Genetic variation analysis and relationships among environmental strains of Scedosporium apiospermum sensu stricto in Bangkok, Thailand

PLOS ONE, Jul 2017

The Scedosporium apiospermum species complex is an emerging filamentous fungi that has been isolated from environment. It can cause a wide range of infections in both immunocompetent and immunocompromised individuals. We aimed to study the genetic variation and relationships between 48 strains of S. apiospermum sensu stricto isolated from soil in Bangkok, Thailand. For PCR, sequencing and phylogenetic analysis, we used the following genes: actin; calmodulin exons 3 and 4; the second largest subunit of the RNA polymerase II; ß-tubulin exon 2–4; manganese superoxide dismutase; internal transcribed spacer; transcription elongation factor 1α; and beta-tubulin exons 5 and 6. The present study is the first phylogenetic analysis of relationships among S. apiospermum sensu stricto in Thailand and South-east Asia. This result provides useful information for future epidemiological study and may be correlated to clinical manifestation.

A PDF file should load here. If you do not see its contents the file may be temporarily unavailable at the journal website or you do not have a PDF plug-in installed and enabled in your browser.

Alternatively, you can download the file locally and open with any standalone PDF reader:

http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0181083&type=printable

Genetic variation analysis and relationships among environmental strains of Scedosporium apiospermum sensu stricto in Bangkok, Thailand

July Genetic variation analysis and relationships among environmental strains of Scedosporium apiospermum sensu stricto in Bangkok, Thailand Thanwa Wongsuk 0 1 Potjaman Pumeesat 0 1 Natthanej Luplertlop 0 1 0 Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University , Bangkok , Thailand , 2 Department of Clinical Pathology, Faculty of Medicine, Vajira Hospital, Navamindradhiraj University , Bangkok , Thailand , 3 Department of Medical Technology, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University , Bangkok , Thailand 1 Editor: Craig Eliot Coleman, Brigham Young University , UNITED STATES The Scedosporium apiospermum species complex is an emerging filamentous fungi that has been isolated from environment. It can cause a wide range of infections in both immunocompetent and immunocompromised individuals. We aimed to study the genetic variation and relationships between 48 strains of S. apiospermum sensu stricto isolated from soil in Bangkok, Thailand. For PCR, sequencing and phylogenetic analysis, we used the following genes: actin; calmodulin exons 3 and 4; the second largest subunit of the RNA polymerase II; û-tubulin exon 2±4; manganese superoxide dismutase; internal transcribed spacer; transcription elongation factor 1α; and beta-tubulin exons 5 and 6. The present study is the first phylogenetic analysis of relationships among S. apiospermum sensu stricto in Thailand and South-east Asia. This result provides useful information for future epidemiological study and may be correlated to clinical manifestation. - Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: This study was supported by Health System Research Institute (HSRI) 2016, National Research Council of Thailand (NRCT) 2016 and Tropical Medicine grant 2014, Faculty of Tropical Medicine, Mahidol University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Introduction Competing interests: The authors have declared that no competing interests exist. level is important as epidemiology, clinical outcomes, and antifungal susceptibility are species-specific [ 9,10 ]. In