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Avivi MY, Touitou N, Rohana H, Lerrer B, Shav-Tal Y, Peretz A, Cohen HY. Nucleic acid hybridization-based detection of pathogenic RNA using microscale thermophoresis. J Biol Chem 2024; 300:105676. [PMID: 38278326 PMCID: PMC10881438 DOI: 10.1016/j.jbc.2024.105676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/28/2024] Open
Abstract
Infectious diseases are one of the world's leading causes of morbidity. Their rapid spread emphasizes the need for accurate and fast diagnostic methods for large-scale screening. Here, we describe a robust method for the detection of pathogens based on microscale thermophoresis (MST). The method involves the hybridization of a fluorescently labeled DNA probe to a target RNA and the assessment of thermophoretic migration of the resulting complex in solution within a 2 to 30-time window. We found that the thermophoretic migration of the nucleic acid-based probes is primarily determined by the fluorescent molecule used, rather than the nucleic acid sequence of the probe. Furthermore, a panel of uniformly labeled probes that bind to the same target RNA yields a more responsive detection pattern than a single probe, and moreover, can be used for the detection of specific pathogen variants. In addition, intercalating agents (ICA) can be used to alter migration directionality to improve detection sensitivity and resolving power by several orders of magnitude. We show that this approach can rapidly diagnose viral SARS-CoV2, influenza H1N1, artificial pathogen targets, and bacterial infections. Furthermore, it can be used for anti-microbial resistance testing within 2 h, demonstrating its diagnostic potential for early pathogen detection.
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Affiliation(s)
- Matan Yosef Avivi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Noga Touitou
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Hanan Rohana
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Tiberias, Israel; Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Batia Lerrer
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Avi Peretz
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Tiberias, Israel; Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Haim Yosef Cohen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
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2
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Inglis TJJ. A systematic approach to microbial forensics. J Med Microbiol 2024; 73. [PMID: 38305344 DOI: 10.1099/jmm.0.001802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
The coronavirus disease 2019 pandemic accelerated developments in biotechnology that underpin infection science. These advances present an opportunity to refresh the microbial forensic toolkit. Integration of novel analytical techniques with established forensic methods will speed up acquisition of evidence and better support lines of enquiry. A critical part of any such investigation is demonstration of a robust causal relationship and attribution of responsibility for an incident. In the wider context of a formal investigation into agency, motivation and intent, the quick and efficient assembly of microbiological evidence sets the tone and tempo of the entire investigation. Integration of established and novel analytical techniques from infection science into a systematic approach to microbial forensics will therefore ensure that major perspectives are correctly used to frame and shape the evidence into a clear narrative, while recognizing that forensic hypothesis generation, testing and refinement comprise an iterative process. Development of multidisciplinary training exercises that use this approach will enable translation into practice and efficient implementation when the need arises.
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Affiliation(s)
- T J J Inglis
- Pathology and Laboratory Medicine, School of Medicine, University of Western Australia, Crawley, WA 6009, Australia
- PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA 6009, Australia
- Western Australian Country Health Service, Perth, WA 6000, Australia
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Salvas J, Merker P, Dingle M, Joossen C, Knutsen C, Govezensky D, Cannon J, Villari P, Cundell A, Navarro V, Franz-Riethdorf M, Scott A. Understanding the Non-Equivalency of Bio-Fluorescent Particle Counts versus the Colony-Forming Unit. PDA J Pharm Sci Technol 2023; 77:514-518. [PMID: 37451837 DOI: 10.5731/pdajpst.2022.012790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Adopting emerging microbiological methods is often desirable because it enables more advantageous, real-time monitoring practices. However, when the newer method measures contamination based on a different detection principle and provides results that are based on different units of measure, a paradigm shift is necessary. That shift can be one of the most difficult challenges in any such project and requires careful consideration. In this article, we explore the challenges presented by the bio-fluorescent particle counting (BFPC) technology, when considering that the traditional colony-forming unit (CFU) is the gold standard that any change is measured against. We examine why attempts to correlate newer units of measure used by biofluorescent particle counters, namely the auto-fluorescent units (AFUs), to the traditional CFUs are not necessarily appropriate. The article explores in depth why there is no consistent correlation factor between the two units of measure, and why that should not be a barrier to fully leveraging, implementing, and using such modern technologies in routine monitoring.
