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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. -
Congo DRC, Kamwiziku. Mycoses 2021
Received: 8 April 2021 | Revised: 1 June 2021 | Accepted: 10 June 2021 DOI: 10.1111/myc.13339 REVIEW ARTICLE Serious fungal diseases in Democratic Republic of Congo – Incidence and prevalence estimates Guyguy K. Kamwiziku1 | Jean- Claude C. Makangara1 | Emma Orefuwa2 | David W. Denning2,3 1Department of Microbiology, Kinshasa University Hospital, University of Abstract Kinshasa, Kinshasa, Democratic Republic A literature review was conducted to assess the burden of serious fungal infections of Congo 2Global Action Fund for Fungal Infections, in the Democratic Republic of the Congo (DRC) (population 95,326,000). English and Geneva, Switzerland French publications were listed and analysed using PubMed/Medline, Google Scholar 3 Manchester Fungal Infection Group, The and the African Journals database. Publication dates spanning 1943– 2020 were in- University of Manchester, Manchester Academic Health Science Centre, cluded in the scope of the review. From the analysis of published articles, we estimate Manchester, UK a total of about 5,177,000 people (5.4%) suffer from serious fungal infections in the Correspondence DRC annually. The incidence of cryptococcal meningitis, Pneumocystis jirovecii pneu- Guyguy K. Kamwiziku, Department monia in adults and invasive aspergillosis in AIDS patients was estimated at 6168, of Microbiology, Kinshasa University Hospital, University of Kinshasa, Congo. 2800 and 380 cases per year. Oral and oesophageal candidiasis represent 50,470 Email: [email protected] and 28,800 HIV- infected patients respectively. Chronic pulmonary aspergillosis post- tuberculosis incidence and prevalence was estimated to be 54,700. Fungal asthma (allergic bronchopulmonary aspergillosis and severe asthma with fungal sensitiza- tion) probably has a prevalence of 88,800 and 117,200. -
Glossary for Narrative Writing
Periodontal Assessment and Treatment Planning Gingival description Color: o pink o erythematous o cyanotic o racial pigmentation o metallic pigmentation o uniformity Contour: o recession o clefts o enlarged papillae o cratered papillae o blunted papillae o highly rolled o bulbous o knife-edged o scalloped o stippled Consistency: o firm o edematous o hyperplastic o fibrotic Band of gingiva: o amount o quality o location o treatability Bleeding tendency: o sulcus base, lining o gingival margins Suppuration Sinus tract formation Pocket depths Pseudopockets Frena Pain Other pathology Dental Description Defective restorations: o overhangs o open contacts o poor contours Fractured cusps 1 ww.links2success.biz [email protected] 914-303-6464 Caries Deposits: o Type . plaque . calculus . stain . matera alba o Location . supragingival . subgingival o Severity . mild . moderate . severe Wear facets Percussion sensitivity Tooth vitality Attrition, erosion, abrasion Occlusal plane level Occlusion findings Furcations Mobility Fremitus Radiographic findings Film dates Crown:root ratio Amount of bone loss o horizontal; vertical o localized; generalized Root length and shape Overhangs Bulbous crowns Fenestrations Dehiscences Tooth resorption Retained root tips Impacted teeth Root proximities Tilted teeth Radiolucencies/opacities Etiologic factors Local: o plaque o calculus o overhangs 2 ww.links2success.biz [email protected] 914-303-6464 o orthodontic apparatus o open margins o open contacts o improper -
Pediatric Invasive Gastrointestinal Fungal Infections: Causative Agents and Diagnostic Modalities
