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Original article
n,1 Eszter To
Krisztina Krizsa th,1 La
szlo
G. Nagy,1 La
szlo
Galgo
czy,1 Palanisamy Manikandan,2,3
Muthusamy Chandrasekaran, Shine Kadaikunnan, Naiyf S. Alharbi,4 Csaba Va
4 4
gvo
€ lgyi1,4 and
Tamas Papp 1
1
Faculty of Science and Informatics, Department of Microbiology, University of Szeged, Szeged, Hungary, 2Aravind Eye Hospital and Postgraduate Institute
of Ophthalmology, Coimbatore, India, 3Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Riyadh,
Saudi Arabia and 4Botany and Microbiology Department, King Saud University, Riyadh, Saudi Arabia
Summary A reliable identification method was developed for three closely related Curvularia
species, which are frequently isolated from human keratomycoses. Since the tradi-
tionally used morphological method and the increasingly used internal transcribed
spacer (ITS)-based molecular method proved to be insufficient to discern C. aus-
traliensis, C. hawaiiensis and C. spicifera, other molecular targets, such as b-tubulin,
translation elongation factor 1-a and the nuclear ribosomal intergenic spacer (IGS),
were tested. Among them, the use of the highly divergent IGS sequence is suggested
and the species-specific discriminating characters were determined in appropriate ref-
erence strains. It was also concluded that C. hawaiiensis and C. spicifera can be pre-
dominantly isolated from eye infections among the three species. The in vitro
antifungal susceptibility of 10 currently used antifungal agents against 32 Curvularia
isolates was also investigated. MICs were determined in each case. Isolates of C. spi-
cifera proved to be less susceptible to the tested antifungals than those of C. hawaiien-
sis, which underline the importance of the correct identification of these species.
Key words: Bipolaris, Cochliobolus, keratomycosis, nuclear ribosomal intergenic spacer, reference strain.
depending on the isolate, age of the colony or culture Statistical analysis was performed by Kruskal–Wallis
conditions, which makes species discrimination chal- test in RSTUDIO (Version 0.97.336; Boston, MA.
lenging with many misidentifications, especially in Retrieved May 20, 2012. RStudio: Integrated develop-
cases of C. australiensis and C. spicifera. Because of the ment environment for R. http://www.rstudio.org/).
lack of clear discriminating characteristics, clinical
microbiologists often report these fungi just as Bipolaris
DNA extraction and PCR
or Curvularia sp. without further identification.12,14–16
Recently, sequencing of the internal transcribed spacer Strains were grown in potato dextrose broth (PDB;
(ITS) region of the nuclear ribosomal RNA coding Difco) for 5 days at 28 °C on a rotary shaker at
cluster and comparison of the sequence data with the 200 rpm. Genomic DNA was extracted from 10 mg of
entries in GenBank have been used to confirm the spe- mycelia ground to a fine powder in liquid nitrogen and
cies-level diagnosis of Bipolaris/Curvularia isolates.16–19 purified by using the MasterPure Yeast DNA purifica-
Unfortunately, only a few data are available con- tion kit (Epicentre, Madison, Wisconsin, USA) accord-
cerning the antifungal susceptibility of these fungi20 ing to the instructions of the manufacturer. The
and categorical breakpoints are not available for sus- complete ITS (including ITS1 – 5.8S rRNA – ITS2) and
ceptibility testing. Bipolaris/Curvularia infections have IGS regions and fragments of the tef and tub genes were
often been reported to be refractory to amphotericin B amplified by PCR, using the following primers: ITS1
treatment, whereas sinusitis and keratitis responded and ITS4 for ITS,21 invSR1R and LR12R for IGS,22
well to itraconazole therapy in some studies.3,4 983F and 2218R for tef23 and T12 and T22 for tub 24
In the present study, Curvularia isolates obtained (for primer sequences see Table S2). Each reaction mix-
from human keratomycoses were examined to improve ture contained 10 Taq polymerase buffer (Zenon,
discrimination among C. australiensis, C. spicifera and Szeged, Hungary), 200 lmol l1 dNTPs, 1 lmol l1 of
C. hawaiiensis. Therefore, their most important mor- each primer, 5 U Taq polymerase (Zenon) and 50 ng of
phological characters and several molecular markers, genomic DNA in a final volume of 25 ll (amplification
such as the whole nuclear ribosomal transcribed conditions are detailed in Table S3).
