Species Complex Isolates Research Articles

Species composition, toxigenic potential and pathogenicity of Fusarium graminearum species complex isolates from southern Brazilian rice

This study aimed to assess the extent and distribution of Fusarium graminearum species complex (FGSC) diversity in rice seeds produced in southern Brazil. Four species and two trichothecene genotypes were detected among 89 FGSC isolates, based on a multilocus genotyping assay: F. asiaticum (69·6%) with the nivalenol (NIV) genotype, F. graminearum (14·6%) with the 15‐acetyldeoxynivalenol (ADON) genotype, and F. cortaderiae (14·6%) and F. meridionale (1·1%), both with the NIV genotype. Seven selected F. asiaticum isolates from rice produced NIV in rice‐based substrate in vitro, at levels ranging from 4·7 to 84·1 μg g−1. Similarly, two F. graminearum isolates from rice produced mainly 15‐ADON (c. 15–41 μg g−1) and a smaller amount of 3‐ADON (c. 6–12 μg g−1). One F. meridionale and two F. cortaderiae isolates did not produce detectable levels of trichothecenes. Two F. asiaticum isolates from rice and two from wheat (from a previous study), and one F. graminearum isolate from wheat, were pathogenic to both crops at various levels of aggressiveness based on measures of disease severity in wheat spikes and rice kernel infection in a greenhouse assay. Fusarium asiaticum and the reference F. graminearum isolate from wheat produced NIV, and deoxynivalenol and acetylates, respectively, in the kernels of inoculated wheat heads. No trichothecene was produced in kernels from inoculated rice panicles by any of the isolates. These findings constitute the first report of FGSC composition in rice outside Asia, and confirm the dominance of F. asiaticum in rice agroecosystems.

Antifungal susceptibilities of Candida glabrata species complex, Candida krusei, Candida parapsilosis species complex and Candida tropicalis causing invasive candidiasis in China: 3 year national surveillance.

To define the antifungal susceptibility patterns of the most common non-albicans Candida spp. in China. We evaluated the susceptibilities to nine antifungal drugs of Candida parapsilosis species complex, Candida tropicalis, Candida glabrata species complex and Candida krusei isolates from patients with invasive candidiasis at 11 hospitals over 3 years. Isolates were identified by MALDI-TOF MS supplemented by DNA sequencing. MICs were determined by Sensititre YeastOne(TM) using current clinical breakpoints/epidemiological cut-off values to assign susceptibility (or WT), and by CLSI M44-A2 disc diffusion for fluconazole and voriconazole. Of 1072 isolates, 392 (36.6%) were C. parapsilosis species complex. C. tropicalis, C. glabrata species complex and C. krusei comprised 35.4%, 24.3% and 3.7% of the isolates, respectively. Over 99.3% of the isolates were of WT phenotype to amphotericin B and 5-flucytosine. Susceptibility/WT rates to azoles among C. parapsilosis species complex were ≥97.5%. However, 11.6% and 9.5% of C. tropicalis isolates were non-susceptible to fluconazole and voriconazole, respectively (7.1% were resistant to both). Approximately 14.3% of C. glabrata sensu stricto isolates (n = 258) were fluconazole resistant, and 11.6% of C. glabrata sensu stricto isolates were cross-resistant to fluconazole and voriconazole. All C. krusei isolates were susceptible/WT to voriconazole, posaconazole and itraconazole. Overall, 97.7%-100% of isolates were susceptible to caspofungin, micafungin and anidulafungin, but 2.3% of C. glabrata were non-susceptible to anidulafungin. There was no azole/echinocandin co-resistance. Disc diffusion and Sensititre YeastOne(TM) methods showed >95% categorical agreement for fluconazole and voriconazole. In summary, reduced azole susceptibility was seen among C. tropicalis. Resistance to echinocandins was uncommon.

European Confederation of Medical Mycology (ECMM) epidemiological survey on invasive infections due to Fusarium species in Europe.

