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Lucini C, Obrová K, Krickl I, Nogueira F, Kocmanová I, Herndlhofer S, Gleixner KV, Sperr WR, Frank T, Andrade N, Peters C, Engstler G, Dworzak M, Attarbaschi A, van Grotel M, van den Heuvel-Eibrink MM, Moiseev IS, Rogacheva Y, Zubarovskaya L, Zubarovskaya N, Pichler H, Lawitschka A, Koller E, Keil F, Mayer J, Weinbergerová B, Valent P, Lion T. Prevalence of fungal DNAemia mediated by putatively non-pathogenic fungi in immunocompromised patients with febrile neutropenia: a prospective cohort study. J Hematol Oncol 2024; 17:63. [PMID: 39113112 PMCID: PMC11304904 DOI: 10.1186/s13045-024-01583-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 07/24/2024] [Indexed: 08/11/2024] Open
Abstract
Invasive fungal disease (IFD) presents a life-threatening condition in immunocompromised patients, thus often prompting empirical administration of antifungal treatment, without adequate mycological evidence. Over the past years, wide use of antifungal prophylaxis resulted in decreased occurrence of IFD but has contributed to changes in the spectrum of fungal pathogens, revealing the occurrence of previously rare fungal genera causing breakthrough infections. The expanding spectrum of clinically relevant fungal pathogens required the implementation of screening approaches permitting broad rather than targeted fungus detection to support timely onset of pre-emptive antifungal treatment. To address this diagnostically important aspect in a prospective setting, we analyzed 935 serial peripheral blood (PB) samples from 195 pediatric and adult patients at high risk for IFD, involving individuals displaying febrile neutropenia during treatment of hematological malignancies or following allogeneic hematopoietic stem cell transplantation. Two different panfungal-PCR-screening methods combined with ensuing fungal genus identification by Sanger sequencing were employed. In the great majority of PB-specimens displaying fungal DNAemia, the findings were transient and revealed fungi commonly regarded as non-pathogenic or rarely pathogenic even in the highly immunocompromised patient setting. Hence, to adequately exploit the diagnostic potential of panfungal-PCR approaches for detecting IFD, particularly if caused by hitherto rarely observed fungal pathogens, it is necessary to confirm the findings by repeated testing and to identify the fungal genus present by ensuing analysis. If applied appropriately, panfungal-PCR-screening can help prevent unnecessary empirical therapy, and conversely, contribute to timely employment of effective pre-emptive antifungal treatment strategies.
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Affiliation(s)
- Chantal Lucini
- St. Anna Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, Vienna, A-1090, Austria
| | - Klára Obrová
- St. Anna Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, Vienna, A-1090, Austria
| | - Isabella Krickl
- St. Anna Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, Vienna, A-1090, Austria
| | - Filomena Nogueira
- St. Anna Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, Vienna, A-1090, Austria
| | - Iva Kocmanová
- Department of Clinical Microbiology and Immunology, University Hospital Brno, Brno, Czech Republic
| | - Susanne Herndlhofer
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Karoline V Gleixner
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang R Sperr
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Tijana Frank
- St. Anna Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, Vienna, A-1090, Austria
| | - Nuno Andrade
- St. Anna Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, Vienna, A-1090, Austria
| | - Christina Peters
- St. Anna Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, Vienna, A-1090, Austria
- Department of Pediatrics, St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | - Gernot Engstler
- Department of Pediatrics, St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | - Michael Dworzak
- St. Anna Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, Vienna, A-1090, Austria
- Department of Pediatrics, St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | - Andishe Attarbaschi
- St. Anna Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, Vienna, A-1090, Austria
- Department of Pediatrics, St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | - Martine van Grotel
- Princess Máxima Centre for Paediatric Oncology, Utrecht, the Netherlands
| | - Marry M van den Heuvel-Eibrink
- Princess Máxima Centre for Paediatric Oncology, Utrecht, the Netherlands
- Division of Childhealth, Wilhelmina Childrens Hospital, University of Utrecht, Utrecht, the Netherlands
| | - Ivan S Moiseev
- RM Gorbacheva Children Research Institute, Pavlov University, Saint Petersburg, Russian Federation
| | - Yuliya Rogacheva
- RM Gorbacheva Children Research Institute, Pavlov University, Saint Petersburg, Russian Federation
| | - Ludmilla Zubarovskaya
- RM Gorbacheva Children Research Institute, Pavlov University, Saint Petersburg, Russian Federation
| | - Natalia Zubarovskaya
- Department of Pediatrics, St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | - Herbert Pichler
- Department of Pediatrics, St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | - Anita Lawitschka
- St. Anna Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, Vienna, A-1090, Austria
- Department of Pediatrics, St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | | | - Felix Keil
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
- 3rd Medical Dept, Hanusch Hospital, Vienna, Austria
| | - Jiří Mayer
- Department of Internal Medicine-Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine-Haematology and Oncology, Masaryk University, Brno, Czech Republic
| | - Barbora Weinbergerová
- Department of Internal Medicine-Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine-Haematology and Oncology, Masaryk University, Brno, Czech Republic
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Thomas Lion
- St. Anna Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, Vienna, A-1090, Austria.
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria.
- Department of Paediatrics, Medical University of Vienna, Vienna, Austria.
