Chapter 2 Athlete's Foot
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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. -
Estimated Burden of Serious Fungal Infections in Ghana
Journal of Fungi Article Estimated Burden of Serious Fungal Infections in Ghana Bright K. Ocansey 1, George A. Pesewu 2,*, Francis S. Codjoe 2, Samuel Osei-Djarbeng 3, Patrick K. Feglo 4 and David W. Denning 5 1 Laboratory Unit, New Hope Specialist Hospital, Aflao 00233, Ghana; [email protected] 2 Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, P.O. Box KB-143, Korle-Bu, Accra 00233, Ghana; [email protected] 3 Department of Pharmaceutical Sciences, Faculty of Health Sciences, Kumasi Technical University, P.O. Box 854, Kumasi 00233, Ghana; [email protected] 4 Department of Clinical Microbiology, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi 00233, Ghana; [email protected] 5 National Aspergillosis Centre, Wythenshawe Hospital and the University of Manchester, Manchester M23 9LT, UK; [email protected] * Correspondence: [email protected] or [email protected] or [email protected]; Tel.: +233-277-301-300; Fax: +233-240-190-737 Received: 5 March 2019; Accepted: 14 April 2019; Published: 11 May 2019 Abstract: Fungal infections are increasingly becoming common and yet often neglected in developing countries. Information on the burden of these infections is important for improved patient outcomes. The burden of serious fungal infections in Ghana is unknown. We aimed to estimate this burden. Using local, regional, or global data and estimates of population and at-risk groups, deterministic modelling was employed to estimate national incidence or prevalence. Our study revealed that about 4% of Ghanaians suffer from serious fungal infections yearly, with over 35,000 affected by life-threatening invasive fungal infections. -
Microsporum Canis Genesig Standard
Primerdesign TM Ltd Microsporum canis PQ-loop repeat protein gene genesig® Standard Kit 150 tests For general laboratory and research use only Quantification of Microsporum canis genomes. 1 genesig Standard kit handbook HB10.04.10 Published Date: 09/11/2018 Introduction to Microsporum canis Microsporum canis is a zoophilic dermatophyte which is responsible for dermatophytosis in dogs and cats. They cause superficial infections of the scalp (tinea capitis) in humans and ringworm in cats and dogs. They belong to the family Arthrodermataceae and are most commonly found in humid and warm climates. They have numerous multi-celled macroconidia which are typically spindle-shaped with 5-15 cells, verrucose, thick-walled, often having a terminal knob and 35-110 by 12-25 µm. In addition, they produce septate hyphae and microconidia and the Microsporum canis genome is estimated at 23 Mb. The fungus is transmitted from animals to humans when handling infected animals or by contact with arthrospores contaminating the environment. Spores are very resistant and can live up to two years infecting animals and humans. They will attach to the skin and germinate producing hyphae, which will then grow in the dead, superficial layers of the skin, hair or nails. They secrete a 31.5 kDa keratinolytic subtilisin-like protease as well as three other subtilisin- like proteases (SUBs), SUB1, SUB2 and SUB3, which cause damage to the skin and hair follicle. Keratinolytic protease also provides the fungus nutrients by degrading keratin structures into easily absorbable metabolites. Infection leads to a hypersensitive reaction of the skin. The skin becomes inflamed causing the fungus to move away from the site to normal, uninfected skin. -
Introduction
