Species Distinction in the Trichophyton rubrum Complex

[Conventional and molecular diagnostics in onychomycosis-part 1 : Conventional differentiation of dermatophytes-Trichophyton rubrum, Trichophyton interdigitale]

Onychomycosis is a common infectious nail disease occurring worldwide. The mycological diagnosis of onychomycosis is primarily used for differential diagnostic differentiation from other, mostly inflammatory nail diseases, such as nail psoriasis or onychodystrophies of other causes. Conventional laboratory diagnostics when onychomycosis is suspected is based on microscopic detection of fungi in the nail material using fluorescence-optical potassium hydroxide preparations and culture of the pathogen. Molecular amplification methods allow a more sensitive and specific identification of the causative dermatophyte. Here, in 108 patients with onychomycosis, the dermatophytes were identified by culture and/or molecular biology using polymerase chain reaction (PCR) and the species identification was confirmed with subsequent sequencing. The dermatophytes were analyzed based on macromorphological and microscopic features. A dermatophyte was cultured in 56 of the 108 patients. Among them were 31 isolates of Trichophyton (T.) rubrum and 25 of T. interdigitale. All species identifications were subsequently confirmed by rDNA sequencing with concordant results in 54 of 56 patients. Two primarily as T. interdigitale identified specimens were revealed to be T. quinckeanum and T. tonsurans by molecular methods. T. quinckeanum, which is a zoophilic dermatophyte and a so-called emerging pathogen in dermatomycology, was isolated here for the first time as the causative agent of onychomycosis. The other dermatophyte, initially thought to be T. interdigitale, turned out to be T. tonsurans on molecular biology. This anthropophilic dermatophyte is also a rarity in onychomycosis. In addition, T. rubrum was identified by PCR in 34 of the 52 nail specimens that did not grow culture, and T. interdigitale in 18 nail specimens. However, the morphological identification of the four different dermatophytes species proved problematic. Neither the colony morphology nor the microscopic features of the dermatophytes allow clear differentiation of the pathogens. Microconidia, macroconidia, chlamydospores, and arthrospores are inconsistent in occurrence, number, microscopic distribution, and shape. The urease activity also did not allow an assignment of the dermatophyte species. These results indicate that the most sensitive detection and reliable identification of causative dermatophytes in onychomycosis is only possible by molecular methods.

Molecular Verification of Trichophyton in the Brazilian URM Culture Collection

Trichophyton species cause dermatophytosis in humans, with a high, worldwide frequency of reports and important public health relevance. We evaluated 61 Trichophyton strains from different sources deposited in the University Recife Mycology (URM) culture collection of the Universidade Federal de Pernambuco, Brazil. Strains were phenotypically identified and confirmed by sequencing Internal Transcribed Spacers rDNA and partial beta-tubulin 2-exon. Additionally, we evaluated their susceptibility to terbinafine and itraconazole. Physiological analyses included urease activity and growth in casein medium. Phenotypic methods allowed the reliable identification of T. rubrum only, whereas, for other species, molecular methods were mandatory. All Trichophyton species exhibited susceptibility profiles to itraconazole (0.04-5.33 μg/mL) and terbinafine (0.17-3.33 μg/mL). Our analyses revealed a heterogeneous distribution of T. mentagrophytes, which does not support the current distribution within the species complex of T. mentagrophytes and its genotypes.

