Oral mycobiome identification in atopic dermatitis, leukemia, and HIV patients – a systematic review

References

• Bass D, Richards TA. Three reasons to re-evaluate fungal diversity on earth and in the ocean. Fungal Biol Rev. 2011;25:159–19.
   Google Scholar
• Brown GD, Denning DW, Levitz SM. Tackling human fungal infections. Science. 2012;336:647.
   PubMed Web of Science ®Google Scholar
• Anonymous. Stop neglecting fungi. Nat Microbiol. 2017;17120. DOI:10.1038/nmicrobiol.2017.120
   Google Scholar
• Casadevall A. Fungal diseases in the 21st century: the near and far horizons. Pathog Immun. 2019;3:183–196.
   Google Scholar
• Gostincar C, Grube M, Gunde - Cimerman N. Evolution of fungal pathogens in domestic environments? Fungal Biol. 2011;115:1008–1018.
   PubMed Web of Science ®Google Scholar
• Garcia-Solache MA, Casadevall A. Global warming will bring new fungal diseases for mammals. mBio. 2010;1(1):e00061–10.
   PubMed Web of Science ®Google Scholar
• Chandra J, Retuerto M, Mukherjee PK, et al. The fungal biome of the oral cavity. Methods Mol Biol. 2016;1356:107–135.
   Google Scholar
• Ghannoum MA, Jurevic RJ, Mukherjee PK, et al. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PloS Pathog. 2010;6(1):e1000713.
   PubMed Web of Science ®Google Scholar
• Dupuy AK, David MS, Li L, et al. Redefining the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal. PLoS One. 2014;9(3):e90899.
   PubMed Web of Science ®Google Scholar
• Neville BW, Damm DD, Allen CM, et al. Oral & Maxillofacial Pathology. Missouri: Elsevier; 2016.
   Google Scholar
• Sherman RG, Prusinski L, Ravenel MC, et al. Oral Candidoses. Quintessence Int. 2002;33:521–532.
   PubMedGoogle Scholar
• Simões RJ, Fonseca P, Figueira MH. Infecções por Candida spp na Cavidade Oral. Odontol Clín Cient. 2013;12:19–22.
   Google Scholar
• Budtz-Jorgensen E. Etiology, pathogenesis, therapy and prophylaxis of oral yeast infections. Acta Odontol Scand. 1990;48:61–69.
   PubMed Web of Science ®Google Scholar
• Cui L, Morris A, Ghedin E. The human mycobiome in health and disease. Genome Med. 2013;5:63.
   PubMed Web of Science ®Google Scholar
• Peters BA, Wu J, Hayes RB, et al. The oral fungal mycobiome: characteristics and relation to periodontitis in a pilot study. BMC Microbiol. 2017;17:157.
   Web of Science ®Google Scholar
• Binder U, Lass-Flörl C. Epidemiology of invasive fungal infections in the mediterranean area. Mediterr J Hematol Infect Dis. 2011;3. DOI:10.4084/MJHID.2011.0016.
   Google Scholar
• Armstrong-James D, Meintjes G, Brown GD. A neglected epidemic: fungal infections in HIV/AIDS. Trends Microbiol. 2014;22:120–127.
   PubMed Web of Science ®Google Scholar
• Okoye AA, Picker LJ. CD4(+) T-cell depletion in HIV infection: mechanisms of immunological failure. Immunol Rev. 2013;254(1):54–64.
   PubMed Web of Science ®Google Scholar
• Myers RC. STAT4-Dependent and -Independent Th2 Responses Correlate with Protective Immunity against Lung Infection with Pneumocystis murina. Immunol. 2013;190:6287–6294.
   Web of Science ®Google Scholar
• Patil S, Majumdar B, Sarode SC, et al. Oropharyngeal Candidosis in HIV-Infected Patients-An Update. Front Microbiol. 2018;9:980.
   Web of Science ®Google Scholar
• Tamí-Maury IM, Willig JH, Jolly PE, et al. Prevalence, incidence, and recurrence of oral lesions among HIV-infected patients on HAART in Alabama: a two-year longitudinal study. South Med J. 2011;104(8):561–566.