Notes Introduction 1. In the book, we use the terms ‘fungal infections’ and ‘mycoses’ (or singular fungal infection and mycosis) interchangeably, mostly following the usage of our historical actors in time and place. 2. The term ‘ringworm’ is very old and came from the circular patches of peeled, inflamed skin that characterised the infection. In medicine at least, no one understood it to be associated with worms of any description. 3. Porter, R., ‘The patient’s view: Doing medical history from below’, Theory and Society, 1985, 14: 175–198; Condrau, F., ‘The patient’s view meets the clinical gaze’, Social History of Medicine, 2007, 20: 525–540. 4. Burnham, J. C., ‘American medicine’s golden age: What happened to it?’, Sci- ence, 1982, 215: 1474–1479; Brandt, A. M. and Gardner, M., ‘The golden age of medicine’, in Cooter, R. and Pickstone, J. V., eds, Medicine in the Twentieth Century, Amsterdam, Harwood, 2000, 21–38. 5. The Oxford English Dictionary states that the first use of ‘side-effect’ was in 1939, in H. N. G. Wright and M. L. Montag’s textbook: Materia Med Pharma- col & Therapeutics, 112, when it referred to ‘The effects which are not desired in any particular case are referred to as “side effects” or “side actions” and, in some instances, these may be so powerful as to limit seriously the therapeutic usefulness of the drug.’ 6. Illich, I., Medical Nemesis: The Expropriation of Health, London, Calder & Boyars, 1975. 7. Beck, U., Risk Society: Towards a New Society, New Delhi, Sage, 1992, 56 and 63; Greene, J., Prescribing by Numbers: Drugs and the Definition of Dis- ease, Baltimore, Johns Hopkins University Press, 2007; Timmermann, C., ‘To treat or not to treat: Drug research and the changing nature of essential hypertension’, Schlich, T. -
Serious Fungal Infections in Peru
Eur J Clin Microbiol Infect Dis DOI 10.1007/s10096-017-2924-9 ORIGINAL ARTICLE Serious fungal infections in Peru B. Bustamante1 & D. W. Denning2 & P. E. Campos3 Received: 21 December 2016 /Accepted: 21 December 2016 # Springer-Verlag Berlin Heidelberg 2017 Abstract Epidemiological data about mycotic diseases are This first attempt to assess the fungal burden in Peru needs limited in Peru and estimation of the fungal burden has not to be refined. We believe the figure obtained is an underesti- been previously attempted. Data were obtained from the mation, because of under diagnosis, non-mandatory reporting Peruvian National Institute of Statistics and Informatics, and lack of a surveillance system and of good data about the UNAIDS and from the Ministry of Health’s publications. size of populations at risk. We also searched the bibliography for Peruvian data on my- cotic diseases, asthma, COPD, cancer and transplants. Incidence or prevalence for each fungal disease were estimat- Introduction ed in specific populations at risk. The Peruvian population for 2015 was 31,151,543. In 2014, the estimated number of HIV/ While candidemia and invasive aspergillosis (IA) are clearly AIDS and pulmonary tuberculosis cases was 88,625, 38,581 recognized as important causes of morbidity and mortality, of them not on ART, and 22,027, respectively. A total of other mycotic agents or different clinical presentations are im- 581,174 cases of fungal diseases were estimated, representing portant in specific regions. Socio-economic and geo- approximately 1.9% of the Peruvian population. This figure ecological characteristics and size of susceptible populations includes 498,606, 17,361 and 4,431 vulvovaginal, oral and are the main determinants of variations on incidence of fungal esophageal candidiasis, respectively, 1,557 candidemia cases, infections across the world. -
Updating the Taxonomy of Dermatophytes of the BCCM/ IHEM Collection According to the New Standard: a Phylogenetic Approach
Mycopathologia https://doi.org/10.1007/s11046-019-00338-7 (0123456789().,-volV)( 0123456789().,-volV) ORIGINAL ARTICLE Updating the Taxonomy of Dermatophytes of the BCCM/ IHEM Collection According to the New Standard: A Phylogenetic Approach F. Baert . D. Stubbe . E. D’hooge . A. Packeu . M. Hendrickx Received: 23 January 2019 / Accepted: 30 April 2019 Ó Springer Nature B.V. 2019 Abstract Recent taxonomical revisions based on floccosum as the only representative, fell within the multilocus gene sequencing have provided some Nannizzia clade, whereas the phylogenetic analysis, clarifications to dermatophyte (Arthrodermataceae) based on the ITS region alone, differentiates Epider- family tree. These changes promoted us to investigate mophyton from Nannizzia as a separate genus. Re- the impact of the changed nomenclature