scholarly journals Scedosporium and Lomentospora Infections: Contemporary Microbiological Tools for the Diagnosis of Invasive Disease

2021 ◽  
Vol 7 (1) ◽  
pp. 23
Author(s):  
Sharon C.-A. Chen ◽  
Catriona L. Halliday ◽  
Martin Hoenigl ◽  
Oliver A. Cornely ◽  
Wieland Meyer
Keyword(s):  
Species Identification ◽  
Antifungal Susceptibility ◽  
Invasive Disease ◽  
Molecular Methods ◽  
Sequencing Technologies ◽  
Flight Mass Spectrometry ◽  
Good Potential ◽  
Detection And Diagnosis ◽  
Panfungal Pcr ◽  
Species Specific

Scedosporium/Lomentospora fungi are increasingly recognized pathogens. As these fungi are resistant to many antifungal agents, early diagnosis is essential for initiating targeted drug therapy. Here, we review the microbiological tools for the detection and diagnosis of invasive scedosporiosis and lomentosporiosis. Of over 10 species, Lomentospora prolificans, Scedosporium apiospermum, S. boydii and S. aurantiacum cause the majority of infections. Definitive diagnosis relies on one or more of visualization, isolation or detection of the fungus from clinical specimens by microscopy techniques, culture and molecular methods such as panfungal PCR or genus-/species-specific multiplex PCR. For isolation from respiratory tract specimens, selective media have shown improved isolation rates. Species identification is achieved by macroscopic and microscopic examination of colonies, but species should be confirmed by ITS with or without β-tubulin gene sequencing or other molecular methods. Matrix-assisted laser desorption ionization-time of flight mass spectrometry databases are improving but may need supplementation by in-house spectra for species identification. Reference broth microdilution methods is preferred for antifungal susceptibility testing. Next-generation sequencing technologies have good potential for characterization of these pathogens. Diagnosis of Scedosporium/Lomentospora infections relies on multiple approaches encompassing both phenotypic- and molecular-based methods.

scholarly journals Identification of Nocardia species using Autof MS 1000 and Bruker MALDI-TOF MS systems: A comparison

2021 ◽  
Author(s):  
Bing Ma ◽  
Yunqi Tian ◽  
Yungang Han ◽  
Lifang Ban ◽  
Junwen Yang ◽  
...  
Keyword(s):  
Species Identification ◽  
Protein Extraction ◽  
Reference Method ◽  
Invasive Disease ◽  
Species Level ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Significant Difference ◽  
Tof Ms

ABSTRACTNocardia is an important cause of clinically invasive disease, but for most clinical laboratories, identification of these isolates to the species level is challenging. Recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used for identification of most bacterial and fungal isolates. In this multicenter study, we evaluated the identification of Nocardia isolates using Autof MS1000 and Bruker Biotyper. A total of 86 non-duplicate Nocardia isolates from 7 hospital laboratories were evaluated. Further, we carried out sequence analysis of 16S rRNA, gyrB, secA1, hsp65, and rpoB genes as a reference method for Nocardia species identification. The 86 isolates were directly spotted on the target plate and plate protein extraction was performed. Data were analyzed by SPSS 19.0. In total, 72 (83.7%) strains (score ≥ 9.0) and 70 (81.4%) strains (score ≥ 2.0) were correctly identified by the Autof MS1000 and Bruker Biotyper systems, respectively, at the species level. There was no significant difference (P > 0.05) between the two systems using the same protein extraction method. In conclusion, the Autof MS 1000 and Bruker MALDI-TOF systems showed no difference in identification of Nocardia spp. to the species level and could meet the most important clinical requirement for species identification.

scholarly journals Species Identification and Antifungal Susceptibility Patterns of Species Belonging to Aspergillus Section Nigri

2009 ◽  
Vol 53 (10) ◽  
pp. 4514-4517 ◽  
Author(s):  
Laura Alcazar-Fuoli ◽  
Emilia Mellado ◽  
Ana Alastruey-Izquierdo ◽  
Manuel Cuenca-Estrella ◽  
Juan L. Rodriguez-Tudela
Keyword(s):  
Phylogenetic Analysis ◽  
Species Identification ◽  
Antifungal Susceptibility ◽  
Morphological Features ◽  
Correct Classification ◽  
Paradoxical Effect ◽  
Aspergillus Section Nigri ◽  
Susceptibility Patterns ◽  
Aspergillus Section

ABSTRACT A phylogenetic analysis was performed for 34 Aspergillus strains belonging to section Nigri. Molecular methods allowed for the correct classification into three different clades (A. niger, A. tubingensis, and A. foetidus). Correlation with in vitro itraconazole susceptibility distinguished the following three profiles: susceptible, resistant, and showing a paradoxical effect. A number of different species whose morphological features resemble those of A. niger showed unusual MICs to itraconazole that have never been described for the Aspergillus genus.

scholarly journals Rapid Species Identification of Cooked Poisonous Mushrooms by Using Real-Time PCR