order to overcome the difficulties in identifying Scedosporium species by routine microbiological methods, several molecular techniques have been proposed such as quantitative real-time PCR (qPCR), PCR-based reverse line blot (PCR-RLB), and loop-mediated isothermal amplification (LAMP) [ 11,12 ]. Additionally, globally standardized genotyping of S. apiospermum and S. boydii, the Multi-Locus Sequences Typing (MLST) scheme, was developed by Bernhardt et al. [13]. The MLST scheme amplifies sequences at five genetic loci±actin (ACT), calmodulin exons 3 and 4 (CAL), the second largest subunit of RNA polymerase II gene (RPB2), û-tubulin exons 2±4 (BT2), and manganese superoxide dismutase (SOD2) and has been found to have strong repeatability [13±15]. The allele types (ATs) and sequences types (STs) numbers of the consensus MLST scheme can be obtained through the Fungal MLST Database (http://mlst.mycologylab.org/). In our previous study, we investigated the spatial distribution of the S. apiospermum species complex in soil in Bangkok, Thailand. We found that the S. apiospermum species complex is widespread in soil across Bangkok and detected predominance of S. apiospermum sensu stricto (72%) [ 16 ]. Here, we continue the study by considering the genetic variation and relationships among S. apiospermum sensu stricto isolated from soil in Bangkok. The data may be used for further epidemiological research, for which it is important to recognize different strains and subspecies. Materials and methods Strains We used 48 isolates of S. apiospermum sensu stricto from our stock collection. Each isolate originated from soil and had previously been typed by PCR of the beta-tubulin gene (exons 5 and 6) [ 16 ]. Each isolate was labeled as TMMI (Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University yeast and moulds culture collection) with a unique identification number (Table 1). DNA extraction DNA was extracted with an E.Z.N.A. Fungal DNA mini kit (Omega Bio-tek). The DNA samples were quantified and the quality was checked with a NanoDrop 2000 spectrophotometer (Thermo Fisher, Wilmington, DE, USA) and stored at −20ÊC until further use. Molecular biology technique For PCR, sequencing and phylogenetic analysis we used eight genes: ACT, CAL, RPB2, BT2, SOD2, internal transcribed spacer (ITS), transcription elongation factor 1α (TEF-1α), and 28S large subunit ribosomal RNA (LSU). PCR amplification of eight gene regions was carried out with the specific primer pairs listed in Table 2. Each PCR reaction mixture was performed in 25-μl final volume containing: 0.5 μM of each primer, KAPA 2G Fast HS ReadyMix PCR kit with loading dye (KAPA Biosystems, USA), nuclease-free water and genomic DNA. PCR amplifications were carried out in a T100 Thermal Cycler (Bio-Rad) according to the following protocol: an initial step of 96ÊC for 6 min, followed by 35 cycles of 94ÊC for 1 min, an annealing temperature that specific with each gene (Table 2) for 1 min and 72ÊC for 45 s and a final extension step of 72ÊC for 10 min. Then, 5 μL of the PCR products were electrophoresed in a 1.5% agarose gel containing SERVA DNA Stain G (SERVA Electrophoresis GmbH, Germany) in 1X TBE buffer, and photographed using a Gel Doc XR+ system (Bio-Rad). 