Insertional Mutagenesis of Candida auris using Agrobacterium tumefaciens

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Drug resistance is arguably one of the most pressing problems in infectious disease. Resistance can occur naturally, where organisms exhbit natural low-level antibiotic susceptibility or it can occur spontaneously after exposure to antibiotics. Fungi pose special problems to antibiotic development because there are very limited antibiotic choices for treatment. Many promising lead compounds that are toxic to fungi unfortunately are toxic to mamals due to the similar eukaryoctic cellular organization. Consequently antifungal development has always been difficult for fungi. Candida auris is an emerging fungal pathogen that displays a high frequency of natural resistance to first line antifungal treatment, but also has been shown to develop resistance to all know antifugals. The extremely rapid spread of this fungus around the world and high mortality rate (~30-80% depending on country) has amplified known problems in treating systemic mycosis: the lack of antifungal choices for fungal infections. Most of what we know about antifungal drug research is derived from studies of non-pathogenic model fungi, such as Saccharomyces cerevisiae, which are unsuitable as pan-fungal models. To address this issue, we will develop a method that rapidly interrogates the C. auris genome to reveal genes that are potential antifungal targets by virtue of their function being essential to cell survival. The major objective of this study will be to develop a way to rapidly and inexpensively identify these targets. To accomplish this goal we will develop an insertional mutagenesis system based on the bacterial pathogen, Agrobacterium tumefaciens for C. auris. The first aim will be to improve the existing Agrobacterium tumefaciens transformation efficiency to yield enough transformants to produce a saturated insertional mutagenesis map. We will next develop a capture-probe based enrichment method for recovering insertion site fragments from the predominating non-junctional genomic DNA background. Finally, we will apply deep sequencing to these enriched fragments to identify each insertion site and its neighboring flanking genomic DNA, and ultimately assemble a high density insertion map that will be used to identify genes that are essential for survival, and therefore, potential antifungal targets.