Identification of Paecilomyces variotii in Clinical Samples and Settings

Abstract

Paecilomyces variotii is a commonly occurring species in air and food, but it is also associated with many types of human infections and is among
the emerging causative agents of opportunistic mycoses in immunocompromised hosts. Paecilomyces can cause hyalohyphomycosis, and two species, Paecilomyces lilacinus and P. variotii, are the most frequently encountered organisms. In the present study, a set of 34 clinical isolates morphologically identified
as P. variotii or P. lilacinus were formally identified by sequencing intergenic transcribed spacer regions 1 and 2 (including 5.8S rDNA) and a part of
the β-tubulin gene. Three isolates were identified as P. lilacinus, and five of the presumptive P. variotii isolates did not belong to the genus Paecilomyces but were identified as Talaromyces eburneus (anamorph, Geosmithia argillacea) or Hamigera avellanea (anamorph, Merimbla ingelheimense). Applying the most recent taxonomy, we found that the clinical P. variotii isolates could be identified as P. variotii sensu stricto (14 strains), P. formosus (11 strains), and P. dactylethromorphus (1 strain). These data indicate that P. formosus occurs in clinical samples as commonly as P. variotii. Susceptibility tests showed that the antifungal susceptibility profiles of P. variotii, P. formosus, and P. dactylethromorphus are similar and that all strains tested were susceptible to amphotericin B in vitro. P. lilanicus, T. eburneus, and H. avellanea had different susceptibility profiles; and flucytosine and voriconazole were the least active of the antifungal drugs tested
against these species. Our results indicate that correct species identification is important to help guide appropriate antifungal
therapy.

Full text

JOURNAL OF CLINICAL MICROBIOLOGY, Aug. 2010, p. 2754–2761 Vol. 48, No. 8
0095-1137/10/$12.00 doi:10.1128/JCM.00764-10
Copyright © 2010, American Society for Microbiology. All Rights Reserved.
Identification of Paecilomyces variotii in Clinical
Samples and Settings
䌤
Jos Houbraken,
1
* Paul E. Verweij,
2
Anthonius J. M. M. Rijs,
2
Andrew M. Borman,
3
and Robert A. Samson
1
CBS-KNAW Fungal Biodiversity Centre, Department of Applied and Industrial Mycology, Utrecht, Netherlands
1
;
Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
2
;
and HPA Mycology Reference Laboratory, HPA Southwest, Bristol, United Kingdom
3
Received 15 April 2010/Returned for modification 10 May 2010/Accepted 21 May 2010
Paecilomyces variotii is a commonly occurring species in air and food, but it is also associated with many types
of human infections and is among the emerging causative agents of opportunistic mycoses in immunocom-
promised hosts. Paecilomyces can cause hyalohyphomycosis, and two species, Paecilomyces lilacinus and P.
variotii, are the most frequently encountered organisms. In the present study, a set of 34 clinical isolates
morphologically identified as P. variotii or P. lilacinus were formally identified by sequencing intergenic
transcribed spacer regions 1 and 2 (including 5.8S rDNA) and a part of the ␤-tubulin gene. Three isolates were
identified as P. lilacinus, and five of the presumptive P. variotii isolates did not belong to the genus Paecilomyces
but were identified as Talaromyces eburneus (anamorph, Geosmithia argillacea)orHamigera avellanea (ana-
morph, Merimbla ingelheimense). Applying the most recent taxonomy, we found that the clinical P. variotii
isolates could be identified as P. variotii sensu stricto (14 strains), P. formosus (11 strains), and P. dactylethro-
morphus (1 strain). These data indicate that P. formosus occurs in clinical samples as commonly as P. variotii.
Susceptibility tests showed that the antifungal susceptibility profiles of P. variotii,P. formosus, and P. dac-
tylethromorphus are similar and that all strains tested were susceptible to amphotericin B in vitro.P. lilanicus,
T. eburneus, and H. avellanea had different susceptibility profiles; and flucytosine and voriconazole were the
least active of the antifungal drugs tested against these species. Our results indicate that correct species
identification is important to help guide appropriate antifungal therapy.
Paecilomyces variotii is a commonly occurring species that
has previously been isolated from various substrates, including
(pasteurized) foods, soil, indoor air, and wood (23, 36, 41, 42,
43). However, it is also associated with many types of human
infections and is listed among the emerging causative agents of
opportunistic mycoses in immunocompromised hosts. Paecilo-
myces can cause hyalohyphomycosis (1), and two species, Pae-
cilomyces lilacinus and P. variotii, are the most frequently en-
countered (20, 52). Both species are morphologically similar
but can be differentiated on the basis of conidial color and
growth rates (41). However, small-subunit ribosomal gene se-
quences showed that the two species are unrelated: P. variotii
belongs to the order Eurotiales, while P. lilacinus is a member
of the order Hypocreales (27). Although they are uncommon,
Paecilomyces infections are associated with almost any organ
or system of the human body (40). Most cases concern immu-
nocompromised patients and are cutaneous or catheter re-
lated. However, dissemination, for example, that involving the
central nervous system, has been observed in a number of cases
(15, 24). Ocular infections associated with prolonged contact
lens use or ocular surgery have also been reported (40), as
has peritonitis in patients with continuous ambulatory peri-
toneal dialysis (24), which apparently responded well to an-
tifungal therapy, with cures occurring in 11 of the 13 cases.
However, the majority of these patients were treated for Pae-
cilomyces peritonitis and were not severely immunocompro-
mised. In vitro amphotericin B was active against clinical P.
variotii isolates but not against P. lilacinus (8). Among the
azoles, only itraconazole and posaconazole showed clinically
relevant activity against P. variotii. The geometric mean MICs
of voriconazole and ravuconazole were above 4 mg/liter, indi-
cating that these azoles will not be effective in vivo. Interest-
ingly, the echinocandins, especially micafungin and anidula-
fungin, were highly active against P. variotii, with MIC values
being as low as 0.016 mg/liter. Conversely, P. lilacinus was not
inhibited by the echinocandins, underscoring the importance
of correct species identification (8).