   PubMed Web of Science ®Google Scholar
• Thompson MA, Aberg JA, Cahn P, et al. Antiretroviral treatment of adult HIV infection: 2010 recommendations of the International AIDS Society-USA panel. JAMA. 2010;304(3):321–333.
   PubMed Web of Science ®Google Scholar
• Walker NF, Scriven J, Meintjes G, et al. Immune reconstitution inflammatory syndrome in HIV-infected patients. HIV/AIDS (Auckland, N Z). 2015;7:49–64.
   Google Scholar
• Bhatt VR, Shostrom V, Gundabolu K, et al. Utilization of initial chemotherapy for newly diagnosed acute myeloid leukemia in the USA. Blood Adv. 2018;2(11):1277–1282.
   PubMed Web of Science ®Google Scholar
• Hansen BA, Ø W, Ø B, et al. Febrile Neutropenia in Acute Leukemia. Epidemiology, Etiology, Pathophysiology and Treatment. Mediterr J Hematol Infect Dis. 2020;12(1):e2020009.
   PubMedGoogle Scholar
• Terwilliger T, Abdul-Hay M. Acute lymphoblastic leukemia: a comprehensive review and 2017 update. Blood Cancer J. 2017;7(6):e577.
   PubMed Web of Science ®Google Scholar
• Pagano L, Caira M, Candoni A, et al. The epidemiology of fungal infections in patients with hematologic malignancies: the SEIFEM-2004 study. Haematol. 2006;91(8):1068–1075.
   PubMed Web of Science ®Google Scholar
• Montassier E, Gastinne T, Vangay P, et al. Chemotherapy-driven dysbiosis in the intestinal microbiome. Aliment Pharm Ther. 2015;42(5):515–528.
   PubMed Web of Science ®Google Scholar
• Robinson S, Peterson CB, Sahasrabhojane P, et al. Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia. mSphere. 2020;5(2):e00048–20.
   Web of Science ®Google Scholar
• Roesner LM, Werfel T, Heratizadeh A. The adaptive immune system in atopic dermatitis and implications on therapy. Expert Rev Clin Immunol. 2016;12(7):787–796.
   PubMed Web of Science ®Google Scholar
• Boguniewicz M, Leung DY. Atopic dermatitis: a disease of altered skin barrier and immune dysregulation. Immunol Rev. 2011;242(1):233–246.
   PubMed Web of Science ®Google Scholar
• Faergemann J. Atopic dermatitis and fungi. Clin Microbiol Rev. 2002;15:545–563.
   PubMed Web of Science ®Google Scholar
• Kortekangas-Savolainen O, Lammintausta K, Kalimo K. Skin prick test reactions to brewer’s yeast (Saccharomyces cerevisiae) in adult atopic dermatitis patients. Allergy. 1993;48(3):147–150.
   Web of Science ®Google Scholar
• Oliveira A, Sodré CS, Ferreira DC, et al. Oral aspects identified in atopic dermatitis patients: a literature review. Open Dent J. 2018;12:424–434.
   Web of Science ®Google Scholar
• Wheeler ML, Limon JJ, Underhill DM. Immunity to commensal fungi: detente and disease. Annu Rev Pathol. 2017;12:359–385.
   PubMed Web of Science ®Google Scholar
• Javad G, Taheri SM, Hedayati MT, et al. Evaluation of candida colonization and specific humoral responses against candida albicans in patients with atopic dermatitis. Biomed Res Int. 2015. DOI:10.1155/2015/849206.
   Web of Science ®Google Scholar
• Wickes BL, Wiederhold NP. Molecular diagnostics in medical mycology. Nat Commun. 2018;9:5135.
   PubMed Web of Science ®Google Scholar
• Kozel TR, Wickes B. Fungal diagnostics. Cold Spring Harb Perspect Med. 2014;4:a019299.
   Web of Science ®Google Scholar
• Temfack E, Kouanfack C, Mossiang L, et al. Cryptococcal antigen screening in asymptomatic HIV-infected antiretroviral native patients in Cameroon and evaluation of the new semi-quantitative BioSynex Crypto PS test. Front Microbiol. 2018;9:409.
