Spectrum of zygomycete species identified in clinically significant specimens in the United States

Abstract

Several members of the order Mucorales (subphylum Mucoromycotina) are important agents of severe human infections. The identification of these fungi by using standard mycologic methods is often difficult and time consuming. Frequently, the etiological agent in clinical cases is reported either as a Mucor sp., which is not the most frequent genus of zygomycetes, or only as a member of the Mucorales. For this reason, the actual spectrum of species of zygomycetes and their incidences in the clinical setting is not well known. The goals of this study were to compare the results of the molecular identification of an important set of clinical isolates, received in a mycological reference center from different regions of the United States, with those obtained by using the traditional morphological methods and to determine the spectrum of species involved. We tested 190 isolates morphologically identified as zygomycetes by using sequencing of the internal transcribed spacer (ITS) region of the ribosomal DNA. Molecular identification revealed that Rhizopus oryzae represented approximately half (44.7%) of these isolates. The remainder was identified as Rhizopus microsporus (22.1%), Mucor circinelloides (9.5%), Mycocladus corymbifer (formerly Absidia corymbifera) (5.3%), Rhizomucor pusillus (3.7%), Cunninghamella bertholletiae (3.2%), Mucor indicus (2.6%), Cunninghamella echinulata (1%), and Apophysomyces elegans (0.5%). The most common anatomic sites for clinically significant zygomycetes, as determined by isolates sent to the Fungus Testing Laboratory for identification and/or susceptibility testing and included in this study, were the sinuses, lungs, and various cutaneous locations, at 25.8%, 26.8%, and 28%, respectively. These sites represented approximately 80% of the isolates evaluated. A high level of correlation (92.6%) between morphological and molecular identifications was found.

FIG. 1.

NJ tree based on maximum composite likelihood-corrected nucleotide distances among 5.8S rRNA gene sequences of representative isolates of the species listed in Table 1. In the tree, branch lengths are proportional to distance. Bootstrap iteration frequencies (1,000 iterations) above 70% are indicated on the nodes. Type or reference strains are indicated in boldface. ^T, type strain; ^NT, neotype strain.

FIG. 2.

NJ tree based on maximum composite likelihood-corrected nucleotide distances among the ribosomal ITS regions and 5.8S rRNA gene sequences of the isolates included in the Mucor clade shown in Fig. 1. In the tree, branch lengths are proportional to distance. Bootstrap iteration frequencies (1,000 iterations) above 70% are indicated on the nodes. Type strains are indicated in boldface. ^T, type strain.