A Comparative Description of Dermatophyte Genomes: A State-of-the-Art Review

The nomenclature and phylogeny of dermatophytes is currently based on the nucleotide sequence polymorphisms of a few genomic regions. However, the limitations of this multilocus sequence-based approach makes dermatophyte species identification difficult. Variation and adaptation are key to the persistence of species. Nevertheless, this heterogeneity poses a genuine problem for the classification and nomenclature of dermatophytes. The relatively high intra-species and low inter-species polymorphisms of this keratinophilic group of fungi hampers both species delineation and identification. Establishing the taxonomic boundaries of dermatophyte species complexes remains controversial. Furthermore, until recently, knowledge of molecular biology, genetics and genomics remained limited. This systematic review highlights the added value of whole genome sequencing and analysis data in dermatophyte classification that might enhance identification and, consequently, the diagnosis and management of dermatophytoses. Our approach consisted in describing and comparing the dermatophyte mitochondrial genomes, secretomes (Adhesins, LysM domains, proteases) and metabolic pathways, with the aim to provide new insights and a better understanding of the phylogeny and evolution of dermatophytes.

The in vitro Activity of Echinocandins Against Clinical Trichophyton rubrum Isolates and Review of the Susceptibility of T. rubrum to Echinocandins Worldwide

Introduction

The emergence of resistance in Trichophyton rubrum to azoles and terbinafine has become increasingly evident in recent years, necessitating the development of novel antifungal drugs and the exploration of new indications for existing agents.

Methods

In this study, we retrospectively evaluated the in vitro antifungal activity of 3 echinocandins (anidulafungin, caspofungin, and micafungin) against 73 clinical isolates of T. rubrum collected from a teaching hospital in Shanghai, China, using EUCAST E.DEF 9.3.1 with minor modification. We also reviewed the susceptibility of T. rubrum to echinocandins globally by literature searching.

Results

Our findings revealed that micafungin exhibited the lowest modal minimum effective concentration (MEC) value (0.08 mg/L, n = 28) and the lowest geometric mean (GM) MEC value (0.014 mg/L) among the 73 isolates of T. rubrum tested, followed by anidulafungin with a modal MEC value of 0.016 mg/L (n = 67) and a GM of 0.018 mg/L. Caspofungin displayed a higher modal MEC value of 0.5 mg/L (n = 35) and a GM of 0.308 mg/L. Despite variations in methodologies, similar results were obtained from the review of five relevant studies included in our analysis.

Discussion

Echinocandins exhibited excellent in vitro activity against T. rubrum isolates, with micafungin and anidulafungin demonstrating greater potency than caspofungin. These findings suggest that echinocandins could be considered as potential treatment options for managing recalcitrant dermatophytoses resulting from the emergence of resistance. However, it is important to note that the clinical efficacy of these in vitro findings has yet to be established and warrants further investigation.

Cutaneous Fungal Infections Caused by Dermatophytes and Non-Dermatophytes: An Updated Comprehensive Review of Epidemiology, Clinical Presentations, and Diagnostic Testing

Cutaneous fungal infection of the skin and nails poses a significant global public health challenge. Dermatophyte infection, mainly caused by Trichophyton spp., is the primary pathogenic agent responsible for skin, hair, and nail infections worldwide. The epidemiology of these infections varies depending on the geographic location and specific population. However, epidemiological pattern changes have occurred over the past decade. The widespread availability of antimicrobials has led to an increased risk of promoting resistant strains through inappropriate treatment. The escalating prevalence of resistant Trichophyton spp. infections in the past decade has raised serious healthcare concerns on a global scale. Non-dermatophyte infections, on the other hand, present even greater challenges in terms of treatment due to the high failure rate of antifungal therapy. These organisms primarily target the nails, feet, and hands. The diagnosis of cutaneous fungal infections relies on clinical presentation, laboratory investigations, and other ancillary tools available in an outpatient care setting. This review aims to present an updated and comprehensive analysis of the epidemiology, clinical manifestations, and diagnostic testing methods for cutaneous fungal infections caused by dermatophytes and non-dermatophytes. An accurate diagnosis is crucial for effective management and minimizing the risk of antifungal resistance.