   Web of Science ®Google Scholar
• Frau A, Kenny JG, Lenzi L, et al. DNA extraction and amplicon production strategies deeply inffluence the outcome of gut mycobiome studies. Sci Rep. 2019;9:9328.
   PubMed Web of Science ®Google Scholar
• Galloway-Peña JR, Kontoyiannis DP. The gut mycobiome: the overlooked constituent of clinical outcomes and treatment complications in patients with cancer and other immunosuppressive conditions. PLoS Pathog. 2020;16(4):e1008353.
   Web of Science ®Google Scholar
• Moher D, Liberati A, Tetzlaff J, et al. The PRISMA group. preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. PLoS Med. 2009;6. DOI:10.1371/journal.pmed.1000097.
   Web of Science ®Google Scholar
• Arendorf TM, Walker DM. The prevalence and intra-oral distribution of Candida albicans in man. Arch Oral Biol. 1980;25:1–10.
   PubMed Web of Science ®Google Scholar
• Mukherjee PK, Chandra J, Retuerto M, et al. Oral mycobiome analysis of HIV-infected patients: identification of pichia as an antagonist of opportunistic fungi. PloS Pathog. 2014;10. DOI:10.1371/journal.ppat.1003996.
   Web of Science ®Google Scholar
• Fukui Y, Kotaro A, Yoshikazu I, et al. The palatine tonsil bacteriome, but not the mycobiome, is altered in HIV infection. BMC Microbiol. 2018;18:127.
   Web of Science ®Google Scholar
• Vijendran LCP, Verma R, Hazra N, et al. A comparative study of the various patterns of oro-cutaneous fungi and their sensitivity to anti fungals between HIV patients and normal healthy individuals. Med J Armed Forces India. 2018;75:50–57.
   Google Scholar
• Li YY, Chen WY, Li X, et al. Asymptomatic oral yeast carriage and antifungal susceptibility profile of HIV-infected patients in Kunming, Yunnan Province of China. BMC Infect Dis. 2013;13:46.
   PubMed Web of Science ®Google Scholar
• Hager CL, Ghannoum MA. The mycobiome in HIV. Curr Opin HIV AIDS. 2018;13(1):69–72.
   Web of Science ®Google Scholar
• Annavajhala MK, Khan SD, Sullivan SB, et al. Oral and gut microbial diversity and immune regulation in patients with HIV on antiretroviral therapy. mSphere 2020;5(1):e0079819.
   Google Scholar
• Das Chagas MS, Portela MB, Cerqueira DF, et al. Reduction of Candida species colonization in the oral cavity of children infected with human immunodeficiency virus after dental treatment. Oral Surg Oral Med Oral Pathol Oral Radiol Endod. 2009;108. DOI:10.1016/j.tripleo.2009.04.038.
   Web of Science ®Google Scholar
• Junqueira JC, Vilela SFG, Rossoni RD, et al. Oral colonization by yeasts in HIV-positive patients in Brazil. Rev Inst Med Trop. 2012;54:17–24.
   PubMed Web of Science ®Google Scholar
• Moris DV, Melhem MSC, Martins MA, et al. Prevalence and antifungal susceptibility of Candida parapsilosis complex isolates collected from oral cavities of HIV-infected individuals. J Med Microbiol. 2012;61:1758–1765.
   Web of Science ®Google Scholar
• Mukherjee PK, Chandra J, Retuerto M, et al. Dysbiosis in the oral bacterial and fungal microbiome of HIV- infected subjects is associated with clinical and immunologic variables of HIV infection. Plos One. 2018;13(7):e0200285.
   Web of Science ®Google Scholar
• Dos Santos Abrantes PM, McArthur CP, Africa CWJ. Multi-drug resistant (MDR) oral Candida species isolated from HIV-positive patients in South Africa and Cameroon. Diagn Microbiol Infect Dis. 2013;79:222–227.
   Web of Science ®Google Scholar
• Merenstein D, Haihong H, Wang C, et al. Colonization by Candida Species of the Oral and Vaginal Mucosa in HIV-Infected and Noninfected Women. AIDS Res Hum Retrov. 2013;29(1):30–34.