2008 ◽  
Vol 74 (10) ◽  
pp. 3306-3309 ◽  
Author(s):  
Kazuhiko Maeta ◽  
Tomoya Ochi ◽  
Keisuke Tokimoto ◽  
Norihiro Shimomura ◽  
Nitaro Maekawa ◽  
...  
Keyword(s):  
Real Time ◽  
Species Identification ◽  
Real Time Pcr ◽  
Specific Test ◽  
Specific Identification ◽  
Specific Fluorescence ◽  
Species Specific ◽  
Poisonous Mushrooms

ABSTRACT Species-specific identification of the major cooked and fresh poisonous mushrooms in Japan was performed using a real-time PCR system. Specific fluorescence signals were detected, and no nonspecific signals were detected. Therefore, we succeeded in developing a species-specific test for the identification of poisonous mushrooms within 1.5 h.

scholarly journals Molecular Identification and Antifungal Susceptibility of Yeast Isolates Causing Fungemia Collected in a Population-Based Study in Spain in 2010 and 2011

2013 ◽  
Vol 58 (3) ◽  
pp. 1529-1537 ◽  
Author(s):  
Jesús Guinea ◽  
Óscar Zaragoza ◽  
Pilar Escribano ◽  
Estrella Martín-Mazuelos ◽  
Javier Pemán ◽  
...  
Keyword(s):  
Hot Spot ◽  
Antifungal Susceptibility ◽  
Point Mutations ◽  
Population Based ◽  
Candida Guilliermondii ◽  
Population Based Study ◽  
Content Type ◽  
Candida Lusitaniae ◽  
Species Specific

ABSTRACTWe report the molecular identifications and antifungal susceptibilities of the isolates causing fungemia collected in the CANDIPOP population-based study conducted in 29 Spanish hospitals. A total of 781 isolates (from 767 patients, 14 of them having mixed fungemia) were collected. The species found most frequently wereCandida albicans(44.6%),Candida parapsilosis(24.5%),Candida glabrata(13.2%),Candida tropicalis(7.6%),Candida krusei(1.9%),Candida guilliermondii(1.7%), andCandida lusitaniae(1.3%). OtherCandidaand non-Candidaspecies accounted for approximately 5% of the isolates. The presence of cryptic species was low. Compared to findings of previous studies conducted in Spain, the frequency ofC. glabratahas increased. Antifungal susceptibility testing was performed by using EUCAST and CLSI M27-A3 reference procedures; the two methods were comparable. The rate of fluconazole-susceptible isolates was 80%, which appears to be a decrease compared to findings of previous studies, explained mainly by the higher frequency ofC. glabrata. Using the species-specific breakpoints and epidemiological cutoff values, the rate of voriconazole and posaconazolein vitroresistance was low (<2%). In the case ofC. tropicalis, using the EUCAST procedure, the rate of azole resistance was around 20%. There was a correlation between the previous use of azoles and the presence of fluconazole-resistant isolates. Resistance to echinocandins was very rare (2%), and resistance to amphotericin B also was very uncommon. The sequencing of the hot spot (HS) regions fromFKS1orFKS2genes in echinocandin-resistant isolates revealed previously described point mutations. The decrease in the susceptibility to fluconazole in Spanish isolates should be closely monitored in future studies.

Use of molecular methods in identification of species, age and sex of insects useful in forensic entomology

2014 ◽  
Vol 286 ◽  
pp. 66-69
Author(s):  
Joanna Stojak ◽  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Environmental Conditions ◽  
Forensic Entomology ◽  
Sex Identification ◽  
The Body ◽  
Molecular Methods ◽  
Insect Larvae ◽  
Identification Of Species ◽  
Age And Sex

Forensic entomology uses insects to determine the time, cause and place of death. To this end, two entomological methods are used. The development-based method uses the patterns of insect larvae development under the specific thermal and environmental conditions. The succession-based method analyzes the sequence of insect succession on the body in various environmental conditions. The proper insect species identification is essential in both methods. In this article, the molecular methods of species, age and sex identification are presented such as DNA barcoding or DNA-HRM-PCR.

Conventional PCR as a reliable method for diagnosing invasive mucormycosis in resource-limited settings

2021 ◽  
Vol 70 (5) ◽  
Author(s):  
Mragnayani Pandey ◽  
Immaculata Xess ◽  
Gagandeep Singh ◽  
Rakesh Kumar ◽  
Manoranjan Mahapatra ◽  
...  
Keyword(s):  
Antifungal Susceptibility ◽  
Tertiary Care ◽  
Care Hospital ◽  
Direct Microscopy ◽  
Specific Pcr ◽  
Resource Limited ◽  
Valuable Adjunct ◽  
Panfungal Pcr ◽  
A Prospective Study