spacer (ITS) and two segments of the nuclear riboso-
mal intergenic spacer (IGS) region, as well as the pro-
Sequence analysis
tein coding genes, translation elongation factor 1-a
(tef) and b-tubulin (tub) were analysed. Antimicrobial The ITS, IGS, tef and tub amplicons were sequenced at
susceptibility of the involved fungal isolates against LGC Genomics (Germany) with the primers used in the
the most important and currently used antifungal PCR experiments. Individual sequence readings were
agents was also evaluated. assembled to contigs by using the PREGAP and GAP4 pro-
grammes of the STADEN Package.25 In case of IGS,
instead of the whole region, two partial sequences were
Materials and methods
determined, the 1920-bp partial 18S rDNA – 18S-28S
intergenic spacer and the 877-bp partial 28S rDNA –
Strains
18S-28S intergenic spacer named in this study as
Fungal strains involved in the study are presented in IGS_1 and IGS_2, respectively. All sequences have been
Table S1. The strains from human keratomycoses deposited in NCBI GenBank (for the accession numbers
were isolated in the years 2007 and 2008 from see Table S1). Sequences were aligned using the Proba-
immunocompetent patients 11–75 years old at the bilistic Alignment Kit (PRANK version 091016).26 The
Aravind Eye Hospital and Postgraduate Institute of concatenated alignment of the ITS, tef, tub, IGS_1 and
Ophthalmology, Coimbatore, Tamil Nadu, India. IGS_2 was used in the phylogenetic analyses. For the
phylogenetic analysis, the best fit models were deter-
mined by using JMODELTEST 0.1.1.27,28 For the tub and
Morphological study
tef sequences the Hasegawa, Kishino and Yano (HKY)
Strains were grown on potato dextrose agar (PDA; model, for the ITS, IGS_1 and IGS_2 the generalised
Difco, Becton Dickinson, Franklin Lakes, New Jersey, time reversible (GTR + G + c model) were applied. Phy-
USA) medium for 14 days at 28 °C. Size and number logenetic reconstruction was carried out by Bayesian
of septa of 50 conidia per isolates were measured MCMC using MRBAYES v 3.1.2.29 Four Markov chains
using an ocular micrometre fitted on a light micro- were run for 3 9 107 generations, with a burn-in
scope (Zeiss Axiolab, Carl Zeiss, Jena, Germany). value of 7.5 9 104. Trees were sampled every 100th
Figure 1 Fifty per cent majority rule consensus tree of 26 990 post-burn-in trees obtained from the Bayesian analysis of the
ITS + tef + tub + IGS_1 + IGS_2 concatenated alignment, which was generated with the MRBAYES v 3.1.2. The Bipolaris sorokiniana CBS
110.14 was used as out-group. On the phylogram, four well-defined clades can be discerned, which correspond to C. spicifera, C. hawai-
iensis, C. australiensis and C. geniculata and Curvularia sp. Neotype strains of Curvularia spicifera, C. hawaiiensis and C. australiensis are
indicated by *. IGS, intergenic spacer; ITS, internal transcribed spacer.
generations. Post-burn-in trees (altogether 26 990 plates by both visual inspection and measuring the
trees) were used to compute a 50% Majority Rule con- optical density of the cultures at 620 nm after 48 and
sensus phylogram. Posterior probabilities ≥0.95 were 72 h incubations at 28 °C in standard RPMI-1640
considered as significant. In all phylogenetic analysis, medium (Sigma, St. Louis, Missouri, USA). Inocula
appropriate sequences of Bipolaris sorokiniana strain were prepared from 14-day cultures grown on PDA;
SZMC 13012 were used as the outgroup (Table S1). the final conidial suspensions contained 1–
5 9 104 CFU ml1. Final concentrations of the drugs
In vitro antifungal susceptibility tests ranged from 0.03 to 16 lg ml1, except those of NAT
In vitro antifungal activity of amphotericin B (AMB), and FLC, which ranged from 0.125 to 64 lg ml1.
