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Next-Generation Sequencing for Hypothesis-Free Genomic Detection
Frickmann et al. BMC Microbiology (2019) 19:75 https://doi.org/10.1186/s12866-019-1448-0 RESEARCH ARTICLE Open Access Next-generation sequencing for hypothesis- free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment Hagen Frickmann1,2* , Carsten Künne3, Ralf Matthias Hagen4, Andreas Podbielski2, Jana Normann2, Sven Poppert5,6, Mario Looso3 and Bernd Kreikemeyer2 Abstract Background: The potential of next-generation sequencing (NGS) for hypothesis-free pathogen diagnosis from (poly-)microbially contaminated, formalin-fixed, paraffin embedded tissue samples from patients with invasive fungal infections and amebiasis was investigated. Samples from patients with chromoblastomycosis (n = 3), coccidioidomycosis (n = 2), histoplasmosis (n = 4), histoplasmosis or cryptococcosis with poor histological discriminability (n = 1), mucormycosis (n = 2), mycetoma (n = 3), rhinosporidiosis (n = 2), and invasive Entamoeba histolytica infections (n = 6) were analyzed by NGS (each one Illumina v3 run per sample). To discriminate contamination from putative infections in NGS analysis, mean and standard deviation of the number of specific sequence fragments (paired reads) were determined and compared in all samples examined for the pathogens in question. Results: For matches between NGS results and histological diagnoses, a percentage of species-specific reads greater than the 4th standard deviation above the mean value of all 23 assessed sample materials was required. Potentially etiologically relevant pathogens could be identified by NGS in 5 out of 17 samples of patients with invasive mycoses and in 1 out of 6 samples of patients with amebiasis. Conclusions: The use of NGS for hypothesis-free pathogen diagnosis from contamination-prone formalin- fixed, paraffin-embedded tissue requires further standardization. -
Severe Chromoblastomycosis-Like Cutaneous Infection Caused by Chrysosporium Keratinophilum
fmicb-08-00083 January 25, 2017 Time: 11:0 # 1 CASE REPORT published: 25 January 2017 doi: 10.3389/fmicb.2017.00083 Severe Chromoblastomycosis-Like Cutaneous Infection Caused by Chrysosporium keratinophilum Juhaer Mijiti1†, Bo Pan2,3†, Sybren de Hoog4, Yoshikazu Horie5, Tetsuhiro Matsuzawa6, Yilixiati Yilifan1, Yong Liu1, Parida Abliz7, Weihua Pan2,3, Danqi Deng8, Yun Guo8, Peiliang Zhang8, Wanqing Liao2,3* and Shuwen Deng2,3,7* 1 Department of Dermatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China, 2 Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China, 3 Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China, 4 CBS-KNAW Fungal Biodiversity Centre, Royal Netherlands Academy of Arts and Sciences, Utrecht, Netherlands, 5 Medical Mycology Research Center, Chiba University, Chiba, Japan, 6 Department of Nutrition Science, University of Nagasaki, Nagasaki, Japan, 7 Department of Dermatology, First Hospital of Xinjiang Medical University, Urumqi, China, 8 Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China Chrysosporium species are saprophytic filamentous fungi commonly found in the Edited by: soil, dung, and animal fur. Subcutaneous infection caused by this organism is Leonard Peruski, rare in humans. We report a case of subcutaneous fungal infection caused by US Centers for Disease Control and Prevention, USA Chrysosporium keratinophilum in a 38-year-old woman. The patient presented with Reviewed by: severe chromoblastomycosis-like lesions on the left side of the jaw and neck for 6 years. Nasib Singh, She also got tinea corporis on her trunk since she was 10 years old. -
Tinea Faciei Presenting Butterfly Erythema in a Boy
TINEA FACIEI PRESENTING BUTTERFLY ERYTHEMA IN A BOY Serpil Şener Department of Dermatology, Beydagi State Hospital, Malatya, Turkey Tinea faciei is the most frequently misdiagnosed entity among cutaneous fungal infections. The atypical clinical features support the separation of this disease from tinea corporis. This often lacks a distinct raised scaly border, and may mimic a photodermatosis such as lupus erythematosus or dermatomyositis. Other photodermatoses to consider include polymorphous light eruption, contact dermatitis, and rosacea. In this article, a 9-year-old boy with tinea faciei presenting butterfly rash was reported because of its rarity. Key words: Dermatophytosis, tinea faciei, butterfly rash Eur J Gen Med 