Insights into Changing Dermatophyte Spectrum in India Through Analysis of Cumulative 161,245 Cases Between 1939 and 2021

Dermatophytosis is one of the most common superficial infections of the skin affecting nearly one-fifth of the world population at any given time. With nearly 30% of worldwide terbinafine-resistance cases in Trichophyton mentagrophytes/Trichophyton interdigitale and Trichophyton rubrum reported from India in recent years, there is a significant burden of the emerging drug resistance epidemic on India. Here, we carry out a comprehensive retrospective analysis of dermatophytosis in India using 1038 research articles pertaining to 161,245 cases reported from 1939 to 2021. We find that dermatophytosis is prevalent in all parts of the country despite variable climatic conditions in different regions. Our results show T. rubrum as the most prevalent until 2015, with a sudden change in dermatophyte spectrum towards T. mentagrophytes/T. interdigitale complex since then. We also carried out an 18S rRNA-based phylogenetics and an average nucleotide identity-and single nucleotide polymorphism-based analysis of available whole genomes and find very high relatedness among the prevalent dermatophytes, suggesting geographic specificity. The comprehensive epidemiological and phylogenomics analysis of dermatophytosis in India over the last 80 years, presented here, would help in region-specific prevention, control and treatment of dermatophyte infections, especially considering the large number of emerging resistance cases.

[Clinical picture, causative agents and diagnostics of dermatomycoses]

Dermatomycoses affect free skin, hairy scalp, fingernails and toenails. In addition, oral mucosa and genital mucosa can also be affected by fungal infections. The most common pathogens causing skin fungal infections are dermatophytes. They are responsible for, among others, tinea corporis, tinea capitis and onychomycosis (tinea unguium). Mainly anthropophilic dermatophytes are found as pathogens. In the case of tinea capitis-at least in Europe and in German-speaking countries-zoophilic skin fungi must also be considered. Rarely, geophilic dermatophytes can also be isolated. Yeast infections of the skin, mostly caused by Candida albicans, primarily affect the intertriginous skin areas, for example, the groin region, but also the submammary area and the spaces between the fingers and toes. Elderly patients are often affected, but also infants and, in particular, immunocompromised patients. These patient groups are also more frequently affected by oral mucosal infections caused by Candida albicans and other Candida species. Pseudomembranous candidiasis of the oral mucosa and tongue typically affects patients with HIV/AIDS. Mold infections in dermatology are relevant in onychomycosis of the big toenail. The causative agent is usually Scopulariopsis brevicaulis. Cutaneous mold infections are rare and only occur in immunocompromised patients. The mycological diagnosis of dermatomycoses is based on the microscopic, if possible fluorescence-optical detection of fungal hyphae and spores from skin scales, nail shavings and hair roots. The culture detection of dermatophytes, yeasts and molds allows the identification of the causative fungal species, but often fails, especially in patients who have already been treated with antifungal agents. In view of the high sensitivity and specificity of the molecular methods for fungal detection compared to culture, polymerase chain reaction (PCR) must realistically be regarded as the gold standard for dermatophytosis diagnostics. However, it should not be neglected that the three pillars of diagnostics-preparation, culture, PCR-currently deliver the best results.

Detection of emerging genotypes in Trichophyton mentagrophytes species complex: A proposal for handling biodiversity in dermatophytes

A resistant and hypervirulent dermatophyte from India has been described as a taxonomic novelty, Trichophyton indotineae, a species of the Trichophyton mentagrophytes complex. Rapid detection and correct identification of closely similar dermatophytes with different predilections are essential for efficient clinical management. We evaluated the efficacy of rapid diagnostic methods clinical and environmental strains in the T. mentagrophytes complex. The methods included Real-time-PCR, DermaGenius, LAMP, and MALDI-ToF MS, using rDNA ITS sequences as taxonomic standard. The results show that only MALDI-ToF MS can distinguish 96.97% T. indotineae from other closely related species. The complex comprises numerous clones which may differ in anonymous markers but with similar evolutionary behavior. Therefore, we recommend to distinguish species only when they show an appreciable degree of adaptation and thus are clinically significant. The distinction of remaining clonal diversity is an epidemiological query and can be solved by haplotype numbering.