of the identification and reclassification of many strains in dermatophyte strains in the BCCM/IHEM fungal the collection have had a profound impact on the collection, which contains strains of all dermatophyte composition of the BCCM/IHEM dermatophyte col- genera except for Ctenomyces. For 688 strains from lection. The biggest change is the decline of preva- this collection, both internal transcribed spacer region lence of Arthroderma strains; starting with 103 strains, (ITS) and partial b-tubulin (BT) sequences were only 22 strains remain in the genus after reassessment. aligned and a multilocus phylogenetic tree was Most Arthroderma strains were reclassified into Tri- constructed. The ITS ? BT phylogentic tree was able chophyton, with A. benhamiae and A. van- to distinguish the genera Arthroderma, Lophophyton, breuseghemii leaving the genus. The amount of Microsporum, Paraphyton, Nannizzia and Trichophy- Microsporum strains also dropped significantly with ton with high certainty. -
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. -
Managing Athlete's Foot
South African Family Practice 2018; 60(5):37-41 S Afr Fam Pract Open Access article distributed under the terms of the ISSN 2078-6190 EISSN 2078-6204 Creative Commons License [CC BY-NC-ND 4.0] © 2018 The Author(s) http://creativecommons.org/licenses/by-nc-nd/4.0 REVIEW Managing athlete’s foot Nkatoko Freddy Makola,1 Nicholus Malesela Magongwa,1 Boikgantsho Matsaung,1 Gustav Schellack,2 Natalie Schellack3 1 Academic interns, School of Pharmacy, Sefako Makgatho Health Sciences University 2 Clinical research professional, pharmaceutical industry 3 Professor, School of Pharmacy, Sefako Makgatho Health Sciences University *Corresponding author, email: [email protected] Abstract This article is aimed at providing a succinct overview of the condition tinea pedis, commonly referred to as athlete’s foot. Tinea pedis is a very common fungal infection that affects a significantly large number of people globally. The presentation of tinea pedis can vary based on the different clinical forms of the condition. The symptoms of tinea pedis may range from asymptomatic, to mild- to-severe forms of pain, itchiness, difficulty walking and other debilitating symptoms. There is a range of precautionary measures available to prevent infection, and both oral and topical drugs can be used for treating tinea pedis. This article briefly highlights what athlete’s foot is, the different causes and how they present, the prevalence of the condition, the variety of diagnostic methods available, and the pharmacological and non-pharmacological management of the -
Mucormycosis of the Central Nervous System
Journal of Fungi Review Mucormycosis of the Central Nervous System 1 1,2, , 3, , Amanda Chikley , Ronen Ben-Ami * y and Dimitrios P Kontoyiannis * y 1 Infectious Diseases Unit, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel 2 Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 64239, Israel 3 Department of Infectious Diseases, The University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA * Correspondence: [email protected] (R.B.-A.); [email protected] (D.P.K.) These authors contribute equally to this paper. y Received: 6 June 2019; Accepted: 7 July 2019; Published: 8 July 2019 Abstract: Mucormycosis involves the central nervous system by direct extension from infected paranasal sinuses or hematogenous dissemination from the lungs. Incidence rates of this rare disease seem to be rising, with a shift from the rhino-orbital-cerebral syndrome typical of patients with diabetes mellitus and ketoacidosis, to disseminated disease in patients with hematological malignancies. We present our current understanding of the pathobiology, clinical features, and diagnostic and treatment strategies of cerebral mucormycosis. Despite advances in imaging and the availability of novel drugs, cerebral mucormycosis continues to be associated with high rates of death and disability. Emerging molecular diagnostics, advances in experimental systems and the establishment of large patient registries are key components of ongoing efforts to provide a timely diagnosis and effective treatment to patients with cerebral mucormycosis. Keywords: central nervous system; mucormycosis; Mucorales; zygomycosis 1. Introduction Mucormycosis is the second most frequent invasive mold disease after aspergillosis [1–3], with rising incidence reported in some countries [4–7]. -