Paecilomyces variotii grows rapidly on standard agar and
forms velvety olive brown colonies. Conidiophores of P. variotii
are irregularly branched, and the phialides have a broad base
ending in a long and slender neck. Samson (41) noted that P.
variotii is a morphologically variable species, and the taxonomy
of P. variotii and the related Byssochlamys teleomorphs has
recently been revised (45). This revision is based on morphol-
ogy, extrolites, and molecules and shows that P. variotii sensu
lato comprises five species, namely, Byssochlamys spectabilis
(the sexual state of P. variotii), P. brunneolus,P. formosus,P.
divaricatus, and P. dactylethromorphus. The last species was
incorrectly named P. saturatus because P. dactylethromorphus
was validly described in 1957 and has priority. The aim of the
present study was to determine the prevalence of these species
in clinical samples and settings. A total of 34 isolates originat-
ing from various clinical specimens and settings were identified
by sequencing the intergenic transcribed spacer (ITS) regions,
* Corresponding author. Mailing address: CBS-KNAW Fungal Biodi-
versity Centre, Department of Applied and Industrial Mycology, Utrecht
3584 CT, Netherlands. Phone: 31 (0)30 2122600. Fax: 31 (0)30 2512097.
E-mail: j.houbraken@cbs.knaw.nl.
䌤
Published ahead of print on 2 June 2010.
2754

including the 5.8S rDNA, and a part of the ␤-tubulin gene.
Furthermore, the antifungal susceptibility profiles of these spe-
cies and ex-type strains are reported.
MATERIALS AND METHODS
Strains. This study includes 34 strains isolated from clinical specimens and
hospital environments. These strains were identified on the basis of macro- and
microscopic characters and were maintained in various culture collections as P.
variotii or P.lilacinus. In additional, ex-type strains and freshly isolated strains
were also included in this study.
Morphological examination. Isolates (Table 1) were grown for 3 days on malt
extract agar (MEA) and were incubated in the dark at 25, 30, and 37°C. Fur-
thermore, three-point inoculations were made on MEA, Czapek yeast agar
(CYA), and creatine agar (CREA); and the isolates were incubated for 7 days at
25°C (the medium compositions are described by Samson et al. [43]). After
TABLE 1. Isolates used in this study
Strain no.
a
Species Source
CBS 100.11
NT
** Byssochlamys nivea Unknown
CBS 146.48
NT
** Byssochlamys fulva Bottled fruit, UK
CBS 373.70
T
** Byssochlamys lagunculariae Wood of Laguncularia racemosa (mangue), Brazil
CBS 605.74
HT
** Byssochlamys verrucosa Nesting material of Leipoa ocellata, Australia
CBS 374.70
isoT
** Byssochlamys zollerniae Wood of Zollernia ilicifolia and Protium heptaphyllum, Brazil
UMCN V63-56, DTO 63F6 Hamigera avellanea Human, ear swab; Nijmegen, Netherlands (2007)
CBS 295.48
isoT
*Hamigera avellanea Soil; San Antonio, TX
CBS 370.70
T
** P. brunneolus Nonfat dry milk, Canada
CBS 110430* P. divaricatum Soil, Thailand
CBS 284.48
T
P. divaricatum Mucilage bottle with library paste, USA
UMCN V54-40, DTO 63F3 P. formosus Human, sputum; Nijmegen, Netherlands (2006)
CBS 296.93 P. formosus Human, bone marrow of patient; Taskent, Uzbekistan
CBS 297.93 P. formosus Human, blood of patient; Taskent, Uzbekistan
CBS 298.93 P. formosus Human, breast milk of patient; Taskent, Uzbekistan
CBS 990.73B
T
P. formosus Unknown
DTO 45H8 P. formosus Pseudo-outbreak in hospital, blood culture, United Kingdom
UMCN 1274, DTO 63E3 P. formosus (lecythidis type) Human, bronchoalveolar lavage fluid; Nijmegen, Netherlands
UMCN V49-58, DTO 63F1 P. formosus (lecythidis type) Human, sputum; Zwolle, Netherlands (2006)
UMCN V56-25, DTO 63F4 P. formosus (lecythidis type) Human, sputum; Nijmegen, Netherlands (2006)
CBS 372.70 P. formosus (lecythidis type) Type of P. lecythidis,Lecythis unsitata (Lecythidaceae), wood, Brazil
DTO 45I1 P. formosus (lecythidis type) Pseudo-outbreak in hospital, blood culture; UK
NCPF 2825, DTO 49D5 P. formosus (lecythidis type) Brain abscess, United Kingdom (1991)
NCPF 2837, DTO 49D6 P. formosus (lecythidis type) Brain abscess, same patient as NCPF 2825, United Kingdom (1991)
CBS 113247* P. formosus (maximus type) Soil, Thailand
CBS 371.70 P. formosus (maximus type) Type of P. maximus,Annona squamosa, Brazil
UMCN 1156,* DTO 63E1 P. lilacinus Unknown source
UMCN 2419,* DTO 63E5 P. lilacinus Human, skin swab; Nijmegen, Netherlands (1994)
CBS 284.36
T
*P. lilacinus Soil; Ithaca, NY
V52-21,* DTO 63F2 P. lilacinus Human, sputum; Nijmegen, Netherlands (2006)
UMCN V66-47, DTO 63F7 P. dactylethromorphus Human, cornea scrapings from keratomycosis; Nijmegen, Netherlands (2008)
CBS 323.34
T
P. dactylethromorphus Unknown source
CBS 492.84* P. dactylethromorphus Lepidium sativum, Denmark
CBS 110036, DTO 34C8 P. variotii Cerebrospinal fluid of 60-year-old female with diabetes and cancer;
Istanbul, Turkey
UMCN 1157*, DTO 63E2 P. variotii Unknown source
UMCN 2266, DTO 63E4 P. variotii Human, feces; Nijmegen, Netherlands (1994)