Microbiology Research Journal International 19(2): 1-11, 2017; Article no.MRJI.32231 Previously known as British Microbiology Research Journal ISSN: 2231-0886, NLM ID: 101608140 SCIENCEDOMAIN international www.sciencedomain.org Pediatric Invasive Gastrointestinal Fungal Infections: Causative Agents and Diagnostic Modalities Mortada H. F. El-Shabrawi 1, Lamiaa A. Madkour 2* , Naglaa Kamal 1 and Kerstin Voigt 3 1Department of Pediatrics, Faculty of Medicine, Cairo University, Egypt. 2Department of Microbiology and Immunology, Faculty of Medicine, Cairo University, Egypt. 3Department of Microbiology and Molecular Biology, University of Jena, Germany. Authors’ contributions This work was carried out in collaboration between all authors. Author MHFES specified the topic of the research. Author LAM designed the study, managed the literature research and wrote the first draft of the manuscript. Authors NK and KV wrote the subsequent drafts. Author MHFES revised the manuscript. All authors read and approved the final manuscript. Article Information DOI: 10.9734/MRJI/2017/32231 Editor(s): (1) Raúl Rodríguez-Herrera, Autonomous University of Coahuila, México. Reviewers: (1) Hasibe Vural, Necmettin Erbakan Üniversity, Turkey. (2) Berdicevsky Israela, Technion Faculty of Medicine, Haifa, Israel. (3) Vassiliki Pitiriga, University of Athens, Greece. Complete Peer review History: http://www.sciencedomain.org/review-history/18327 Received 16 th February 2017 th Review Article Accepted 18 March 2017 Published 24 th March 2017 ABSTRACT Invasive gastrointestinal fungal infections are posing a serious threat to the ever-expanding population of immunocompromised children, as well as some healthy children at risk. In this narrative review, we collate and explore the etiologies and diagnostic modalities of these overlooked infections. -
Pulmonary Basidiobolomycosis: an Unusual Presentation in a Cancer Patient: a Case Report and Mini Review of Cases in India
Int.J.Curr.Microbiol.App.Sci (2015) 4(5): 798-805 ISSN: 2319-7706 Volume 4 Number 5 (2015) pp. 798-805 http://www.ijcmas.com Case Study Pulmonary Basidiobolomycosis: An unusual presentation in a cancer patient: A case report and mini review of cases in India Deba Dulal Biswal1, Manisa Sahu2* and Pallavi Bhaleker3 1Department of Medical Oncology, S L Raheja Hospital (A Fortis Associate) Mahim (W), Mumbai-400016, India 2Department of Microbiology, S L Raheja Hospital (A Fortis Associate) Mahim(W), Mumbai-400016, India *Corresponding author A B S T R A C T K e y w o r d s Basidiobolomycosis is an uncommon disease caused by Basidiobolus Basidiobolo- ranarum. The clinical presentation varies from localized subcutaneous mycosis, infection to widespread dissemination involving different viscera s, notably Basidio-bolus the gastrointestinal tract. Pulmonary involvement is rarer; we report a case ranarum, of pulmonary Basidiobolomycosis in a lung cancer patient. lung cancer Introduction Basidiobolo mycosis is caused by the fungus cases are from Southern part.( Sujatha S et Basidiobolus ranarum, which is a al., 2003; Chandrasekhar HR et al., 1998; zygomycetes belonging to order Prasad PV et al., 2002; Krishnan et al., Entomophthorales. (Gugnani, H. C et al., 1998) Rare dissemination with visceral 1999) This filamentous fungus is usually involvement by Basidiobolus are quoted by associated with subcutaneous zygomycosis various authors such as gastrointestinal tract, of trunk and limbs in immune competent uterus, urinary bladder and retro peritoneum. individuals (Ribes JA et al., 2000) It is an (Bigliazzi C et al., 2004; Khan ZU et al., environmental saprophyte isolated mostly 2001; Nazir Z et al., 1997; Choonhakarn C from decaying vegetation, foodstuffs, fruits, et al., 2004) Pulmonary involvement are and soil. -
Subcutaneous Phycomycosis: a Review of 31 Cases Seen in Uganda
