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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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Schwartz IS, Wiederhold NP, Hanson KE, Patterson TF, Sigler L. Blastomyces helicus, a New Dimorphic Fungus Causing Fatal Pulmonary and Systemic Disease in Humans and Animals in Western Canada and the United States. Clin Infect Dis 2020; 68:188-195. [PMID: 29878145 PMCID: PMC6321858 DOI: 10.1093/cid/ciy483] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 06/04/2018] [Indexed: 11/29/2022] Open
Abstract
Background Blastomyces helicus (formerly Emmonsia helica) is a dimorphic fungus first isolated from a man with fungal encephalitis in Alberta, Canada. The geographic range, epidemiology, and clinical features of disease are unknown. Methods We reviewed human and veterinary isolates of B. helicus identified among Blastomyces and Emmonsia isolates at the University of Alberta Microfungus Collection and Herbarium, University of Texas Health San Antonio’s Fungus Testing Laboratory, and Associated Regional and University Pathologists Laboratories. Isolates were selected based on low Blastomyces dermatitidis DNA probe values and/or atypical morphology. Species identification was confirmed for most isolates by DNA sequence analysis of the internal transcribed spacer with or without D1/D2 ribosomal RNA regions. Epidemiological and clinical data were analyzed. Results We identified isolates from 10 human and 5 veterinary cases of B. helicus infection; all were referred from western regions of Canada and the United States. Isolates remained sterile in culture, producing neither conidia nor sexual spores in the mycelial phase, but often producing coiled hyphae. Isolates were most frequently cultured from blood and bronchoalveolar lavage in humans and lungs in animals. Most infected persons were immunocompromised. Histopathological findings included pleomorphic, small or variably sized yeast-like cells, with single or multiple budding, sometimes proliferating to form short, branching, hyphal-like elements. Disease carried a high case-fatality rate. Conclusions Blastomyces helicus causes fatal pulmonary and systemic disease in humans and companion animals. It differs from B. dermatitidis in morphological presentation in culture and in histopathology, by primarily affecting immunocompromised persons, and in a geographic range that includes western regions of North America.
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Affiliation(s)
- Ilan S Schwartz
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada.,San Antonio Center for Medical Mycology
| | - Nathan P Wiederhold
- San Antonio Center for Medical Mycology.,Fungus Testing Laboratory, University of Texas Health San Antonio
| | - Kimberly E Hanson
- Division of Infectious Diseases, Department of Medicine.,Clinical Microbiology Division, Department of Pathology, University of Utah, Salt Lake City
| | - Thomas F Patterson
- San Antonio Center for Medical Mycology.,South Texas Veterans Health Care System, San Antonio
| | - Lynne Sigler
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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Sha SP, Suryavanshi MV, Jani K, Sharma A, Shouche Y, Tamang JP. Diversity of Yeasts and Molds by Culture-Dependent and Culture-Independent Methods for Mycobiome Surveillance of Traditionally Prepared Dried Starters for the Production of Indian Alcoholic Beverages. Front Microbiol 2018; 9:2237. [PMID: 30319566 PMCID: PMC6169615 DOI: 10.3389/fmicb.2018.02237] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/03/2018] [Indexed: 12/25/2022] Open
Abstract
Marcha, thiat, dawdim, hamei, humao, khekhrii, chowan, and phut are traditionally prepared dried starters used for production of various ethnic alcoholic beverages in North East states of India. The surveillance of mycobiome associated with these starters have been revealed by culture-dependent methods using phenotypic and molecular tools. We identified Wickerhamomyces anomalus, Pichia anomala, Saccharomycopsis fibuligera, Pichia terricola, Pichia kudriavzevii, and Candida glabrata by ITS-PCR. The diversity of yeasts and molds in all 40 samples was also investigated by culture-independent method using PCR-DGGE analysis. The average distributions of yeasts showed Saccharomyces cerevisiae (16.5%), Saccharomycopsis fibuligera (15.3%), Wickerhamomyces anomalus (11.3%), S. malanga (11.7%), Kluyveromyces marxianus (5.3%), Meyerozyma sp. (2.7%), Candida glabrata (2.7%), and many strains below 2%. About 12 strains of molds were also identified based on PCR-DGGE analysis which included Aspergillus penicillioides (5.0%), Rhizopus oryzae (3.3%), and sub-phylum: Mucoromycotina (2.1%). Different techniques used in this paper revealed the diversity and differences of mycobiome species in starter cultures of India which may be referred as baseline data for further research.