2 / 16 KY123063 KY123064 KY123065 KY123066 KY123067 KY123068 KY123069 KY123070 KY123071 KY123072 KY123073 KY123074 KY123075 KY123076 KY123077 KY123078 KY123079 KY123080 KY123081 KY123082 KY123083 KY123084 KY123085 KY123086 KY123087 KY123088 KY123089 KY123090 KY123091 KY123092 KY123093 KY123094 KY123095 KY123096 KY123097 KY123098 KY123099 KY123100 KY123101 KY123102 KY123103 KY123104 KY123105 KY123106 KY123107 (Continued) 3 / 16 RPB2 TEF-1α KY122772 KY122820 KY122773 KY122821 KY122774 KY122822 GenBank accession numbers ITS LSU ACT CAL SOD2 KY122868 KY122916 KY122964 KY123012 KY123060 KY122869 KY122917 KY122965 KY123013 KY123061 KY122870 KY122918 KY122966 KY123014 KY123062 Each PCR product was purified using a FavorPrepTM GEL/PCR Purification Mini Kit (Favorgen Biotech Corporation, Taiwan) and sequenced using gene-specific both forward and reverse primers at the AITbiotech Pty Ltd (Singapore). The retrieved sequence files were analyses using BioEdit software (http://www.mbio.ncsu.edu/bioedit/bioedit.html) and compared with existing sequences in GenBank using BLASTn (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Genotyping variation and relationship analysis of eight housekeeping genes Nucleotide sequences of seven genes (ACT, CAL, RPB2, BT2, SOD2, ITS, TEF-1α) were used for genetic variation and relationship analysis together with û-tubulin exons 5 and 6 gene (TUB). The following TUB sequences were downloaded from GenBank: KU533691, KU533702, KU533711, KU533712, KU533691, KU533656, KU533658, KU533655, KU533649, KU533673, KU533713, KU533674, KU533675, KU533695, KU533676, KU533703, KU533723, KU533704, KU533692, KU533693, KU533694, KU533677, KU533705, KU533678, KU533659, KU533679, KU533696, KU533680, KU533681, KU533682, KU533683, KU533707, KU533660, KU533684, KU533708, KU533706, KU533666, KU533697, KU533685, KU533650, KU533651, KU533652, KU533709, KU533710, KU533657, KU533716, KU533698, and KU533717. Each sequence was trimmed to the correct length with the start and the end of each gene (shown in Table 3). Genotype variation of each gene was analyzed by MLSTest v1.0.1.23 software, which was downloaded from http://ipe.unsa.edu.ar/software [ 21 ]. The ATs number was created by 4 / 16 using the same software and allele profiles were used to assign the STs number. A phylogenetic network of each loci was performed with the neighbor-net algorithm by SplitsTree4 and downloaded from http://www.splitstree.org/ [ 22 ]. Sequences were concatenated by the following order respectively; ACT, CAL, RPB2, BT2, SOD2, ITS, TEF-1α and TUB. The best model of evolution for concatenated data set were selected from the Bayesian Information Criterion (BIC) in MEGA7 [ 23 ]. Model with the lowest BIC score was chosen to construct a maximum likelihood phylogenetic tree. A phylogenetic tree of the 48 aligned sequences excluding gaps and missing data for the heuristic search was obtained by applying the neighbor-joining method to a matrix of pairwise distances estimated using the maximum likelihood approach based on the best model in MEGA7 [ 23 ]. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Codon positions included were 1st+2nd+3rd+Noncoding. There were a total of 4,841 positions in the final dataset. A bootstrap analysis was conducted with 1000 replications and bootstrap values 50% were shown above branches. Phylogenetic analysis of the concatenated sequences of ACT, CAL, RPB2, BT2 and SOD2 genes To assess evolutionary relationships among isolates, all 48 generated concatenated of ACT, CAL, RPB2, BT2 and SOD2 genes sequences as well as 27 concatenated sequences of S. apiospermum sensu stricto (isolate IHEM 15555, IHEM 15553, IHEM 15552, IHEM 15551, IHEM 15148, IHEM 15146, IHEM 14764, IHEM 14763, IHEM 14762, IHEM 14465, IHEM 14463, IHEM 14462, IHEM 15151, IHEM 15149, IHEM 15643, IHEM 14276, IHEM 14275, IHEM 14273, IHEM 14270, IHEM 14269, IHEM 14268), BMU07462, BMU04729, BMU04111, BMU03882, BMU01117 and BMU00491) from other regions of the world and three S. boydii (isolate IHEM 14362, IHEM 14638 and IHEM 14457) concatenated sequences downloaded