Although A. fumigatus strains are generally susceptible to azoles, recently, acquired resistance to a number of antifungal compounds has been reported, especially to triazoles possibly due to widespread clinical use of triazoles or through exposure to azole fungicides in the environment. The significant clinical problem of azole resistance has led to study the antifungal resistance mechanisms for developing effective therapeutic strategies. Of 230 clinical A. fumigatus isolates submitted during 2008 and 2009 to the Mycology Reference Centre Manchester, UK (MRCM), 64 (28%) were azole resistant and 14% and 20% of patients had resistant isolates, respectively. Among the resistant isolates, 62 of 64 (97%) were itraconazole resistant, 2 of 64 (3%) were only voriconazole resistant and 78% were multi-azole resistant. The gene encoding 14-α sterol demethylase (cyp51A) was analyzed in 63 itraconazole resistant (ITR-R) and 16 ITR-susceptible clinical and environmental isolates of A. fumigatus respectively. Amino acid substitutions in the cyp51A, the commonest known mechanism of azole resistance in A. fumigatus, were found in some ITR-R isolates. Fifteen different amino acid substitutions were found in the cyp51A three of which, A284T, M220R and M220W, have not been previously reported. In addition, several mutations were found in the cyp51A gene in one of the A. fumigatus environmental isolates. Importantly, a remarkably increased frequency of azole-resistant isolates without cyp51A mutations was observed in 43% of isolates and 54% of patients. Other mechanisms of resistance must be responsible for resistance. In order to assess the contribution of transporters and other genes to resistance, particular resistant isolates that did not carry a cyp51A mutation were studied. The relative expression of three novel transporter genes; ABC11, MFS56 and M85 as well as cyp51A, cyp51B, AfuMDR1, AfuMDR2 AfuMDR3, AfuMDR4 and atrF were assessed using real-time RT-PCR in both azole susceptible and resistant isolates, without cyp51A mutations. Interestingly, deletion of ABC11, MFS56 and M85 from a wild-type strain increased A. fumigatus susceptibility to azoles and these genes showed changes in expression levels in many ITR-R isolates. Most ITR-R isolates without cyp51A mutations showed either constitutive high-level expression of the three novel genes or induction of expression upon exposure to itraconazole. One isolate highly over-expressed cyp51B, a novel finding. Our results are most consistent with over-expression of one or more of these genes in ITR-R A. fumigatus without cyp51A mutations being at least partially responsible for ITR resistance. Multiple concurrent possible resistance mechanisms were found in some isolates. My work probably explains the mechanism(s) of resistance in A. fumigatus isolates with cyp51A mutations. Other ITR resistance mechanisms are also possible. To determine taxonomic relationships among A. fumigatus clinical and environmental isolates, the sequences of the ITS, β-tubulin, actin and calmodulin gene of 23 clinical and 16 environmental isolates were analyzed phylogenetically. Actin and calmodulin sequences proved to be good for species differentiation of A. fumigatus while both ITS, β-tubulin regions did not, in this dataset. Many cryptic species of A. fumigates (complex) were found. All environmental A. fumigates complex isolates were ITR susceptible and no cross resistance was found.

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