Mould Sequencing

Lactophenol analine blue prep of Coccidioides immitis
Figure 1. Lactophenol analine blue prep of Coccidioides immitis

(Mold ID by sequencing, Mold Identification by sequencing, Mold PCR and sequencing, Aspergillus PCR and sequencing)

Accurate identification of mold isolates is an essential task of the clinical microbiology laboratory that enables initiation of proper antimicrobial therapy. For many molds, traditional phenotypic identification is difficult, laborious and time-consuming. Identification often takes 4 weeks or more to identify an isolate to the species level. This issue is confounded by phenotypic variation within species, many newly described pathogenic species and the limited battery of phenotypic tests available to distinguish among all established and potential fungal pathogens. It is sometimes essential to identify mold isolates to species level in order to detect unsuspected pathogens, ascribe pathogenicity to species so far considered to be nonpathogenic and to identify new mold species. PCR amplification and sequencing of mold 26S ribosomal RNA (rRNA) and Internal Transcribed Spacer 1 and 2 regions (ITS1 & ITS2) provides rapid, accurate identification of clinically significant molds. These target DNA fragments contain signature sequences useful for mold identification to species level, flanked by conserved regions that are useful for the design of universal PCR primers.

UWMC Molecular Diagnosis section maintains a rapidly growing DNA database that contains 28S and Internal Transcribed Spacer (ITS) sequences from mold strains that were identified using phenotypic methods. The final identification of organism is based on sequence alignment (BLAST) with our local database, as well as the public database at NCBI.