Anti-dermatophytic activity of cold atmospheric plasma against Trichophyton rubrum via affecting fungal growth, morphology, drug susceptibility and HSP90 gene expression

Trichophyton rubrum, a major human pathogenic dermatophyte, is responsible for the most recurrent dermatophytoses as globally important superficial fungal infections. Typical chemotherapy is used to handle such infections; however, emerging drug resistance and side effects necessitate the new remedial method development. Cold atmospheric plasma (CAP) is an emerging technology, consisted of neutral and charged particles and photons newly developed as a potent and safe antimicrobial technique to combat drug-resistant microbial pathogens. In the present study, the vast effects of CAP irradiation containing oxygen (2%) and helium (98%) on T. rubrum growth and pathogenicity were explored. After exposure of T. rubrum to CAP jet for 90, 120, 150, 180, and 210 s in 96-well microtiter plates, cell morphology and viability, ergosterol content of fungal hyphae, HSP90 gene expression, and the pattern of drug susceptibility were studied by using electron microscopy, RT-qPCR, spectrophotometry, disk diffusion and CLSI microbroth dilution methods. CAP irradiation significantly inhibited the fungal growth by 25.83 to 89.10%, reduced fungal cell viability by 11.68 to 87.71%, disrupted cellular membranous organelles and structures of the fungal hyphae, and suppressed efficiently the expression of HSP90 gene by 2 folds in 210 s exposure. Taken together, our results demonstrated that CAP is an efficient tool with potential in-vivo therapeutic applications against chronic dermatophytosis caused by T. rubrum due to its effectiveness, harmless, and ease of access.

Phylogenetic and ecological reevaluation of the order Onygenales

The order Onygenales is classified in the class Eurotiomycetes of the subphylum Pezizomycotina. Families in this order have classically been isolated from soil and dung, and two lineages contain causative agents of superficial, cutaneous and systemic infections in mammals. The ecology and habitat choices of the species are driven mainly by the keratin and cellulose degradation abilities. The present study aimed to investigate whether the ecological trends of the members of Onygenales can be interpreted in an evolutionary sense, linking phylogenetic parameters with habitat preferences, to achieve polyphasic definitions of the main taxonomic groups. Evolutionary processes were estimated by multiple gene genealogies and divergence time analysis. Previously described families, namely, Arthrodermataceae, Ajellomycetaceae, Ascosphaeraceae, Eremascaceae, Gymnoascaceae, Onygenaceae and Spiromastigoidaceae, were accepted in Onygenales, and two new families, Malbrancheaceae and Neogymnomycetaceae, were introduced. A number of species could not be assigned to any of the defined families. Our study provides a revised overview of the main lines of taxonomy of Onygenales, supported by multilocus analyses of ITS, LSU, TUB, TEF1, TEF3, RPB1, RPB2, and ribosomal protein 60S L10 (L1) (RP60S) sequences, combined with available data on ecology, physiology, morphology, and genomics.

Investigations upon the Improvement of Dermatophyte Identification Using an Online Mass Spectrometry Application

Online MALDI-TOF mass spectrometry applications, such as MSI-2, have been shown to help identify dermatophytes, but recurrent errors are still observed between phylogenetically close species. The objective of this study was to assess different approaches to reduce the occurrence of such errors by adding new reference spectra to the MSI-2 application. Nine libraries were set up, comprising an increasing number of spectra obtained from reference strains that were submitted to various culture durations on two distinct culture media: Sabouraud gentamicin chloramphenicol medium and IDFP Conidia medium. The final library included spectra from 111 strains of 20 species obtained from cultures on both media collected every three days after the appearance of the colony. The performance of each library was then analyzed using a cross-validation approach. The spectra acquisitions were carried out using a Microflex Bruker spectrometer. Diversifying the references and adding spectra from various culture media and culture durations improved identification performance. The percentage of correct identification at the species level rose from 63.4 to 91.7% when combining all approaches. Nevertheless, residual confusion between close species, such as Trichophyton rubrum, Trichophyton violaceum and Trichophyton soudanense, remained. To distinguish between these species, mass spectrometry identification should take into account basic morphological and/or clinico-epidemiological features.