clotrimazole (CLT), econazole (ECO), fluconazole (FLC), Each plate contained a sterile control (containing med-
itraconazole (ITC), ketoconazole (KTC), miconazole ium alone) and a growth control (containing inocu-
(MCZ), voriconazole (VRC), natamycin (NAT) and ter- lated medium without the drugs). The uninoculated
binafine (TRB) against the isolates was tested using a medium was used as background for the spectrophoto-
broth microdilution method according to the CLSI metric calibration. Each experiment was repeated three
guideline M38-A2.30 Minimal inhibitory concentration times; Paecilomyces variotii ATCC 22319 was used as
(MIC) values were determined in 96-well microtiter the quality control strain.
Table 1 Length and width of the conidia and number of the conidial septa measured in case of the studied Curvularia species.
seven-nucleotide motif was identified (at the position Table 2 In vitro minimal inhibitory concentration (MIC) values
260–266 in Fig. S4), which was unique in each spe- (lg ml1) of selected antifungal agents against the Curvularia
isolates.
cies. Many species-specific single nucleotide differences
(19 for C. australiensis, six for C. hawaiiensis and two MIC (lg ml1)
Species (number
for C. spicifera) and several 2- to 43-nucleotide motifs
of isolates) Agents Range MIC MIC50 MIC90
were detected in the IGS_2 partial sequence (Fig. S5).
Among them, there is a 17-nucleotide motif at the C. australiensis (3) AMB 1 1 n.d.1
position 782–798 (Fig. S5), which contain unique NAT 4 4 n.d.
characters for each species. CLT 0.25–0.5 0.5 n.d.
ECO 0.25–≥16 0.5 n.d.
FLC 16–64 32 n.d.
Conidial morphology ITC 0.125–0.5 0.125 n.d.
KTC 0.5–1 0.5 n.d.
Length, width and the number of septa of 50 conidia MCZ 0.25–0.5 0.5 n.d.
were measured for each tested isolate (Table 1). Differ- VRC 0.5–1 0.5 n.d.
TRB 0.5 0.5 n.d.
ences in the length and width of the conidia of the C. hawaiiensis (12) AMB 0.125–1 0.5 1
C. australiensis, C. spicifera and C. hawaiiensis isolates NAT 2–4 1–2 2
proved to be not significant. Although conidia of the CLT 0.5–2 0.5–1 1
C. geniculata isolates also had similar dimensions, these ECO 0.25–≥16 2 16
isolates could be easily differentiated from those of the FLC 32–≥64 32 64
ITC 0.06–1 0.125 1
three other species based on their typical, curved, KTC 0.25–1 0.5–1 1
Curvularia-type conidia. MCZ 0.25–2 0.5–1 1
VRC 0.5–4 1 4
TRB 0.25–4 2 4
Antimicrobial susceptibility assay C. spicifera (12) AMB 0.125–2 0.5–1 1
NAT 1–4 2 4
Minimal inhibitory concentrations (MIC50 and MIC90 CLT 0.125–8 1 8
values) of the tested antifungal agents are shown in ECO 0.5–≥16 8–16 >16
Table 2. The MIC50 of ITC was found to be FLC 32–64 32–64 64
0.125 lg ml1 for C. autraliensis and C. hawaiiensis, ITC 0.25–4 0.5 2
0.25 lg ml1 for C. genicluata and 0.5 lg ml1 for KTC 0.125–8 2 4
MCZ 0.5–4 2 4
C. spicifera, while the MIC90 value was 1 lg ml1 for VRC 2–4 2 4
C. hawaiiensis and 2 lg ml1 for C. spicifera. FLC dis- TRB 0.25–8 2 4
played MIC50 values in the range of 8–64 lg ml1 and C. geniculata (3) AMB 0.5–1 1 n.d.
