Clinical Mycology Research Articles

Sino-Orbital Invasive Fungal Infections in Immunocompetent Hosts

This review describes the clinical presentation, predisposing factors, pathophysiology, mycology, diagnosis, and therapy of sino-orbital invasive fungal infections in immunocompetent individuals. Recent advances published in the literature were reviewed with special consideration of current diagnostic methods and treatment regimens. Owing to the rarity of this condition literature is scarce. Majority of the studies are from tropical countries such as India where the disease is relatively more common. Treatment strategies are variable and response to medical treatment is favorable in significant number of patients. Invasive sino-orbital fungal infection in immunocompetent hosts is a rare clinical condition. Aspergillus and Mucorales group of fungi cause infection in the presence of certain risk factors. Other species of fungi may occasionally be involved. Diagnosis requires imaging and laboratory back up. CT scan remains the primary imaging modality of choice although MRI is more sensitive in picking up orbital soft tissue inflammation. With early diagnosis and appropriate medical and surgical therapy, globe salvage and visual recovery may be achieved.

Updates in Laboratory Diagnostics for Invasive Fungal Infections.

Appropriate diagnosis of invasive fungal infections (IFIs) is critical due to the high rates of morbidity and mortality, as well as the substantial economic burden, associated with the management of these diseases. The recognition of IFI and differentiation from other infections with similar clinical presentations can be challenging, which can lead to diagnostic error that not only has an impact on individual patient health outcomes but also on antimicrobial drug usage and the growing threat of antimicrobial resistance in bacteria. Therefore, there is a significant need for improved stewardship related to diagnostic testing for and treatment of IFIs. The purpose of this review is to highlight recent advances related to current fungal diagnostics, as well as explore some of the most innovative technology that has emerged with the potential to shift the paradigm of clinical mycology. In general, this review will discuss research related to enhanced fungal culture utilization and identification techniques, expanded applications of fungal antigen testing, and recently developed molecular assays and other novel nonculture fungal diagnostic approaches. Specifically, the application of mass spectrometry, novel glycobiomarker detection, and detection of fungal-specific volatile organic compounds will be reviewed, along with other key updates, to provide the reader with an updated review that extends beyond the basics of IFI laboratory diagnostics. Where appropriate, the reader will be directed to more comprehensive reviews of certain aspects of clinical mycology laboratory testing to provide a broader context for the critical consideration of these updates.

Clinical mycology today: A synopsis of the mycoses study group education and research consortium (MSGERC) second biennial meeting, September 27-30, 2018, Big Sky, Montana, a proposed global research agenda.

Clinical mycology today: A synopsis of the mycoses study group education and research consortium (MSGERC) second biennial meeting, September 27-30, 2018, Big Sky, Montana, a proposed global research agenda.

Use of MALDI-TOF MS for fungal species distribution of interdigital intertrigo in seafarers, Dakar, Senegal

To determine fungal species distribution of interdigital intertrigo among seafarers in Dakar, Senegal, a cross-sectional study was carried out from May to August 2017 among seafarers clinically diagnosed with interdigital intertrigo. A questionnaire was filled to each patient before sampling the affected folds and transporting to Aristide Le Dantec University Hospital where mycological analyses were realized. Species identification by MALDI-TOF MS was performed in Marseille, France. In total, 169 men (21–66 years) were included. Few of them (3%) had a high level of education and the duration of the mycosis exceed 10 years for 88% of patients. Direct microscopic examination (ME) was positive in 34.3%. Among samples with positive ME, 58.6% had positive culture. An overall incidence of 30.2% was found. Patients with confirmed cases aged between 28 and 66 years. Among them, those between 36–50 years were predominant (52.9%). Those with a high level of education were less representative (2%). For 52.1% of patients, the duration of the mycosis was superior to 10 years. Furthermore, 57% of cases were significantly associated with other types of tinea pedis and/or onychomycosis (P=0.03). Culture was positive in 23.7% isolating 43 strains successfully identified at the species level by MALDI-TOF MS for 31 isolates: 20 Candida and 11 dermatophytes. The rest was identified only at the genus level belonged to Fusarium. In definitive, MALDI-TOF MS could be a useful tool for routine and fast identification of dermatophytes, yeasts and NDFF in clinical mycology laboratories.