UMCN 3796, DTO 63E6 P. variotii Human, mouthwash; Nijmegen, Netherlands (1995)
UMCN 45H9*, DTO 45H9 P. variotii Liver biopsy; London, UK
UMCN 577, DTO 63D6 P. variotii Human, mouthwash; Nijmegen, Netherlands
UMCN 654, DTO 63D7 P. variotii Human, feces, Nijmegen; Netherlands
UMCN 730, DTO 63D8 P. variotii Hospital environment, elevator shaft; Nijmegen, Netherlands
UMCN 731, DTO 63D9 P. variotii Human, mouthwash; Nijmegen, Netherlands
UMCN 7845, DTO 63E7 P. variotii Human, cerebrospinal fluid; Nijmegen, Netherlands (1998)
UMCN 8490, DTO 63E9 P. variotii Human, mouthwash; Nijmegen, Netherlands (1999)
UMCN V57-21, DTO 63F5 P. variotii Human, abscess; Zwolle, Netherlands (2007)
CBS 101075 P. variotii Type of B. spectabilis, heat-processed fruit beverage, Japan
CBS 102.74
T
P. variotii Unknown source
CBS 124.97 P. variotii Human, vitreous tumor left eye, neutropenic leukemic patient with acute
endophthalmitis, Hong Kong
CBS 339.51 P. variotii Human, sputum, Netherlands
DTO 45I3 Talaromyces eburneus Pseudo-outbreak in hospital, blood culture, UK
NCPF 2801, DTO 49D4 Talaromyces eburneus Sputum, cystic fibrosis patient, UK (1991)
NCPF 7594, DTO 49D7 Talaromyces eburneus Blood culture, patient with peritonitis, UK (2002)
NCPF 7596, DTO 49D9 Talaromyces eburneus Peritoneal dialysis fluid (same patient source as NCPF 7594)
a
Strains indicated with one asterisk are not included in the phylogenetic analysis; these strains are used only in the susceptibility tests. The strains labeled with two asterisks
are included in the phylogenetic study but not in the susceptibility tests. NT, neotype; HT, holotype; isoT, isotype. CBS, culture collection of the CBS-Fungal Biodiversity
Centre, Utrecht, Netherlands; UMCN, culture collection of Radboud University Nijmegen Medical Center; DTO, internal culture collection of CBS-Fungal Biodiversity
Centre.
VOL. 48, 2010 IDENTIFICATION OF PAECILOMYCES VARIOTII 2755

incubation, the colony diameters were measured and the reactions on creatine
agar recorded.
Phylogeny and molecular identification. Strains were grown on MEA (Oxoid)
for 4 to 7 days at 25°C. Genomic DNA was isolated using an Ultraclean microbial
DNA isolation kit (MoBio), according to the manufacturer’s instructions. Frag-
ments containing ITS region 1 (ITS1) and ITS2, including 5.8S rDNA) and a part
of the ␤-tubulin gene were amplified and subsequently sequenced and analyzed
according to the procedure described previously (22). For parsimony analyses,
PAUP (version 4.0) software was used (48) and Byssochlamys verrucosa CBS
605.74 was used as the outgroup.
Antifungal susceptibility tests. The susceptibilities of the majority of the
strains listed in Table 1 were tested; exceptions were the (ex type) strains of
uncommon species in clinical environments, such as Byssochlamys nivea,B. fulva,
B. verrucosa,B. lagunculariae,B. zollerniae, and P. brunneolus.Paecilomyces
divaricatus is also uncommon, but it is included to provide a representative
overview of the susceptibility of the members of the Paecilomyces variotii com-
plex. Isolates were revived by subculturing twice on Sabouraud dextrose agar
tubes for 5 to 7 days at 35°C. Conidial suspensions were adjusted spectrophoto-
metrically and were further diluted in RPMI 1640 medium (with L-glutamine and
without bicarbonate; Gibco BRL, Life Technologies, Woerden, Netherlands).
Microtiter plates were inoculated with an initial concentration of 1 ⫻10
4
to 5 ⫻
10
4
conidia/ml, as recommended by the CLSI (formerly the NCCLS) for mold
testing (30).
The antifungal activities of amphotericin B (Bristol-Myers Squibb, Woerden,
Netherlands), flucytosine (5FC; Valeant, Zoetermeer, Netherlands), itracon-
azole (Janssen Pharmaceutica BV, Tilburg, Netherlands), voriconazole (Pfizer,
Capelle aan de IJssel, Netherlands), posaconazole (Schering-Plough, Maarssen,
Netherlands), terbinafine (Novartis Pharma, Arnhem, Netherlands), and caspo-
fungin (Merck, Sharpe, and Dohme, Haarlem, Netherlands) were determined in
vitro using a broth microdilution method, according to CLSI guidelines (M38-A)
(30). The concentration range for amphotericin B, terbinafine, itraconazole,
voriconazole, and posaconazole was 0.016 to 16 mg/liter; a range of 0.062 to 64
mg/liter was used for 5FC and caspofungin. MICs were determined after 24 and
48 h of incubation. For amphotericin B and the azoles itraconazole, voriconazole,
and posaconazole, the MIC was defined as the lowest concentration that showed
no visible growth. For 5FC and terbinafine, the MIC was defined as the lowest
concentration at which 50% inhibition of growth compared with that of the
control was measured (32). For caspofungin, the minimum effective concentra-
tion was determined. All susceptibility tests were performed in duplicate.
Nucleotide sequence accession numbers. The sequences newly generated in
the present study are deposited in GenBank under accession numbers GU968650
to GU968703.