   Web of Science ®Google Scholar
• Sharifzadeh A, Khosravi AR, Shokri H. Oral microflora and their relation to risk factors in HIV + patients with oropharyngeal candidiasis. J Mycol Med. 2013;23:105–112.
   Web of Science ®Google Scholar
• Jiang L, Yong X, Li R, et al. Dynamic analysis of oral Candida carriage, distribution, and antifungal susceptibility in HIV-infected patients during the first year of highly active antiretroviral therapy in Guangxi, China. J Oral Pathol Med. 2014;43:696–703.
   PubMed Web of Science ®Google Scholar
• Thanyasrisung P, Kesakomol P, Pipattanagonvit P, et al. Oral Candida carriage and immune status in Thai human immunodeficiency virus-infected individuals. J Med Microbiol. 2014;63:753–759.
   Web of Science ®Google Scholar
• Menezes RP, Borges AS, Araujo LB, et al. Related factors for colonization by Candida species in the oral cavity of HIV-infected individuals. Ver Inst Med Trop. 2015;57:413–419.
   Web of Science ®Google Scholar
• Lourenço AG, Ribeiro AERA, Nakao C, et al. Oral Candida spp carriage and periodontal diseases in HIV-infected patients in Ribeirão Preto, Brazil. Rev Inst Med Trop. 2017;59:e29.
   Web of Science ®Google Scholar
• De Mendonça RM, Araújo MD, Levy CE, et al. Oral mucositis in pediatric acute lymphoblastic leukemia patients: evaluation of microbiological and hematological factors. Pediatr Hematol Oncol. 2015;32(5):322–330.
   Web of Science ®Google Scholar
• De Mendonça RM, De Araújo M, Levy CE, et al. Prospective evaluation of HSV, Candida spp., and oral bacteria on the severity of oral mucositis in pediatric acute lymphoblastic leukemia. Support Care Cancer. 2012;20:1101–1107.
   Web of Science ®Google Scholar
• Akdis CA, Akdis M, Bieber T, et al. European Academy of Allergology and Clinical Immunology/American Academy of Allergy Asthma and Immunology: diagnosis and treatment of atopic dermatitis in children and adults: european Academy of Allergology and Clinical Immunology/American Academy of Allergy, Asthma and Immunology/PRACTALL Consensus Report. J Allergy Clin Immunol. 2006;118:152–169.
   PubMed Web of Science ®Google Scholar
• Fonacier LS, Dreskin SC, Leung DYM. Allergic skin diseases. J Allergy Clin Immunol. 2010;125:138–149.
   PubMed Web of Science ®Google Scholar
• Incorvaia C, Frati F, Verna N, et al. Allergy and the skin. Clin Exp Immunol. 2008;153:27–29.
   Web of Science ®Google Scholar
• Luis A, Schaub B. Lesson from the farm environment. Curr Opin Allergy Clin Immunol. 2012;12:153–163.
   Web of Science ®Google Scholar
• Glatz M, Bosshard P, Grendelmeier PS. The role of fungi in atopic dermatitis. Immunol Allergy Clin. 2017;37:63–74.
   Web of Science ®Google Scholar
• Feja KN, Wu F, Roberts K, et al. Risk factors for candidemia in critically ill infants: a matched case-control study. J Pediatr. 2005;147(2):156–161.
   Web of Science ®Google Scholar
• Williams DW, Lewis MA. Isolation and identification of candida from the oral cavity. Oral Dis. 2000;6:3–11.
   Web of Science ®Google Scholar
• Mane A, Kulkami A, Risbud A. Biofilm production in oral Candida isolates from HIV-positive individuals from Pune, India. Mycoses. 2012;56(2):182–186.
   Web of Science ®Google Scholar
• Silva JO, Candido RC. Avaliação do sistema API20C AUX na identificação de leveduras de interesse clínico. Rev Soc Bras Med Trop. 2005;38(3):261–263.
   Google Scholar
• Blignaut E, van Heerden WF. Molecular and histological association between candida albicans from oral soft tissue and carious dentine of HIV-positive children. Mycopathologia. 2015;180:193–201.