A national survey on fungal infection diagnostic capacity in the clinical mycology laboratories of tertiary care hospitals in China.

As the incidence of fungal infections in China increases, the demand for rapid and accurate diagnosis of mycoses is growing. Yet, information on current diagnostic capacity is scarce. An online survey was conducted in February 2018 to collect information on mycology testing from tertiary care hospitals across China. Responses from 348 hospitals were analyzed, and a scoring system was designed and employed to assess the overall diagnostic capacity. Most of the surveyed hospitals did not have separate laboratory space, manpower, or equipment dedicated for fungal testing. Conventional staining methods were widely available (>70%), whereas GMS and fluorescent staining were less common. Fungal identification services were offered mostly with chromogenic medium, morphological characterization or automated identification systems, other than more advanced methods such as MALDI-TOF MS and DNA sequencing. Fungal serology testing was available in 81.1%, with G test being the most often used. Though 91.8% of the respondents had the ability to perform antifungal susceptibility testing for yeasts, less than 13% conducted such testing for molds. The percentage of laboratories participating in External Quality Assessment programs and research was 57.5% and 32.5%, respectively. The average score for the 348 surveyed hospitals was 37.2 (out of a maximum of 89 points), with only 15 hospitals scoring >60, suggesting a general lack of high-quality mycology laboratories. The overall clinical testing capacity for fungal infection in China is insufficient. More investment and training efforts are warranted to establish centers of excellence and promote access to high-quality diagnostic services.

Genotyping of different clinical Candida albicans isolates using RAPD Analysis

Random Amplification of Polymorphic DNA (RAPD–PCR) is a powerful discriminative assay comparing several clinical isolates by amplifying the target DNA genome by a group of short random primers. In clinical mycology the infections with Candida species increase, especially Candida albicans and their complications become a serious problem, So this work aims to determine the genetic typing of clinical C. Albicans isolated from ICU patient's (urine, blood, vaginal secretions, and bronchoalveolar lavage) who existing in Elarreish hospital, Egypt based on RAPD-PCR assay. To investigate their genetic relationships. Totally one hundred samples of 40 samples of urine, 30 samples of blood, 20 samples of vaginal secretions and 10 samples of Bronchoalveolar lavage were collected. About 50 different species of Candida were isolated, 28 species out of them were identified by standard-taxonomic criteria and molecular technique as Candida albicans (n =28). Candida albicans represents 14 samples of urine (35%), 7 samples of blood (23%), 3 samples of vaginal secretions (10%), and 4 samples of bronchoalveolar lavage (40%). Genetic relevance of the different 28 Candida albicans was analyzed by (RAPD) assay using 6 different primers OPA1, OPA2, OPA3, OPA7, OPA8, and OPA9. Only three primers OPA3, OPA7, and OPA9 allow discrimination among the Candida albicans isolates. PCR bands were scored as present or absent and the genetic similarity between them was determined using Jaccard's coefficient(Sj). Dendrograms constructed using the UPGMA method showed that 12, 14, and 20 different genotypes can be identified by OPA3, OPA7, and OPA9 primers respectively since they showed a high degree of genetic heterogeneity. Data indicated that RAPD analysis is useful for providing genotypic characteristics for C. albicans in the epidemiological investigation.

Fishing for a Diagnosis, the Impact of Delayed Diagnosis on the Course of Mycobacterium marinum Infection: 21 Years of Experience at a Tertiary Care Hospital.

