Strain identification in Aspergillus fumigatus

Russell Poulter, Margi Butler

Author address: 

University of Otago, Dunedin, New Zealand


Purpose: Genome sequencing can be employed in species and strain identification. The use of PCR to target specific sequences can make the identification of fungal species or isolates more accurate and rapid. This would be valuable in situations such as the identification and monitoring of strains in a disease outbreak. This approach is, however, difficult in A. fumigatus because this species shows very little sequence variation among strains. Our study uses as a target the PCR and sequencing of specific orthologs of the repetitious Afut1 mobile elements that are present in the A. fumigatus genome. Methods: We used standard end-point PCR and sequencing methods. Afut1 orthologs were selected using the published genome of strain Af293. The Afut1 elements of A. fumigatus show clear evidence of repeat-induced point mutation (RIP). This was noted when Afut1 was first described. Our study is the first attempt to compare an orthologous series of Afut1 elements derived from a group of strains. Orthologous elements are found at a specific site in the genomes of different strains and are related by vertical descent from an element that transposed into that site in the common ancestor of the group of strains. Results: Orthologous Afut1 elements are highly variable in sequence between strains. This indicates that RIP has occurred in diverse strains since this species evolved. Some strains show minimal RIP, while others show high frequency of RIP at a particular ortholog. The sequence data permits strain recognition and the study of the intra-specific phylogeny. Conclusions: The analysis of Afut1 sequences permits strain recognition in A. fumigatus. In other fungi, RIP occurs exclusively during sexual reproduction. The occurrence of RIP in diverse strains of A. fumigatus therefore suggests that there has been sexual reproduction within the species. In addition, sequence data from orthologous sites in multiple strains provides an indication of re-assortment between loci confirming sexual recombination

abstract No: 


Full conference title: 

    • ECFG 9th (2008)