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Affiliation(s)
- Shankar Prasad Sha
- DAICENTRE (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Mangesh Vasant Suryavanshi
- DAICENTRE (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India.,National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Kunal Jani
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Jyoti Prakash Tamang
- DAICENTRE (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
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Badali H, Alian S, Fakhim H, Falahatinejad M, Moradi A, Mohammad Davoudi M, Hagen F, Meis JF. Cryptococcal meningitis due to Cryptococcus neoformans genotype AFLP1/VNI in Iran: a review of the literature. Mycoses 2015; 58:689-93. [PMID: 26444438 DOI: 10.1111/myc.12415] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 09/06/2015] [Accepted: 09/07/2015] [Indexed: 12/14/2022]
Abstract
Cryptococcal meningitis is the most important opportunistic fungal infection with a high mortality in HIV-patients in less developed regions. Here, we report a case of cryptococcal meningitis in a 49-year-old HIV-positive female due to Cryptococcus neoformans (serotype A, mating-type alpha, genotype AFLP1/VNI) in Sari, Iran. In vitro antifungal susceptibility tests showed MICs of isavuconazole (0.016 μg ml(-1) ), voriconazole (0.031 μg ml(-1) ), posaconazole (0.031 μg ml(-1) ), itraconazole (0.063 μg ml(-1) ), amphotericin B (0.125 μg ml(-1) ) and fluconazole (8 μg ml(-1) ). Despite immediate antifungal therapy, the patient died 4 days later due to respiratory failure. Cryptococcal infections have been infrequently reported from Iran and therefore we analysed all published cases of cryptococcosis in Iran since the first reported case from 1969.
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Affiliation(s)
- Hamid Badali
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - Shahriar Alian
- Department of Infectious Disease, Antimicrobial Resistance Research Center (ARRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - Hamed Fakhim
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahsa Falahatinejad
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ali Moradi
- Department of Infectious Disease, Antimicrobial Resistance Research Center (ARRC), Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.,Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands
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Kiraz N, Oz Y, Aslan H, Erturan Z, Ener B, Akdagli SA, Muslumanoglu H, Cetinkaya Z. Is the extraction by Whatman FTA filter matrix technology and sequencing of large ribosomal subunit D1-D2 region sufficient for identification of clinical fungi? Mycoses 2015; 58:588-97. [PMID: 26293550 DOI: 10.1111/myc.12365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/05/2015] [Accepted: 07/07/2015] [Indexed: 11/30/2022]
Abstract
Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour-intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1-D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA; extremely rapid, practical and successful. Sequence analysis strategy of D1-D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis.
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Affiliation(s)
- Nuri Kiraz
- Cerrahpasa Medical Faculty, Department of Microbiology, Division of Mycology, Istanbul University, Istanbul, Turkey
| | - Yasemin Oz
- Faculty of Medicine, Department of Microbiology, Division of Mycology, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Huseyin Aslan
- Faculty of Medicine, Department of Medical Genetics, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Zayre Erturan
- Faculty of Medicine, Department of Microbiology, Division of Mycology, Istanbul University, Istanbul, Turkey
| | - Beyza Ener
- Faculty of Medicine, Department of Microbiology, Uludag University, Bursa, Turkey
| | - Sevtap Arikan Akdagli
- Faculty of Medicine, Department of Microbiology, Hacettepe University, Ankara, Turkey
| | - Hamza Muslumanoglu
- Faculty of Science and Arts, Department of Molecular Biology, Yildiz Technical University, Istanbul, Turkey
| | - Zafer Cetinkaya
- Department of Microbiology, Goztepe Research and Education Hospital, Istanbul, Turkey
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Barker AP, Horan JL, Slechta ES, Alexander BD, Hanson KE. Complexities associated with the molecular and proteomic identification of Paecilomyces species in the clinical mycology laboratory. Med Mycol 2014; 52:537-45. [PMID: 24687961 DOI: 10.1093/mmy/myu001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Paecilomyces species are emerging fungal pathogens. Morphological identifications are complicated by similarities among the members of the P. variotii complex as well as to some Rasamsonia and Hamigera species. The purpose of this study was to compare matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) with molecular diagnostic standards (i.e., multilocus DNA sequencing of the internal transcribed spacer regions 1 and 2, D1/D2 regions, and part of the β-tubulin gene) for the identification of Paecilomyces spp. encountered in two clinical mycology laboratories. A total of 77 clinical isolates identified morphologically as P. variotii (n = 21), P. lilacinus (n = 52), and Paecilomyces spp. not otherwise specified (n = 4) were included. In accord with the most recent taxonomy, all P. lilacinus isolates were confirmed as Purpureocillium lilacinum by both sequencing and MALDI-TOF MS. Fungi phenotypically resembling P. variotii or Paecilomyces spp. were identified by molecular techniques as P. variotii sensu stricto (n = 12), P. formosus (n = 3), P. dactylethromorphus (n = 3), Rasamsonia argillacea (n = 4), or R. piperina (n = 1) and at the genus level as an isolate of a Hamigera sp. and a Paecilomyces sp. There was 92.2% (71/77) agreement between the molecular and proteomic methods only after supplementation of the MALDI-TOF MS database with type strains. Paecilomyces variotii-like organisms required multilocus DNA interrogations for differentiation and account for all of the fungi whose identification was missed by MALDI-TOF MS. Overall, MALDI-TOF MS was a rapid and reliable alternative to multilocus sequencing. However, significant augmentation of the commercially available database was required to reproducibly identify this group of important human pathogens.
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Affiliation(s)
- Adam P Barker
- Department of Pathology, University of Utah, ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Jennifer L Horan
- Department of Medicine/Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - E Susan Slechta
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Barbara D Alexander
- Department of Medicine/Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Kimberly E Hanson
- Department of Medicine and Department of Pathology, University of Utah, Salt Lake City, UT, USA
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