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Mishra K, Isali I, Sindhani M, Prunty M, Bell S, Mahran A, Damiani G, Ghannoum M, Retuerto M, Kutikov A, Ross J, Woo LL, Abbosh PH, Bukavina L. Characterization of Changes in Penile Microbiome Following Pediatric Circumcision. Eur Urol Focus 2022:S2405-4569(22)00290-5. [PMID: 36566099 DOI: 10.1016/j.euf.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/25/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND While microbiome and host regulation contribute independently to many disease states, it is unclear how circumcision in pediatric population influences subsequent changes in penile microbiome. OBJECTIVE Our study aims to analyze jointly paired taxonomic profiles and assess pathways implicated in inflammation, barrier protection, and energy metabolism. DESIGN, SETTING, AND PARTICIPANTS We analyzed 11 paired samples, periurethral collection, before and after circumcision, to generate microbiome and mycobiome profiling. Sample preparation of 16S ribosomal RNA and internal transcribed spacer sequencing was adapted from the methods developed by the National Institutes of Health Human Microbiome Project. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We obtained the predictive functional attributes of the microbial communities between samples using Silva-Tax4Fun and the Greengenes-Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) approach. The predictive functioning of the microbial communities was determined by linearly combining the normalized taxonomic abundances into the precomputed association matrix of Kyoto Encyclopedia of Genes and Genomes orthology reference profiles. RESULTS AND LIMITATIONS Several notable microbiome and mycobiome compositional differences were observed between pre- and postcircumcision patients. Pairwise comparisons across taxa revealed a significant decrease (p < 0.05, false discovery rate corrected) of microbiome organisms (Clostridiales, Bacteroidales, and Campylobacterales) and mycobiome (Saccharomycetales and Pleosporales) following circumcision. A total of 14 pathways were found to differ in abundance between the pre- and postcircumcision groups (p < 0.005, false discovery rate <0.1 and linear discriminant analysis score >3; five enriched and nine depleted). The pathways reduced after circumcision were mostly involved with amino acid and glucose metabolism, while pathways prior to circumcision were enriched in genetic information processing and transcription processes. As expected, enrichment in methyl-accepting chemotaxis protein, an integral membrane protein involved in directed motility of microbes to chemical cues and environment, occurred prior to circumcision, while the filamentous hemagglutinin pathway (a strong immunogenic protein) was depleted after circumcision CONCLUSIONS: Our results offer greater insight into the host-microbiota relationship of penile circumcision and may serve to lay the groundwork for future studies focused on drivers of inflammation, infection, and oncogenesis. PATIENT SUMMARY Our study showed a significant reduction in bacteria and fungi after circumcision, particularly anaerobic bacteria, which are known to be potential inducers of inflammation and cancer. This is the first study of its kind showing the changes in microbiome after circumcision, and some of the changes that occur in healthy infants after circumcision that may explain the differences in cancer and inflammatory disorders in adulthood.
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Affiliation(s)
- Kirtishri Mishra
- Department of Urology, New York University, Langone Medical Center, New York, NY, USA; Department of Urology, University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
| | - Ilaha Isali
- Department of Urology, University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
| | | | - Megan Prunty
- Department of Urology, University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
| | | | - Amr Mahran
- Department of Urology, University of Tennessee, Knoxville, TN, USA; Department of Urology, Assiut University, Assiut, Egypt
| | - Giovanni Damiani
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA; Department of Biomedical, Surgical, and Dental Sciences, University of Milan, Milan, Italy
| | - Mahmoud Ghannoum
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA; Case Western Reserve School of Medicine, Center for Medical Mycology, Cleveland, OH, USA
| | - Mauricio Retuerto
- Case Western Reserve School of Medicine, Center for Medical Mycology, Cleveland, OH, USA
| | | | - Jonathan Ross
- Department of Urology, Rush University, Chicago, IL, USA
| | - Lynn L Woo
- Einstein Medical Center, Department of Urology, Philadelphia, PA, USA
| | - Philip H Abbosh
- Fox Chase Cancer Center, Philadelphia, PA, USA; Department of Urology, Rainbow Babies and Children's Hospital, Cleveland, OH, USA
| | - Laura Bukavina
- Department of Urology, University Hospitals, Cleveland Medical Center, Cleveland, OH, USA; Fox Chase Cancer Center, Philadelphia, PA, USA.
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Li H, Sun J, Wang X, Shi J. Oral microbial diversity analysis among atrophic glossitis patients and healthy individuals. J Oral Microbiol 2021; 13:1984063. [PMID: 34676060 PMCID: PMC8526005 DOI: 10.1080/20002297.2021.1984063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Atrophic glossitis is a common disease in oral mucosal diseases. The Current studies have found the human oral cavity contains numerous and diverse microorganisms, their composition and diversity can be changed by various oral diseases. To understand the composition and diversity of oral microbiome in atrophic glossitis is better to explore the cause and mechanism of atrophic glossitis. The salivary microbiome is comprised of indigenous oral microorganisms that are specific to each person, exhibits long-term stability. We used llumina MiSeq high-throughput sequencing based on the V3-V4 region of the bacterial 16S rRNA gene and the internal transcribed spacer (ITS) region of fungal rRNA genes from saliva in atrophic glossitis patients and healthy individuals to explore the composition and diversity of oral microbiome. In our reports, it showed a lower diversity of bacteria and fungi in atrophic glossitis patients than in healthy individuals. The data further suggests that Lactobacillus and Saccharomycetales were potential indicators for the initiation and development of atrophic glossitis. Moreover, we also discuss the relationship between the oral microbial ecology and atrophic glossitis.