Oral Antifungals Month/Year of Review: July 2015 Date of Last
© Copyright 2012 Oregon State University. All Rights Reserved Drug Use Research & Management Program Oregon State University, 500 Summer Street NE, E35 Salem, Oregon 97301-1079 Phone 503-947-5220 | Fax 503-947-1119 Class Update with New Drug Evaluation: Oral Antifungals Month/Year of Review: July 2015 Date of Last Review: March 2013 New Drug: isavuconazole (a.k.a. isavunconazonium sulfate) Brand Name (Manufacturer): Cresemba™ (Astellas Pharma US, Inc.) Current Status of PDL Class: See Appendix 1. Dossier Received: Yes1 Research Questions: Is there any new evidence of effectiveness or safety for oral antifungals since the last review that would change current PDL or prior authorization recommendations? Is there evidence of superior clinical cure rates or morbidity rates for invasive aspergillosis and invasive mucormycosis for isavuconazole over currently available oral antifungals? Is there evidence of superior safety or tolerability of isavuconazole over currently available oral antifungals? • Is there evidence of superior effectiveness or safety of isavuconazole for invasive aspergillosis and invasive mucormycosis in specific subpopulations? Conclusions: There is low level evidence that griseofulvin has lower mycological cure rates and higher relapse rates than terbinafine and itraconazole for adult 1 onychomycosis.2 There is high level evidence that terbinafine has more complete cure rates than itraconazole (55% vs. 26%) for adult onychomycosis caused by dermatophyte with similar discontinuation rates for both drugs.2 There is low -
Therapeutic Class Overview Onychomycosis Agents
Therapeutic Class Overview Onychomycosis Agents Therapeutic Class • Overview/Summary: This review will focus on the antifungal agents Food and Drug Administration (FDA)-approved for the treatment of onychomycosis.1-9 Onychomycosis is a progressive infection of the nail bed which may extend into the matrix or plate, leading to destruction, deformity, thickening and discoloration. Of note, these agents are only indicated when specific types of fungus have caused the infection, and are listed in Table 1. Additionally, ciclopirox is only FDA-approved for mild to moderate onychomycosis without lunula involvement.1 The mechanisms by which these agents exhibit their antifungal effects are varied. For ciclopirox (Penlac®) the exact mechanism is unknown. It is believed to block fungal transmembrane transport, causing intracellular depletion of essential substrates and/or ions and to interfere with ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).1 The azole antifungals, efinaconazole (Jublia®) and itraconazole tablets (Onmel®) and capsules (Sporanox®) works via inhibition of fungal lanosterol 14-alpha-demethylase, an enzyme necessary for the biosynthesis of ergosterol. By decreasing ergosterol concentrations, the fungal cell membrane permeability is increased, which results in leakage of cellular contents.2,5,6 Griseofulvin microsize (Grifulvin V®) and ultramicrosize (GRIS-PEG®) disrupts the mitotic spindle, arresting metaphase of cell division. Griseofulvin may also produce defective DNA that is unable to replicate. The ultramicrosize tablets are absorbed from the gastrointestinal tract at approximately one and one-half times that of microsize griseofulvin, which allows for a lower dose of griseofulvin to be administered.3,4 Tavaborole (Kerydin®), is an oxaborole antifungal that interferes with protein biosynthesis by inhibiting leucyl-transfer ribonucleic acid (tRNA) synthase (LeuRS), which prevents translation of tRNA by LeuRS.7 The final agent used for the treatment of onychomycosis, terbinafine hydrochloride (Lamisil®), is an allylamine antifungal. -
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.