Genetic diversity and reproductive modes of aflatoxin-producing Aspergillus flavus isolated from cashew nuts in coastal Kenya

Pauline Wambui Gachanja, Manase Aloo Onyango, Eugene Mwanza Muzami, Kyalo Katua, Colletah Rhoda Musangi, Dennis Wamalabe Mukhebi, Bicko Steve Juma, Cecilia Mbithe Mweu, Virginia Gathoni Gichuru, Wilton Mwema Mbinda

World J Microbiol Biotechnol.; 2025 Oct 13; 41(10):379. doi: 10.1007/s11274-025-04612-3.

Abstract

Cashew (Anacardium occidentale L.) is a major cash crop in the coastal region of Kenya, as a source of livelihood for small-scale farmers in Kilifi, Kwale and Lamu counties. Despite being an important food crop, cashew nuts are highly susceptible to aflatoxin-producing Aspergillus flavus, primarily due to their nutritional profile and poor pre-harvest and post-harvest practices. The presence of aflatoxins poses significant health risks to consumers of cashew nuts due to the carcinogenic, genotoxic, and hepatotoxic nature of these toxins. The detection of aflatoxin-producing Aspergillus flavus in cashew nuts from coastal Kenya demonstrates the necessity for comprehensive research aimed at mitigating the risk of aflatoxicosis outbreaks, which continue to pose a major public health challenge in the country. In this study, we report for the first time the genetic diversity and modes of reproduction of aflatoxigenic A. flavus using genome-wide single-nucleotide polymorphism (SNP) markers. 33,752 bi-allelic SNPs obtained from 17 A. flavus isolates from Kilifi, Kwale and Lamu counties were used. Our analyses revealed a lack of differentiation and low genetic diversity among A. flavus populations from cashew nuts in the coastal region. Both heterothallic and homothallic A. flavus isolates were observed, with heterothallic and MAT1-2 genes being more predominant. Clonal reproduction was evidenced by the unequal distribution of mating type genes and the observed low genetic diversity. Further analysis of the extent of recombination and linkage disequilibrium (LD) found A. flavus population to be sexually recombining, although we hesitate to interpret these results due to the small sample sizes. Our phylogenetic analyses indicated that our populations are likely to produce low levels of aflatoxins. Overall, these findings provide valuable insights into the population genetics of A. flavus, which can inform future research and strategies to mitigate aflatoxin contamination in cashew nuts, ensuring consumer safety and safeguarding the source of income for the people of the coastal region of Kenya.