27 June 1964 Myelomatosis-Speed et al. BRITISH 1669 Case 10 (19 October 1962); Case 12 (24 February 1964); REFERNCES Case 14 (9 September 1962); and Case 16 (17 February 1963). N. (1947). Lancet, 2, 388. Alwall, Campgn, Case 5 received 10 further courses of melphalan, and the disease Bergel, F., and Stock, J. A. (1953). A.R. Brit. Emp. Cancer Br Med J: first published as 10.1136/bmj.1.5399.1669 on 27 June 1964. Downloaded from 31, 6. remained well controlled until the last 10 weeks of life, when Bergsagel, D. E. (1962). Cancer Chemother. Rep., No. 16, p. 261. the growth extended extremely rapidly. He received one further - Sprague, C. C., Austin, C., and Griffith, K. M. (1962). Ibid., No. 21, p. 87. course of radiotherapy for local pain. Case 9 received eight Bernard, J., Seligmann, M., and Danon, F. (1962). Nouv. Rev. franc. further courses of melphalan, and the disease was well controlled Himat., 2, 611. of ribs which Blokhin, N., Larionov, L., Perevodchikova, N., Chebotareva, L., and except for local pain from pathological fractures Merkulova, N. (1958). Ann. N.Y. Acad. Sci., 68, 1128. was relieved by irradiation. At post-mortem examination a Innes, J. (1963). Proc. roy. Soc. Med., 56, 648. gastric carcinoma, suspected in the last three months of life, - and Rider, W. D. (1955). Blood, 10, 252. Larionov, L. F., Khokhlov, A. S., Shkodinskaja, E. N., Vasina, 0. S., was found. Cases 8, 9, 12, 14, and 16 did not benefit from Troosheikina, V. I., and Novikova, M. A. (1955). Bull. -
Pulmonary Geotrichosis Confirms the Diagnosis of Geotrichosis.A'3 Radiologically, Urinary Bladder Carcinoma Initially Manifested
150 LETTERS TO THE EDITOR Postgrad Med J: first published as 10.1136/pgmj.68.796.150 on 1 February 1992. Downloaded from References ricin B and 5-fluorocytosine have been shown to have in vitro activity at attainable concentrations.4 1. Langgand, H. & Smith, W.O. Self-induced water intoxication without predisposing illness. N Engl J Med 1962, 266: 378-383. Rama Ramani 2. Kennedy, R.M. & Earley, L.E. Profound hyponatraemia P. Vittal Rao' resulting from a thiazide induced decrease in urinary diluting Girija R. Kumari capacity in a patient with primary polydipsia. N Engl J Med P.G. Shivananda 1970, 282: 1185-1186. Departments of Microbiology & 'Medicine, 3. Beresford, H.R. Polydipsia, hydrochlorothiazide and water Kasturba Medical College, intoxication. JAMA 1970, 214: 879-883. Manipal 576 119, 4. Raskind, M. Psychosis, polydipsia and water intoxication. India. Arch Gen Psychiatry 1974, 30: 112-114. 5. Gossain, V.V., Hagen, G.A. & Sugawara, M. Drug-induced hyponatraemia in psychogenic polydipsia. Postgrad Med J 1976, 52: 720-722. References 6. Fowler, R.C., Kronfol, Z.A. & Perry, P.J. Water intoxication, psychosis, and inappropriate secretion of antidiuretic hor- 1. Rippon, J.W. Medical Mycology; The pathogenicfungi and the mone. Arch Gen Psychiatry 1977, 34: 1097-1099. pathogenic actinomycetes, 2nd ed. W.B. Saunders, Phila- 7. Smith, W.O. & Clark, M.L. Self-induced water intoxication in delphia, 1982, pp. 642-645. schizophrenic patients. Am J Psychiatry 1980, 137: 1055-1060. 2. Pahwa, R.K., Yadav, V.K., Singh, M.M. & Chaturvedi, V.P. 8. Emsley, R.A. & Gledhill, R.F. -
A Case of Disseminated Histoplasmosis Detected in Peripheral Blood Smear Staining Revealing AIDS at Terminal Phase in a Female Patient from Cameroon
Hindawi Publishing Corporation Case Reports in Medicine Volume 2012, Article ID 215207, 3 pages doi:10.1155/2012/215207 Case Report A Case of Disseminated Histoplasmosis Detected in Peripheral Blood Smear Staining Revealing AIDS at Terminal Phase in a Female Patient from Cameroon Christine Mandengue Ebenye Cliniques Universitaires des Montagnes, Bangangt´e, Cameroon Correspondence should be addressed to Christine Mandengue Ebenye, [email protected] Received 28 August 2012; Revised 2 November 2012; Accepted 5 November 2012 Academic Editor: Ingo W. Husstedt Copyright © 2012 Christine Mandengue Ebenye. