Fusarium: more than a node or a foot-shaped basal cell

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org)

İstanbul ilinde hastanelerin içinde ve dışında hava ile taşınan funguslar üzerine araştırmalar

Bu çalışma Şubat 2005 ile Ocak 2006 arasında yapılmıştır. Çalışmada İstanbul’daki altı farklı hastanenin (Marmara Üniversitesi Hastanesi, Dr. Siyami Ersek Göğüs, Kalp ve Damar Cerrahisi Hastalıkları Eğitim ve Araştırma Hastanesi, Haydarpaşa Numune Eğitim ve Araştırma Hastanesi, Göztepe Eğitim ve Araştırma Hastanesi, Kartal Devlet Hastanesi, Çamlıca Medicana Hastanesi (Hayat Hastanesi)) 5 farklı bölümünün (Mikrobiyoloji Laboratuarları, tuvaletleri, bekleme salonları, bahçeleri, kütüphaneleri) fungal florasının belirlenmesi amaçlanmıştır. Örnekler Rose Bengal Pepton Dekstroz Agarın belirtilen bölümlerde yerden 75-85 cm yükseklikte Petri kapağının 15-30 dakika açık bırakılarak havayla temas ettirilmesiyle alınmıştır. Araştırmada toplam 900 fungus (mantar) mantar kolonisi izole edilerek incelenmiştir. 15 cinse ait 40 tür izole edilmiştir. Elde edilen cinsler; Cladosporium, Penicillium, Alternaria, Aspergillus, Aureobasidium, Mycelia sterilia, Scopulariopsis, Rhizopus, Ulocladium, Fusarium, Paecilomyces, Gliocladium, Trichoderma, Drechslera ve Acremonium’ dur. Bunların içinde en fazla izole edilen cinsler; Cladosporium, Penicillium, Alternaria, Aspergillus ve Aureobasidium olmuştur. Çalışmada en fazla izole edilen türler; Cladosporium cladosporioides, Alternaria alternata, Penicillium glabrum, Cladosporium herbarum, Penicillium brevicompactum, Aureobasidium pullulans ve Aspergillus niger olmuştur. Cladosporium en fazla Mayıs, Haziran, Temmuz, Ağustos, Eylül’de; Penicillium Ocak, Şubat, Ekim, Kasım ve Aralık’ta; Alternaria Mayıs, Haziran, Temmuz ve Ağustos’ ta; Aspergillus Ocak ve Mart’ta; Aureobasidium Mayıs ve Haziran aylarında en yüksek miktarlarda izole edilmişlerdir. Tüm aylar boyunca en yüksek fungus konsantrasyonu Mayıs ayında, en az ise Ocak ayında elde edildi. En fazla fungus yaz mevsiminde izole edilirken en az ise kış mevsiminde izole edildi. Çalışma boyunca örnek alınan alanların sıcaklık ve nem değerleri ölçüldü ve fungus konsantrasyonun havanın sıcaklık ve neminin artmasına bağlı olarak arttığı görüldü. Çalışmada elde edilen funguslardan allerjen olanları belirtildi. ABSTRACT Conducted between February 2005 and January 2006, this study aims to identify the fungal flora of five varied parts (Microbiology laboratories, toilets, waiting saloons, gardens, libraries) of six different hospitals (Marmara University Hospital, Dr. Siyami Ersek Cardiovascular Diseases, Training and Research Hospital, Haydarpaşa Numune Training and Research Hospital, Göztepe Training and Research Hospital, Kartal State Hospital, Çamlıca Medicana Hospital (Hayat Hospital)). Samples were taken by leaving open the cover of the Petri dish which contain of Rose Bengal Peptone Dextrose Agar for 15-30 minutes to enable air communication at a height of 75-85 centimeters at the mentioned locations. A total of 900 fungus colonies were examined in the research and 40 species belonging to 15 genus were isolated. The obtained genus are; Cladosporium, Penicillium, Alternaria, Aspergillus, Aureobasidium, Mycelia sterilia, Scopulariopsis, Rhizopus, Ulocladium, Fusarium, Paecilomyces, Gliocladium, Trichoderma, Drechslera and Acremonium. The most isolated genera among them have been Cladosporium, Penicillium, Alternaria, Aspergillus and Aureobasidium. The most frequently encountered species in the study are Cladosporium cladosporioides, Alternaria alternata, Penicillium glabrum, Cladosporium herbarum, Penicillium brevicompactum, Aureobasidium pullulans and Aspergillus niger. The highest isolation of Cladosporium was observed in May, June, July, August and September; of Penicillium in January, February, October, November and December; of Alternaria in May, June, July and August; of Aspergillus in January and March and of Aureobasidium in May and June. The highest fungus concentration has been obtained in May whereas the lowest concentration was in January. The largest number of fungus was isolated in summer and the lowest number of fungus isolation was performed in winter. Heat and moisture measurements have also been made as samples were taken and a positive correlation between fungus concentration and it was seen consantration of fungi increased depending on high of air temperature and moisture. The allergens among the fungi acquired in course of this study have also been listed

