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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. -
An Overview of the Management of the Most Important Invasive Fungal Infections in Patients with Blood Malignancies
Infection and Drug Resistance Dovepress open access to scientific and medical research Open Access Full Text Article REVIEW An Overview of the Management of the Most Important Invasive Fungal Infections in Patients with Blood Malignancies This article was published in the following Dove Press journal: Infection and Drug Resistance Aref Shariati 1 Abstract: In patients with hematologic malignancies due to immune system disorders, espe- Alireza Moradabadi2 cially persistent febrile neutropenia, invasive fungal infections (IFI) occur with high mortality. Zahra Chegini3 Aspergillosis, candidiasis, fusariosis, mucormycosis, cryptococcosis and trichosporonosis are Amin Khoshbayan 4 the most important infections reported in patients with hematologic malignancies that undergo Mojtaba Didehdar2 hematopoietic stem cell transplantation. These infections are caused by opportunistic fungal pathogens that do not cause severe issues in healthy individuals, but in patients with hematologic 1 Department of Microbiology, School of malignancies lead to disseminated infection with different clinical manifestations. Prophylaxis Medicine, Shahid Beheshti University of fi Medical Sciences, Tehran, Iran; and creating a safe environment with proper lters and air pressure for patients to avoid contact 2Department of Medical Parasitology and with the pathogens in the surrounding environment can prevent IFI. Furthermore, due to the Mycology, Arak University of Medical fi For personal use only. absence of speci c symptoms in IFI, rapid and accurate diagnosis reduces -
Oral Candidiasis: a Review
International Journal of Pharmacy and Pharmaceutical Sciences ISSN- 0975-1491 Vol 2, Issue 4, 2010 Review Article ORAL CANDIDIASIS: A REVIEW YUVRAJ SINGH DANGI1, MURARI LAL SONI1, KAMTA PRASAD NAMDEO1 Institute of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur (C.G.) – 49500 Email: [email protected] Received: 13 Jun 2010, Revised and Accepted: 16 July 2010 ABSTRACT Candidiasis, a common opportunistic fungal infection of the oral cavity, may be a cause of discomfort in dental patients. The article reviews common clinical types of candidiasis, its diagnosis current treatment modalities with emphasis on the role of prevention of recurrence in the susceptible dental patient. The dental hygienist can play an important role in education of patients to prevent recurrence. The frequency of invasive fungal infections (IFIs) has increased over the last decade with the rise in at‐risk populations of patients. The morbidity and mortality of IFIs are high and management of these conditions is a great challenge. With the widespread adoption of antifungal prophylaxis, the epidemiology of invasive fungal pathogens has changed. Non‐albicans Candida, non‐fumigatus Aspergillus and moulds other than Aspergillus have become increasingly recognised causes of invasive diseases. These emerging fungi are characterised by resistance or lower susceptibility to standard antifungal agents. Oral candidiasis is a common fungal infection in patients with an impaired immune system, such as those undergoing chemotherapy for cancer and patients with AIDS. It has a high morbidity amongst the latter group with approximately 85% of patients being infected at some point during the course of their illness. A major predisposing factor in HIV‐infected patients is a decreased CD4 T‐cell count. -
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. -
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. -
Epidemiology of Invasive Fungal Diseases in Patients With
Journal of Fungi Article Epidemiology of Invasive Fungal Diseases in Patients with Hematologic Malignancies and Hematopoietic Cell Transplantation Recipients Managed with an Antifungal Diagnostic Driven Approach Maria Daniela Bergamasco 1 , Carlos Alberto P. Pereira 1, Celso Arrais-Rodrigues 2, Diogo B. Ferreira 1 , Otavio Baiocchi 2, Fabio Kerbauy 2, Marcio Nucci 3 and Arnaldo Lopes Colombo 1,* 1 Division of Infectious Diseases, Hospital São Paulo-University Hospital, Universidade Federal de São Paulo, São Paulo 04024-002, Brazil; [email protected] (M.D.B.); [email protected] (C.A.P.P.); [email protected] (D.B.F.) 2 Division of Hematology, Hospital São Paulo-University Hospital, Universidade Federal de São Paulo, São Paulo 04024-002, Brazil; [email protected] (C.A.