MIC90 at 64 lg ml1. The four groups of isolates NAT 2–4 2 n.d.
showed high variability in their susceptibility to ECO as CLT 0.25–2 0.5 n.d.
ECO 0.5–4 0.5 n.d.
the MIC50 values ranged from 0.25 to 16 lg ml1. FLC 8–64 8 n.d.
MIC50 and MIC90 values of the other tested azoles (CLT, ITC 0.125–2 0.25 n.d.
KTZ, MCZ and VRC) were found in the ranges of 0.25–4 KTC 0.25–2 0.5 n.d.
and 1–8 lg ml1, respectively. MIC50 values of AMB MCZ 0.125–2 0.5 n.d.
were found at 1 lg ml1 for C. australiensis, C. spicifera VRC 0.5–2 0.5 n.d.
TRB 0.5–2 1 n.d.
and C. geniculata and at 0.5 lg ml1 for C. hawaiiensis,
whereas the MIC90 value was determined to 1 lg ml1 AMB, amphotericin B; CLT, clotrimazole; ECO, econazole; FLC,
for C. hawaiiensis and C. spicifera. MIC50 of NAT for fluconazole; ITC, itraconazole; KTC, ketoconazole; MCZ, micona-
C. hawaiiensis, C. spicifera and C. geniculata was found at zole; VRC, voriconazole; NAT, natamycin; TRB, terbinafine.
1
2 lg ml1, while it was 4 lg ml1 for the C. australien- n.d., not defined. MIC50 and MIC90 were defined as the lowest
concentrations inhibiting the growth of 50 or 90% of the isolates
sis isolates. The MIC90 values were 2 lg ml1 for of a species, respectively. MIC90 could not be defined for species
C. hawaiiensis and 4 lg ml1 for C. spicifera. For TRB, represented by <10 isolates.
MIC values ranged from 0.25 to 8 lg ml1.
Original article
n,1 Eszter To
Krisztina Krizsa th,1 La
szlo
G. Nagy,1 La
szlo
Galgo
czy,1 Palanisamy Manikandan,2,3
Muthusamy Chandrasekaran, Shine Kadaikunnan, Naiyf S. Alharbi,4 Csaba Va
4 4
gvo
€ lgyi1,4 and
Tamas Papp 1
1
Faculty of Science and Informatics, Department of Microbiology, University of Szeged, Szeged, Hungary, 2Aravind Eye Hospital and Postgraduate Institute
of Ophthalmology, Coimbatore, India, 3Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Riyadh,
Saudi Arabia and 4Botany and Microbiology Department, King Saud University, Riyadh, Saudi Arabia
Summary A reliable identification method was developed for three closely related Curvularia
species, which are frequently isolated from human keratomycoses. Since the tradi-
tionally used morphological method and the increasingly used internal transcribed
spacer (ITS)-based molecular method proved to be insufficient to discern C. aus-
traliensis, C. hawaiiensis and C. spicifera, other molecular targets, such as b-tubulin,
translation elongation factor 1-a and the nuclear ribosomal intergenic spacer (IGS),
were tested. Among them, the use of the highly divergent IGS sequence is suggested
and the species-specific discriminating characters were determined in appropriate ref-
erence strains. It was also concluded that C. hawaiiensis and C. spicifera can be pre-
dominantly isolated from eye infections among the three species. The in vitro
antifungal susceptibility of 10 currently used antifungal agents against 32 Curvularia
isolates was also investigated. MICs were determined in each case. Isolates of C. spi-
cifera proved to be less susceptible to the tested antifungals than those of C. hawaiien-
sis, which underline the importance of the correct identification of these species.
Key words: Bipolaris, Cochliobolus, keratomycosis, nuclear ribosomal intergenic spacer, reference strain.
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Figure S5. Alignment of IGS_2 sequences of Curvu-
broth dilution antifungal susceptibility testing of filamentous fungi; laria species.