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Affiliation(s)
- Hong Li
- Department of Oral Medicine, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University, Taiyuan Shanxi Province, China
| | - Jing Sun
- Department of Oral Medicine, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University, Taiyuan Shanxi Province, China
| | - Xiaoyan Wang
- Department of Oral Medicine, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University, Taiyuan Shanxi Province, China
| | - Jing Shi
- Department of Oral Medicine, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University, Taiyuan Shanxi Province, China
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Mycobiome in the Gut: A Multiperspective Review. Mediators Inflamm 2020; 2020:9560684. [PMID: 32322167 PMCID: PMC7160717 DOI: 10.1155/2020/9560684] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/23/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022] Open
Abstract
Human gut is home to a diverse and complex microbial ecosystem encompassing bacteria, viruses, parasites, fungi, and other microorganisms that have an undisputable role in maintaining good health for the host. Studies on the interplay between microbiota in the gut and various human diseases remain the key focus among many researchers. Nevertheless, advances in sequencing technologies and computational biology have helped us to identify a diversity of fungal community that reside in the gut known as the mycobiome. Although studies on gut mycobiome are still in its infancy, numerous sources have reported its potential role in host homeostasis and disease development. Nonetheless, the actual mechanism of its involvement remains largely unknown and underexplored. Thus, in this review, we attempt to discuss the recent advances in gut mycobiome research from multiple perspectives. This includes understanding the composition of fungal communities in the gut and the involvement of gut mycobiome in host immunity and gut-brain axis. Further, we also discuss on multibiome interactions in the gut with emphasis on fungi-bacteria interaction and the influence of diet in shaping gut mycobiome composition. This review also highlights the relation between fungal metabolites and gut mycobiota in human homeostasis and the role of gut mycobiome in various human diseases. This multiperspective review on gut mycobiome could perhaps shed new light for future studies in the mycobiome research area.
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Haridy M, Abdo W, Hashem M, Yanai T. Candida parapsilosis and Candida tropicalis infections in an Okhotsk snailfish (Liparis ochotensis). J Vet Med Sci 2018; 80:1676-1680. [PMID: 30185722 PMCID: PMC6261807 DOI: 10.1292/jvms.18-0133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
An Okhotsk snailfish (Liparis ochotensis) kept at Nagoya aquarium exhibited sudden death. Microscopically, the fish showed multiple granulomatous foci in the gills, liver
and kidney. Multiple yeast-like organisms as well as pseudohyphal elements were observed within granulomatous lesions. Immunohistochemically, the hyphae were negative for both
Asperigullus and Mucor spp., and a weak positive for Candida sp. The seminated-PCR product was consistent with Candida
parapsilosis and C. tropicalis. This is the first record of disseminated mycotic granulomatous lesion due to C. parapsilosis and C.
tropicalis infection in fish.
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Affiliation(s)
- Mohie Haridy
- Department of Pathology & Clinical Pathology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Walied Abdo
- Department of Pathology, Faculty of Veterinary Medicine, Kafr-Elsheikh University, Kafr-Elsheikh 33516, Egypt
| | - Mahmoud Hashem
- Department of Fish Diseases and Mangment, Faculty of Veterinary Medicine, New Valley Branch, Assuit University, El-Kharja 72511, Egypt
| | - Tokuma Yanai
- Department of Pathogenetic Veterinary Science, United Graduated School of Veterinary Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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6
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Robledo-Leal E, Rivera-Morales LG, Sangorrín MP, González GM, Ramos-Alfano G, Adame-Rodriguez JM, Alcocer-Gonzalez JM, Arechiga-Carvajal ET, Rodriguez-Padilla C. Identification and susceptibility of clinical isolates of Candida spp. to killer toxins. BRAZ J BIOL 2018; 78:742-749. [PMID: 29412252 DOI: 10.1590/1519-6984.175635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/11/2017] [Indexed: 01/07/2023] Open
Abstract
Although invasive infections and mortality caused by Candida species are increasing among compromised patients, resistance to common antifungal agents is also an increasing problem. We analyzed 60 yeasts isolated from patients with invasive candidiasis using a PCR/RFLP strategy based on the internal transcribed spacer (ITS2) region to identify different Candida pathogenic species. PCR analysis was performed from genomic DNA with a primer pair of the ITS2-5.8S rDNA region. PCR-positive samples were characterized by RFLP. Restriction resulted in 23 isolates identified as C. albicans using AlwI, 24 isolates as C. parapsilosis using RsaI, and 13 as C. tropicalis using XmaI. Then, a group of all isolates were evaluated for their susceptibility to a panel of previously described killer yeasts, resulting in 75% being susceptible to at least one killer yeast while the remaining were not inhibited by any strain. C. albicans was the most susceptible group while C. tropicalis had the fewest inhibitions. No species-specific pattern of inhibition was obtained with this panel of killer yeasts. Metschnikowia pulcherrima, Pichia kluyveri and Wickerhamomyces anomalus were the strains that inhibited the most isolates of Candida spp.