   Web of Science ®Google Scholar
• Mushi MF, Mitsemitika CI, Bader O, et al. High Oral Carriage of Non-albicans Candida spp. among HIV-infected individuals. Int J Infect Dis. 2016;49:185–188.
   PubMed Web of Science ®Google Scholar
• Forth FL, Hoper D. Highly efficient library preparation for Ion Torrent sequencing using Y-adapters. Biotechniques. 2019;67(5):229–237.
   Web of Science ®Google Scholar
• Carvalho MCCG, Silva DCG. Sequenciamento de DNA de nova geração e suas aplicações na genômica de plantas. Ciênc Rural. 2010;40(3):735–744.
   Google Scholar
• Amjad M. An overview of the molecular methods in the diagnosis of gastrointestinal infectious diseases. Int J Microbiol. 2020. DOI:10.1155/2020/8135724
   Web of Science ®Google Scholar
• Diaz PI, Hong BY, Dupuy AK, et al. Mining the oral mycobiome: methods, components, and meaning. Virulence. 2017;8(3):313–323. . 1252015
   PubMed Web of Science ®Google Scholar
• Huseyin CE, O’Toole PW, Cotter PD, et al. Forgotten fungi-the gut mycobiome in human health and disease. FEMS Microbiol Rev. 2017;41(4):479–511.
   PubMed Web of Science ®Google Scholar
• Rhoads DD, Wolcott RD, Sun Y, et al. Comparison of culture and molecular identification of bacteria in chronic wounds. Int J Mol Sci. 2012;13(3):2535–2550.
   Web of Science ®Google Scholar
• Low CY, Rotstein C. Emerging fungal infections in immunocompromised patients. F1000 Med Rep. 2011;3:14.
   PubMedGoogle Scholar
• Rees JA. Regulation and private participation in the water and sanitation sector. Nat Resour Forum. 1998;22:95–105.
   Google Scholar
• Denning DW, Kibbler CC, Barnes RA. British society for medical mycology proposed standards of care for patients with invasive fungal infections. Lancet Infect Dis. 2003;3:230–240.
   PubMed Web of Science ®Google Scholar
• Garey KW, Rege M, Manjunath PP, et al. Time to initiation of fluconazole therapy impacts mortality in patients with candidemia: a multi-institutional study. Clin Infect Dis. 2006;43:25–31.
   PubMed Web of Science ®Google Scholar
• Nolla-Salas J, Sitges-Serra A, León-Gil C, et al. Candidemia in non-neutropenic critically ill patients: analysis of prognostic factors and assessment of systemic antifungal therapy. Intensive Care Med. 1997;23:23–30.
   PubMed Web of Science ®Google Scholar
• Qian J, Cutler JE, Cole RB, et al. MALDI-TOF mass signatures for differentiation of yeast species, strain grouping and monitoring of morphogenesis markers. Anal Bioanal Chem. 2008;392:439–449.
   PubMed Web of Science ®Google Scholar
• Dhiman N, Hall L, Wohlfiel SL, et al. Performance and cost analysis of matrix-assisted laser desorption ionization–time of flight mass spectrometry for routine identification of yeast. J Clin Microbiol. 2011;49:1614–1616.
   PubMed Web of Science ®Google Scholar
• Alanio A, Beretti JL, Dauphin B, et al. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for fast and accurate identification of clinically relevant Aspergillus species. Clin Microbiol Infect. 2011;17:750–755.
   PubMed Web of Science ®Google Scholar
• De Carolis E, Osteraro B, Lass-Flörl C, et al. Species identification of Aspergillus, Fusarium and Mucorales with direct surface analysis by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Microbiol Infect. 2011;18(5):475–484.
   Web of Science ®Google Scholar
• Bader O, Weig M, Thaverne-Gadhwal L, et al. Improved clinical laboratory identification of human pathogenic yeasts by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Microbiol Infect. 2011;17:1359–1365.
