 394 laboratory personnel in biosafety and biosecurity, creating a pool of personnel to support the implementation of comprehensive and sustainable biosafety and biosecurity procedures and practices at the health facility level.
  • Laboratory supply chain management: Trained and mentored 428 laboratory personnel in logistics management to support the purchase and management of diagnostic commodities. We are providing buffer microbiology laboratory reagents for two regional laboratories as a stop-gap measure.
  • Specimen referral and transport system: Established mechanisms to ensure that specimens from over 300 health facilities (i.e. >90% of health facilities) are transported to 20 hub laboratories and two national reference laboratories.


Baylor Uganda works in collaboration with the Ministry of Health and other partners to strengthen surveillance systems that are able to detect events of public health significance early to facilitate a timely response. We support surveillance by providing both financial and technical resources for the development and review of national guidelines, support both national and subnational training in surveillance, and second technical staff to both the National Emergency Operation Centre (EOC) and the Department of Integrated Epidemiology, Surveillance and Public Health Emergencies (IES&PHEs) of Ministry of Health. This support is aligned to the IHR core capacity requirements for surveillance including; ensuring a functional surveillance system to identify potential events of concern for public health and health security is in place; the surveillance system is supported by electronic tools, and supporting systematic analysis of surveillance data for action.

Integrated Disease Surveillance and Response

Since 2020, together with other stakeholders, we have provided technical assistance to the MoH to strengthen surveillance systems. We supported the development of the National Integrated Epidemiology Surveillance and Response Strategic Plan 2021-2025, adaptation and rollout of the 3rd edition Integrated Disease Surveillance and Response (IDSR) Strategy, a framework for implementing indicator and event-based surveillance.

Event-based surveillance

Baylor Foundation Uganda is supporting MoH in the implementation of electronic tools in surveillance in the following ways:

  • At the national level, consultants seconded to the Division of Health Information at MoH have provided technical assistance in the development of a Centralised Surveillance Data Warehouse, which is increasing access to available data for analysis, visualisation and use to inform epidemic intelligence;
  • Provided capacity building in the implementation of electronic tools for surveillance, including DHIS2, electronic laboratory information system, electronic IDSR and GoData; and
  • Supported MoH in development of an event management system.

Sentinel surveillance

Baylor Foundation Uganda is championing the routine analysis and utilization of data for action including monitoring, evaluating, and improving policies, programs, and services and facilitating the better allocation of resources.

  • At the national level, the epidemiologists seconded to the IES&PHEs produce weekly epidemiological reports; the National EOC also produces dashboards and disseminates situation reports of events and ongoing outbreaks.
  • The national and regional EOCs produce analyses and disseminate epidemiologic interpretations of all major events at all levels.
  • Through the routine analysis of surveillance data at both national and regional levels, the epidemiologists were able to identify bottlenecks to both timeliness and completeness of reporting in Rwenzori, Bunyoro, and Kampala Capital City Authority. The implementation of targeted mentorships has since improved completeness in the three regions to the national target of 80%.


  • Supported 3rd edition IDSR adaptation and development of the Integrated Epidemiology, Surveillance and Response Strategic Plan 2021 – 2025.
  • Provided technical support in IDSR rollout of in 48/148 districts in 6 Regions (Karamoja, Lango, North Central, West Nile, Rwenzori and Bunyoro) of the country.
  • Provided direct support to IDSR rollout in 17 districts and 2 cities in Rwenzori and Bunyoro Regions where 100 IDSR district-based mentors/trainers; 184 health facilities and 600 health workers have been trained.
  • Provided technical assistance to MoH in the development of protocols for Acute Febrile Illnesses (AFI) and Severe Acute Respiratory Illness (SARI) Influenza Like Illness (ILI) surveillance, including COVID-19 genomic sequencing and Pan Respiratory Disease Surveillance (PRDS). AFI implementation has begun in Jinja Regional Referral Hospital, while SARI/ILI/COVID19/PRDS protocol is currently under review and approval.
  • Developed one health event-based surveillance technical documents (one health priority list, signal list, Event-Based Surveillance (EBS) manual and M&E plan), which are under approval by MoH.
  • Developed of one-health EBS training curriculum for national, district, sub-county, facility and community level, under approval by MoH.
  • Supported national one health EBS training of trainers, where 56 national trainers were trained.
  • Spearheaded development and piloting of the Regional EOC-led one health EBS implementation in Kabarole District and Fort portal City in Rwenzori Region, where:
    1. 22 district based one-health trainers/mentors have been trained in Fort Portal and Kabarole;
    2. 138 sub-county one-health EBS supervisors were trained in Fort Portal and Kabarole;
    3. Surveillance focal persons and Incharges from 26 facilities in Fort Port Portal and 36 in Kabarole were trained in Fort Portal and Kabarole; and
    4. 800 VHTs in Fort Portal and Kabarole were trained.


  • STAR

With CDC funding, Baylor Uganda supported the set up the Fort portal Regional Emergency Operation Centre (REOC) located and managed by the regional referral hospital. The REOC is now able to respond to future public health emergencies in the Rwenzori region. In the photograph is the Minister of State for Health with the Director General of Health Services, the CDC Country Global Health Security Director, Director Regional Referral Hospital, representatives of the president in the districts/city and the Executive Director of Baylor-Uganda at the official launch of the REOC.

Outbreak response

Early warning alert and response: Baylor-Uganda successfully integrated EMS into the alert management system to support preparedness and response measures.

Viral Hemorrhagic Fevers

EVD response: Baylor-Uganda seconded 12 health workers to the Ebola Treatment Units to support clinical management, trauma counseling and nutritional support to infants below 2 years of age who were separated from their mothers. Baylor-Uganda also provided technical, financial, and logistical support to the incident management team and nine response pillars by seconding 29 additional surge staff.

Yellow Fever

Rift Valley Fever




  • IPC
  • RCCE



Area of Operations

The project currently operates at the national level, in the Rwenzori (9 districts, one city) and Bunyoro (8 districts, 1 city) regions, and other regions as the need arises, especially for emergency response work.

Project Objectives

  • Improve the prevention of avoidable epidemics;
  • Improve the ability to detect threats early; and
  • Strengthen the capacity to respond rapidly and effectively to public health threats of national and international concern.