2007; 4(3):141-142 INTRODUCTION DISCUSSION Tinea faciei is a superficial dermatophyte Tinea faciei is a relatively uncommon infection limited to the glabrous skin of the superficial dermatophyte infection limited to face. In pediatric and female patients, the the glabrous skin of the face. It can be found infection may appear on any surface of the worldwide, but has a predilection for tropical face. In men, the condition is known as tinea humid climates (4). The causative agent varies barbae when a dermatophyte infection of according to the geographic region. In Asia, bearded areas occurs (1). The clinical features Trychophyton mentagrophytes and T. rubrum vary considerable. Annular or circinate are the most frequent etiologic agents (1,5). lesions, plaques with a raised margin, simple Infection results either from direct contact to papular lesions, and flat patches of erythema, an external source, for example a domestic as well as scaling, itching and exacerbation animal, or there may be secondary spread after sun exposure may occur (1-3). -
Fungal Infections in HIV-Positive Peruvian Patients: Could the Venezuelan Migration Cause a Health Warning Related-Infectious Diseases?
Moya-Salazar J, Salazar-Hernández R, Rojas-Zumaran V, Quispe WC. Fungal Infections in HIV-positive Peruvian Patients: Could the Venezuelan Migration Cause a Health Warning Related-infectious Diseases?. J Infectiology. 2019; 2(2): 3-10 Journal of Infectiology Journal of Infectiology Research Article Open Access Fungal Infections in HIV-positive Peruvian Patients: Could the Venezuelan Migration Cause a Health Warning Related-infectious Diseases? Jeel Moya-Salazar1,2*, Richard Salazar-Hernández3, Victor Rojas-Zumaran2, Wanda C. Quispe3 1School of Medicine, Faculties of Health Science, Universidad Privada Norbert Wiener, Lima, Peru 2Pathology Department, Hospital Nacional Docente Madre Niño San Bartolomé, Lima, Peru 3Cytopathology and Genetics Service, Department of Pathology, Hospital Nacional Guillermo Almenara Irigoyen, Lima, Peru Article Info Abstract Article Notes In patients with human immunodeficiency virus (HIV), opportunistic Received: December 22, 2018 infections occur that could compromise the health of patients. In order to Accepted: March 7, 2019 determine the frequency of fungal opportunistic and superficial infections *Correspondence: in HIV-positive men-who-have-sex-with-men (MSM) patients at the Hospital Jeel Moya-Salazar, M.T, M.Sc., 957 Pacific Street, Urb. Sn Nacional Guillermo Almenara, we conducted a cross-sectional retrospective Felipe, 07 Lima, Lima 51001, Peru; Telephone No: +51 986- study. We include Peruvian patients >18 years-old, derived from infectious or 014-954; Email: [email protected]. gynecological offices, with or without antiretroviral treatment. © 2019 Moya-Salazar J. This article is distributed under the One hundred thirteen patients were enrolled (36.7±10, range: 21 to terms of the Creative Commons Attribution 4.0 International 68 years), which 46 (40.7%) has an opportunistic fungal infection, mainly License. -
Histopathology of Important Fungal Infections
Journal of Pathology of Nepal (2019) Vol. 9, 1490 - 1496 al Patholo Journal of linic gist C of of N n e o p ti a a l- u i 2 c 0 d o n s 1 s 0 a PATHOLOGY A m h t N a e K , p d of Nepal a l a M o R e d n i io ca it l A ib ss xh www.acpnepal.com oc g E iation Buildin Review Article Histopathology of important fungal infections – a summary Arnab Ghosh1, Dilasma Gharti Magar1, Sushma Thapa1, Niranjan Nayak2, OP Talwar1 1Department of Pathology, Manipal College of Medical Sciences, Pokhara, Nepal. 2Department of Microbiology, Manipal College of Medical Sciences , Pokhara, Nepal. ABSTRACT Keywords: Fungus; Fungal infections due to pathogenic or opportunistic fungi may be superficial, cutaneous, subcutaneous Mycosis; and systemic. With the upsurge of at risk population systemic fungal infections are increasingly common. Opportunistic; Diagnosis of fungal infections may include several modalities including histopathology of affected tissue Systemic which reveal the morphology of fungi and tissue reaction. Fungi can be in yeast and / or hyphae forms and tissue reactions may range from minimal to acute or chronic granulomatous inflammation. Different fungi should be differentiated from each other as well as bacteria on the basis of morphology and also clinical correlation. Special stains like GMS and PAS are helpful to identify fungi in tissue sections. INTRODUCTION Correspondence: Dr Arnab Ghosh, MD Fungal infections or mycoses may be caused by Department of Pathology, pathogenic fungi which infect healthy individuals or by Manipal College of Medical Sciences, Pokhara, Nepal. -
