Multi-Locus Sequence Typing Environmental Fungal Samples from Western Kenya

Sponsor: Burroughs Wellcome Fund

Location(s): Kenya


Among HIV infected individuals, opportunistic infections pose a major public health burden. Opportunistic Cryptococcus neoformans infection is considered an AIDS-defining illness and is a leading cause of HIV-related death. In sub-Saharan Africa there are an estimated 700,000 cryptococcal meningitis cases per year, with a 3-month mortality rate of up to 70%.

Cryptococcal infections are likely acquired from the environment, though the exact environmental niches in sub-Saharan Africa are not known. The environmental reservoir of the fungus and the mechanism(s) by which it is transmitted from the environment to humans in Kenya are unknown. This lack of information is a critical impediment to efforts to reduce the rates of invasive cryptococcal infections and subsequent deaths due to invasive cryptococcal disease.

In this pilot study, we will use previously collected clinical isolates of Cryptococcus spp. from patients enrolled in an ongoing Phase IIb clinical trial (An Open Label Randomized Controlled Phase IIb Trial to Determine the Safety of Oral Fluconazole in Combination with Flucytosine as Compared to Fluconazole Alone, Identifier: NCT01562132). We will then compare these clinical isolates to isolates collected from the homes and surrounding environment of the participants by Multi-Locus Sequence Typing (MLST) to identify possible environmental reservoirs of pathogenic Cryptococcus spp.

MLST is a genetic sequencing technique for characterizing bacterial or fungal species by using the sequence variation of several housekeeping genes. For each housekeeping gene, the varying sequences identified for the species are assigned and cataloged as distinct alleles.  Subsequently, the alleles at each of the loci will in combination define the sequence type (ST) or allelic profile for each isolate. We will use this technique to determine if any fungal isolates recovered from the homes or environment of the Cryptococcus-infected participants are genetically similar to the fungal isolate found in their blood.