RESULTS
Identification. Identification of the strains was performed by
combining phenotypic characteristics and the sequences of the
ITS regions and part of the ␤-tubulin gene. The investigated
clinical strains were maintained in various collections as P.
variotii or P. lilacinus. Critical examination of the cultures
showed that one Hamigera avellanea isolate and four Talaro-
myces eburneus isolates were present among the isolates which
had previously been identified as P. variotii. The ITS sequences
of three T. eburneus isolates (NCPF 7594, NCPF 7596, and
DTO 45I3) were identical and had 99.8% homology with the
type strain of T. eburneus (CBS 100538). Isolate DTO 49D4
was more divergent and shared 96.4% homology with the type
strain of T. eburneus and 98.8% similarity with the type strain
of Geosmithia argillaea (NRRL 5177). Although this strain is
more closely related to G. argillaea, we identified this strain as
T. eburneus, since both species are claimed to be conspecific
(53). The T. eburneus strains were isolated from patient mate-
rial in three separate cases: from the sputum of a patient with
cystic fibrosis (NCPF 2801), from a blood culture (DTO 45I3),
and from the peritoneal dialysis fluid and blood of a patient
(NCPF 7594 and NCPF 7596). P. variotii superficially resem-
bles T. eburneus in its olive brown conidial colors and thermo-
philic nature. However, it differs in growing very slowly at 25°C
(attaining a diameter of between 10 and 25 mm) and having a
Geosmithia anamorph. Geosmithia anamorphs are character-
ized by cylindrical phialides, ornamented conidiophores and
phialides, and cylindrical conidia (Fig. 1). A further presump-
tive isolate of P. variotii was identified as H. avellanea. The ITS
sequence of this strain had a similarity of 98.0% with the type
strain of this species (CBS 295.48). This species macroscopi-
cally resembles P. variotii in many respects and also forms
powdery olive brown colonies, and it has a high growth rate at
25°C and 37°C. However, H. avellanea can be distinguished
from P. variotii by the presence of a Merimbla-type anamorph
(Fig. 1). Three strains were identified as P. lilacinus, and the
ITS sequences of these strains have 100% homology with the
type strain of P. lilacinus (CBS 284.36).
In the present study, we have adopted the taxonomy of
Paecilomyces variotii and related species proposed by Samson
et al. (45), which uses morphological characteristics, in combi-
nation with extrolite data and sequences. Combined molecular
and morphological examination of the remaining P. variotii
sensu lato isolates showed that three different species were
present, namely, P. variotii,P. formosus, and P. dactylethromor-
phus.P. variotii was the species encountered the most fre-
quently (12), 11 isolates were identified as P. formosus, and 1
isolate was identified as P. dactylethromorphus. These three
species can be differentiated on the basis of morphological
criteria. P. variotii morphologically resembles P. formosus, but
the latter produces acid components on creatine agar and
grows faster at 30°C than at 37°C. P. dactylethromorphus can be
differentiated from the other two species by its cylindrical
conidia and regular branched conidiophores (Fig. 1). Figure 2
shows the results of the phylogenetic analysis of the ITS and
partial tubulin sequences. Both sequenced regions gave similar
identification results, and all the species of the P. variotii com-
plex can be differentiated by either their ITS or partial tubulin
sequences. A high degree of variation was present in the ITS
and tubulin sequences of the P. formosus isolates. Two distinct
groups, with high bootstrap support, were observed. A propor-
tion of the isolates (5) formed a group together with the type
strain of P. formosus, and the other group clustered together
with the type strain of P. lecythidis. These two groups could
represent two cryptic species but were not treated as such since
they are morphologically similar and produce the same pattern
of extrolites (45). Three strains (CBS 296.93, CBS 297.93, and
CBS 298.93) received as P. variotii var. zaaminella and claimed
to be the causal agent of zaaminellosis (11) were identified as
P. formosus.
Susceptibility testing. Susceptibility data, i.e., the geometric
mean (GM) of the MIC and the MIC range, are shown in
Table 2. For those isolates that were not inhibited by the
highest drug concentration, the next higher concentration was
used to calculate the GM MIC; if no growth was observed in
the well with the lowest drug concentration, the next lower
concentration was used. The activities of most of the antifungal
agents differed between the seven different species. Posacon-
azole and terbinafine showed good in vitro activity against all
the species tested. Posaconazole showed the lowest MICs, as
all isolates except T. eburneus were inhibited by a concentra-
tion of 0.25 mg/liter; T. eburneus had slightly higher MIC val-
ues (MIC range, 0.25 to 1 mg/liter). All isolates (except one P.
2756 HOUBRAKEN ET AL. J. CLIN.MICROBIOL.

FIG. 1. Macro- and micromorphological features of various species related to P. variotii. Columns, from left to right, MEA, conidiophores, and
conidia, respectively; rows, from top to bottom, P. variotii,P. formosus,P. dactylethromorphus,Hamigera avellanea,Talaromyces eburneus, and
Paecilomyces lilacinus, respectively. Bars, 10 ␮m.
2757

formosus isolate) were inhibited by terbinafine at a concentra-
tion of 1 mg/liter or lower. Itraconazole was the second most
active azole, having in vitro activity against all Paecilomyces
species except P. lilanicus and T. eburneus. The P. lilanicus
isolates were not inhibited by itraconazole, which was also true
for three of four of T. eburneus isolates. H. avellanea was
moderately susceptible to itraconazole, but only two isolates
were available for testing. Voriconazole was the least active
azole and had in vitro activity only against P. lilanicus and H.
avellanea. Amphotericin B was active in vitro against all species
tested with the exception of P. lilanicus and T. eburneus. Flucy-
tosine was also active against most of the species tested; the
exceptions were P. lilanicus and H. avellanea. For amphotericin
B, itraconazole, posaconazole, voriconazole, and flucytosine,
little intraspecific variation in antifungal susceptibility was
noted. This was not the case for caspofungin, where minimal
effective concentration values varied between 0.063 and 4 mg/
liter for different isolates of the same species.