Founder Effects Contribute to the Population Genetic Structure of the Major Dermatophytosis Pathogen Trichophyton rubrum on Hainan Island, China

Background

Founder events have been observed among numerous plants and animal species living on oceanic islands due to the geographic separation of these islands and the small amount of original life they harbor. However, there has been little research on the ecological characteristics of pathogenic microorganisms on islands. Trichophyton rubrum ranks the most common isolated dermatophyte causing dermatophytosis in clinic and has become an epidemic strain worldwide in recent decades.

Objective

To study the phylogenetic characteristics and the distribution pattern of genetic polymorphism of T. rubrum in China, which further provide theoretical basis for the prevention and control of T. rubrum.

Methods

In the present study, we sequenced and analyzed the genetic characteristics of 204 T. rubrum isolates from Hainan Island and other sites in China. Phylogenetic analysis and genetic polymorphisms were studied based on a total of 41,409 high-quality whole-genome SNPs.

Results

The majority of the isolates from Hainan Island clustered together. Mixed T. rubrum population differentiation was observed among the strains of different geographical origins. In addition, the genetic diversity (π) of the Hainan isolates was low and showed no significant difference from that of isolates from other sites.

Conclusion

This study is the first to discuss general ecological and evolutionary principles related to pathogenic fungi. Our findings reveal a founder effect during the origination of T. rubrum on Hainan Island and provide guidance regarding prevention and treatment strategies.

The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach

The medically relevant Trichophyton rubrum species complex has a variety of phenotypic presentations but shows relatively little genetic differences. Conventional barcodes, such as the internal transcribed spacer (ITS) region or the beta-tubulin gene, are not able to completely resolve the relationships between these closely related taxa. T. rubrum, T. soudanense and T. violaceum are currently accepted as separate species. However, the status of certain variants, including the T. rubrum morphotypes megninii and kuryangei and the T. violaceum morphotype yaoundei, remains to be deciphered. We conducted the first phylogenomic analysis of the T. rubrum species complex by studying 3105 core genes of 18 new strains from the BCCM/IHEM culture collection and nine publicly available genomes. Our analyses revealed a highly resolved phylogenomic tree with six separate clades. Trichophyton rubrum, T. violaceum and T. soudanense were confirmed in their status of species. The morphotypes T. megninii, T. kuryangei and T. yaoundei all grouped in their own respective clade with high support, suggesting that these morphotypes should be reinstituted to the species-level. Robinson-Foulds distance analyses showed that a combination of two markers (a ubiquitin-protein transferase and a MYB DNA-binding domain-containing protein) can mirror the phylogeny obtained using genomic data, and thus represent potential new markers to accurately distinguish the species belonging to the T. rubrum complex.

Recent developments in less known and multi-resistant fungal opportunists

Fungal infections have increased in recent years due to host factors, such as oncohaematological and transplant-related disorders, immunosuppressive therapy, and AIDS. Additionally, molecular and proteomic facilities have become available to identify previously unrecognizable opportunists. For these reasons, reports on less-known and recalcitrant mycoses, such as those caused by black fungi, hyaline filamentous fungi, coelomycetes, Mucorales, and non-Candida yeasts have emerged. In this review, novel taxonomy in these groups, which often are multi-resistant to one or several classes of antifungals, is discussed. Clinical presentations, diagnosis and current treatment of some major groups are summarised.