from GenBank were multiply-aligned using BioEdit. The concatenated sequences of S. aurantiacum isolate IHEM 15458, S. angusta isolate BMU01115, Pseudallescheria fusoidea isolate BMU01297 and Pseudallescheria ellipsoidea isolate BMU01118 were included in the phylogenetic analysis. GenBank accession numbers are listed in S1 Table. MEGA7 [ 23 ] was used to selected the best model of evolution and a phylogenetic tree was constructed as described above. The analysis involved 82 nucleotides sequences. All position containing gaps and missing data were eliminated. There were a total of 2,958 positions in the final dataset. A bootstrap analysis was conducted with 1000 replications and bootstrap values 50% were shown above branches also. 5 / 16 Nucleotide sequences accession numbers The generated nucleotide sequences were deposited in GenBank under accession numbers and listed in Table 1. Results PCR amplification of the eight genes was successful for all strains, with a single band investigated on gels after electrophoresis. The BLASTn algorithm was used for sequence similarity searching in the NCBI database. Sequence-based identities with a cutoff of 99% were considered significant [ 24,25 ]. Genotypic variation profiling of S. apiospermum sensu stricto was generated and showed 37 good different STs from 48 strains (Table 4). The numbers of ATs variation at each loci were 8 (ACT), 7 (CAL), 11 (RPB2), 12 (BT2), 18 (SOD2), 15 (ITS), 6 (TEF-1α), and 8 (TUB) (Table 5). The number of polymorphisms, typing efficacy, and power of discrimination (95% confidential interval) were calculated (Table 3). We found diverse genetic relationships among the genotyped variants of 48 S. apiospermum sensu stricto after analyzing each gene with a neighbor-net algorithm (Fig 1). The best model for concatenated data set (ACT, CAL, RPB2, BT2, SOD2, ITS, TEF-1α and TUB, respectively) analyses was HKY+G+I (HKY: Hasegawa-Kishino-Yano; +G: Gamma distribution; +I: invariable sites) and the BIC score was 18004.65987. Therefore, the maximum likelihood phylogenetic tree of concatenated data set was created based on the HKY model [ 26 ]. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.0500). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 48.7606% sites) (Fig 2). To compare the genetic relationship of strains in Thailand with other regions of the world, the ACT, CAL, RPB2, BT2 and SOD2 sequences from previous studies in France, China and Japan were downloaded from GenBank. Data for these five genes were concatenated. TN93+G +I model (TN93: Tamura-Nei) was chosen according the best model of evolution analyses (the BIC score was 17282.89945). Then, a phylogenetic tree constructed by maximum likelihood analysis based on the TN93 model [ 27 ]. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.1587)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 42.7147% sites). As a tree (Fig 3), 82 nucleotide sequences comprised 2,958 positions were involved. S. apiospermum sensu stricto was strongly clustered together among Thai, French, Chinese and Japanese isolates (strongly supported by bootstrap value of 100%) and were subdivided into two groups (Group I and Group II). Discussion The Scedosporium apiospermum species complex contains important opportunistic species. Giraud and Bouchara [ 8 ] and the European Confederation of Medical Mycology (ECMM)/ International Society for Human and Animal Mycology (ISHAM) classify the novel nomenclature of the S. apiospermum species complex as comprising five species: S. apiospermum sensu stricto, S. boydii (= Pseudallescheria boydii), S. aurantiacum, S. dehoogii, and S. minutispora. In contrast, a recent study [ 7 ] defined the S. apiospermum species complex as only S. apiospermum, S. boydii, and S. angusta (= Pseudalleschelia angusta) because phylogenetic analysis of βtubulin (BT2), γ-actin, transcriptional elongation factor 1α (TEF-1α), and internal transcribed spacer of the small ribosomal protein 60sS L10 (L1) distinguished S. minutispora, S. aurantiacum, and S. dehoogii from these three species. These days, there are numerous molecular 6 / 16 7 / 16 CAL RPB2 BT2 SOD2 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 1 2 3 4 5 6 7 8 9 1 2 3 4 5 6 7 8 9 10 11 10 11 12 1 14 21 6 2 2 1 1 1 6 9 18 8 3 2 1 10 19 4 3 1 5 1 2 1 1 1 6 6 2 2 1 1 1 1 1 1 1 10 16 TMMI015 TMMI058 TMMI063 TMMI070 TMMI053 TMMI057, TMMI067 TMMI005, TMMI009 TMMI006, TMMI015 TMMI025 TMMI053 TMMI061 TMMI063 TMMI067 TMMI070 TMMI001 (Continued) 8 / 16 Gene ATs Frequency Gene ATs Frequency 2 2 3 2 4 4 5 14 techniques to determine genetic diversity that are robust and reproducible. MLST has been proposed as one of the best tools for genotypic and evolutionary studies. In the fungal research field, four working groups have established public MLST schemes: (1) ISHAM established an MLST scheme for Cryptococcus gattii, Cryptococcus neoformans, S. apiospermum, S. boydii, S. aurantiacum, Bipolaris australiensis, Bipolaris. hawaiiensis, Bipolaris spicifera (http://mlst.mycologylab.org/); (2) Westerdijk Fungal Biodiversity Institute (CBS-KNAW Fungal Biodiversity Centre) established an MLST scheme for Fusarium spp. (http://www.westerdijkinstitute.nl/fusarium/); (3) Imperial College established an MLST scheme for Candida albicans and Candida glabrata (http://www.mlst.net/); and (4) Oxford University established an MLST scheme for Aspergillus fumigatus, Pichia kudriavzevii (Candida krusei) and Candida tropicalis (http://pubmlst.org/). MLST is clearly a powerful method for typing and studying genetic variation in microorganisms. In this study, we used the MLST tool to study S. apiospermum sensu stricto previously isolated from soil samples. We chose eight housekeeping gene loci (ACT, BT2, CAL, ITS, RPB2, SOD2, TEF-1α, LSU) coupled with the TUB gene from our previous study to analyze the genetic variation and relationships among S. apiospermum sensu stricto strains, which are currently unknown and have not been previously analyzed genetically in Thailand or South-east Asia. We successfully sequenced all selected loci, but only the LSU sequences showed no polymorphisms (data not show). We identified 37 STs after combining the 8 genes (except LSU). In each gene fragment, the number of alleles varied; 8, 12, 8, 15, 11, 18, 6, 8 for ACT, BT2, CAL, ITS, RPB2, SOD2, TEF-1α, and TUB, respectively. The number of polymorphisms for each gene fragment varied from 6 (TEF-1α) to 41 (BT2). The sequences of the 48 S. apiospermum sensu stricto strains were accessed by a neighbor-net algorithm in SplitsTree4. SplitsTree4 graphs of ACT, CAL, RPB2, BT2, SOD2, ITS, TEF-1α, and TUB sequence data showed parallelograms that implied the character is shared by a set of species. In terms of discriminatory power (DP) evaluation, SOD2 showed the highest DP (0.932); TUB showed the lowest DP, which was 0.688. Additionally, there were 37 STs, which could be grouped; each isolate had one ST type except ST3, ST9, ST11, ST13, ST18, and ST21, which had 2, 5, 2, 4, 2, and 2 ST types, respectively. In our study, SOD2 provided the highest number of alleles (18), and another study showed a similar high number of alleles for SOD2 [ 13 ]. Moreover, we combined five loci (ACT, CAL, RPB2, BT2 and SOD2) for objective genetic relationship analysis between Thailand (representing South-east Asia), China and Japan (Asia), and France (Europe): (i) to assess the relationship between clinical and environmental strains of S. apiospermum; and (ii) to assess the global variation between S. apiospermum strains. Our results detected a close relationship between the environmental strains from Thailand and the clinical strains from France [ 15 ], China and Japan [ 28 ]. Therefore, French, Chinese and 10 / 16 Fig 1. Phylogenetic network (A±H). SplitTree decomposition analysis using the neighbor-net algorithm of each of the eight genes i.e. A. ACT, B. CAL, C. RPB2, D. BT2, E. SOD2, F. ITS, G. TEF-1α and H. TUB (in blanket to show the number of the collection name of each strain). 11 / 16 Fig 2. Molecular phylogenetic maximum likelihood analysis of the concatenated sequences of ACT, CAL, RPB2, BT2, SOD2, ITS, TEF-1α, and TUB genes. The tree with the highest log likelihood (-8390.7037) is shown. 12 / 16 Fig 3. Molecular phylogenetic maximum likelihood analysis of the concatenated sequences of ACT, CAL, RPB2, BT2 and SOD2 genes. The tree with the highest log likelihood (-1105.3764) is shown. The black 13 / 16 circle represents the strains from Thailand (environmental isolates), the blue circle represents the strains from France (clinical isolates), the green circle represents the strains from China (clinical isolates) and the pink circle represents the strains from Japan (clinical isolates). Japan isolates originated in Thailand also. These data suggest that S. apiospermum sensu stricto isolates retrieved from different regions and different countries shared a close genetic relatedness. One limitation of our study was a lack of clinical isolates from Thailand to compare with our environmental strains. We hope that our data may be useful for other researchers in future study. Interestingly, TEF-1α used as a marker in an MLST scheme for S. aurantiacum (http://mlst.mycologylab.org/) including other filamentous fungi such as Fusarium [ 29 ], did not use S. apiospermum or S. boydii. In our data, TEF-1α presented the lowest number of alleles (6) and the DP was also quite low (0.688). This result may explain why TEF-1α was not used for S. apiospermum or S. boydii. In summary, we here present the first phylogenetic analysis of relationships among S. apiospermum sensu stricto in Thailand and the South-east Asian region. The results provide valuable knowledge to assist future study and perhaps link the relationships of species in clinical settings. Supporting information CAL, RPB2, BT2 and SOD2.) (DOCX) Acknowledgments S1 Table. Strains, specimens, countries and GenBank accession numbers of 34 sequences. (All sequences were using for phylogenetic analysis of the concatenated sequences of ACT, We thank Dr. Ana Alastruey-Izquierdo (National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda 228220, España) for her valuable assistance. Author Contributions Conceptualization: Natthanej Luplertlop. Data curation: Natthanej Luplertlop. Formal analysis: Natthanej Luplertlop. Investigation: Thanwa Wongsuk, Potjaman Pumeesat. Methodology: Thanwa Wongsuk, Potjaman Pumeesat, Natthanej Luplertlop. Writing ± original draft: Thanwa Wongsuk, Potjaman Pumeesat. Writing ± review & editing: Natthanej Luplertlop. 14 / 16 15 / 16 1. Borghi E , Iatta R , Manca A , Montagna MT , Morace G . Chronic airway colonization by Scedosporium apiospermum with a fatal outcome in a patient with cystic fibrosis . Med Mycol 2010 ; 48 Suppl 1 : S108 ± 13 . https://doi.org/10.3109/13693786. 2010 .504239 PMID: 21067322 2. Rougeron A , Schuliar G , Leto J , Sitterle E , Landry D , Bougnoux ME , et al. Human-impacted areas of France are environmental reservoirs of the Pseudallescheria boydii/Scedosporium apiospermum species complex . Environ Microbiol . 