Aflatoxins are secondary metabolites produced by members of the fungal genus Aspergillus. Immunosuppressive and carcinogenic activities of these toxins negatively impact human health especially in developing countries. Severity of contamination is influenced by both fungal community structure and the environment to which the crop is exposed either prior to or after harvest. In 2004, a severe episode of lethal human aflatoxicosis occurred in the Eastern Province of Kenya. Analysis of fungal community structure revealed that this event was caused by a previously unknown fungal lineage closely resembling the S strain morphotype of Aspergillus flavus. Fungal communities associated with maize produced in affected regions of Kenya were invariably dominated by the new fungal lineage and its incidence was strongly correlated with maize aflatoxin content. Analyses of fungal communities of maize grown in adjacent Kenyan provinces showed that incidences of the new lineage are limited outside the Eastern Province where the aflatoxicoses outbreaks occurred. Multi-locus phylogenetic analyses suggest the newly identified Kenyan lineage is closely related to the B and G aflatoxin producing species A. minisclerotigenes, and more distantly related to both the A. flavus S strain and an unnamed taxon with similar morphology endemic in West Africa (strain SBG). Sequence analyses of the cypA aflatoxin biosynthesis gene identified a previously unknown 2.2 kb deletion unique to the Kenyan lineage and coherent with its phylogenetic placement. A polyphasic approach was used to study aflatoxin-producing fungal communities, with emphasis on occurrence of fungi with S strain morphology, in Sub-Saharan Africa. Four phylogenetically distinct groups of fungi with S strain morphology were identified with restrictions to West Africa (strain SBG) or Central and East Africa (A. flavus S strain, A. minisclerotigenes, the new lineage). Aflatoxin production in synthetic media was a poor predictor of aflatoxin production in viable maize grain. An in vitro assay was developed to predict the aflatoxin-producing potential of fungal isolates in maize. This screen was used to identify atoxigenic isolates of A. flavus with potential value for biological control within highly toxic Aspergillus communities associated with maize production in Kenya. These atoxigenic isolates have potential value for mitigating aflatoxin contamination in Kenya.

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