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Affiliation(s)
- E Robledo-Leal
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León - UANL, Av. Universidad, s/n, Ciudad Universitaria, CP 66455, San Nicolás de los Garza, Nuevo León, México
| | - L G Rivera-Morales
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León - UANL, Av. Universidad, s/n, Ciudad Universitaria, CP 66455, San Nicolás de los Garza, Nuevo León, México
| | - M P Sangorrín
- Grupo de Biodiversidad y Biotecnología de Levaduras, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Facultad de Ingeniería, Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas - PROBIEN, Universidad Nacional del Comahue, Buenos Aires, 1400, CP 8300, Neuquén, Argentina
| | - G M González
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León - UANL, Av. Francisco I. Madero Pte, s/n y Av. Gonzalitos, Monterrey, CP 64460, Nuevo León, México
| | - G Ramos-Alfano
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León - UANL, Av. Universidad, s/n, Ciudad Universitaria, CP 66455, San Nicolás de los Garza, Nuevo León, México
| | - J M Adame-Rodriguez
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León - UANL, Av. Universidad, s/n, Ciudad Universitaria, CP 66455, San Nicolás de los Garza, Nuevo León, México
| | - J M Alcocer-Gonzalez
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León - UANL, Av. Universidad, s/n, Ciudad Universitaria, CP 66455, San Nicolás de los Garza, Nuevo León, México
| | - E T Arechiga-Carvajal
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León - UANL, Av. Universidad, s/n, Ciudad Universitaria, CP 66455, San Nicolás de los Garza, Nuevo León, México
| | - C Rodriguez-Padilla
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León - UANL, Av. Universidad, s/n, Ciudad Universitaria, CP 66455, San Nicolás de los Garza, Nuevo León, México
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Huseyin CE, O'Toole PW, Cotter PD, Scanlan PD. Forgotten fungi-the gut mycobiome in human health and disease. FEMS Microbiol Rev 2017; 41:479-511. [PMID: 28430946 DOI: 10.1093/femsre/fuw047] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/04/2017] [Indexed: 12/11/2022] Open
Abstract
The human body is home to a complex and diverse microbial ecosystem that plays a central role in host health. This includes a diversity of fungal species that is collectively referred to as our 'mycobiome'. Although research into the mycobiome is still in its infancy, its potential role in human disease is increasingly recognised. Here we review the existing literature available on the human mycobiota with an emphasis on the gut mycobiome, including how fungi interact with the human host and other microbes. In doing so, we provide a comprehensive critique of the methodologies available to research the human mycobiota as well as highlighting the latest research findings from mycological surveys of different groups of interest including infants, obese and inflammatory bowel disease cohorts. This in turn provides new insights and directions for future studies in this burgeoning research area.
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Affiliation(s)
- Chloe E Huseyin
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland.,APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland.,School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Paul W O'Toole
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland.,School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland.,APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland
| | - Pauline D Scanlan
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland
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Real-Time Polymerase Chain Reaction (PCR) Based Identification and Detection of Fungi Belongs to Genus Fusarium. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Evaluation of Fluorescent Capillary Electrophoresis for Rapid Identification of Candida Fungal Infections. J Clin Microbiol 2016; 54:1295-303. [PMID: 26935732 DOI: 10.1128/jcm.00118-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022] Open
Abstract
Early diagnosis of fungal infection is critical for initiating antifungal therapy and reducing the high mortality rate in immunocompromised patients. In this study, we focused on rapid and sensitive identification of clinically important Candida species, utilizing the variability in the length of the ITS2 rRNA gene and fluorescent capillary electrophoresis (f-ITS2-PCR-CE). The method was developed and optimized on 29 various Candida reference strains from which 26 Candida species were clearly identified, while Candida guilliermondii, C. fermentati, and C. carpophila, which are closely related, could not be distinguished. The method was subsequently validated on 143 blinded monofungal clinical isolates (comprising 26 species) and was able to identify 88% of species unambiguously. This indicated a higher resolution power than the classical phenotypic approach which correctly identified 73%. Finally, the culture-independent potential of this technique was addressed by the analysis of 55 retrospective DNA samples extracted directly from clinical material. The method showed 100% sensitivity and specificity compared to those of the combined results of cultivation and panfungal PCR followed by sequencing used as a gold standard. In conclusion, this newly developed f-ITS2-PCR-CE analytical approach was shown to be a fast, sensitive, and highly reproducible tool for both culture-dependent and culture-independent identification of clinically important Candida strains, including species of the "psilosis" complex.
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10
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van Diepeningen AD, Brankovics B, Iltes J, van der Lee TAJ, Waalwijk C. Diagnosis of Fusarium Infections: Approaches to Identification by the Clinical Mycology Laboratory. CURRENT FUNGAL INFECTION REPORTS 2015; 9:135-143. [PMID: 26301000 PMCID: PMC4537702 DOI: 10.1007/s12281-015-0225-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Infections caused by the genus Fusarium have emerged over the past decades and range from onychomycosis and keratitis in healthy individuals to deep and disseminated infections with high mortality rates in immune-compromised patients. As antifungal susceptibility can differ between the different Fusarium species, identification at species level is recommended. Several clinical observations as hyaline hyphae in tissue, necrotic lesions in the skin and positive blood tests with fungal growth or presence of fungal cell wall components may be the first hints for fusariosis. Many laboratories rely on morphological identification, but especially multi-locus sequencing proves better to discriminate among members of the species complexes involved in human infection. DNA-based diagnostic tools have best discriminatory power when based on translation elongation factor 1-α or the RNA polymerase II second largest subunit. However, assays based on the detection of other fusarial cell compounds such as peptides and cell wall components may also be used for identification. The purpose of this review is to provide an overview and a comparison of the different tools currently available for the diagnosis of fusariosis.