2015 ; 17 ( 4 ): 1039 ± 48 . https://doi.org/10.1111/ 1462 - 2920 .12472 PMID: 24684308 3. Leechawengwongs M , Milindankura S , Liengudom A , Chanakul K , Viranuvatti K , Clongsusuek P. Multiple Scedosporium apiospermum brain abscesses after near-drowning successfully treated with surgery and long-term voriconazole: a case report . Mycoses . 2007 ; 50 ( 6 ): 512 ±6. https://doi.org/10.1111/j.1439- 0507 . 2007 . 01410 . x PMID : 17944716 4. Larbcharoensub N , Chongtrakool P , Wirojtananugoon C , Watcharananan SP , Sumethkul V , Boongird A , et al. Treatment of a brain abscess caused by Scedosporium apiospermum and Phaeoacremonium parasiticum in a renal transplant recipient . Southeast Asian J Trop Med Public Health . 2013 ; 44 ( 3 ): 484 ± 9 . PMID: 24050081 5. Satirapoj B , Ruangkanchanasetr P , Treewatchareekorn S , Supasyndh O , Luesutthiviboon L , Supaporn T. Pseudallescheria boydii brain abscess in a renal transplant recipient: first case report in Southeast Asia . Transplant Proc . 2008 ; 40 ( 7 ): 2425 ±7. https://doi.org/10.1016/j.transproceed. 2008 . 07 .030 PMID: 18790255 6. Garzoni C , Emonet S , Legout L , Benedict R , Hoffmeyer P , Bernard L , et al. Atypical infections in tsunami survivors . Emerg Infect Dis . 2005 ; 11 ( 10 ): 1591 ±3. https://doi.org/10.3201/eid1110.050715 PMID: 16318701 7. Chen M , Zeng J , de Hoog GS , Stielow B , Gerrits Van Den Ende AH , Liao W , et al. ( 2016 ) The 'species complex' issue in clinically relevant fungi: a case study in Scedosporium apiospermum . Fungal Biol . 2016 ; 120 ( 2 ): 137 ± 46 . https://doi.org/10.1016/j.funbio. 2015 . 09 .003 PMID: 26781369 8. Giraud S , Bouchara JP . Scedosporium apiospermum complex: diagnosis and species identification . Curr Fungal Infect Rep . 2014 ; 8(3):211±9 . https://doi.org/10.1007/s12281-014-0192-z 9. Gilgado F , Serena C , Cano J , Gene J , Guarro J . Antifungal susceptibilities of the species of the Pseudallescheria boydii complex . Antimicrob Agents Chemother . 2006 ; 50 ( 12 ): 4211 ±3. https://doi.org/10. 1128/AAC.00981-06 PMID: 17015631 10. Heath CH , Slavin MA , Sorrell TC , Handke R , Harun A , Phillips M , et al. Population-based surveillance for scedosporiosis in Australia: epidemiology, disease manifestations and emergence of Scedosporium aurantiacum infection . Clin Microbiol Infect . 2009 ; 15 ( 7 ): 689 ± 93 . https://doi.org/10.1111/j.1469- 0691 . 2009 . 02802 . x PMID : 19549223 11. Lu Q , Gerrits van den Ende AH , Bakkers JM , Sun J , Lackner M , Najafzadeh MJ , et al. Identification of Pseudallescheria and Scedosporium species by three molecular methods . J Clin Microbiol . 2011 ; 49 ( 3 ): 960 ±7. https://doi.org/10.1128/JCM.01813-10 PMID: 21177887 12. Ramsperger M , Duan S , Sorrell TC , Meyer W , Chen SC . The genus Scedosporium and Pseudallescheria: current challenges in laboratory diagnosis . Curr Clin Microbiol Rep . 2014 ; 1 ( 1 ±2): 27 ± 36 . https://doi.org/10.1007/s40588-014-0001-z 13. Bernhardt A , Sedlacek L , Wagner S , Schwarz C , Wurstl B , Tintelnot K. Multilocus sequence typing of Scedosporium apiospermum and Pseudallescheria boydii isolates from cystic fibrosis patients . J Cyst Fibros . 2013 ; 12 ( 6 ): 592 ±8. https://doi.org/10.1016/j.jcf. 2013 . 05 .007 PMID: 23764085 14. Bernhardt A , Seibold M , Rickerts V , Tintelnot K. Cluster analysis of Scedosporium boydii infections in a single hospital . Int J Med Microbiol . 2015 ; 305 ( 7 ): 724 ±8. https://doi.org/10.1016/j.ijmm. 2015 . 08 .024 PMID: 26330287 15. Matray O , Mouhajir A , Giraud S , Godon C , Gargala G , Labbe F , et al. Semi-automated repetitive sequence-based PCR amplification for species of the Scedosporium apiospermum complex . Med Mycol . 