Diagnostic capacity for invasive fungal infections in advanced HIV disease in Africa: a continent-wide survey

Lakoh S, Kamudumuli PS, Penney ROS, et al

21 December 2022

Access via The Lancet Infectious Diseases

Publication summary

The African continent is home to approximately 67% of the world’s people who are living with HIV, and recent analyses have found that global funding and investments in HIV care across Africa have had an inadequate effect on preventing AIDS-related mortality. Among people living with advanced HIV disease, opportunistic fungal infections—notably, cryptococcal meningitis, histoplasmosis, and Pneumocystis pneumonia—are a leading cause of morbidity and death. 

This first-ever study of diagnostic capacity for invasive fungal infections in people living with HIV across Africa assesses the availability of CD4 cell counts, cryptococcal antigen testing, lumbar puncture, India ink microscopy, histoplasmosis urinary antigen testing, Pneumocystis microscopy or polymerase chain reaction (PCR) testing, fungal culture, and magnetic resonance imaging (MRI) in public and private healthcare facilities in 48 African countries from October 2020 to October 2022. 

The authors included countries that had a population of more than 1 million people, and the study methods involved questionnaires, video conference calls, data validation from public and private sources and country Ministry of Health officials, and five regional webinars with the Africa Centres for Disease Control and Prevention.

Who this is for

  • Ministry of Health officials and policymakers across Africa
  • Diagnostic developers and companies
  • Global, regional, and national HIV funding and care organizations

Key findings

Availability of CD4 cell counts. CD4 cell counts, which can help to identify people living with advanced HIV disease who have a higher risk of fungal infection, were available in public facilities in 29 countries. In 14 countries, access to CD4 cell counts were limited to new patients, patients who were receiving antiretroviral treatment, or people who were ill and/or hospitalized. CD4 cell counts were rarely or never done in Burundi, Cameroon, Mozambique, South Sudan, and Sudan, where approximately 2.9 million people are living with HIV.

Availability of Cryptococcus diagnostics

  • Cryptococcal antigen testing. Cryptococcal antigen testing was regularly available in public healthcare facilities across 14 countries and occasionally publicly available in 9 countries. In private healthcare settings, testing was available regularly in Cameroon and Mozambique, and occasionally in Angola and the autonomous state of Puntland in Somalia. In 22 countries, representing a population of about 613 million people, cryptococcal antigen testing was not available.
  • Lumbar puncture. Lumbar puncture, a mainstay of fungal meningitis diagnosis, was available in 35 countries. The procedure was offered regularly or occasionally in community settings in Algeria, Burkina Faso, Chad, The Gambia, Niger, and Togo. In 16 countries and the state of Somaliland, only teaching hospitals performed lumbar puncture. The procedure was not available in Guinea-Bissau, Libya, and Somalia (excluding the autonomous states of Puntland and Somaliland), and was rarely performed in Egypt, Equatorial Guinea, Gabon, the state of Somaliland, and Sudan.
  • India ink microscopy. India ink preparation of cerebrospinal fluid is another method for diagnosing cryptococcal meningitis, and the procedure was available regularly in 23 countries and occasionally in 13 countries. Countries that performed neither cryptococcal antigen testing nor India ink microscopy included Equatorial Guinea, Guinea-Bissau, and Somalia (excluding the state of Puntland).

Availability of histoplasmosis diagnostics. Histoplasmosis urine antigen testing was not regularly available in public healthcare facilities in any of the countries surveyed, though it was occasionally available publicly in Burundi, Mozambique, Niger, and the state of Somaliland. Rare availability in public facilities was documented in Angola, Egypt, Kenya, South Africa, Tanzania, and Tunisia. The test was regularly available in private settings in Eswatini, Kenya, Mozambique, the state of Somaliland, and South Africa and occasionally privately available in Burundi and Niger. Neither public nor private facilities offered histoplasmosis urine antigen testing in Botswana, Egypt, Guinea, Guinea-Bissau, Liberia, and Zimbabwe. Given sporadic availability across the continent, the authors estimate that more than 1 billion people living across 40 African countries do not have access to histoplasmosis urine antigen testing.

Availability of Pneumocystis diagnostics. Microscopy on respiratory secretions or PCR testing are typical methods for diagnosing Pneumocysistis jirovecii pneumonia, and one or both of the procedures was offered regularly in public healthcare settings in Burundi, Madagascar, and South Africa. Testing was occasionally available publicly in Côte d’Ivoire, Eswatini, Morocco, and Tunisia. Regular testing was available in private healthcare settings in Kenya and South Africa.

Availability of fungal culture. Most countries (41) had some capacity for fungal culture. Fungal culture was performed regularly in public facilities in 22 countries and in private facilities in 13 countries. Angola and Kenya only offered fungal culture in private healthcare settings. Eight countries (Equatorial Guinea, Guinea, Liberia, Libya, Sierra Leone, Somalia, South Sudan, and Zambia) were not able to perform fungal culture in the public or private healthcare sector.

Availability of MRI. MRI was regularly accessible to people in 15 countries, though it was not available in public healthcare settings in Burkina Faso, Central African Republic, Democratic Republic of the Congo, Equatorial Guinea, Eswatini, Guinea-Bissau, Libya, Namibia, Sierra Leone, Somalia, South Sudan, and Zimbabwe. Neither public nor private facilities offered MRI in Central African Republic, Guinea-Bissau, and South Sudan.

Recommendations. The authors recommend that, given the disappointing effects of global HIV/AIDS funding on AIDS-related mortality across Africa, national and continent-wide governance should seek to apply funding and resources in ways that better prevent and manage opportunistic infections and the progression of advanced HIV disease that places people at higher risk of infection. Gaps in fungal diagnostic capacity across Africa, especially in the public healthcare sphere, may also inadvertently create conditions that foster a lack of awareness and suspicion for opportunistic fungal infections in people living with HIV, thus prolonging time to appropriate treatment.


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