In order to better understand the epidemiology of fusariosis in Europe, a survey collecting information on the clinical characteristics of the patients infected by Fusarium as well as on the infecting isolates was launched. A total of 76 cases of invasive fusariosis occurring from January 2007 to June 2012 were collected and Fusarium isolates were identified by sequencing the translation elongation factor 1α (TEF) gene. Also, antifungal susceptibility was tested by broth microdilution according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and the Etest. Disseminated disease was considered proven in 46 cases and probable in 17 cases. Localised infection was seen in 13 cases. Gibberella fujikuroi species complex (SC), including Fusarium verticillioides and F. proliferatum, and F. solani SC were the most frequent aetiology of disseminated and localised infections, respectively. The crude mortality rate was 46 %, the highest associated with F. solani SC (67 %) and F. proliferatum (62.5 %). A wide range of antifungal susceptibilities was observed. Amphotericin B was the most potent antifungal in vitro, and itraconazole the least effective. The azoles exhibited lower minimum inhibitory concentrations (MICs) against F. verticillioides strains, with posaconazole having a slightly better performance, while F. solani SC isolates were resistant to all three azoles tested. The essential agreement between the Etest and the EUCAST method was 100 % for itraconazole and voriconazole, and 96 % for amphotericin B and posaconazole. In conclusion, we confirm that fusariosis is a rare but severe event in Europe, that G. fujikuroi SC is the predominant cause of deep infections and that different species have different antifungal in vitro susceptibility patterns.

Antifungal susceptibilities of Cryptococcus species complex isolates from AIDS and non-AIDS patients in Southeast China

Cryptococcus spp. are common causes of mycoses in immunocompromised patients. To determine the drug susceptibilities of clinical Cryptococcus spp. isolates, the characteristics of 61 clinical Cryptococcus spp. complex isolates and their antifungal susceptibilities were investigated, including 52 C. neoformans and 9 C. gattii isolates collected at Shanghai between 1993 and 2009. Antifungal susceptibility of clinical isolates to amphotericin B, fluconazole, itraconazole, and flucytosine were determined by the microdilution method M27-A2 and the ATB FUNGUS 3 kit. The 90% minimum inhibitory concentration (MIC90) and susceptibility ranges were as follows: 1 (0.0625-1) µg/mL for amphotericin B, 4 (0.125-16) µg/ mL for fluconazole, 0.25 (0.0313-4) µg/mL for itraconazole, and 4 (0.125-8) µg/mL for flucytosine. Fluconazole, itraconazole, and flucytosine have excellent in vitro activity against all tested clinical Cryptococcus spp., and we also found a high rate of tolerance to amphotericin B (MICs ranging from 0.55-1 µg/mL). Furthermore, C. neoformans isolates from acquired immune deficiency syndrome (AIDS) patients were less susceptible to fluconazole and flucytosine than those from non-AIDS patients. These data suggest that use of amphotericin B may lead to tolerance or resistance of the pathogen over time. There were also no significant associations between species, genotypes, and in vitro susceptibilities of these clinical isolates.

Antifungal susceptibilities of Cryptococcus species complex isolates from AIDS and non-AIDS patients in Southeast China

Cryptococcus spp. are common causes of mycoses in immunocompromised patients. To determine the drug susceptibilities of clinical Cryptococcus spp. isolates, the characteristics of 61 clinical Cryptococcus spp. complex isolates and their antifungal susceptibilities were investigated, including 52 C. neoformans and 9 C. gattii isolates collected at Shanghai between 1993 and 2009. Antifungal susceptibility of clinical isolates to amphotericin B, fluconazole, itraconazole, and flucytosine were determined by the microdilution method M27-A2 and the ATB FUNGUS 3 kit. The 90% minimum inhibitory concentration (MIC90) and susceptibility ranges were as follows: 1 (0.0625–1) μg/mL for amphotericin B, 4 (0.125–16) μg/mL for fluconazole, 0.25 (0.0313–4) μg/mL for itraconazole, and 4 (0.125–8) μg/mL for flucytosine. Fluconazole, itraconazole, and flucytosine have excellent in vitro activity against all tested clinical Cryptococcus spp., and we also found a high rate of tolerance to amphotericin B (MICs ranging from 0.55–1μg/mL). Furthermore, C. neoformans isolates from acquired immune deficiency syndrome (AIDS) patients were less susceptible to fluconazole and flucytosine than those from non-AIDS patients. These data suggest that use of amphotericin B may lead to tolerance or resistance of the pathogen over time. There were also no significant associations between species, genotypes, and in vitro susceptibilities of these clinical isolates.