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Affiliation(s)
| | - Balázs Brankovics
- />CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Jearidienne Iltes
- />CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Theo A. J. van der Lee
- />Plant Research International Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Cees Waalwijk
- />Plant Research International Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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11
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Tortorano AM, Richardson M, Roilides E, van Diepeningen A, Caira M, Munoz P, Johnson E, Meletiadis J, Pana ZD, Lackner M, Verweij P, Freiberger T, Cornely OA, Arikan-Akdagli S, Dannaoui E, Groll AH, Lagrou K, Chakrabarti A, Lanternier F, Pagano L, Skiada A, Akova M, Arendrup MC, Boekhout T, Chowdhary A, Cuenca-Estrella M, Guinea J, Guarro J, de Hoog S, Hope W, Kathuria S, Lortholary O, Meis JF, Ullmann AJ, Petrikkos G, Lass-Flörl C. ESCMID and ECMM joint guidelines on diagnosis and management of hyalohyphomycosis: Fusarium spp., Scedosporium spp. and others. Clin Microbiol Infect 2014; 20 Suppl 3:27-46. [PMID: 24548001 DOI: 10.1111/1469-0691.12465] [Citation(s) in RCA: 324] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 11/18/2013] [Accepted: 11/18/2013] [Indexed: 01/03/2023]
Abstract
Mycoses summarized in the hyalohyphomycosis group are heterogeneous, defined by the presence of hyaline (non-dematiaceous) hyphae. The number of organisms implicated in hyalohyphomycosis is increasing and the most clinically important species belong to the genera Fusarium, Scedosporium, Acremonium, Scopulariopsis, Purpureocillium and Paecilomyces. Severely immunocompromised patients are particularly vulnerable to infection, and clinical manifestations range from colonization to chronic localized lesions to acute invasive and/or disseminated diseases. Diagnosis usually requires isolation and identification of the infecting pathogen. A poor prognosis is associated with fusariosis and early therapy of localized disease is important to prevent progression to a more aggressive or disseminated infection. Therapy should include voriconazole and surgical debridement where possible or posaconazole as salvage treatment. Voriconazole represents the first-line treatment of infections due to members of the genus Scedosporium. For Acremonium spp., Scopulariopsis spp., Purpureocillium spp. and Paecilomyces spp. the optimal antifungal treatment has not been established. Management usually consists of surgery and antifungal treatment, depending on the clinical presentation.
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Affiliation(s)
- A M Tortorano
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milano, Italy
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Mukherjee PK, Chandra J, Retuerto M, Sikaroodi M, Brown RE, Jurevic R, Salata RA, Lederman MM, Gillevet PM, Ghannoum MA. Oral mycobiome analysis of HIV-infected patients: identification of Pichia as an antagonist of opportunistic fungi. PLoS Pathog 2014; 10:e1003996. [PMID: 24626467 PMCID: PMC3953492 DOI: 10.1371/journal.ppat.1003996] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 01/21/2014] [Indexed: 11/19/2022] Open
Abstract
Oral microbiota contribute to health and disease, and their disruption may influence the course of oral diseases. Here, we used pyrosequencing to characterize the oral bacteriome and mycobiome of 12 HIV-infected patients and matched 12 uninfected controls. The number of bacterial and fungal genera in individuals ranged between 8-14 and 1-9, among uninfected and HIV-infected participants, respectively. The core oral bacteriome (COB) comprised 14 genera, of which 13 were common between the two groups. In contrast, the core oral mycobiome (COM) differed between HIV-infected and uninfected individuals, with Candida being the predominant fungus in both groups. Among Candida species, C. albicans was the most common (58% in uninfected and 83% in HIV-infected participants). Furthermore, 15 and 12 bacteria-fungi pairs were correlated significantly within uninfected and HIV-infected groups, respectively. Increase in Candida colonization was associated with a concomitant decrease in the abundance of Pichia, suggesting antagonism. We found that Pichia spent medium (PSM) inhibited growth of Candida, Aspergillus and Fusarium. Moreover, Pichia cells and PSM inhibited Candida biofilms (P = .002 and .02, respectively, compared to untreated controls). The mechanism by which Pichia inhibited Candida involved nutrient limitation, and modulation of growth and virulence factors. Finally, in an experimental murine model of oral candidiasis, we demonstrated that mice treated with PSM exhibited significantly lower infection score (P = .011) and fungal burden (P = .04) compared to untreated mice. Moreover, tongues of PSM-treated mice had few hyphae and intact epithelium, while vehicle- and nystatin-treated mice exhibited extensive fungal invasion of tissue with epithelial disruption. These results showed that PSM was efficacious against oral candidiasis in vitro and in vivo. The inhibitory activity of PSM was associated with secretory protein/s. Our findings provide the first evidence of interaction among members of the oral mycobiota, and identifies a potential novel antifungal.
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Affiliation(s)
- Pranab K. Mukherjee
- OHARA/ACTG Mycology Unit at Case Western Reserve University, Department of Dermatology, Cleveland, Ohio, United States of America
- Center for Medical Microbiology, Department of Dermatology, School of Medicine, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, Ohio, United States of America
| | - Jyotsna Chandra
- OHARA/ACTG Mycology Unit at Case Western Reserve University, Department of Dermatology, Cleveland, Ohio, United States of America
| | - Mauricio Retuerto
- OHARA/ACTG Mycology Unit at Case Western Reserve University, Department of Dermatology, Cleveland, Ohio, United States of America
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, United States of America
| | - Robert E. Brown
- Microbiome Analysis Center, Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, United States of America
| | - Richard Jurevic
- Microbiome Analysis Center, Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, United States of America
| | - Robert A. Salata
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Michael M. Lederman
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, University Hospitals Case Medical Center, Cleveland, Ohio, United States of America
| | - Patrick M. Gillevet
- Microbiome Analysis Center, Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, United States of America
| | - Mahmoud A. Ghannoum
- OHARA/ACTG Mycology Unit at Case Western Reserve University, Department of Dermatology, Cleveland, Ohio, United States of America
- Center for Medical Microbiology, Department of Dermatology, School of Medicine, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, Ohio, United States of America
- * E-mail:
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Preuner S, Lion T. Towards molecular diagnostics of invasive fungal infections. Expert Rev Mol Diagn 2014; 9:397-9. [DOI: 10.1586/erm.09.27] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Buchta V, Feuermannová A, Váša M, Bašková L, Kutová R, Kubátová A, Vejsová M. Outbreak of fungal endophthalmitis due to Fusarium oxysporum following cataract surgery. Mycopathologia 2014; 177:115-21. [PMID: 24381050 DOI: 10.1007/s11046-013-9721-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 12/08/2013] [Indexed: 11/29/2022]
Abstract
Outbreak of exogenous Fusarium endophthalmitis after cataract surgery was evaluated. Twenty patients developed postoperative endophthalmitis. In 19 eyes, pars plana vitrectomy (PPV) was performed, in 14 cases (74 %) with primary intraocular lens explantation. In one case, the PPV was not performed because of poor general condition of the patient. Symptoms of endophthalmitis (damaged vision, iritis, tyndallization in anterior chamber, hypopyon) occurred at intervals of 16-79 days (mean 31.3 days). Fungal etiology was documented in 12 eyes (60 %). Fusarium oxysporum was evidenced by culture and/or microscopy and confirmed by PCR and sequencing analysis. Eighteen (90 %) patients were treated with oral voriconazole (400 mg/day) for a period of 4-6 weeks. The final visual acuity was 6/15 in 1 case (5 %), 6/60 and worse in 17 eyes (85 %), and in 2 cases (10 %), enucleation had to be performed. Viscoelastic filling material was suggested the most likely source of infection. Endophthalmitis caused by Fusarium spp. are a potentially big threat for patients with serious impact on vision. Successful management of the infection is highly dependent on early diagnosis including species identification and antifungal susceptibility testing, and on aggressive and long-term treatment.