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Histoplasmosis is endemic in the American continent and also in Sub-Saharan Africa, coexisting with the African histoplasmosis. Immunosuppressed patients, especially those with advanced HIV infection develop a severe disseminated histoplasmosis with fatal prognosis. The definitive diagnosis of disseminated histoplasmosis is based on the detection of Histoplasma capsulatum from patient’ tissues samples or body fluids. Among the diagnostic tests peripheral blood smear staining is not commonly used. Nonetheless a few publications reveal that Histoplasma capsulatum has been discovered by chance using this method in HIV infected patients with chronic fever and hence revealed AIDS at the terminal phase. We report a new case detected in a Cameroonian woman without any previous history of HIV infection. Peripheral blood smear staining should be commonly used for the diagnosis of disseminated histoplasmosis in the Sub-Saharan Africa, where facilities for mycology laboratories are unavailable. 1. Introduction 1987 [2]. -
Clinical Biotechnology and Microbiology ISSN: 2575-4750
Page 47 to 49 Volume 1 • Issue 1 • 2017 Research Article Clinical Biotechnology and Microbiology ISSN: 2575-4750 Aspergillosis: A Highly Infectious Global Mycosis of Human and Animal Mahendra Pal* Narayan Consultancy on Veterinary Public Health and Microbiology, 4 Aangan, Ganesh Dairy Road, Anand-388001, India *Corresponding Author: Mahendra Pal, Narayan Consultancy on Veterinary Public Health and Microbiology, 4 Aangan, Ganesh Dairy Road, Anand-388001, India. Received: June 09, 2017; Published: June 19, 2017 Abstract Aspergillosis is an important opportunistic fungal saprozoonosis of worldwide distribution. The disease is reported in humans and animals including birds, and is caused primarily by Aspergillus fumigatus, a saprobic fungus of ubiquitous distribution. It occurs in aspergillosis are re- sporadic and epidemic form causing significant morbidity and mortality. Globally, over 200,000 cases of invasive ported each year. The source of infection is exogenous and respiratory tract is the chief portal of entry of fungus. A variety of clinical aspergillosis. The pathogen can signs are observed in humans and animals. Direct demonstration of fungal agent in clinical material and its isolation in pure growth be easily isolated on APRM agar. Detailed morphology of fungus is studied in Narayan stain. Numerous antifungal drugs are used in on mycological medium is still considered the gold standard to confirm an unequivocal diagnosis of clinical practice to treat cases of aspergillosis - . Certain high risk groups should use face mask to prevent inhalation of fungal spores from immediate environment. It is recommended that “APRM medium” and “Narayan stain”, which are easy to prepare and less ex including Aspergillus pensive than other stains and media, should be routinely used in microbiology and public health laboratories for the study of fungi consequences of disease. -
Sporothrix Schenckii: ➢ Thermal Dimorphic
Subcutaneous mycoses ➢1-Mycetoma ➢2-Sporotrichosis ➢3-Chromoblastomycosis ➢4-Rhinosporidiosis ➢5- Lobomycosis ➢6- Entomophthoramycosis Sporotrichosis Rose gardener’s disease Chronic desease Agent Sporothrix schenckii: ➢ Thermal dimorphic ➢ In soil ➢ On decaying vegetation,plants,plant products (hay, straw, sphagnum moss), and a variety of animals (cats) ➢ less than 37° C (hyphal) ➢ 37° C (yeast) ➢ Sporothrix brasiliensis ➢ Sporothrix globosa Epidemiology ➢Worldwide ➢Tropical regions ➢Mexico ➢Brazile ➢France ➢USA Occupational disease: ➢Farmers ➢ ➢Workers ➢Gardeners ➢Florists Predisposing factors: ➢Trauma ➢Inhalation (very rarely) ➢HIV Clinical Syndromes 1-lymphocutaneous 2-Fixed cutaneous 3- Osteoarticular involvement 4-Pulmonary 5-Systemic Primary infection 1-Lymphocutaneous sporotrichosis 2-Fixed cutaneous sporotrichosis: Fixed cutaneous sporotrichosis verrucous-type sporotrichosis localized cutaneous type Paronychia sporotrichosis Osteoarticular involvement Pulmonary sporotrichosis: ➢Alcoholic ➢Pulmonary tuberculosis, diabetes mellitus and steroid ➢A productive cough ➢Low-grade fever ➢Weight loss Systemic sporotrichosis Transmission: ➢Dog bite ➢parrot bite ➢Insects bite ➢Cases of animal-to-human transmission Laboratory Diagnosis: 1-Collection of samples: ➢Drainage from skin lesions ➢Exudates ➢Pus ➢Blood ➢Pulmonary secretions ➢Tissue biopsy specimens 2-Direct examination ➢Gram ➢PAS ➢GMS ➢H & E ❖Yeast Cells ❖Asteroid body: Elongated Buds (“Cigar Body”) Wet Mount BHI Blood 37˚C Yeast with Elongated Daughter Cell Biopsy of subcutaneous tissue -