Genetic diversity and mycotoxin production of Fusarium lactis species complex isolates from sweet pepper

An internal fruit rot disease of sweet peppers was first detected in Belgium in 2003. Research conducted mostly in Canada indicates that this disease is primarily caused by Fusarium lactis Pirotta. Ninety-eight Fusarium isolates obtained from diseased sweet peppers from Belgium, as well as from other countries (Canada, the Netherlands and the United Kingdom) were identified by sequencing the translation elongation factor 1α (EF). Of these 98 isolates, 13 were identified as F. oxysporum Schltdl., nine as F. proliferatum (Matsush.) Nirenberg and two belonged to clade 3 of the F. solani species complex. Of the 74 remaining isolates, the EF sequence showed 97% to 98% similarity to F. lactis. Of these isolates, the β-tubulin (TUB), calmodulin (CAM) and the second largest subunit of RNA polymerase II (RPB2) genes were also sequenced. Analysis of the combined sequences revealed that the 74 isolates share nine combined sequences that correspond to nine multilocus sequence types (STs), while the F. lactis neotype strain and one other strain, both isolated from figs, form a separate ST. Together, these 10 STs represent a monophyletic F. lactis species complex (FLASC). An unusually high level of genetic diversity was observed between (groups of) these STs. Two of them (ST5 and ST6) fulfilled the criteria for species recognition based on genealogical exclusivity and together represent a new monophyletic species lineage (FLASC-1). The seven other STs, together with the F. lactis neotype ST, form a paraphyletic species lineage in the African clade of the Gibberella fujikuroi species complex (GFSC). From each of the 10 STs, the mycotoxin production was assessed using a multi-mycotoxin liquid chromatography mass spectrometry method. Out of the 27 analyzed mycotoxins, beauvericin and fumonisins were detected in sweet pepper tissue and in maize kernels. The 10 STs clearly differed in the amount of mycotoxin produced, but there was only limited congruence between the production profile and the phylogenetic analysis. Furthermore, the morphological characterization (based on mycelial growth rate and the length of macroconidia) showed distinct differences between the 10 STs, but again there was limited congruence with the phylogenetic results. In conclusion, the data presented in this study demonstrate that 75% of the isolates obtained from sweet pepper with internal fruit rot belong to a F. lactis species complex (FLASC), including a new FLASC-1 monophyletic species, and that the members of this complex display great genetic and phenotypic diversity.

Acinetobacter calcoaceticus–Acinetobacter baumannii complex species in clinical specimens in Singapore

This study was performed to determine the prevalence, distribution of specimen sources, and antimicrobial susceptibility of the Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) species complex in Singapore. One hundred and ninety-three non-replicate Acb species complex clinical isolates were collected from six hospitals over a 1-month period in 2006. Of these, 152 (78·7%) were identified as A. baumannii, 18 (9·3%) as 'Acinetobacter pittii' [genomic species (gen. sp.) 3], and 23 (11·9%) as 'Acinetobacter nosocomialis' (gen. sp. 13TU). Carbapenem resistance was highest in A. baumannii (72·4%), followed by A. pittii (38·9%), and A. nosocomialis (34·8%). Most carbapenem-resistant A. baumannii and A. nosocomialis possessed the bla(OXA-23-like) gene whereas carbapenem-resistant A. pittii possessed the bla(OXA-58-like) gene. Two imipenem-resistant strains (A. baumannii and A. pittii) had the bla(IMP-like) gene. Representatives of carbapenem-resistant A. baumannii were related to European clones I and II.