DISCUSSION
Of 32 isolates which were identified as P. variotii by their
phenotypic characteristics, 5 were shown here not to belong to
the genus Paecilomyces and instead proved to be Talaromyces
eburneus (anamorph, Geosmithia argillacea)orHamigera avel-
lanea (anamorph, Merimbla ingelheimense). These two species
superficially resemble P. variotii, but the micromorphology is
distinct from that of Paecilomyces (35). The occurrence of
these two species in clinical environments might be more com-
mon than has been noted to date. Screening of the StrainInfo
bioportal (www.straininfo.net) identified two other Hamigera
isolates that have been reported from clinical environments.
One isolate (CBS 128.90) originates from continuous ambulatory
peritoneal dialysis liquid of a dialysis patient, and the other
(UAMH 2531), maintained under the anamorphic name M. in-
gelheimense, was isolated from skin between the toes of a man.
Multiple isolates of G. argillacea originating from bronchial wash-
ings (UAMH 7717, UAMH 8639, UAMH 9714, UAMH 9854,
UAMH 10232), a brain abscess (UAMH 9833), and a dissemi-
nated infection in a German shepherd dog (UAMH 10932,
UAMH 10933 [21]) are also present in the UAMH culture
collection. In addition, this species has recently been proposed
to be a potential new pathogen that colonizes patients with
cystic fibrosis lung disease (6, 19). The remaining isolates be-
longed to three different Paecilomyces species. P. variotii and P.
formosus predominated, although one isolate of P. dactylethro-
morphus was also detected. The presence of these species in
the clinical samples might be explained by the fact that these
species occur more commonly in food and indoor environ-
ments than the other members of the P. variotii complex (J.
Houbraken, unpublished results).
FIG. 2. One of the most parsimonious trees from each of the two analyzed loci sequenced. (A) ITS1, ITS2, and 5.8S rDNA (consistency index ⫽
0.796; retention index ⫽0.938, rescaled consistency index ⫽0.747); (B) partial beta-tubulin data (consistency index ⫽0.745; retention index ⫽
0.909; rescaled consistency index ⫽0.677).
2758 HOUBRAKEN ET AL. J. CLIN.MICROBIOL.

Species identification of fungi in the past has primarily been
based on morphological features. However, identification
solely on the basis of morphology appears to be difficult, and
trained staff is required for correct identification. Identification
of fungi from clinical samples might even encounter the prob-
lem that isolates grow atypically on inappropriate agars or
become atypical if antimycotics are used (31). Therefore, mo-
lecular-based methods, such as sequencing, appear to be more
reliable and are a robust alternative to discriminate fungal
species (4, 9, 17, 39). Sequencing data are objective and fast,
and reliable identification of uncommon species can be ob-
tained. The ITS regions are recommended for use for identi-
fication of species in a clinical setting, since they are easy to
amplify and large data sets are present in various databases,
such as GenBank and European Molecular Biology Labora-
tory Nucleotide Sequence Database. These databases will ex-
pand dramatically in the near future since the ITS region has
become the prime bar coding region (5, 46; U. Eberhardt,
personal communication). The disadvantage of the ITS region
is that it does not have sufficient discriminatory power in
various genera, for example, the genera Aspergillus,Penicil-
lium, and Fusarium (5, 18, 33, 47). In this study, the ITS
regions and part of the ␤-tubulin gene were used, and both
loci were shown to exhibit sufficient interspecific variation
for identification purposes.
Paecilomyces variotii is a commonly occurring species and
has previously been isolated from various substrates. Immuno-
suppression is the critical risk factor for infection; and cases of
pneumonia (7), sinusitis (13, 34, 50), endophthalmitis (25, 49),
otitis media (12), wound infection in a transplant recipient
(26), cutaneous hyalohyphomycoses (3, 29), onychomycosis
(2), osteomyelitis in a patient with granulomatous disorder
(10), and dialysis-related peritonitis (38) have all been re-
ported to be caused by this fungus. This species can be con-
sidered extremotolerant and is able to grow at high tempera-
tures, on decaying wood, and on creosote treated wooden
utility poles (E. de Meyere et al., unpublished data). The ability
to grow on creosote-treated wooden poles suggests that this
species is able to break down aromatics and is able to grow
under stressful conditions (very hot conditions, dry conditions,
conditions very low in micronutrients). Additionally, P. formo-
sus has also been isolated from toluene gas biofilters. However,
these isolates were misidentified as P. sinensis and P. variotii,
and the correct name for these isolates is P. formosus (14, 16,
37). The extremotolerant nature is suggested to contribute to
the pathogenic potential of fungi. Prenafeta-Boldu´ et al. (37)
speculated that there might be a link between neurotropism
and assimilation of aromatic substrates, and this might be one
of the factors that enable fungi to grow in the human brain,
with its unique chemical properties. This suggested link is also
found in our study, as we have also encountered four strains of
three independent cases originating from brain or cerebrospi-
nal fluid.
Correlations of species identities with susceptibility profiles.
Major differences in in vitro antifungal susceptibility profiles
were found between the investigated species. In general, vori-
conazole is not active against members of the Paecilomyces
variotii complex but is active against P. lilanicus and H. avella-
nea. Treatment of infections due to P. lilanicus may be com-
plicated, as amphotericin B also showed no activity in vitro.