Inferring genetic fitness from genomic data

The genetic composition of a naturally developing population is considered as due to mutation, selection, genetic drift, and recombination. Selection is modeled as single-locus terms (additive fitness) and two-loci terms (pairwise epistatic fitness). The problem is posed to infer epistatic fitness from population-wide whole-genome data from a time series of a developing population. We generate such data in silico and show that in the quasilinkage equilibrium phase of Kimura, Neher, and Shraiman, which pertains at high enough recombination rates and low enough mutation rates, epistatic fitness can be quantitatively correctly inferred using inverse Ising-Potts methods.

Regional Differences in Antifungal Susceptibility of the Prevalent Dermatophyte Trichophyton rubrum

In vitro susceptibility testing for Trichophyton rubrum has shown resistance to terbinafine, azoles and amorolfine, locally, but epidemiological cutoffs are not available. In order to assess the appropriateness of current first-line antifungal treatment for T. rubrum in China, we characterized antifungal susceptibility patterns of Chinese T. rubrum strains to nine antifungals and also described the upper limits of wild-type (WT) minimal inhibitory concentrations (MIC) (UL-WT) based on our study and another six studies published during the last decades. Sixty-two clinical isolates originating from seven provinces in China were identified as T. rubrum sensu stricto; all Chinese strains showed low MICs to eight out of nine antifungal drugs. Terbinafine (TBF) showed the lowest MICs of all antifungal classes tested in both the Chinese and global groups, with a 97.5% UL-WT MIC-value of 0.03 mg/L. No non-WT isolates were observed for TBF in China, but were reported in 18.5% of the global group. Our study indicated that TBF was still the most active drug for Chinese T. rubrum isolates, and all strains were within the WT-population. TBF therefore remains recommended for primary therapy to dermatophytosis caused by T. rubrum in China now, but regular surveillance of dermatophytes and antifungal susceptibility is recommended.

Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

BACKGROUND

The Trichophyton rubrum species group consists of prevalent causative agents of human skin, nail and hair infections, including T rubrum sensu stricto and T violaceum, as well as other less well-established or debatable taxa like T soudanense, T kuryangei and T megninii. Our previous study provided limited evidence in favour of the existence of two genetic lineages in the Russian T rubrum sensu stricto population.

OBJECTIVES

We aimed to study the genetic structure of the Russian population of T rubrum and to identify factors shaping this structure.

METHODS

We analysed the polymorphism of 12 simple sequence repeat (SSR or microsatellite) markers and single nucleotide polymorphism in the TERG_02941 protein-coding gene in 70 T rubrum isolates and performed a phylogenomic reconstruction.

RESULTS

All three types of data provided conclusive evidence that the population consists of two genetic lineages. Clustering, performed by means of microsatellite length polymorphism analysis, was strongly dependent on the number of nucleotide repeats in the 5'-area of the fructose-1,6-bisphosphate aldolase gene. Analysis of molecular variance (AMOVA) on the basis of SSR typing data indicated that 22%-48% of the variability was among groups within T rubrum. There was no clear connection of population structure with types of infection, places of geographic origin, aldolase gene expression or urease activity.

CONCLUSION

Our results suggest that the Russian population of T rubrum consists of two cosmopolitan genetic lineages.

Towards Genomic Criteria for Delineating Fungal Species

The discussion of fungal species delineation has yet to reach a consensus, despite the advancements in technology, which helped modernise traditional approaches. In particular, the phylogenetic species concept was one of the tools that has been used with considerable success across the fungal kingdom. The fast rise of fungal genomics provides an unprecedented opportunity to expand measuring the relatedness of fungal strains to the level of whole genomes. However, the use of genomic information in taxonomy has only just begun, and few methodological guidelines have been suggested so far. Here, a simple approach of computationally measuring genomic distances and their use as a standard for species delineation is investigated. A fixed threshold genomic distance calculated by the quick and easy-to-use tools Mash and Dashing proved to be an unexpectedly widely applicable and robust criterion for determining whether two genomes belong to the same or to different species. The accuracy of species delineation in an uncurated dataset of GenBank fungal genomes was close to 90%—and exceeded 90% with minimal curation. As expected, the discriminative power of this approach was lower at higher taxonomic ranks, but still significantly larger than zero. Simple instructions for calculation of a genomic distance between two genomes and species similarity thresholds at different k-mer sizes are suggested. The calculation of genomic distance is identified as a powerful approach for delineating fungal species and is proposed—not as the only criterion—but as an additional tool in the versatile toolbox of fungal taxonomy.