Therapies for Common Cutaneous Fungal Infections
MedicineToday 2014; 15(6): 35-47 PEER REVIEWED FEATURE 2 CPD POINTS Therapies for common cutaneous fungal infections KENG-EE THAI MB BS(Hons), BMedSci(Hons), FACD Key points A practical approach to the diagnosis and treatment of common fungal • Fungal infection should infections of the skin and hair is provided. Topical antifungal therapies always be in the differential are effective and usually used as first-line therapy, with oral antifungals diagnosis of any scaly rash. being saved for recalcitrant infections. Treatment should be for several • Topical antifungal agents are typically adequate treatment weeks at least. for simple tinea. • Oral antifungal therapy may inea and yeast infections are among the dermatophytoses (tinea) and yeast infections be required for extensive most common diagnoses found in general and their differential diagnoses and treatments disease, fungal folliculitis and practice and dermatology. Although are then discussed (Table). tinea involving the face, hair- antifungal therapies are effective in these bearing areas, palms and T infections, an accurate diagnosis is required to ANTIFUNGAL THERAPIES soles. avoid misuse of these or other topical agents. Topical antifungal preparations are the most • Tinea should be suspected if Furthermore, subsequent active prevention is commonly prescribed agents for dermatomy- there is unilateral hand just as important as the initial treatment of the coses, with systemic agents being used for dermatitis and rash on both fungal infection. complex, widespread tinea or when topical agents feet – ‘one hand and two feet’ This article provides a practical approach fail for tinea or yeast infections. The pharmacol- involvement. to antifungal therapy for common fungal infec- ogy of the systemic agents is discussed first here. -
Tinea Faciei Presenting Butterfly Erythema in a Boy
TINEA FACIEI PRESENTING BUTTERFLY ERYTHEMA IN A BOY Serpil Şener Department of Dermatology, Beydagi State Hospital, Malatya, Turkey Tinea faciei is the most frequently misdiagnosed entity among cutaneous fungal infections. The atypical clinical features support the separation of this disease from tinea corporis. This often lacks a distinct raised scaly border, and may mimic a photodermatosis such as lupus erythematosus or dermatomyositis. Other photodermatoses to consider include polymorphous light eruption, contact dermatitis, and rosacea. In this article, a 9-year-old boy with tinea faciei presenting butterfly rash was reported because of its rarity. Key words: Dermatophytosis, tinea faciei, butterfly rash Eur J Gen Med 2007; 4(3):141-142 INTRODUCTION DISCUSSION Tinea faciei is a superficial dermatophyte Tinea faciei is a relatively uncommon infection limited to the glabrous skin of the superficial dermatophyte infection limited to face. In pediatric and female patients, the the glabrous skin of the face. It can be found infection may appear on any surface of the worldwide, but has a predilection for tropical face. In men, the condition is known as tinea humid climates (4). The causative agent varies barbae when a dermatophyte infection of according to the geographic region. In Asia, bearded areas occurs (1). The clinical features Trychophyton mentagrophytes and T. rubrum vary considerable. Annular or circinate are the most frequent etiologic agents (1,5). lesions, plaques with a raised margin, simple Infection results either from direct contact to papular lesions, and flat patches of erythema, an external source, for example a domestic as well as scaling, itching and exacerbation animal, or there may be secondary spread after sun exposure may occur (1-3). -
Chromoblastomycosis Patricia Chang1, Elba Arana2, Roberto Arenas3