Background Mycobacterium marinum is a common but underreported mycobacterial infection. We conducted a large retrospective study to determine risk factors and describe the therapeutic interventions and outcomes in patients with uncomplicated and complicated M. marinum infection.MethodsCulture-confirmed M. marinum infection cases were identified from the Mayo Clinic Clinical Mycology Laboratory from January 1998 to December 2018. Complicated M. marinum infection was defined as the presence of tenosynovitis, septic arthritis, or osteomyelitis. Differences in complicated vs uncomplicated M. marinum infections were analyzed using statistical comparisons.ResultsTwelve cases had a complicated M. marinum infection. Patients with a complicated infection were older (64.3 ± 11.1 vs 55.8 ± 14.5; P = .03), had longer duration of symptoms (5 vs 3 months; P = .011), and had more surgical debridements (1 vs 0; P < .001). Length of treatment and number of drugs used were not statistically significant. Complicated M. marinum cases received more medications (2 vs 1; P = .263) and were treated longer (5.7 vs 3.5 months; P = .067). Antibiotic susceptibilities were performed in 59% of the patients. All isolates were susceptible to clarithromycin. From the tetracyclines, doxycycline had a better susceptibility pattern.Conclusions M. marinum infection is an important cause of skin and soft tissue infection. Poor water exposure documentation, unusual clinical presentation, and empiric antibiotic treatment before definitive M. marinum diagnosis often contribute to a delayed diagnosis. Complicated M. marinum cases had longer duration of symptoms and more surgical debridements. No difference in the number of drugs used or clinical outcome was observed.

Report of the Korean Association of External Quality Assessment Service on Clinical Bacteriology and Mycology (2016)

Report of the Korean Association of External Quality Assessment Service on Clinical Bacteriology and Mycology (2016)

Is Candida auris here to stay? An interview with Dimitrios Kontoyiannis.

In this exclusive interview, Dimitrios P Kontoyiannis discusses current mycology hot topic, Candida auris. With a focus on the current knowns and unknowns for the pathogenesis, resistance and transmission of this emerging fungal pathogen, in addition to a look at therapeutics and future perspectives. This interview was conducted by Ellen Colvin, Commissioning Editor of Future Microbiology. Dimitrios P Kontoyiannis is the Texas 4000 distinguished endowed professor and deputy head in the Division of Internal Medicine at MD Anderson Cancer Center in Houston (TX, USA). Dr Kontoyiannis has authored over 550 peer-reviewed manuscripts and has given over 330 lectures in national and international conferences and academic institutions in the USA and abroad. He is considered a leading mycology expert world-wide with an H index of 101 and over 43,000 citations. His research group is credited for many and sustained contributions to clinical, translational and experimental mycology. He is the recipient of many national and international awards and is the past president elect of Immunocompromised Host Society (2016-2018).

English

Antimicrobials have been playing an important role in preventing illness and death associated with infections due to bacteria. However, the emergence and spread of resistance by pathogens have decreased the effectiveness of the commonly prescribed antimicrobials. Intestinal Escherichia coli are among bacterial pathogens that are endowed with such resistance traits because they are important source and reservoir of genes that encode antimicrobial resistance. To determine the antimicrobial resistance profile of fecal isolates of E. coli from diarrheic patients. Stool samples were collected consecutively from 100 individuals who visited Selam Health Center during the study period, April to June 2018. Samples were collected and transported under sterile condition to the National Clinical Bacteriology and Mycology reference Laboratory, Ethiopian Public Health Institute. The samples were streaked on MacConkey agar and incubated overnight at 37°C. E. coli isolates were further confirmed using conventional biochemical tests. Antimicrobial susceptibility status was determined using the disk diffusion method on Mueller Hinton agar as recommended by the Clinical Laboratory Standard Institute. The raw data was compiled and entered to spreadsheet and analysis was done using SPSS Version 20 with p-value ≤0.05 considered statistically significant. Out of the 100 patients, 43 were female and the rest were male. Confirmed E. coli were isolated from 73 individuals. Antimicrobial susceptibility testing showed that E. coli isolated in this study were highly resistant to trimethoprim-sulfamethoxazole 49 (67.1%) and amoxicillin-clavulanic acid 47(64.4 %). No isolates showed resistance to gentamicin and tobramicin. Of all the isolates, 11(15.1%) were multidrug resistant. No association was observed between antimicrobial resistance status and sex of individuals included in this study. However, there was an association between age and resistance patterns. Resistance to commonly prescribed antibiotics among E. coli isolated in this study was high and a considerable proportions of the strains were multidrug resistant. This is an indication for an alarming rate of resistance of intestinal E. coli to first line antimicrobials. To reduce the problem, regular monitoring and education for the community are very important. Key words: Escherichia coli, antibiotic susceptibility, multidrug resistant, Ethiopia, biochemical tests, disk diffusion.

Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities \u2013 a proof of concept under laboratory conditions

High-throughput sequencing (HTS) enables the generation of large amounts of genome sequence data at a reasonable cost. Organisms in mixed microbial communities can now be sequenced and identified in a culture-independent way, usually using amplicon sequencing of a DNA barcode. Bulk RNA-seq (metatranscriptomics) has several advantages over DNA-based amplicon sequencing: it is less susceptible to amplification biases, it captures only living organisms, and it enables a larger set of genes to be used for taxonomic identification. Using a model mock community comprising 17 fungal isolates, we evaluated whether metatranscriptomics can accurately identify fungal species and subspecies in mixed communities. Overall, 72.9% of the RNA transcripts were classified, from which the vast majority (99.5%) were correctly identified at the species level. Of the 15 species sequenced, 13 were retrieved and identified correctly. We also detected strain-level variation within the Cryptococcus species complexes: 99.3% of transcripts assigned to Cryptococcus were classified as one of the four strains used in the mock community. Laboratory contaminants and/or misclassifications were diverse, but represented only 0.44% of the transcripts. Hence, these results show that it is possible to obtain accurate species- and strain-level fungal identification from metatranscriptome data as long as taxa identified at low abundance are discarded to avoid false-positives derived from contamination or misclassifications. This study highlights both the advantages and current challenges in the application of metatranscriptomics in clinical mycology and ecological studies.

Emerging Fungal Infections: New Patients, New Patterns, and New Pathogens.

The landscape of clinical mycology is constantly changing. New therapies for malignant and autoimmune diseases have led to new risk factors for unusual mycoses. Invasive candidiasis is increasingly caused by non-albicans Candida spp., including C. auris, a multidrug-resistant yeast with the potential for nosocomial transmission that has rapidly spread globally. The use of mould-active antifungal prophylaxis in patients with cancer or transplantation has decreased the incidence of invasive fungal disease, but shifted the balance of mould disease in these patients to those from non-fumigatus Aspergillus species, Mucorales, and Scedosporium/Lomentospora spp. The agricultural application of triazole pesticides has driven an emergence of azole-resistant A. fumigatus in environmental and clinical isolates. The widespread use of topical antifungals with corticosteroids in India has resulted in Trichophyton mentagrophytes causing recalcitrant dermatophytosis. New dimorphic fungal pathogens have emerged, including Emergomyces, which cause disseminated mycoses globally, primarily in HIV infected patients, and Blastomyces helicus and B. percursus, causes of atypical blastomycosis in western parts of North America and in Africa, respectively. In North America, regions of geographic risk for coccidioidomycosis, histoplasmosis, and blastomycosis have expanded, possibly related to climate change. In Brazil, zoonotic sporotrichosis caused by Sporothrix brasiliensis has emerged as an important disease of felines and people.

Defining breakthrough invasive fungal infection-Position paper of the mycoses study group education and research consortium and the European Confederation of Medical Mycology.

Breakthrough invasive fungal infections (IFIs) have emerged as a significant problem in patients receiving systemic antifungals; however, consensus criteria for defining breakthrough IFI are missing. This position paper establishes broadly applicable definitions of breakthrough IFI for clinical research. Representatives of the Mycoses Study Group Education and Research Consortium (MSG-ERC) and the European Confederation of Medical Mycology (ECMM) reviewed the relevant English literature for definitions applied and published through 2018. A draft proposal for definitions was developed and circulated to all members of the two organisations for comment and suggestions. The authors addressed comments received and circulated the updated document for approval. Breakthrough IFI was defined as any IFI occurring during exposure to an antifungal drug, including fungi outside the spectrum of activity of an antifungal. The time of breakthrough IFI was defined as the first attributable clinical sign or symptom, mycological finding or radiological feature. The period defining breakthrough IFI depends on pharmacokinetic properties and extends at least until one dosing interval after drug discontinuation. Persistent IFI describes IFI that is unchanged/stable since treatment initiation with ongoing need for antifungal therapy. It is distinct from refractory IFI, defined as progression of disease and therefore similar to non-response to treatment. Relapsed IFI occurs after treatment and is caused by the same pathogen at the same site, although dissemination can occur. These proposed definitions are intended to support the design of future clinical trials and epidemiological research in clinical mycology, with the ultimate goal of increasing the comparability of clinical trial results.