TABLE 2. Susceptibility results for Paecilomyces species, Hamigera avellanea, and Talaromcyes eburneus strains, by species and antifungal agent
Species No. of
isolates
Geometric mean (range) MIC (mg/liter)
a
AMB 5FC ITZ VCZ POS TB CAS
P. variotii 16 0.11 (0.03–0.5) 0.03 0.04 (0.008–4) 11.3 (1–32) 0.02 (0.008–0.125) 0.08 (0.031–0.5) 0.52 (0.063–4)
P. lilanicus 4 32 128 5.7 (0.063–32) 0.15 (0.063–0.25) 0.2 (0.008–0.25) 0.04 (0.031–0.063) 0.59 (0.5–1)
P. formosus 14 0.13 (0.063–0.25) 0.04 (0.031–0.25) 0.13 (0.063–1) 26.25 (16–32) 0.08 (0.031–0.25) 0.12 (0.031–2) 1.16 (0.063–4)
P. dactylethromorphus 3 0.16 (0.125–0.25) 0.05 (0.031–0.125) 0.08 (0.031–0.125) 32 0.03 0.31 (0.125–1) 0.25 (0.125–0.5)
P. divaricatus 2 0.25 (0.125–0.5) 0.008 0.5 (0.25–1) 32 0.18 (0.125–0.25) 0.06 (0.031–0.125) 0.71 (0.25–2)
H. avellanea 2 0.5 2 (1–4) 0.031 0.09 (0.063–0.125) 0.031 0.04 (0.031–0.063) 0.063
T. eburneus 4 3.3 (1–8) 0.032 12.5 (1–32) 28 (16–32) 0.69 (0.25–1) 0.032 0.31 (0.25–0.5)
a
For caspofungin, the minimum effective concentration was determined. AMB, amphotericin B; 5FC, flucytosine; ITZ, itraconazole; VCZ, voriconazole; POS, posaconazole; TB, terbinafine; CAS, caspofungin.
VOL. 48, 2010 IDENTIFICATION OF PAECILOMYCES VARIOTII 2759

Posaconazole may be the only appropriate alternative agent,
although the lack of an intravenous formulation and limited
penetration into the cerebrospinal fluid might limit its use.
Amphotericin B showed good activity against all other species
tested, as was also the case for flucytosine. The combination of
amphotericin B and flucytosine may therefore be an option in
complicated infections due to Paecilomyces species other than
P. lilanicus. Flucytosine was recently shown to be active in vitro
and in vivo against A. fumigatus, with the MIC measured at pH
5.0 being found to correlate better with the outcome in a
murine model of disseminated aspergillosis than that deter-
mined at pH 7.0 (51). It would be of interest to determine the
activity of flucytosine at pH 5.0 against other molds, including
Paecilomyces species. As published previously, terbinafine also
shows potent activity against all species tested (8). However,
the clinical use of this drug for the treatment of invasive fungal
infections remains limited due to its pharmacological proper-
ties. The role of the echinocandins remains unclear, as the in
vitro activity of caspofungin was variable, with the MIC ranges
within species being broad. This indicates that the activity of
the drug is not easily predictable, thereby precluding a prom-
inent role in the first-line therapy of Paecilomyces infections. In
general, the antifungal susceptibility profiles of P. variotii,P.
formosus,P. dactylethromorphus, and P. divaricatus appeared to
be similar, although a limited number of species have been
tested. The profiles of P. lilanicus,T. eburneus, and H. avellanea
are different. This is in agreement with the phylogeny, since T.
eburneus and H. avellanea are not related to Paecilomyces or
Byssochlamys (45, 53) and P. lilacinus will shortly be accom-
modated in a new genus because it is only distantly related to
P. variotii and the other species hitherto placed in the genus
Paecilomyces (27, 28). In summary, it is clear that correct spe-
cies identification of Paecilomyces isolates is important to help
guide appropriate antifungal therapy. The correlation between
the in vitro activity and the in vivo efficacy of these agents
against Paecilomyces species remains to be investigated fur-
ther.
ACKNOWLEDGMENT
Andrew Borman thanks Elizabeth Johnson for her interest in the
study and permitting him to collaborate in this study.
REFERENCES
1. Ajello, L. 1986. Hyalohyphomycosis and phaeohyphomycosis: two global
disease entities of public health importance. Eur. J. Epidemiol. 2:243–251.
2. Arenas, R., M. Arce, H. Munoz, and J. Ruiz-Esmenjaud. 1998. Onychomy-
cosis due to Paecilomyces variotii. Case report and review. J. Mycol. Med.
8:32–33.
3. Athar, M. A., A. S. Sekhon, J. V. Mcgrath, and R. M. Malone. 1996. Hyalo-
hyphomycosis caused by Paecilomyces variotii in an obstetrical patient. Eur.
J. Epidemiol. 12:33–35.
4. Balajee, S. A., J. Gribskov, M. Brandt, J. Ito, A. Fothergill, and K. A. Marr.
2005. Mistaken identity: Neosartorya pseudofischeri and its anamorph mas-
querading as Aspergillus fumigatus. J. Clin. Microbiol. 43:5996–5999.
5. Balajee, S. A., A. M. Borman, M. E. Brandt, J. Cano, M. Cuenca-Estrella, E.
Dannaoui, J. Guarro, G. Haase, C. C. Kibbler, W. Meyer, K. O’Donnell,
C. A. Petti, J. L. Rodriguez-Tudela, D. Sutton, A. Velegraki, and B. L.
Wickes. 2009. Sequence-based identification of Aspergillus, Fusarium and
the Mucorales in the clinical mycology laboratory: where are we and where
should we go from here? J. Clin. Microbiol. 47:877–884.
6. Barton, R. C., A. M. Borman, E. M. Johnson, J. Houbraken, R. P. Hobson,
M. Denton, S. P. Conway, K. G. Brownlee, D. Peckham, and T. W. R. Lee. 26
April 2010, posting date. Isolation of the fungus Geosmithia argillacea in the
sputum of people with cystic fibrosis. J. Clin. Microbiol. doi:10.1128/JCM.
7. Byrd, R. P., Jr., T. M. Roy, C. L. Fields, and J. A. Lynch. 1992. Paecilomyces
variotii pneumonia in a patient with diabetes mellitus. J. Diabetes Complicat.
6:150–153.