Candida ve aspergillus enfeksiyonlarının real time PCR yöntemi ile hızlı tanısının kültür yöntemi ile karşılaştırılması ve antifungal direncin kolorimetrik yöntemle tayini

ÖZETCANDİDA ve ASPERGİLLUS ENFEKSİYONLARININ REAL TIME PCR YÖNTEMİ ile HIZLI TANISININ KÜLTÜR YÖNTEMİ ile KARŞILAŞTIRILMASI ve ANTİFUNGAL DİRENCİN KOLORİMETRİK YÖNTEMLE TAYİNİBu çalışma 2009 - 2011 yılları arasında Yeditepe Üniversitesi Hastanesi Tıbbi Mikrobiyoloji Anabilim Dalı’na başvuran hastalardan alınan örnekler kullanılarak gerçekleştirilmiştir. Toplamda 139 adet örnek çalışılmış ve 139 adet suş izole edilmiştir. Bu suşlar, hastalardan alınan abse, ağız sürüntsü, balgam, BAL (Bronkoalveolar Lavaj), idrar ve idrar sondası, kan kültürü, kateter, kulak akıntısı ve sürüntüsü, trakeal aspirat, steril vücut sıvısı örneklerinden elde edilmiştir. Çalışmada kültür yöntemi ile tanımlanan Candida ve Aspergillus türleri, moleküler yöntemlerle tanımlanmıştır, bu iki yöntemin sonuçları karşılaştırılmıştır. Çalışmamızda Aspergillus cinsine ait Aspergillus flavus (Link, 1809), Aspergillus fumigatus (Fresen, 1863), Aspergillus niger (Tiegh, 1867), Aspergillus terreus (Thom, 1918) ile Candida cinsine ait Candida albicans ((C.P. Robin) Berkhout 1923), Candida glabrata ((H.W. Anderson) S.A. Mey. & Yarrow, 1978), Candida parapsilosis ((Ashford) Langeron & Talice, 1932), Candida tropicalis ((Castell.) Berkhout, 1923), Candida dubliniensis (D.J. Sullivan, Western., K.A. Haynes, Dés.E. Benn. & D.C. Coleman, 1995), Candida krusei ((Castell.) Berkhout, 1923) türleri izole edilmiştir. Sybr green boyası ile panfungal PCR yapılarak öncelikle cins düzeyinde Aspergillus ve Candida ayrımı yapılmıştır. Daha sonra Taqman PCR ile 4 farklı Candida türü (Candida albicans, Candida glabrata, Candida tropicalis ve Candida parapsilosis) tanımlanmıştır. Kültür yöntemi ile tanımlanan 57 adet Candida albicans; 12 adet C. glabrata; 21 adet C. parapsilosis; 17 adet C. tropicalis suşlarının tamamı Taqman PCR ile de doğrulanmıştır ve bu iki yöntem ile yapılan identifikasyon sonuçları arasındaki uyumun %100 olduğu belirlenmiştir. Ayrıca Candida türlerinin kolorimetrik bir yöntem ile 7 farklı antifungale (Flukonazol, Kaspofungin, Vorikonazol, Amfoterisin B, Posakonazol, İtrakonazol ve 5-Flusitosin) karşı duyarlılık deneyleri yapılmıştır. Kaspofungine dirençli bir suşa rastlanmazken, en fazla direnç azol grubu antifungallerde saptanmıştır.ABSTRACTREAL TIME PCR for RAPID DIAGNOSIS OF CANDIDA and ASPERGILLUS INFECTIONS with COMPARISON of CULTURE METHOD and DETERMINATION of ANTIFUNGAL RESISTANCE COLORIMETRIC METHODIn this study, specimen, collected from the patients who applied to Medical Microbiology Laboratory of Yeditepe University Hospital between 2009-2011 were evaluated. 139 specimen were studied and 139 strains were isolated. These strains were isolated from abscesses, oral swabs, sputum, BAL (Bronchoalveolar lavage), urine, and urinary catheter, blood cultures, catheter, ear discharge and swabs, tracheal aspirates, sterile body fluid samples. In the study Aspergillus flavus (Link, 1809), Aspergillus fumigatus (Fresen, 1863), Aspergillus niger (Tiegh, 1867), Aspergillus terreus (Thom, 1918) species, which were belong to Aspergilus genus and Candida albicans ((C.P. Robin) Berkhout 1923), Candida glabrata ((H.W. Anderson) S.A. Mey. & Yarrow, 1978), Candida parapsilosis ((Ashford) Langeron & Talice, 1932), Candida tropicalis ((Castell.) Berkhout, 1923), Candida dubliniensis (D.J. Sullivan, Western., K.A. Haynes, Dés.E. Benn. & D.C. Coleman, 1995), Candida krusei ((Castell.) Berkhout, 1923) species which were belong to Candida genus were isolated. Primarily panfungal PCR was made by Sybr green dye to distinguish Candida and Aspergillus at species level. Then four different Candida species (Candida albicans, Candida glabrata, Candida tropicalis ve Candida parapsilosis) have been identified by Taqman PCR. 57 Candida albicans, 12 C. glabrata, 21 C. parapsilosis, 17 C. tropicalis; which were defined by culture method confirmed by Taqman PCR. The results of identification with these two methods were found 100% compatible.In addition, antifungal susceptibility of Candida species against 7 different antifungals (Fluconazole, Caspofungin, Voriconazole, Amphotericin B, Posaconazole, Itrakonazole ve 5-Flucytosine) determined by colorimetric method. Caspofungin resistant strains were not found, the most resistance was determined to azole antifungals