Clinical mycology in Latin America and the Caribbean: Asnapshot of diagnostic and therapeutic capabilities.

Despite the existence of endemic mycoses in Latin America and the Caribbean, in addition to a large population of patients at risk for invasive mycoses, the capability of medical centres to perform a proper diagnosis in mycology has not been studied in the region. Moreover, availability of antifungal drugs in the region is unknown. Here, we report the results of a survey involving 129 centres in 24 countries. Only 9% of centres would have the potential to apply for the minimum standards in mycology, as determined by the European Confederation of Medical Mycology. There is an urgent need to improve diagnostic conditions in Latin America and the Caribbean, as well as providing access to safer and more efficacious antifungal drugs.

From the Clinical Mycology Laboratory: New Species and Changes in Fungal Taxonomy and Nomenclature.

Fungal taxonomy is the branch of mycology by which we classify and group fungi based on similarities or differences. Historically, this was done by morphologic characteristics and other phenotypic traits. However, with the advent of the molecular age in mycology, phylogenetic analysis based on DNA sequences has replaced these classic means for grouping related species. This, along with the abandonment of the dual nomenclature system, has led to a marked increase in the number of new species and reclassification of known species. Although these evaluations and changes are necessary to move the field forward, there is concern among medical mycologists that the rapidity by which fungal nomenclature is changing could cause confusion in the clinical literature. Thus, there is a proposal to allow medical mycologists to adopt changes in taxonomy and nomenclature at a slower pace. In this review, changes in the taxonomy and nomenclature of medically relevant fungi will be discussed along with the impact this may have on clinicians and patient care. Specific examples of changes and current controversies will also be given.

Research and Reviews in Clinical Microbiology: Virology and HIV Medicine-A book Review

Clinical microbiology is a vast subject that covers a wide range of sub categories that include clinical bacteriology, clinical virology, clinical mycology, and clinical parasitology. The present book is a compilation of both research and review pieces related to the field of clinical virology and HIV medicine.

417. Clinical Mycology in Latin America and the Caribbean: Diagnostic Capabilities and Antifungal Therapy

BackgroundNo data are available about diagnostic capabilities and practice in clinical mycology in Latin America and the Caribbean.MethodsHere, we conducted an online survey aimed to assess availability, routine diagnostic procedures and access to therapy. Contacts were made through LIFE initiative (Leading International Fungal Education), SBI (Brazilian Society of Infectious Diseases), SBAC (Brazilian Society of Clinical Analysis), and SBM (Brazilian Society of Microbiology) during the first 2018 trimester.ResultsWe got 128 responses, each one from a single healthcare institution. Countries included Brazil (96), Mexico (9), Colombia (5), Uruguay (3), Guatemala (3), Argentina (2), Chile (2), Paraguay (2), Venezuela (2), Barbados (1), Ecuador (1), Honduras (1), and Peru (1). Most frequent institution profiles were public (38%), private (14%), and university hospitals (22%). Number of hospital beds varied between 12–3,000 (median 200 beds). ICU beds ranged 3–500 (15 beds). Most institutions provided care for hematology (63%) and HIV (31%) patients. Yeast identification was performed by biochemical tests (76%), automated methods (65%), and MALDI-TOF (15%). Twelve percent of responders had access to DNA sequencing. Almost a half (39%) of institutions did not undertake antifungal susceptibility tests, 47% did it only for yeasts, 2% molds. Fifteen (12%) institutions performed antifungal susceptibility tests routinely for all fungal isolates. Automated methods were the most frequently used antifungal susceptibility methodology (38%). Eighty-two (64%) institutions had no access to therapeutic drug monitoring (TDM). Cryptococccal antigen testing was available for 75% of responders.ConclusionThis survey was the largest and most updated snapshot of the clinical mycology scenario in Latin America and Caribbean. Efforts should be made to improve diagnostic capabilities and equalize regional disparities.Disclosures All authors: No reported disclosures.