Tipificación molecular de aislamientos del complejo Cryptococcus neoformans/Cryptococcus gattii

The molecular typing of the Cryptococcus neoformans/Cryptococcus gattii species complex is an useful tool for the molecular surveillance of this important opportunistic pathogen. The aim of this short communication is to inform physicians and laboratory personnel in Colombia about the importance of PCR fingerprinting in the comprehensive study of the genetic diversity of the C. neoformans/C. gattii species complex in the country. Furthermore, the results obtained from this molecular typing will enable us t complement the information gathered during the National Survey about cryptococcosis lead by the Microbiology Group of the Instituto Nacional de Salud.Isolates of the complex can be classified in 8 molecular patterns according to PCR fingerprinting using universal primers, which allows grouping the members of the complex according to species and, for C. neoformans, according to variety.The molecular surveillance of the C. neoformans/ C. gattii species complex isolates has become an epidemiological tool of great value since cryptococcosis has gained an important relevance in recent years due to the increasing number of immune-suppressed patients.

Development of a new MLST scheme for differentiation of Fusarium solani Species Complex (FSSC) isolates

Fungi belonging to the Fusarium solani Species Complex (FSSC) are well known plant pathogens. In addition to being the causative agent of some superficial infections, FSSC has recently emerged as a group of common opportunistic moulds, mainly in patients with haematological malignancies. Molecular typing methods are essential in order to better understand the epidemiology of such opportunistic agents with the final goal of preventing contamination. A three-locus typing scheme has thus been developed for FSSC; based on polymorphisms in the domains of the ITS, EF-1 alpha, and RPB2 genes. This method is now considered to be a useful reference for phylogenetic and taxonomic studies. In other significant clinical fungi (e.g., Candida sp., Cryptococcus neoformans, and Aspergillus fumigatus), genes coding for metabolic enzymes have been widely used and proven to be very informative for diagnosis and epidemiology. The contribution of these genes has never been evaluated for Fusarium sp. and more specifically for F. solani Species Complex.Here, we have evaluated the contribution of 25 genes for diagnosis and epidemiological purposes. We then report a new five-locus MLST scheme useful for diagnosis and typing of clinical FSSC isolates. The method has been validated on 51 epidemiologically unrelated strains of FSSC and presents a high power of discrimination calculated at 0.991.

Molecular epidemiology of Cryptococcus neoformans species complex isolates from HIV-positive and HIV-negative patients in southeast China

This study investigated the molecular types of the Cryptococcus neoformans species complex isolates and their clinical manifestations among human immunodeficiency virus (HIV)-positive and HIV-negative patients in southeast China in the past 15 years. The molecular types of 109 isolates from 108 patients were analyzed by the PCR fingerprinting method, sequences of internal transcribed spacers of rDNA (ITS region), and sequences of the capsule-associated gene (CAP59). In HIV-positive patients, clinical isolates were grouped into molecular types VNI (75%, 15/20), VNII (15%, 3/20), and VNIII (10%, 2/20). In HIV-negative patients, the majority of the clinical isolates were grouped into molecular types VNI (72%, 64/89), VNII (13%, 12/89), VGI (12%, 11/89), VNIII (1%, 1/89), and VGII (1%, 1/89). In reference to the mating type of the isolates, 97% (106/109) were of the MATα, 2% (2/109) were of the MATα/− and 1% (1/109) were of the MATα/a. As for the clinical manifestations of the molecular types among the patients, the average cerebrospinal fluid (CSF) pressure of the patients infected by the C. gattii was higher than that of the patients infected by the C. neoformans. These results suggest that both HIV-positive and HIV-negative cryptococcal patients in the southeast of China are mostly infected by the C. neoformans strains. No C. gattii strains were found in HIV-positive patients.

