Use of multiple methods for genotyping Fusarium during an outbreak of contact lens associated fungal keratitis in Singapore

We assessed the genetic diversity of the isolates using AFLP, Rep-PCR, and ERIC-PCR and compared the usefulness of these typing schemes to characterize the isolates.AFLP was the most discriminative typing scheme and appears to group FSSC from eye infections and from other infections differently.There was a high genomic heterogeneity among the isolates confirming that this was not a point source outbreak.Fusarium spp. are filamentous fungi commonly isolated from environmental sources such as soil, plant roots, plant debris and water systems [1,2]. They may cause invasive infections predominantly in immunocompromised persons [2]. Fusarium species can also cause ocular infections, usually keratitis or endophtalmitis, in immunocompetent persons usually associated with trauma [3-6]. Several morphologically similar species are grouped together in the Fusariun solani species complex (FSSC), but further genotypic characterization of species within this complex is laborious and is usually not done routinely in clinical laboratories. Members of this species complex are usually reported in the literature as Fusarim solani [7]. Nucleic acid based methods are often used in laboratories to identify Fusarium spp. [8-10].Several different methods have been used for molecular typing of fungal isolates associated with outbreaks. Godoy et. al. showed that an enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) and PCR restriction fragment length polymorphism (PCR-RFLP) were useful for genotyping Fusarium isolates [5]. Other methods that have been used include REP-PCR [11], amplified fragment length polymorphism (AFLP) [12,13], and multilocus sequence typing (MLST) [3,14]. Recently, microsphere array-based genotyping was also described [7].In Singapore, there was an outbreak of fungal keratitis caused by members of the FSSC from March 2005 to May 2006 involving 66 patients. Epidemiological investigations in Singapore and the U.S. indicated that improper contact lens wear and