8. Castelli, M. V., A. Alastruey-Izquierdo, I. Cuesta, A. Monzon, E. Mellado,
J. L. Rodriguez-Tudela, and M. Cuenca-Estrella. 2008. Susceptibility testing
and molecular classification of Paecilomyces spp. Antimicrob. Agents Che-
mother. 52:2926–2928.
9. Clinical and Laboratory Standards Institute. 2008. Interpretive criteria for
identification of bacteria and fungi by DNA target sequencing: guideline.
CLSI document MM18-A. Clinical and Laboratory Standards Institute,
Wayne, PA.
10. Cohen-Abbo, A., and K. M. Edwards. 1995. Multifocal osteomyelitis caused
by Paecilomyces variotii in a patient with chronic granulomatous disease.
Infection 23:55–57.
11. Dekhkan-Khodzhayeva, N. 1992. Newly identified fungal disease zaaminel-
losis. Meditsinskaya Gazeta 3:8–9.
12. Dhindsa, M. K., J. Naidu, S. M. Singh, and S. K. Jain. 1995. Chronic
suppurative otitis media caused by Paecilomyces variotii. J. Med. Vet. Mycol.
33:59–61.
13. Eloy, P., B. Bertrand, P. Rombeaux, M. Delos, and J. P. Trigaux. 1997.
Mycotic sinusitis. Acta Otorhinolaryngol. Belg. 51:339–352.
14. Estevez, E., M. C. Veiga, and C. Kennes. 2005. Biodegradation of toluene by
the new fungal isolates Paecilomyces variotii and Exophiala oligosperma.
J. Ind. Microbiol. Biotechnol. 32:33–37.
15. Fagerburg, R., B. Suh, H. R. Buckley, B. Lorber, and J. Karian. 1981.
Cerebrospinal fluid shunt colonization and obstruction by Paecilomyces vari-
otii. J. Neurosurg. 54:257–260.
16. Garcia-Pena, I., S. Hernandez, R. Auria, and S. Revah. 2005. Correlation of
biological activity and reactor performance in biofiltration of toluene with
the fungus Paecilomyces variotii CBS 115145. Appl. Environ. Microbiol.
71:4280–4285.
17. Geiser, D. M., J. I. Pitt, and J. W. Taylor. 1998. Cryptic speciation and
recombination in the aflatoxin-producing fungus Aspergillus flavus. Proc.
Natl. Acad. Sci. U. S. A. 95:388–393.
18. Geiser, D. M., M. A. Klich, J. C. Frisvad, S. W. Peterson, J. Varga, and R. A.
Samson. 2007. The current status of species recognition and identification in
Aspergillus. Stud. Mycol. 59:1–10.
19. Giraud, S., M. Pihet, B. Razafimandimby, J. Carre`re, N. Degand, L. Mely, L.
Favennec, E. Dannaoui, J.-P. Bouchara, and A. Calenda. 12 May 2010,
posting date. Geosmithia argillacea: an emerging pathogen in cystic fibrosis
patients? J. Clin. Microbiol. doi:10.1128/JCM.
20. Groll, A. H., and T. J. Walsh. 2001. Uncommon opportunistic fungi: new
nosocomial threats. Clin. Microbiol. Infect. 7(Suppl. 2):8–24.
21. Grant, D. C., D. A. Sutton, A. Sandberg, R. D. Tyler, E. H. Thompson, A. M.
Romanelli, and B. L. Wickes. 2009. Disseminated Geosmithia argillacea in-
fection in a German shepherd dog. Med. Mycol. 47:221–226.
22. Houbraken, J., M. Due, J. Varga, M. Meijer, J. C. Frisvad, and R. A.
Samson. 2007. Polyphasic taxonomy of Aspergillus section Usti. Stud. Mycol.
59:107–128.
23. Houbraken, J., J. Varga, E. Rico-Munoz, S. Johnson, and R. Samson. 2008.
Sexual reproduction as the cause of heat resistance in the food spoilage
fungus Byssochlamys spectabilis (anamorph Paecilomyces variotii). Appl. En-
viron. Microbiol. 74:1613–1619.
24. Kantarcioglu, A. S., G. Hatemi, A. Yucel, G. S. De Hoog, and N. M. Mandel.
2003. Paecilomyces variotii central nervous system infection in a patient with
cancer. Mycoses 46:45–50.
25. Lam, D. S., A. P. Koehler, D. S. Fan, W. Cheuk, A. T. Leung, and J. S. Ng.
1999. Endogenous fungal endophthalmitis caused by Paecilomyces variotii.
Eye 13:113–116.
26. Lee, J., W. W. Yew, C. S. Chiu, P. C. Wong, C. F. Wong, and E. P. J. Wang.
2002. Delayed sternotomy wound infection due to Paecilomyces variotii in a
lung transplant recipient. Heart Lung Transplant. 21:1131–1134.
27. Luangsa-ard, J. J., N. L. Hywel-Jones, and R. A. Samson. 2004. The
polyphyletic nature of Paecilomyces sensu lato based on 18S-generated
rDNA phylogeny. Mycologia 96:773–780.
28. Luangsa-Ard, J., N. L. Hywel-Jones, L. Manoch, and R. A. Samson. 2005. On
the relationships of Paecilomyces sect. Isarioidea species. Mycol. Res. 109:
581–589.
29. Naidu, J., and S. M. Singh. 1992. Hyalohyphomycosis caused by Paecilomy-
ces variotii: a case report, animal pathogenicity and ‘in vitro’ sensitivity.
Antonie Van Leeuwenhoek 62:225–230.
30. National Committee for Clinical Laboratory Standards. 2002. Reference
method for broth dilution antifungal susceptibility testing of filamentous
fungi. Approved standard M38-A. National Committee for Clinical Labora-
tory Standards, Wayne, PA.
