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<i>Paecilomyces</i> spp. are emerging fungal pathogens, where <i>Paecilomyces</i> <i>lilacinus</i> and <i>Paecilomyces variotii</i> are the most reported species. Taxonomic and phylogenetic revisions in this genus have shown that <i>P. variotii</i> represents a species complex, whereas <i>P. lilacinus</i> is related to another genus called <i>Purpureocillium</i>. The aims of this study were to identify clinical isolates of <i>Paecilomyces</i> spp. at the species level, and to determine their antifungal susceptibility profiles. 70 clinical <i>Paecilomyces</i> spp. isolates were identified by MALDI-TOF Mass Spectrometry (MS) and by multilocus rDNA genes sequencing including ITS and the D1/D2 genes. Among the 70 <i>Paecilomyces</i> spp. isolates, 28 were identified as <i>P. lilacinum</i>, 26 as <i>P. variotii stricto sensu</i>, and 16 as <i>P. maximus</i>. For antifungal susceptibility testing, Minimal Inhibitory Concentrations (MICs) or Minimal Effective Concentrations (MECs) were determined for 8 antifungals. All <i>P. lilacinum</i> isolates had high MICs and MECs of amphotericin B and echinocandins, respectively, unlike <i>P. variotii</i> and <i>P. maximus</i>. For azole drugs, MICs were molecule- and species- dependent. The differences in in vitro susceptibility to antifungals underline the importance of accurate species identification. The MALDI–TOF MS can be a good alternative in routine laboratory to ensure fast identification of <i>Paecilomyces</i> spp. and <i>P. lilacinum</i>.