A fast impedance-based antimicrobial susceptibility test

There is an urgent need to develop simple and fast antimicrobial susceptibility tests (ASTs) that allow informed prescribing of antibiotics. Here, we describe a label-free AST that can deliver results within an hour, using an actively dividing culture as starting material. The bacteria are incubated in the presence of an antibiotic for 30 min, and then approximately 105 cells are analysed one-by-one with microfluidic impedance cytometry for 2-3 min. The measured electrical characteristics reflect the phenotypic response of the bacteria to the mode of action of a particular antibiotic, in a 30-minute incubation window. The results are consistent with those obtained by classical broth microdilution assays for a range of antibiotics and bacterial species.

Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning

It is important that antibiotics prescriptions are based on antimicrobial susceptibility data to ensure effective treatment outcomes. The increasing availability of next-generation sequencing, bacterial whole genome sequencing (WGS) can facilitate a more reliable and faster alternative to traditional phenotyping for the detection and surveillance of AMR. This work proposes a machine learning approach that can predict the minimum inhibitory concentration (MIC) for a given antibiotic, here ciprofloxacin, on the basis of both genome-wide mutation profiles and profiles of acquired antimicrobial resistance genes. We analysed 704 Escherichia coli genomes combined with their respective MIC measurements for ciprofloxacin originating from different countries. The four most important predictors found by the model, mutations in gyrA residues Ser83 and Asp87, a mutation in parC residue Ser80 and presence of the qnrS1 gene, have been experimentally validated before. Using only these four predictors in a linear regression model, 65% and 93% of the test samples’ MIC were correctly predicted within a two- and a four-fold dilution range, respectively. The presented work does not treat machine learning as a black box model concept, but also identifies the genomic features that determine susceptibility. The recent progress in WGS technology in combination with machine learning analysis approaches indicates that in the near future WGS of bacteria might become cheaper and faster than a MIC measurement.

Species identification of dermatophytes isolated in China by matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry

BACKGROUND AND OBJECTIVES

Matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry (MALDI-TOF MS) is a novel technique for identifying dermatophytes. This study aimed to detect the limitation of MALDI-TOF MS applied to dermatophytes.

METHODS

A total of 113 DNA-sequenced dermatophyte isolates preserved at the Research Center for Medical Mycology of Peking University were selected for this study. Forty-two isolates were selected as reference strains used to create a supplementary database. Seventy-one isolates (Trichophyton rubrum series, T benhamiae series, T mentagrophytes series species and T schoenleinii) were used to evaluate the suitability of the MALDI-TOF MS Biotyper system. MALDI Biotyper 4.0 software was employed to construct the main spectrum profile (MSP) dendrograms.

RESULTS

Correct identification rates at the species and genus levels were 90.1% and 91.5%, respectively, using Bruker Filamentous Fungi Library 1.0 combined with the novel database. The MSP dendrogram of the T rubrum series showed unambiguous separation of T rubrum and T violaceum and that of the T benhamiae series distinguished T verrucosum, T benhamiae and T erinacei. Conversely, the MSP dendrogram of the T mentagrophytes series did not successfully distinguish T mentagrophytes, T interdigitale and T tonsurans.

CONCLUSION

MALDI-TOF MS showed good performance in the identification and delineation of the T rubrum series and T benhamiae series, but showed poor performance in T mentagrophytes series.