-R.); [email protected] (O.B.); [email protected] (F.K.) 3 Department of Internal Medicine, Hospital Universitário Clementino Frafa Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-913, Brazil; [email protected] * Correspondence: [email protected] or [email protected] Abstract: Patients with hematologic malignancies and hematopoietic cell transplant recipients (HCT) Citation: Bergamasco, M.D.; Pereira, are at high risk for invasive fungal disease (IFD). The practice of antifungal prophylaxis with mold- C.A.P.; Arrais-Rodrigues, C.; Ferreira, active azoles has been challenged recently because of drug–drug interactions with novel targeted D.B.; Baiocchi, O.; Kerbauy, F.; Nucci, therapies. This is a retrospective, single-center cohort study of consecutive cases of proven or probable M.; Colombo, A.L. Epidemiology of IFD, diagnosed between 2009 and 2019, in adult hematologic patients and HCT recipients managed Invasive Fungal Diseases in Patients with fluconazole prophylaxis and an antifungal diagnostic-driven approach for mold infection. -
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. -
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. -
Identification of Culture-Negative Fungi in Blood and Respiratory Samples
IDENTIFICATION OF CULTURE-NEGATIVE FUNGI IN BLOOD AND RESPIRATORY SAMPLES Farida P. Sidiq A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2014 Committee: Scott O. Rogers, Advisor W. Robert Midden Graduate Faculty Representative George Bullerjahn Raymond Larsen Vipaporn Phuntumart © 2014 Farida P. Sidiq All Rights Reserved iii ABSTRACT Scott O. Rogers, Advisor Fungi were identified as early as the 1800’s as potential human pathogens, and have since been shown as being capable of causing disease in both immunocompetent and immunocompromised people. Clinical diagnosis of fungal infections has largely relied upon traditional microbiological culture techniques and examination of positive cultures and histopathological specimens utilizing microscopy. The first has been shown to be highly insensitive and prone to result in frequent false negatives. This is complicated by atypical phenotypes and organisms that are morphologically indistinguishable in tissues. Delays in diagnosis of fungal infections and inaccurate identification of infectious organisms contribute to increased morbidity and mortality in immunocompromised patients who exhibit increased vulnerability to opportunistic infection by normally nonpathogenic fungi. In this study we have retrospectively examined one-hundred culture negative whole blood samples and one-hundred culture negative respiratory samples obtained from the clinical microbiology lab at the University of Michigan Hospital in Ann Arbor, MI. Samples were obtained from randomized, heterogeneous patient populations collected between 2005 and 2006. Specimens were tested utilizing cetyltrimethylammonium bromide (CTAB) DNA extraction and polymerase chain reaction amplification of internal transcribed spacer (ITS) regions of ribosomal DNA utilizing panfungal ITS primers. -
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. -
Medicinal Product No Longer Authorised
European Medicines Agency EMEA/H/C/611 EUROPEAN PUBLIC ASSESSMENT REPORT (EPAR) POSACONAZOLE SP EPAR summary for the public This document is a summary of the European Public Assessment Report (EPAR). It explains how the Committee for Medicinal Products for Human Use (CHMP) assessed the studies performed, to reach their recommendations on how to use the medicine. If you need more information about your medical condition or your treatment, readauthorised the Package Leaflet (also part of the EPAR) or contact your doctor or pharmacist. If you want more information on the basis of the CHMP recommendations, read the Scientific Discussion (also part of the EPAR). What is Posaconazole SP? Posaconazole SP is an oral suspension that contains the active substance posaconazole (40 mg/ml). What is Posaconazole SP used for? Posaconazole SP is an antifungal medicine. It is used to treatlonger patients with the following diseases, when they cannot tolerate other antifungal medicines (amphotericin B, itraconazole or fluconazole) or have not improved after at least 7 days of treatment with other antifungal medicines: • invasive aspergillosis (a type of fungal infection due to Aspergillus), • fusariosis (another type of fungal infection nodue to Fusarium), • chromoblastomycosis and mycetoma (long-term fungal infections of the skin or the tissue just below the skin, usually caused by fungal spores infecting wounds due to thorns or splinters), • coccidioidomycosis (fungal infection of the lungs caused by breathing in spores). Posaconazole SP is also used to treat patients with oropharyngeal candidiasis or ‘thrush’, a fungal infection of the mouth and throat due to Candida. It is used in patients who have not been treated for this disease before.