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Affiliation(s)
- Vladimír Buchta
- Department of Clinical Microbiology, University Hospital and Charles University Medical Faculty, Sokolska 581, 500 05, Hradec Kralove, Czech Republic,
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Xafranski H, Melo ASA, Machado AM, Briones MRS, Colombo AL. A quick and low-cost PCR-based assay for Candida spp. identification in positive blood culture bottles. BMC Infect Dis 2013; 13:467. [PMID: 24099320 PMCID: PMC3851980 DOI: 10.1186/1471-2334-13-467] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 09/26/2013] [Indexed: 12/26/2022] Open
Abstract
Background Differences in the susceptibility of Candida species to antifungal drugs make identification to the species level important for clinical management of candidemia. Molecular tests are not yet standardized or available in most clinical laboratories, although such tests can reduce the time required for species identification, as compared to the conventional culture-based methods. To decrease laboratory costs and improve diagnostic accuracy, different molecular methods have been proposed, including DNA extraction protocols to produce pure DNA free of PCR inhibitors. The objective of this study was to validate a new format of molecular method, based on the internal transcribed spacer (ITS) of the rDNA gene amplification followed by sequencing, to identify common and cryptic Candida species causing candidemia by analyzing DNA in blood culture bottles positive for yeasts. Methods For DNA extraction, an “in-house” protocol based on organic solvent extraction was tested. Additional steps of liquid nitrogen incubation followed by mechanical disruption ensured complete cell lysis, and highly pure DNA. One hundred sixty blood culture bottles positive for yeasts were processed. PCR assays amplified the ITS region. The DNA fragments of 152 samples were sequenced and these sequences were identified using the GenBank database (NCBI). Molecular yeast identification was compared to results attained by conventional method. Results The organic solvent extraction protocol showed high reproducibility in regards to DNA quantity, as well as high PCR sensitivity (10 pg of C. albicans DNA and 95% amplification on PCR). The identification of species at the molecular level showed 97% concordance with the conventional culturing method. The molecular method tested in the present study also allowed identification of species not commonly implicated in human infections. Conclusions This study demonstrated that our molecular method presents significant advantages over the conventional yeast culture identification method by providing accurate results within 24 hours, in contrast to at least 72 hours required by the automated conventional culture method. Additionally, our molecular method allowed the identification of mixed infections, as well as infections due to emergent fungal pathogens. This economical DNA extraction method developed in our laboratory provided high-quality DNA and 60% cost savings compared to commercial methods.
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Affiliation(s)
- Hemílio Xafranski
- Laboratório Especial de Micologia, Departamento de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo 669 5 andar, São Paulo, SP, Brazil.
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Preuner S, Lion T. Species-specific identification of a wide range of clinically relevant fungal pathogens by the Luminex(®) xMAP technology. Methods Mol Biol 2013; 968:119-39. [PMID: 23296890 DOI: 10.1007/978-1-62703-257-5_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Invasive fungal infections (IFI) are a common cause of life-threatening events in immunocompromised patients. Early detection and identification of the fungal pathogen is an important prerequisite for timely onset of the most appropriate treatment. Methods based on fungal culture are often too slow to be clinically useful. Other approaches to the identification of fungal species, including molecular techniques, are often restricted to a small number of the most commonly occurring pathogens and are therefore of limited use in the clinical setting. The development of assays for the detection and identification of a broad-range of clinically relevant fungal species is therefore an urgently needed step towards optimized diagnostics of IFI.The Luminex(®) xMAP technology offers a platform for the establishment of multiplex assays permitting high-throughput analysis of up to 100 different target molecules in a single test. Here we describe a Luminex(®)-based multiplex assay permitting rapid detection and identification of 10 fungal genera and 29 different species, including both commonly occurring and emerging fungal pathogens.