31. Nosanchuk, J. D., W. Cleare, S. P. Franzot, and A. Casadevall. 1999. Am-
photericin B and fluconazole affect cellular charge, macrophage phagocyto-
sis, and cellular morphology of Cryptococcus neoformans at subinhibitory
concentrations. Antimicrob. Agents Chemother. 43:233–239.
32. Odds, F. C., F. van Gerven, A. Espinel-Ingroff, M. S. Bartlett, M. A. Ghan-
noum, M. V. Lancaster, M. A. Pfaller, J. H. Rex, M. G. Rinaldi, and T. J.
Walsh. 1998. Evaluation of possible correlations between antifungal suscep-
tibilities of filamentous fungi in vitro and antifungal treatment outcomes in
animal infection models. Antimicrob. Agents Chemother. 42:282–288.
33. O’Donnell, K., D. A. Sutton, A. Fothergill, D. McCarthy, M. G. Rinaldi,
2760 HOUBRAKEN ET AL. J. CLIN.MICROBIOL.

M. E. Brandt, N. Zhang, and D. M. Geiser. 2008. Molecular phylogenetic
diversity, multilocus haplotype nomenclature, and in vitro antifungal resis-
tance within the Fusarium solani species complex. J. Clin. Microbiol. 46:
2477–2490.
34. Otcenasek, M., Z. Jirousek, Z. Nozicka, and K. Mencl. 1984. Paecilomycosis
of the maxillary sinus. Mykosen 27:242–251.
35. Pitt, J. I., and A. D. Hocking. 1979. Merimbla gen. nov. for the anamorphic
state of Talaromyces avellaneus. Can. J. Bot. 57:2394–2398.
36. Pitt, J. I., and A. D. Hocking. 2009. Fungi and food spoilage, 3rd ed.
Springer, Berlin, Germany.
37. Prenafeta-Boldu´, F. X., R. Summerbell, and G. Sybren de Hoog. 2006. Fungi
growing on aromatic hydrocarbons: biotechnology’s unexpected encounter
with biohazard? FEMS Microbiol. Rev. 30:109–130.
38. Rinaldi, S., E. Fiscarelli, and G. Rizzoni. 2000. Paecilomyces variotii perito-
nitis in an infant on automated peritoneal dialysis. Pediatr. Nephrol. 14:365–
366.
39. Rinyu, E., J. Varga, and L. Ferenczy. 1995. Phenotypic and genotypic analysis
of variability in Aspergillus fumigatus. J. Clin. Microbiol. 33:2567–2575.
40. Salle, V., E. Lecuyer, T. Chouaki, F. X. Lescure, A. Smail, A. Vaidie, C.
Dayen, J. L. Schmit, J. P. Ducroix, and Y. Douadi. 2005. Paecilomyces variotii
fungemia in a patient with multiple myeloma: case report and literature
review. J. Infect. 51:e93–e95.
41. Samson, R. A. 1974. Paecilomyces and some allied hyphomycetes. Stud.
Mycol. 6:1–119.
42. Samson, R. A., J. Houbraken, R. C. Summerbell, B. Flannigan, and J. D.
Miller. 2001. Common and important species of fungi and actinomycetes in
indoor environment, p. 287–474. In B. Flannigan, R. A. Samson, and J.
Miller (ed.), Microorganisms in home and indoor work environments. CRC
Press LLC, Boca Raton, FL.
43. Samson, R. A., E. S. Hoekstra, and J. C. Frisvad. 2004. Introduction to food-
and airborne fungi, 7th ed. Centraalbureau voor Schimmelcultures, Utrecht,
Netherlands.
44. Reference deleted.
45. Samson, R. A., J. Houbraken, J. Varga, and J. C. Frisvad. 2009. Polyphasic
taxonomy of the heat resistant ascomycete genus Byssochlamys and its Pae-
cilomyces anamorphs. Persoonia 22:14–27.
46. Seifert, K. A. 2009. Barcoding fungi. Progress towards DNA barcoding of
fungi. Mol. Ecol. Resource 9:83–89.
47. Skouboe, P., J. C. Frisvad, J. W. Taylor, D. Lauritsen, M. Boysen, and L.
Rossen. 1999. Phylogenetic analysis of nucleotide sequences from the ITS
region of terverticillate Penicillium species. Mycol. Res. 103:873–881.
48. Swofford, D. L. 2000. PAUP*: phylogenetic analysis using parsimony (*and
other methods), version 4.0b4a. Sinauer Associates, Sunderland, MA.
49. Tarkkanen, A., V. Raivio, V. J. Anttila, P. Tommila, R. Ralli, L. Merenmies,
and I. Immonen. 2004. Fungal endophthalmitis caused by Paecilomyces vari-
otii following cataract surgery: a presumed operating room air-conditioning
system contamination. Acta Ophthalmol. Scand. 82:232–235.
50. Thompson, R. F., R. B. Bode, J. C. Rhodes, and J. L. Gluckman. 1988.
Paecilomyces variotii. An unusual cause of isolated sphenoid sinusitis. Arch.
Otolaryngol. Head Neck Surg. 114:567–569.
51. Verweij, P. E., D. T. A. Te Dorsthorst, W. H. P. Janssen, J. F. G. M. Meis,
and J. W. Mouton. 2008. In vitro activity at pH 5.0 and pH 7.0 and in vivo
efficacy of flucytosine against Aspergillus fumigatus. Antimicrob. Agents Che-
mother. 52:4483–4485.
52. Walsh, T. J., A. Groll, J. Hiemenz, R. Fleming, E. Roilides, and E. Anaissie.
2004. Infections due to emerging and uncommon medically important fungal
pathogens. Clin. Microbiol. Infect. 10:48–66.
53. Yaghuchi, T., S. Udagawa, and K. Nishimura. 2005. Geosmithia argillacea is
the anamorph of Talaromyces eburneus as a heat resistant fungus. Crypto-
gamie Mycol. 26:133–141.
VOL. 48, 2010 IDENTIFICATION OF PAECILOMYCES VARIOTII 2761