Intraspecific Diversity and Taxonomy of Emmonsia crescens

Emmonsia crescens is known as an environmental pathogen causing adiaspiromycosis in small rodents. As the generic name Emmonsia is no longer available for this species, its taxonomic position is re-evaluated. The intraspecific variation of Emmonsia crescens was analyzed using molecular, morphological, and physiological data, and the relationship between frequency of adiaspiromycosis and body temperature of host animals was explored. A North American and a pan-global lineage could be discerned, each with subclusters at low genetic distance. European strains produced the classical type of very large adiaspores, while in the North American lineage adiaspores relatively small, resembling the broad-based budding cells of Blastomyces. Members of the closely related genus Emergomyces may exhibit large, broad-based in addition to small, narrow-based budding cells. We conclude that the morphology of the pathogenic phase in these fungi differs gradationally between species and even populations, and is therefore less suitable as a diagnostic criterion for generic delimitation. Two Emmonsia species are reclassified in Emergomyces.

A rapid and accurate method for the detection of four aminoglycoside modifying enzyme drug resistance gene in clinical strains of Escherichia coli by a multiplex polymerase chain reaction

BACKGROUND

Antibiotics are highly effective drugs used in the treatment of infectious diseases. Aminoglycoside antibiotics are one of the most common antibiotics in the treatment of bacterial infections. However, the development of drug resistance against those medicines is becoming a serious concern.

AIM

This study aimed to develop an efficient, rapid, accurate, and sensitive detection method that is applicable for routine clinical use.

METHODS

Escherichia coli was used as a model organism to develop a rapid, accurate, and reliable multiplex polymerase chain reaction (M-PCR) for the detection of four aminoglycoside modifying enzyme (AME) resistance genes Aac(6')-Ib, Aac(3)-II, Ant(3″)-Ia, and Aph(3')-Ia. M-PCR was used to detect the distribution of AME resistance genes in 237 clinical strains of E. coli. The results were verified by simplex polymerase chain reaction (S-PCR).

RESULTS

Results of M-PCR and S-PCR showed that the detection rates of Aac(6')-Ib, Aac(3)-II, Ant(3″)-Ia, and Aph(3')-Ia were 32.7%, 59.2%, 23.5%, and 16.8%, respectively, in 237 clinical strains of E. coli. Compared with the traditional methods for detection and identification, the rapid and accurate M-PCR detection method was established to detect AME drug resistance genes. This technique can be used for the clinical detection as well as the surveillance and monitoring of the spread of those specific antibiotic resistance genes.

A Comparative Study on Phenotypic versus ITS-Based Molecular Identification of Dermatophytes Isolated in Dakar, Senegal

Classically, dermatophytes are identified by phenotypic methods even if these methods, sometimes, remain difficult or uncertain. On the other hand, nucleotide sequence analysis of internal transcribed spacers (ITS) of rDNA has proved to be a useful method for identification of dermatophytes. The objective of this study was to compare the phenotypic method with DNA sequencing of the ITS regions for identification of dermatophyte species isolated in Dakar, Senegal. A collection of thirty-two strains of dermatophytes were isolated from patients suffering from dermatophytosis. Mycological identification revealed Trichophyton soudanense (n = 13), T. interdigitale (n = 10), Microsporum audouinii (n = 5), and one strain for each of the following species: T. rubrum, T. mentagrophytes, and M. canis and one unidentified strain. For comparison, ITS-based PCR and DNA sequencing were applied for identification of the isolated dermatophytes. ITS sequences showed, in BLAST search analysis, 99-100% of similarity. Identification of dermatophyte isolates by conventional methods was confirmed by DNA sequencing of the ITS regions in 84% of cases. Discrepancies concern mostly T. rubrum misidentified as T. interdigitale. PCR sequencing provided an excellent tool for identifying dermatophyte strains that do not present typical morphological characteristics. It was also able to give correct identification of an atypical strain of M. audouinii responsible of mycetoma of the scalp.