2XU'HUPDWRORJ\2QOLQH Case Report Chromoblastomycosis Patricia Chang1, Elba Arana2, Roberto Arenas3 1Department of Dermatology, Hospital General de Enfermedades IGSS and Hospital Ángeles, Guatemala, 2Elective student, Hospital General de Enfermedades IGSS and Hospital Ángeles, Guatemala, 3Mycology section, “Dr. Manuel Gea González” Hospital, Mexico City, Mexico Corresponding author: Dr. Patricia Chang, E-mail: [email protected] ABSTRACT Chromoblastomycosis is a subcutaneous, chronic, granulomatous mycosis that occurs more frequently in tropical and subtropical countries. We report a case of chromoblastomycosis of the earlobe due to Fonsecaea sp in a male patient of 34 years old, due to its uncommon localization. Key words: Chromoblastomycosis; Fonsecaea pedrosoi; Fonsecaea compacta; Cladosporium carrionii; Fumagoid cells INTRODUCTION plate, hematic crusts and one retroauricular nodule with slightly warty appearance (Figs. 1 and 2). The rest of the The chromoblastomycosis is a sub cutaneous mycosis physical exam was within normal limits. in tropical and subtropical areas considered as an American disease, the main agents are Fonsecaea The patient says that his disease started 3 years ago pedrosoi, in endemic areas of tropical and subtropical with a small asymptomatic “pimple” in his right ear environments; Fonsecaea compacta, Cladosporium that slowly increased its size until he decided to consult. carrionii. The diagnosis of the disease is through the In the last 6 months he had an occasional itch and presence of fumagoids cells. was prescribed different antibiotics and non-specific creams. He does not remember bruising the area. In our environment, chromoblastomycosis is the third most common subcutaneous mycosis. It predominates Three clinical diagnosis were made based on the in the lower limbs in warty form and F pedrosoi is the clinical data: chromoblastomycosis; leishmaniasis; most frequent etiological agent. -
Therapies for Common Cutaneous Fungal Infections
MedicineToday 2014; 15(6): 35-47 PEER REVIEWED FEATURE 2 CPD POINTS Therapies for common cutaneous fungal infections KENG-EE THAI MB BS(Hons), BMedSci(Hons), FACD Key points A practical approach to the diagnosis and treatment of common fungal • Fungal infection should infections of the skin and hair is provided. Topical antifungal therapies always be in the differential are effective and usually used as first-line therapy, with oral antifungals diagnosis of any scaly rash. being saved for recalcitrant infections. Treatment should be for several • Topical antifungal agents are typically adequate treatment weeks at least. for simple tinea. • Oral antifungal therapy may inea and yeast infections are among the dermatophytoses (tinea) and yeast infections be required for extensive most common diagnoses found in general and their differential diagnoses and treatments disease, fungal folliculitis and practice and dermatology. Although are then discussed (Table). tinea involving the face, hair- antifungal therapies are effective in these bearing areas, palms and T infections, an accurate diagnosis is required to ANTIFUNGAL THERAPIES soles. avoid misuse of these or other topical agents. Topical antifungal preparations are the most • Tinea should be suspected if Furthermore, subsequent active prevention is commonly prescribed agents for dermatomy- there is unilateral hand just as important as the initial treatment of the coses, with systemic agents being used for dermatitis and rash on both fungal infection. complex, widespread tinea or when topical agents feet – ‘one hand and two feet’ This article provides a practical approach fail for tinea or yeast infections. The pharmacol- involvement. to antifungal therapy for common fungal infec- ogy of the systemic agents is discussed first here. -
Application to Add Itraconazole and Voriconazole to the Essential List of Medicines for Treatment of Fungal Diseases – Support Document
Application to add itraconazole and voriconazole to the essential list of medicines for treatment of fungal diseases – Support document 1 | Page Contents Page number Summary 3 Centre details supporting the application 3 Information supporting the public health relevance and review of 4 benefits References 7 2 | Page 1. Summary statement of the proposal for inclusion, change or deletion As a growing trend of invasive fungal infections has been noticed worldwide, available few antifungal drugs requires to be used optimally. Invasive aspergillosis, systemic candidiasis, chronic pulmonary aspergillosis, fungal rhinosinusitis, allergic bronchopulmonary aspergillosis, phaeohyphomycosis, histoplasmosis, sporotrichosis, chromoblastomycosis, and relapsed cases of dermatophytosis are few important concern of southeast Asian regional area. Considering the high burden of fungal diseases in Asian countries and its associated high morbidity and mortality (often exceeding 50%), we support the application of including major antifungal drugs against filamentous fungi, itraconazole and voriconazole in the list of WHO Essential Medicines (both available in oral formulation). The inclusion of these oral effective antifungal drugs in the essential list of medicines (EML) would help in increased availability of these agents in this part of the world and better prompt management of patients thereby reducing mortality. The widespread availability of these drugs would also stimulate more research to facilitate the development of better combination therapies. -