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Affiliation(s)
- S Preuner
- Children's Cancer Research Institute (CCRI), Labdia Labordiagnostik, Vienna, Austria
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White JR, Maddox C, White O, Angiuoli SV, Fricke WF. CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota. MICROBIOME 2013; 1:6. [PMID: 24451270 PMCID: PMC3869194 DOI: 10.1186/2049-2618-1-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 11/21/2012] [Indexed: 05/16/2023]
Abstract
BACKGROUND Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as those representing eukaryotic organisms. RESULTS Here we introduce CloVR-ITS, an automated pipeline for comparative analysis of internal transcribed spacer (ITS) pyrosequences amplified from metagenomic DNA isolates and representing fungal species. This pipeline performs a variety of steps similar to those commonly used for 16S rRNA amplicon sequence analysis, including preprocessing for quality, chimera detection, clustering of sequences into operational taxonomic units (OTUs), taxonomic assignment (at class, order, family, genus, and species levels) and statistical analysis of sample groups of interest based on user-provided information. Using ITS amplicon pyrosequencing data from a previous human gastric fluid study, we demonstrate the utility of CloVR-ITS for fungal microbiota analysis and provide runtime and cost examples, including analysis of extremely large datasets on the cloud. We show that the largest fractions of reads from the stomach fluid samples were assigned to Dothideomycetes, Saccharomycetes, Agaricomycetes and Sordariomycetes but that all samples were dominated by sequences that could not be taxonomically classified. Representatives of the Candida genus were identified in all samples, most notably C. quercitrusa, while sequence reads assigned to the Aspergillus genus were only identified in a subset of samples. CloVR-ITS is made available as a pre-installed, automated, and portable software pipeline for cloud-friendly execution as part of the CloVR virtual machine package (http://clovr.org). CONCLUSION The CloVR-ITS pipeline provides fungal microbiota analysis that can be complementary to bacterial 16S rRNA and total metagenome sequence analysis allowing for more comprehensive studies of environmental and host-associated microbial communities.
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Affiliation(s)
- James Robert White
- Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II - 801 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Cynthia Maddox
- Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II - 801 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II - 801 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Samuel V Angiuoli
- Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II - 801 West Baltimore Street, Baltimore, MD, 21201, USA
| | - W Florian Fricke
- Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II - 801 West Baltimore Street, Baltimore, MD, 21201, USA
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Laboratory diagnostics of invasive fungal infections: an overview with emphasis on molecular approach. Folia Microbiol (Praha) 2012; 57:421-30. [PMID: 22566119 DOI: 10.1007/s12223-012-0152-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
Abstract
Although invasive fungal diseases (IFDs) are relatively rare, they have become an increasingly common life-threatening complication in a variety of critically ill patients. Due to changes in treatment strategies, patterns of IFDs have changed substantially as well. Yeast infections have shifted toward a higher proportion of non-albicans Candida species, but their overall incidence has remained stable. In contrast, IFDs caused by molds, including particularly various species of Aspergillus, Fusarium, and Mucorales, have increased in number. In view of the growing incidence and the high mortality rates of IFDs, accurate diagnostic techniques permitting timely onset of adequate antifungal treatment are of paramount importance. Although conventional approaches such as microscopy, cultivation, histopathological examination, and imaging methods still represent the gold standard, the diagnosis remains difficult because of limited sensitivity and specificity. Noninvasive and culture-independent diagnostic techniques, including fungal antigen detection, and different molecular-based techniques are becoming increasingly important. Of the fungal surrogate markers such as cell wall components, galactomannan and (1,3)-β-D-glucan by commercially available diagnostic kits have become widely used, but the results are still controversial. A plethora of PCR-based diagnostic methods targeting different gene regions and exploiting a variety of amplicon detection tools have been published. Molecular assays have the capacity to overcome the limitations of other diagnostic approaches, but the current lack of methodological standardization and validation, together with not always clear interpretation of the results, has prevented broad application in the clinical setting.
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Kraková L, Chovanová K, Puškarová A, Bučková M, Pangallo D. A novel PCR-based approach for the detection and classification of potential cellulolytic fungal strains isolated from museum items and surrounding indoor environment. Lett Appl Microbiol 2012; 54:433-40. [DOI: 10.1111/j.1472-765x.2012.03227.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
The incidence of invasive fungal infections (IFI) has increased substantially and the epidemiology has changed dramatically in recent years. Candida albicans is still most important, but non-albicans species, Aspergillus species, Glomeromycota (formerly Zygomycetes) and Fusarium species are an increasing cause of IFIs. Due to this growing diversity, the identification of the causative organism to genus and species level is important to perform best and adequate treatment. The early, sensitive and specific detection of IFIs remains challenging and current conventional methods are limited. The golden standard for the definite diagnosis of proven pulmonary infection remains either histopathologic, cytopathologic or direct tissue examination. Invasive procedures are necessary to obtain reliable specimens and biopsies may be taken percutaneously, bronchoscopically, via open surgery or via video-assisted thorascopic surgery. Molecular methods, like PCR or in situ hybridization, are a promising diagnostic tool for rapid and reliable species identification and should be performed in addition to microscopic examination and culture to increase the sensitivity for the diagnosis of IFI. Combining culture, microscopy, serology, and PCR in lung tissues and/or bronchial samples will increase the diagnostic yield by 99%. Here, we give an overview of biopsy procedures for molecular tissue diagnosis of IFI.
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Muhammed M, Coleman JJ, Carneiro HA, Mylonakis E. The challenge of managing fusariosis. Virulence 2011; 2:91-6. [PMID: 21304267 DOI: 10.4161/viru.2.2.15015] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Fusarium is the second most frequent mold involved in fungal infections and is particularly important among immunocompromised patients. Culture methods and microscopy are still routinely used in clinical laboratories to identify Fusarium spp, and more sophisticated, timely, and effective methods for detecting Fusarium spp. in laboratory samples could improve the outcome of the patient. These investigational diagnostic approaches include serological assays and specific nested PCR assays that can yield positive and negative predictive values of over 90%. Other assays in development, such as mass spectroscopy techniques, can provide accurate and consistent results. The treatment of fusariosis in immunocompromised patients remains a challenge and the prognosis of systemic fusariosis in this population remains poor. Successful treatment is highly dependent on the particular Fusarium species involved in the infection. High dose intravenous amphotericin B formulation is recommended as the first line of therapy in management of fusariosis in patients. Voriconazole is also effective in treating fusariosis. Intolerance, contraindication, or failure of the amphotericin B formulation warrants the use of voriconazole as an alternative agent, and posaconazole is licensed as salvage therapy against invasive fusariosis. Adjunctive therapies such as surgical debridement of infected tissue, granulocyte colony stimulating factor (G-CSF) or granulocyte-macrophage colony stimulating factor (GM-CSF) infusions, or granulocyte transfusions are also tools for managing fusariosis. In conclusion, Fusarium infection is considered an emerging problem and should be suspected in immunocompromised patients experiencing systemic infection and should be treated accordingly.