Expert Consensus on The Management of Dermatophytosis in India (ECTODERM India)

BackgroundDermatophytosis management has become an important public health issue, with a large void in research in the area of disease pathophysiology and management. Current treatment recommendations appear to lose their relevance in the current clinical scenario. The objective of the current consensus was to provide an experience-driven approach regarding the diagnosis and management of tinea corporis, cruris and pedis.MethodsEleven experts in the field of clinical dermatology and mycology participated in the modified Delphi process consisting of two workshops and five rounds of questionnaires, elaborating definitions, diagnosis and management. Panel members were asked to mark “agree” or “disagree” beside each statement, and provide comments. More than 75% of concordance in response was set to reach the consensus.ResultKOH mount microscopy was recommended as a point of care testing. Fungal culture was recommended in chronic, recurrent, relapse, recalcitrant and multisite tinea cases. Topical monotherapy was recommended for naïve tinea cruris and corporis (localised) cases, while a combination of systemic and topical antifungals was recommended for naïve and recalcitrant tinea pedis, extensive lesions of corporis and recalcitrant cases of cruris and corporis. Because of the anti-inflammatory, antibacterial and broad spectrum activity, topical azoles should be preferred. Terbinafine and itraconazole should be the preferred systemic drugs. Minimum duration of treatment should be 2–4 weeks in naïve cases and > 4 weeks in recalcitrant cases. Topical corticosteroid use in the clinical practice of tinea management was strongly discouraged.ConclusionThis consensus guideline will help to standardise care, provide guidance on the management, and assist in clinical decision-making for healthcare professionals.

Exoproteome Analysis of Human Pathogenic Dermatophyte Species and Identification of Immunoreactive Proteins.

Increasing incidence of onychomycosis and tinea pedis in humans of industrialized countries together with deep tissue infections are a therapeutic challenge in clinical mycology. For a better understanding of the pathology and immunology of infection, the authors analyze the exoproteomes of three reference strains of the most common clinical dermatophyte species (Trichophyton rubrum, Trichophyton interdigitale, Arthroderma benhamiae) and of Trichophyton strains isolated from affected patients. Extracellular proteins of those in vitro grown strains are separated via 2D High Performance Electrophoresis and identified by mass spectrometry to find proteins with provoked host immune reactivity. More than 80 secreted proteins including virulence factors such as peptidases and other hydrolases are identified. By Western blotting with respective patient sera, up to 31 proteins with significant antigen-antibody reactions are detected in comparison with control sera, for example, peptidases as well as several oxidoreductases. One protein, beta-glucosidase F2SZI9 seems to be a commonly processed antigen in all Trichophyton infections. These first global exoproteome data of three dermatophyte species can be a stepping stone on the way to further study the molecular mechanisms of Trichophyton pathogenicity-associated traits. Possible candidates for potential new diagnostic methods or vaccination have to be validated in further investigations.

Ultrastructural changes of Trichophyton rubrum in tinea unguium after itraconazole therapy in vivo observed using scanning electron microscopy.

Tinea unguium is a dermatophyte infection of the nails. Itraconazole is a broad-spectrum antifungal drug used to treat this disease. It works by interfering with the synthesis of ergosterol in the cell membrane, thus causing changes that can be seen under scanning electron microscopy (SEM). To observe under SEM the in vivo ultrastructural changes of tinea unguium caused by Trichophyton rubrum before and after itraconazole (ICZ) therapy, and to explore the in vivo antifungal effect of ICZ. Ten outpatients diagnosed by mycology and SEM as having with tinea unguium caused by T. rubrum were recruited. They received ICZ pulse therapy (200 mg twice/day for 1 week, stop for 3 weeks, repeated for 3-4 months). Clinical change, mycology and SEM results were obtained after therapy. After ICZ therapy, 3 of the 10 cases were positive by both mycology and SEM; the latter showed completely dry, shrivelled, curved and folded hyphae with a relatively smooth surface or local destruction. Several hyphae remained intact with only some local bumps or crimps. The other cases were negative by SEM, but two were positive by mycology. In vivo ultrastructural changes of hyphae of T. rubrum in tinea unguium after ICZ treatment could be seen under SEM, demonstrating that ICZ fungistasis was effective and that SEM is a good tool for evaluating the effectiveness of ICZ in vivo. To our knowledge, this study is the first to show by SEM ICZ permeates the affected nail plate via the nail bed capillaries.