Cytotoxic, anti-proliferative and anti-microbial activities of extract from cladonia pocillum

İstanbul Bilim Üniversitesi, Fen Edebiyat Fakültesi.Lichens produce a wide variety of seconder metabolites which have a potential use as anti-microbial, cytotoxic, fungitoxic, anti-feedant, anti-oxidant, anti-inflammatory [1-3]. Many studies report that, the efficacy of lichen metabolites in the treatment of cancers [4, 5]. The aim of the study is to explore the anti-proliferative, cytotoxic and anti-microbial properties of extract from Cladonia pocillum

Screening of antimicrobial activity and cytotoxic effects of two Cladonia species.

İstanbul Bilim Üniversitesi, Sağlık Hizmetleri Meslek Yüksekokulu.The present study explores the antimicrobial activity and cytotoxic effects in culture assays of two fruticose soil lichens, Cladonia rangiformis Hoffm. and Cladonia convoluta (Lamkey) Cout., to contribute to possible pharmacological uses of lichens. In vitro antimicrobial activities of methanol and chloroform extracts against two Gram-negative bacteria (Pseudomonas aeruginosa and Escherichia coli), two Gram-positive bacteria (Enterococcus faecalis and Staphylococcus aureus), and the yeast Candida albicans were examined using the paper disc method and through determination of minimal inhibitory concentrations (MICs). The data showed the presence of antibiotic substances in the chloroform and the methanol extracts of the lichen species. The chloroform extracts exhibited more signifi cant antimicrobial activity than the methanol extracts. However, a higher antifungal activity was noted in the methanol extract of C. rangiformis. The maximum antimicrobial activity was recorded for the chloroform extract of C. convoluta against E. coli. The cytotoxic effects of the lichen extracts on human breast cancer MCF-7 cells were evaluated by the trypan blue assay yielding IC50 values of ca. 173 and 167 μg/ml for the extracts from C. rangiformis and C. convoluta, respectively