Boards' Fodder
boards’ fodder Medical Mycology By Adriana Schmidt, MD, and Natalie M. Curcio, MD, MPH. (Updated July 2015*) SUPERFICIAL ORGANISM CLINICAL HISTO/KOH TREATMENT MYCOSES* Pityriasis Malessezia furfur Hypo- or hyper-pigmented Spaghetti & meatballs: Antifungal shampoos and/or versicolor macules short hyphae + yeast PO therapy Tinea nigra Hortaea werneckii (formerly Brown-black non-scaly Branching septate hyphae Topical imidazoles or palmaris Phaeoannellomyces werneckii) macules + budding yeast allylamines Black piedra Piedraia hortae Hard firm black Dark hyphae around concretions acrospores Cut hair off, PO terbinafine, White piedra Trichosporon ovoides or inkin Soft loose white Blastoconidia, imidazoles, or triazoles (formely beigelii) concretions arthroconidia Fluorescent small Microsporum Canis KOH: spores on outside spore ectothrix: M. audouinii of the hair shaft; “Cats And Dogs M. distortum Wood’s lamp --> yellow Sometimes Fight T. schoenleinii fluorescence & Growl” M. ferrugineum+/- gypseum Large spore Trichophyton spp. (T. tonsurans in North America; T. violaceum in KOH: spores within hair Topical antifungals; PO endothrix Europe, Asia, parts of Africa). shaft antifungals for T. manuum, Tinea corporis T. rubrum > T. mentag. Majocchi’s granuloma: T. rubrum capitis, unguium T. pedis Moccasin: T. rubrum, E. floccosum. Interdigital/vesicular: T. mentag T. unguium Distal lateral, proximal and proximal white subungual: T. rubrum. White superficial: T. mentag. HIV: T. rubrum SUBQ MYCOSES** ORGANISM TRANSMISSION CLINICAL HISTO/KOH TREATMENT -
Opportunistic Invasive Fungal Infections: Diagnosis & Clinical
Review Article Indian J Med Res 139, February 2014, pp 195-204 Opportunistic invasive fungal infections: diagnosis & clinical management Parisa Badiee & Zahra Hashemizadeh Prof. Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran Received May 14, 2013 Invasive fungal infections are a significant health problem in immunocompromised patients. The clinical manifestations vary and can range from colonization in allergic bronchopulmonary disease to active infection in local aetiologic agents. Many factors influence the virulence and pathogenic capacity of the microorganisms, such as enzymes including extracellular phospholipases, lipases and proteinases, dimorphic growth in some Candida species, melanin production, mannitol secretion, superoxide dismutase, rapid growth and affinity to the blood stream, heat tolerance and toxin production. Infection is confirmed when histopathologic examinationwith special stains demonstrates fungal tissue involvement or when the aetiologic agent is isolated from sterile clinical specimens by culture. Both acquired and congenital immunodeficiency may be associated with increased susceptibility to systemic infections. Fungal infection is difficult to treat because antifungal therapy forCandida infections is still controversial and based on clinical grounds, and for molds, the clinician must assume that the species isolated from the culture medium is the pathogen. Timely initiation of antifungal treatment is a critical component affecting the outcome. Disseminated infection requires the use of systemic agents with or without surgical debridement, and in some cases immunotherapy is also advisable. Preclinical and clinical studies have shown an association between drug dose and treatment outcome. Drug dose monitoring is necessary to ensure that therapeutic levels are achieved for optimal clinical efficacy. The objectives of this review are to discuss opportunistic fungal infections, diagnostic methods and the management of these infections.