   PubMed Web of Science ®Google Scholar
• Wang Z, Nilsson RH, James TY. Future perspectives and challenges of Fungal Systematics in the Age of Big Data. In Li, De-Wei editors. Biology of Microfungi. CT: Springer International Publishing; 2006. 25–46. DOI:10.1007/978-3-319-29137-6
   Google Scholar
• Lutzoni F, Kauff F, Cox CJ, et al. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot. 2004;91:1446–1480.
   PubMed Web of Science ®Google Scholar
• Miotto NML, Yurgel LS, Cherubini K, et al. Métodos laboratoriais de identificação do fungo Candida sp. Revista Da Faculdade De Odontologia De Passo Fundo. 2004;9(1):27–33.
   Google Scholar
• Zhou KM, Lokate M, Deurenberg RH, et al. Use of whole-genome sequencing to trace, control and characterize theregional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae. Sci Rep. 2016;6:20840.
   PubMed Web of Science ®Google Scholar
• Edwards DJ, Holt KE. Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data. Microb Inform Exp. 2013;3(1):2.
   Google Scholar
• Gillevet PM. Multitag Sequencing and Ecogenomic Analysis. U.S. Patent No 8,603,749. Washington, DC: US Patent and Trademark Office; 2006.
   Google Scholar
• Metzker M. Sequencing technologies — the next generation. Nat Rev Genet. 2010;11:31–46.
   PubMed Web of Science ®Google Scholar
• Alanazi H, Semiali A, Chmielewski W, et al. E-Cigarettes Increase Candida albicans Growth and Modulate its Interaction with Gingival Epithelial Cells. Int J Environ Res Public Health. 2019;16:294.
   Web of Science ®Google Scholar
• Mokeem S, Abduliabbar T, Al-Kheraif AA, et al. Oral Candida carriage among cigarette-and waterpipe-smokers, and electronic cigarette users. Oral Dis. 2019;25:319–326.
   PubMed Web of Science ®Google Scholar
• Muzurovic S, Hukic M, Babajic E, et al. The relationship between cigarette smoking and oral colonization with Candida species in healthy adult subjects. Med Glas. 2013;10(2):397–399.
   PubMedGoogle Scholar
• Darwazeh AMG, Dwari ZNA, Al-Zwari AAW. The relationship between tobacco smoking and oral colonization with candida species. J Contemp Dent Pract. 2010;11(3):17–24.
   Google Scholar
• Becker T, Porat D, Gorsky M. The association between smoking habits and candida in the oral cavity. Int J Dent Oral Health. 2015;1:2.
   Google Scholar
• Eigner U, Holfelder M, Oberdorfer K, et al. Performance of a matrix-assisted laser desorption ionization time-of-flight mass spectrometry system for the identification of bacterial isolates in the clinical routine laboratory. Clin Lab. 2009;55(7/8):289–296.
   Web of Science ®Google Scholar
• Angeletti S. Matrix assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology. J Microbiol. 2017;138:20–29.
   Google Scholar
• Barros NEF, Oliveira EMM, Marin VA. Aplicabilidade da metodologia de reação de polimerase em cadeia em tempo real na determinação do percentual de organismos geneticamente modificados em alimentos. Rev Nutr. 2008;21(1):85–92.
   Google Scholar
• Matsumura N, Aiba S, Tanaka M, et al. Comparison of immune reactivity profiles against various environmental allergens between adult patients with atopic dermatitis and patients with allergic respiratory diseases. Acta Derm Venereol. 1997;77(5):388–391.
   Web of Science ®Google Scholar
• Diez B, Pedrós-Alió C, Marsh TL, et al. Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques. App Environ Microbiol. 2001;67:2942–2951.
   PubMed Web of Science ®Google Scholar
• Krsek M, Wellington EM. Comparison of different methods for the isolation and purification of total community DNA from soil. J Microbiol Methods. 1999;39(1):1–16.
   PubMed Web of Science ®Google Scholar
• Ovreas L. Population and community level approaches for analyzing microbial diversity in natural environments. Ecol Lett. 2000;3:236–251.
   Web of Science ®Google Scholar
• Tsiodras S, Kelesidis T, Kelesidis I, et al. Human infections associated with wild birds. J Infect. 2008;56(2):83–98.
   Web of Science ®Google Scholar