Introduction. Invasive mucormycosis (IM) is a life-threatening infection caused by fungi belonging to the order Mucorales. Histopathology, culture and radiology are the mainstay of diagnosis but lack sensitivity, leading to a delay in timely diagnosis and intervention. Recently, PCR-based approaches have been shown to be a promising method in diagnosing IM. Hypothesis/Gap Statement. Molecular-based approaches may be a valuable adjunct to standard conventional methods for diagnosing IM, especially among culture negatives and patients on antifungal therapy. Aim. In the present study we aimed to evaluate the clinical utility of panfungal and Mucorales-specific PCR for diagnosing IM from various clinical specimens. Methodology. This was a prospective study in which 239 clinically suspected cases of IM attending our tertiary care hospital from August 2015 to March 2018 were enrolled. All the cases were defined as ‘proven’, ‘probable’ or ‘possible’ based on EORTC/MSGERC guidelines. In addition to conventional diagnostics (KOH-calcofluor stain and culture), panfungal and Mucorales-specific PCR assays were also performed. The amplified products were sequenced for species identification. In vitro antifungal susceptibility was performed on all the culture-positive isolates. Results. Among 239 clinically suspected cases of IM, only 140 cases were diagnosed by the demonstration of aseptate ribbon-like hyphae on direct microscopy. Culture was positive in 35.7 % (54/140) of direct microscopy-positive samples. Among the proven cases (n=11), the sensitivity for both Mucorales-specific nested PCR and panfungal PCR was 100 %, but specificity was 91.9 and 73.7% respectively. In probable cases (n=129), the sensitivity of both the PCRs was 98.5 % and specificity for panfungal PCR was 73.7 and 91.9 % for Mucorales-specific PCR. Conclusion. Pan fungal PCR in combination with Mucorales-specific PCR, followed by sequencing, may play a significant role in IM diagnosis especially among those negative for both direct microscopy and culture.

scholarly journals Species-Specific Impact of Fusarium Infection on the Root and Shoot Characteristics of Asparagus

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 509 ◽  
Author(s):  
Roxana Djalali Farahani-Kofoet ◽  
Katja Witzel ◽  
Jan Graefe ◽  
Rita Grosch ◽  
Rita Zrenner
Keyword(s):  
Negative Impact ◽  
Fusarium Species ◽  
Asparagus Officinalis ◽  
Root Characteristics ◽  
Disease Symptoms ◽  
Flight Mass Spectrometry ◽  
Significant Negative Impact ◽  
Species Specific ◽  
Specific Impact

Soil-borne pathogens can have considerable detrimental effects on asparagus (Asparagus officinalis) growth and production, notably caused by the Fusarium species F. oxysporum f.sp. asparagi, F. proliferatum and F. redolens. In this study, their species-specific impact regarding disease severity and root morphological traits was analysed. Additionally, various isolates were characterised based on in vitro physiological activities and on protein extracts using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS). The response of two asparagus cultivars to the different Fusarium species was evaluated by inoculating experiments. Differences in aggressiveness were observed between Fusarium species and their isolates on roots, while no clear disease symptoms became visible in ferns eight weeks after inoculation. F. redolens isolates Fred1 and Fred2 were the most aggressive strains followed by the moderate aggressive F. proliferatum and the less and almost non-aggressive F. oxysporum isolates, based on the severity of disease symptoms. Fungal DNA in stem bases and a significant induction of pathogenesis-related gene expression was detectable in both asparagus cultivars. A significant negative impact of the pathogens on the root characteristics total root length, volume, and surface area was detected for each isolate tested, with Fred1 causing the strongest effects. No significant differences between the tested asparagus cultivars were observed.

Black aspergilli: A remaining challenge in fungal taxonomy?

2018 ◽  
Vol 57 (6) ◽  
pp. 773-780 ◽  
Author(s):  
Elizabet D’hooge ◽  
Pierre Becker ◽  
Dirk Stubbe ◽  
Anne-Cécile Normand ◽  
Renaud Piarroux ◽  
...  
Keyword(s):  
Antifungal Susceptibility ◽  
Identification Accuracy ◽  
Clinical Isolates ◽  
Reference Database ◽  
Data Set ◽  
Ionization Time ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

AbstractAspergillus section Nigri is a taxonomically difficult but medically and economically important group. In this study, an update of the taxonomy of A. section Nigri strains within the BCCM/IHEM collection has been conducted. The identification accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was tested and the antifungal susceptibilities of clinical isolates were evaluated. A total of 175 strains were molecularly analyzed. Three regions were amplified (ITS, benA, and caM) and a multi-locus phylogeny of the combined loci was created by using maximum likelihood analysis. The in-house MALDI-TOF MS reference database was extended and an identification data set of 135 strains was run against a reference data set. Antifungal susceptibility was tested for voriconazole, itraconazole, and amphotericin B, using the EUCAST method. Phylogenetic analysis revealed 18 species in our data set. MALDI-TOF MS was able to distinguish between A. brasiliensis, A. brunneoviolaceus, A. neoniger, A. niger, A. tubingensis, and A. welwitschiae of A. sect. Nigri. In the routine clinical lab, isolates of A. sect. Nigri are often identified as A. niger. However, in the clinical isolates of our data set, A. tubingensis (n = 35) and A. welwitschiae (n = 34) are more common than A. niger (n = 9). Decreased antifungal susceptibility to azoles was observed in clinical isolates of the /tubingensis clade. This emphasizes the importance of identification up to species level or at least up to clade level in the clinical lab. Our results indicate that MALDI-TOF MS can be a powerful tool to replace classical morphology.

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