Where the Spores at? Insights into the Residential Indoor Mycobiome of South Africa

Indoor air quality (IAQ) has garnered increasing global attention due to its potential impact on human health, and fungi play a crucial role in contributing to indoor air contamination. Chapter 1 of this thesis reviewed international research on the health implications of fungal proliferation in indoor air, accepted detection and monitoring strategies, and the composition of indoor fungal communities globally and in South Africa. However, IAQ assessment protocols and permissible fungal load thresholds remain heterogeneous, with a variety of sampling, detection, enumeration and predication methods and a lack of dose/response metrics to aid in abundance thresholds. Moreover, the review highlighted a dearth of data from South Africa, where literature indicates that latitude, climatic conditions and other factors likely shape indoor mycobiomes unlike western fungal communities. To address the lack of regional data, Chapter 2 addressed this gap through a ten-year (2014-2024) evaluation of airborne fungi in n = 192 residences in two South African provinces with distinct climatic conditions (Western Cape [WC; winter rainfall] and Gauteng [GP; summer rainfall]). Air samples were collected by impaction and identified to genus level by morphological characteristics. It was found that, in accordance with international findings, fungal abundances remained stable interannually. Additionally, Cladosporium dominated fungal communities in both WC and GP (40-60%), particularly in autumn. Penicillium was the second most abundant genus, surpassing Alternaria, a reversal of trends reported in Europe and North America. Yeasts constituted 12-19% of total counts, peaking in WC during winter, likely due to the increased rainfall. Some genera made up a minor portion of the community (Epicoccum and Fusarium) but did show seasonality despite low abundances. Chapter 2 emphasised that the seasonality and community composition in South African indoor mycobiomes are distinct from international studies, reinforcing the need for region-specific IAQ reference values. The culture-based nature of this study likely underrepresents and misses certain genera and underscores the benefit of including culture-independent molecular approaches. Building on these findings, Chapter 3 aimed to develop a pilot quantitative polymerase chain reaction (qPCR) panel based on the Environmental Relative Mouldiness Index (ERMI), tailored to South African indoor fungi. Ten target species (Penicillium brevicompactum, Aspergillus tubingensis, Aspergillus fumigatus, Cladosporium sphaerospermum, Alternaria alternata, Stachybotrys chlorohalonata, Mucor plumbeus, Candida parapsilosis, Pichia kudriavzevii, and Rhodotorula mucilaginosa) were selected based on local abundance and potential pathogenicity and allergenicity. The indoor air of twelve residences was sampled by impaction, impingement, visible mould swabs and general room swabs. Based on Cochrans’ Q and Wald Χ2 tests, swab-based sampling achieved the highest detection (86-100%) and quantification rates, particularly C. sphaerospermum, P. brevicompactum, and C. parapsilosis, whereas impingement underperformed in detection (14-57%). Both culture-based and qPCR data indicated that the sampling biases are method-specific, where impaction favoured viable fast-growing fungi, while impingement missed hydrophobic taxa. Chapter 3 concludes that combining swab-based molecular detection for sensitive quantification with impaction, for snapshot information may be favourable and highlights the benefit of a tiered approach for indoor air sampling. This study provided an understanding of South African indoor mycobiomes and tested the first use of an ERMI qPCR panel in South Africa. The results of this thesis provide a starting point for further refining molecular detection in South African mycological IAQ, through expanding the qPCR panel to include more region-specific fungal species and complementing culture-dependent research with long-read amplicon sequencing. With further information about indoor mycology and its impact on human health, precise risk assessment modelling could be developed.

Grantor dc:publisher

Stellenbosch : Stellenbosch University

Year dc:date.issued

2026

Author dc:creator

• Van der Want, Saskia Noelle

Advisor dc:contributor.advisor

• Jacobs, Karin

Language dc:language.iso

en

Repository record dc:identifier.uri

https://scholar.sun.ac.za/handle/10019.1/135672

OAI identifier oai:identifier

oai:scholar.sun.ac.za:10019.1/135672