2016 ; 54 ( 4 ): 409 ± 19 . https://doi.org/10.1093/mmy/myv080 PMID: 26486722 16. Luplertlop N , Pumeesat P , Muangkaew W , Wongsuk T , Alastruey-Izquierdo A . Environmental screening for the Scedosporium apiospermum species complex in public parks in Bangkok, Thailand . PLoS One . 2016 ; 11 ( 7 ):e0159869. https://doi.org/10.1371/journal.pone. 0159869 PMID: 27467209 17. Hoffmann K , Discher S , Voigt K. Revision of the genus Absidia (Mucorales, Zygomycetes) based on physiological, phylogenetic, and morphological characters; thermotolerant Absidia spp. form a coherent group, Mycocladiaceae fam . nov. Mycol Res . 2007 ; 111 (Pt 10): 1169 ± 83 . https://doi.org/10.1016/j. mycres. 2007 . 07 .002 PMID: 17997297 18. Liu YJ , Whelen S , Hall BD . Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit . Mol Biol Evol . 1999 ; 16 ( 12 ): 1799 ± 808 . PMID: 10605121 19. Glass NL , Donaldson GC . Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes . Appl Environ Microbiol . 1995 ; 61 ( 4 ): 1323 ± 30 . PMID: 7747954 20. Stielow JB , LeÂvesque CA , Seifert KA , Meyer W , Iriny L , Smits D , et al. One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes . Persoonia . 2015 ; 35 : 242 ± 63 . https://doi.org/10.3767/003158515X689135 PMID: 26823635 21. Tomasini N , Lauthier JJ , Llewellyn MS , Diosque P. MLSTest: novel software for multi-locus sequence data analysis in eukaryotic organisms . Infect Genet Evol . 2013 ; 20 : 188 ± 96 . https://doi.org/10.1016/j. meegid. 2013 . 08 .029 PMID: 24025589 22. Huson DH , Bryant D. Application of phylogenetic networks in evolutionary studies . Mol Biol Evol . 2006 ; 23 ( 2 ): 254 ± 67 . https://doi.org/10.1093/molbev/msj030 PMID: 16221896 23. Kumar S , Stecher G , Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets . Mol Biol Evol . 2016 ; 33 ( 7 ): 1870 ± 4 . https://doi.org/10.1093/molbev/msw054 PMID: 27004904 24. Pounder JI , Simmon KE , Barton CA , Hohmann SL , Brandt ME , Petti CA. Discovering potential pathogens among fungi identified as nonsporulating molds . J Clin Microbiol . 2007 ; 45 ( 2 ): 568 ± 71 . https://doi. org/10.1128/JCM.01684-06 PMID: 17135442 25. Rakeman JL , Bui U , Lafe K , Chen YC , Honeycutt RJ , Cookson BT . Multilocus DNA sequence comparisons rapidly identify pathogenic molds . J Clin Microbiol . 2005 ; 43 ( 7 ): 3324 ± 33 . https://doi.org/10.1128/ JCM.43.7. 3324 - 3333 . 2005 PMID: 16000456 26. Hasegawa M , Kishino H , Yano T. Dating the human-ape split by a molecular clock of mitochondrial DNA . J Mol Evol . 1985 ; 22 ( 2 ): 160 ± 74 . PMID: 3934395 27. Tamura K , Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees . Mol Biol Evol . 1993 ; 10 ( 3 ): 512 ± 26 . PMID: 8336541 28. Wang H , Wan Z , Li R , Lu Q , Yu J ( 2015 ) Molecular identification and susceptibility of clinically relevant Scedosporium spp . in China. Biomed Res Int . 2015 ; 2015 :109656. https://doi.org/10.1155/ 2015 / 109656 PMID: 26550562 29. Debourgogne A , Gueidan C , Hennequin C , Contet-Audonneau N , de Hoog S , Machouart M. Development of a new MLST scheme for differentiation of Fusarium solani species complex (FSSC) isolates . J Microbiol Methods . 2010 ; 82 ( 3 ): 319 ± 23 . https://doi.org/10.1016/j.mimet. 2010 . 07 .008 PMID: 20624428


This is a preview of a remote PDF: http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0181083&type=printable

Thanwa Wongsuk, Potjaman Pumeesat, Natthanej Luplertlop. Genetic variation analysis and relationships among environmental strains of Scedosporium apiospermum sensu stricto in Bangkok, Thailand, PLOS ONE, 2017, DOI: 10.1371/journal.pone.0181083