Sensitivity of Japanese Fusarium graminearum species complex isolates to metconazole

The sensitivity of the Fusarium graminearum species complex, the causal fungus of Fusarium head blight, to metconazole was measured. The minimum inhibitory concentrations (MIC) of 101 isolates ranged from 0.20 to 6.25 mg/l with a single peak at 1.56 mg/l. The effective concentration for 50% growth inhibition (EC50) was <0.1 mg/l in about 80% of isolates, and no isolate was significantly less sensitive to metconazole among this group. Among the F. graminearum species complex, F. asiaticum and F. graminearum s. str. were identified by PCR-RFLP. The trichothecene chemotypes were determined as 3ADON, 15ADON, or NIV by multiplex PCR. Although species-specific geographical distributions and mycotoxin production characteristics were found, the MIC values to metconazole of both species were distributed within a similar range, and no significant difference in sensitivity was observed between the species or trichothecene chemotypes. Next, CYP51 genes from isolates with different sensitivities to metconazole were amplified by PCR, and their sequences were compared. As a result, it was suggested that the differences in sensitivity to metconazole between the isolates were not due to the substitution of amino acids in CYP51, the target enzyme of DMI. Then, macrospores from isolates with various sensitivities to metconazole were sprayed onto wheat ears, and the efficacy of metconazole was examined. Metconazole showed high control activity against every isolate.

Antimicrobial activity of Hymenaea martiana towards dermatophytes and Cryptococcus neoformans

The biological activity of crude extract and fractions of Hymenaea martiana was evaluated against a panel of human pathogenic fungi. The crude extracts and hydroalcoholic fractions (E) showed a high activity against Cryptococcus neoformans species complex isolates with MICs between 2 and 64 μg ml(-1). The methanolic (C) and butanolic (D) fractions were the most active against Trichopyton rubrum, Trichopyton mentagrophytes and Microsporum canis with MICs between 8 and 256 μg ml(-1). None of the extracts was active against the yeast Malassezia furfur, Malassezia obtusa and Malassezia sympodialis.

Molecular typing and antifungal susceptibility of clinical and environmental Cryptococcus neoformans species complex isolates in Goiania, Brazil

A total of 124 Cryptococcus isolates, including 84 clinical strains obtained from cerebrospinal fluid from AIDS patients and 40 environmental isolates from pigeon excreta and from Eucalyptus trees, were studied. The varieties, serotypes, phospholipase activity and molecular profile of these isolates were determined. Cryptococcus neoformans var. grubii serotype A was identified in 120 isolates and Cryptococcus gattii serotype B in four isolates. The clinical isolates showed higher phospholipase activity than environmental isolates. Similar patterns of in vitro susceptibility to amphotericin B, fluconazole, itraconazole and voriconazole and no resistance were found for all isolates. Molecular type VNI (C. neoformans var. grubii) was recovered in 80 clinical and 40 environmental isolates while the type VGIII (C. gattii) was found in four clinical isolates. This study demonstrated for the first time the molecular types of clinical and environmental Cryptococcus isolates in the midwest Brazil region.

Fusarium solani species complex isolates conspecific with Fusarium solani f. sp. cucurbitae race 2 from naturally infected human and plant tissue and environmental sources are equally virulent on plants, grow at 37°C and are interfertile

SummaryIn a previous taxonomic study based on multilocus sequencing of Fusarium from clinical specimens and hospital environments, the most common lineage was Fusarium solani species complex group 1 (FSSC 1) which is conspecific with F. solani f. sp. cucurbitae race 2, a pathogen of cucurbit fruits. The aims of our study were to determine if clinical and environmental isolates of FSSC 1 are plant pathogens and members of the same biological species as cucurbit isolates, and to determine if all isolates can germinate, grow and sporulate at 37°C. Isolates from the different sources did not differ in virulence on zucchini fruits. All FSSC 1 isolates were pathogenic and produced more rot than FSSC isolates from plant hosts other than cucurbits. Both mating types were found among isolates from each of the sources, and all isolates were sexually compatible with cucurbit isolates. All isolates germinated, grew and sporulated at 37°C. This is the first report in which plant pathogenicity has been verified for a collection of human clinical isolates. Our data are consistent with the hypothesis that all FSSC 1 isolates, regardless of source, are a single biological species, equally virulent plant pathogens and tolerant of the human body temperature.

Mango Anthracnose: Economic Impact and Current Options For Integrated Managaement.

Mango Anthracnose: Economic Impact and Current Options For Integrated Managaement.