1. Incidence or Prevalence, per 100,000 Burden, no. of cases per year*
Estimated Burden of Fungal Disease in South Africa
Ilan S. Schwartz1, Tom H. Boyles2, David W. Denning3
1University of Alberta, Canada 2University of Witwatersrand, South Africa 3University of Manchester, UK with
BACKGROUND
RESULTS
Table 2. Estimated rates and burdens of serious fungal infections in South Africa
South Africa is home to at least 200,000 fungal species (Crous et al, 2006), reflecting distinct climatic and ecological features found at the southern tip of Africa.
Some of these fungi cause disease in humans, and these can be expected to flourish in a country reeling from the intertwined epidemics of HIV, tuberculosis, and poverty.
Given these distinctive features of the population and ecology in South Africa, we set out to estimate the prevalence and incidence of serious fungal infections in this country.
Mycosis
Incidence or Prevalence, per 100,000
Burden, no. of cases per year*
Cryptococcal meningitis
14.8
8,357
Pneumocystis pneumonia
7.9
4,452
Invasive aspergillosis
11.8
2,645
Chronic pulmonary aspergillosis
175.8
99,351
Allergic bronchopulmonary aspergillosis
107.2
60,591
Severe asthma with fungal sensitisation
141.5
79,980
Candidaemia
14.6
8,257
Peritoneal candidiasis
5.3
2,984
Oral candidiasis
2,036
1,150,560
Oesophageal candidiasis
1,103
623,598
Recurrent vulvovaginal candidiasis
3,547
1,002,499
Tinea capitis
1,775
1,003,490
Emergomycosis
0.2
100
Histoplasmosis
0.1 60
Sporotrichosis
0.07 40
Blastomycosis
0.02 10
Mucormycosis
113
Chromoblastomycosis
Eumycetoma
Total
4,047,138
*Burden represents new cases per year except for the following chronic conditions, for which this means total number of cases: allergic bronchopulmonary aspergillosis, chronic pulmonary aspergillosis, severe asthma with fungal sensitisation, recurrent vulvovaginal candidiasis, tinea capitis.
METHODS / ASSUMPTIONS
Table 1. Assumptions on which estimates are predicated
Mycosis
Assumptions
Cryptococcosis
Surveillance data, plus 20%
Pneumocystis pneumonia
Adults: 5% of hospitalizations among PLWH with CD4 <100 cells/µL, 10% of whom were assumed to be hospitalized each year.
Children: 21% of childhood pneumonia deaths and assuming that 40% childhood PCP cases were fatal.
Invasive aspergillosis
10% of cases of AML/yr and as many in all other hematologic malignancies;
0.5% of kidney SOT, 4% of lung SOT, 6% of heart SOT, 4% of liver SOT, and 2.6% of cases of lung cancer; 0.5% of patients dying of AIDS, and 1.3% of the worst 10% of COPD patients.
Chronic pulmonary aspergillosis
22% of pulmonary TB cases with cavitation (assumed to comprise 12% of pulmonary TB) and 2% of pulmonary TB cases without cavitation; Pulmonary TB assumed to underlie 80% of cases of chronic pulmonary aspergillosis
Allergic bronchopulmonary aspergillosis
Affects 2.5% of asthmatic adults
Severe asthma with fungal sensitisation
30% of the most severe decile of asthmatic adults
Candidaemia
Rate in adults same in all occupied ICU beds (assuming 90% capacity) across country and based on incidence reported at Chris Hani-Baragwanath Hospital. Ratio of 7:3 ICU to non-ICU cases.
Peritoneal candidiasis
Post-surgical candida peritonitis is half as common as ICU-related candidemia; 1449 PD patients, each experiencing 1.7 episodes of peritonitis per year and 3.8% of these are fungal
Oral candidiasis
38% of PLWH not on ART and 14% taking ART
Oesophageal candidiasis
20% of PLWH not on ART and 5% taking ART
Recurrent vulvovaginal candidiasis
6% of women 15 – 54 years of age
Tinea capitis
6% of children under 15 years of age
Endemic mycoses, mucormycosis, chromoblastomycosis, eumycetoma
Based on literature review
Abbreviations: AML acute myelogenous leukemia, ART antiretroviral therapy, ICU intensive care unit, PD peritoneal dialysis, PLWH persons living with HIV, SOT solid organ transplantation, TB tuberculosis
Over 4 million South Africans are estimated to have a serious fungal disease each year (7.16% of the population).
Estimates show a significant diagnostic gap, notably in PCP in which only 55% of cases were confirmed by microscopy in one S. African study (Chiliza et al, 2018).
In candidaemia, a high proportion of isolates are C. parapsilosis, suggestive of poor infection control measures. The rate of 14.6/100,000 is similar to Brazil and slightly lower than Pakistan. Candida auris is now a problem in South Africa (Govender et al, 2018).
The proportion of patients affected by chronic pulmonary aspergillosis is probably the largest in the world at 175.8/100,000, thanks in part to the high TB rate, and needs validation. The key laboratory diagnostic test (Aspergillus IgG antibody) is not available in South Africa.
CONCLUSION
Fungal infections cause a high burden of disease in South Africa, driven primarily by HIV, TB, and poverty.
Empirical data is generally lacking, with the notable exception of cryptococcosis. National surveillance data is anticipated for candidemia.
Our findings emphasize the importance of improving strategies for the prevention, diagnosis and management of these diseases.