Fungal Infections (Mycoses): Dermatophytoses (Tinea, Ringworm)
Editorial | Journal of Gandaki Medical College-Nepal Fungal Infections (Mycoses): Dermatophytoses (Tinea, Ringworm) Reddy KR Professor & Head Microbiology Department Gandaki Medical College & Teaching Hospital, Pokhara, Nepal Medical Mycology, a study of fungal epidemiology, ecology, pathogenesis, diagnosis, prevention and treatment in human beings, is a newly recognized discipline of biomedical sciences, advancing rapidly. Earlier, the fungi were believed to be mere contaminants, commensals or nonpathogenic agents but now these are commonly recognized as medically relevant organisms causing potentially fatal diseases. The discipline of medical mycology attained recognition as an independent medical speciality in the world sciences in 1910 when French dermatologist Journal of Raymond Jacques Adrien Sabouraud (1864 - 1936) published his seminal treatise Les Teignes. This monumental work was a comprehensive account of most of then GANDAKI known dermatophytes, which is still being referred by the mycologists. Thus he MEDICAL referred as the “Father of Medical Mycology”. COLLEGE- has laid down the foundation of the field of Medical Mycology. He has been aptly There are significant developments in treatment modalities of fungal infections NEPAL antifungal agent available. Nystatin was discovered in 1951 and subsequently and we have achieved new prospects. However, till 1950s there was no specific (J-GMC-N) amphotericin B was introduced in 1957 and was sanctioned for treatment of human beings. In the 1970s, the field was dominated by the azole derivatives. J-GMC-N | Volume 10 | Issue 01 developed to treat fungal infections. By the end of the 20th century, the fungi have Now this is the most active field of interest, where potential drugs are being January-June 2017 been reported to be developing drug resistance, especially among yeasts. -
Treatment of Chronic Vulvovaginal Candidiasis with Posaconazole and Ciclopiroxolamine
Vol.2, No.6, 513-518 (2010) Health doi:10.4236/health.2010.26077 Treatment of chronic vulvovaginal candidiasis with posaconazole and ciclopiroxolamine Hans-Jürgen Tietz Fungal Infection and Microbiology Institute, Berlin, Germany; [email protected] Received 21 January 2010; revised 30 January 2010; accepted 2 February 2010. ABSTRACT re-infection from sexual partner(s), and recurrent disease as a result of persistent colonization have been postu- Therapy of chronic recurrent vulvovaginal can- lated. This last postulate is supported by studies showing didiasis (VVC) caused by Candida glabrata is recurrent disease to be caused by identical strains in the still rare in comparison to C. albicans infection, vast majority of cases [2]. but therapy remains more difficult. Combination Though C. albicans is the main pathogen in more than therapy with topical antifungals may improve 95% of cases of acute infection [4], other species are therapy outcome, but still standard agents as implicated in chronic infection, chiefly C. glabrata. The fluconazole or itraconazole often fail. Posa- characteristic features of Candida albicans and Candida conazole is a new systemic triazole with a wide glabrata are listed in Table 1. antifungal spectrum including rare Candida The pathogenic role of C. glabrata is disputed, but pa- species. Up to now, no clinical trials with posa- tients who present to a physician with fungal disease conazole in chronic recurrent VVC have been caused by these atypical pathogens always report symp- undertaken. Here, first results of the application toms. Though vaginal discharge is rare, redness, agoniz- of a new therapy regimen consisting of oral ing itching, and a sour-smelling sticky discharge are posaconazole in combination with topical ci- characteristic.