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Affiliation(s)
- Maged Muhammed
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
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Lin MT, Tseng LH, Rich RG, Hafez MJ, Harada S, Murphy KM, Eshleman JR, Gocke CD. Δ-PCR, A Simple Method to Detect Translocations and Insertion/Deletion Mutations. J Mol Diagn 2010; 13:85-92. [PMID: 21227398 DOI: 10.1016/j.jmoldx.2010.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Revised: 08/16/2010] [Accepted: 08/18/2010] [Indexed: 12/21/2022] Open
Abstract
PCR detection of chromosomal translocations and small insertion/deletion mutations is challenging when potential amplicon size varies greatly. Molecular diagnostic laboratories face such difficulties with the BCL2-IGH translocation in follicular lymphoma and with internal tandem duplication mutation of the FLT3 gene in leukemia, where breakpoints are widely distributed, mutations may be multiple, signal strength is low, and background noise is elevated. We developed a strategy, called Δ-PCR, that ensures PCR specificity and identifies individual breakpoints. Δ-PCR uses two forward primers (external and internal) and a reverse primer simultaneously. The internal primer functions as a probe with a defined distance Δ from the external primer. For follicular lymphoma, we prepared upstream, BCL2-specific primers for potential breakpoints to pair with a common, downstream VLJH primer. Multiplexed PCR amplicons are sized by capillary electrophoresis. Each of the upstream pairs has a defined interval separating them that uniquely identifies the breakpoint. The presence of two amplicons with a defined size difference confirms validity of the rearrangement and identity of the specific breakpoint, even if signal strength is low. By testing 40 follicular lymphoma and 12 control specimens from formalin-fixed, paraffin-embedded (FFPE) blocks, we showed that multiplex Δ-PCR is a simple, sensitive strategy to identify translocations with multiple breakpoints or partners. The strategy was also applied to detect minor leukemic clones with internal tandem duplication mutations and could have broader applications for other insertion/deletion and duplication mutations.
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Affiliation(s)
- Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, Gillevet PM. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog 2010; 6:e1000713. [PMID: 20072605 PMCID: PMC2795202 DOI: 10.1371/journal.ppat.1000713] [Citation(s) in RCA: 693] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 12/02/2009] [Indexed: 12/28/2022] Open
Abstract
The oral microbiome–organisms residing in the oral cavity and their collective genome–are critical components of health and disease. The fungal component of the oral microbiota has not been characterized. In this study, we used a novel multitag pyrosequencing approach to characterize fungi present in the oral cavity of 20 healthy individuals, using the pan-fungal internal transcribed spacer (ITS) primers. Our results revealed the “basal” oral mycobiome profile of the enrolled individuals, and showed that across all the samples studied, the oral cavity contained 74 culturable and 11 non-culturable fungal genera. Among these genera, 39 were present in only one person, 16 genera were present in two participants, and 5 genera were present in three people, while 15 genera (including non-culturable organisms) were present in ≥4 (20%) participants. Candida species were the most frequent (isolated from 75% of participants), followed by Cladosporium (65%), Aureobasidium, Saccharomycetales (50% for both), Aspergillus (35%), Fusarium (30%), and Cryptococcus (20%). Four of these predominant genera are known to be pathogenic in humans. The low-abundance genera may represent environmental fungi present in the oral cavity and could simply be spores inhaled from the air or material ingested with food. Among the culturable genera, 61 were represented by one species each, while 13 genera comprised between 2 and 6 different species; the total number of species identified were 101. The number of species in the oral cavity of each individual ranged between 9 and 23. Principal component (PCO) analysis of the obtained data set followed by sample clustering and UniFrac analysis revealed that White males and Asian males clustered differently from each other, whereas both Asian and White females clustered together. This is the first study that identified the “basal mycobiome” of healthy individuals, and provides the basis for a detailed characterization of the oral mycobiome in health and disease. We characterized the fungal microbiome (mycobiome) of the oral cavity in healthy individuals. Our results demonstrate that the fungal component of the oral microbiome is diverse as revealed by the presence of 74 culturable and 11 non-culturable fungal genera in the oral cavity. A total of 101 species were identified, with between 9 and 23 culturable species present in each person. Fifteen genera (which included four known pathogenic fungi and non-culturable organisms) were present in ≥20% of the tested samples; Candida species were the most frequently obtained genera, isolated from 75% of all study participants, followed by Cladosporium (65%), Aureobasidium, Saccharomycetales (50% for both), Aspergillus (35%), Fusarium (30%), and Cryptococcus (20%). The remaining fungi detected in the oral wash samples represent organisms likely originating from the environment. This is the first study that identified the “basal mycobiome” of healthy individuals, and provides the basis for a detailed characterization of the oral mycobiome in health and disease.
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Affiliation(s)
- Mahmoud A Ghannoum
- Center for Medical Microbiology, Department of Dermatology, School of Medicine, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, Ohio, USA.
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