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Affiliation(s)
| | - Petra Merker
- Bayer AG, Müllerstr. 178, D-13353 Berlin, Germany/BioPhorum
| | - Mike Dingle
- TSI Incorporated, 500 Cardigan Road, Shoreview, MN 55126 USA/PEMM
| | - Cedric Joossen
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium/OWBA
| | - Chris Knutsen
- Bristol-Myers Squibb, New Brunswick, NJ, USA/BioPhorum
| | - David Govezensky
- Bio-Technology General (Israel) Ltd., POB 571, Be'er Tuvia Industrial Zone, Kiryat Malachi 8310402, Israel/BioPhorum
| | - Jim Cannon
- Mettler-Toledo Thornton, Inc., 900 Middlesex Turnpike, Building 8, Billerica, MA 01821/PEMM
| | | | | | | | - Margit Franz-Riethdorf
- BioPhorum Operations Group Limited, 5 Westbrook Court, Sharrowvale Road, Sheffield, S11 8YZ, United Kingdom; and
| | - Allison Scott
- Azbil North America Research and Development: BioVigilant, 2005 W. Ruthrauff Rd. #151, Tucson, AZ 85705 USA/PEMM
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Prada-Ramírez HA, BeltrÁn-Osuna ÁA, Celeita S, Fonseca JC. Performance Equivalence and Validation of a Rapid Microbiological Method for Detection and Quantification of Yeast and Mold in an Antacid Oral Suspension. PDA J Pharm Sci Technol 2023; 77:268-280. [PMID: 37085183 DOI: 10.5731/pdajpst.2021.012632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 03/21/2023] [Indexed: 04/23/2023]
Abstract
Alternative and rapid microbiological methods can be effective replacements for more traditional plating approaches for ensuring quality and safety in the pharmaceutical industry. This article compares the efficacy of the Soleris automated method and the traditional plate-count method for the quantitative detection of yeasts and molds at three different microbial bioburden levels. Validation testing was carried out using an antacid oral suspension (aluminum hydroxide 4% + magnesium hydroxide 4% + simethicone 0.4%). Equivalence of data between detection time and colony-forming units was established for both the alternative and the conventional methodologies. Using probability of detection, linear Poisson regression, Fisher's test, and multifactorial analysis of variance (ANOVA), all results from the rapid method were shown to be in statistical agreement with the those of the reference plating procedures. The limits of detection and quantification were statistically similar for both methods (Fisher's exact test, P > 0.05), showing that the alternative method is not inferior in performance to the reference method. Essential validation parameters such as precision (standard deviation <5, coefficient of variance <35%), accuracy (>70%), linearity (R2 >0.9025), ruggedness (ANOVA, P < 0.05), operative range, and specificity were determined. It was shown that all the test results obtained using the alternative method were in statistical agreement with the those of the standard plate-count method. Thus, this new technology was found to meet all the validation criteria needed to be considered as an alternative method for yeast and mold quantification in the antacid oral suspension tested. However, taking into account that the present validation was carried out utilizing A. brasiliensis and C. albicans as suitable models for yeasts and molds and with an antacid oral suspension as a pharmaceutical matrix, further investigation will be required to qualify Soleris technology for other environmental isolates and recovery of these isolates from production batches.
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Affiliation(s)
| | | | - Sandra Celeita
- Laboratorios Coaspharma S.A.S., CL 18A 28A-43, Bogotá, Colombia; and
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Murata M, Kosai K, Akamatsu N, Matsuyama Y, Oda M, Wakamatsu A, Izumikawa K, Mukae H, Yanagihara K. Diagnostic Performance of BD Phoenix CPO Detect Panels for Detection and Classification of Carbapenemase-Producing Gram-Negative Bacteria. Microbiol Spectr 2023; 11:e0089723. [PMID: 37162344 PMCID: PMC10269800 DOI: 10.1128/spectrum.00897-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/11/2023] [Indexed: 05/11/2023] Open
Abstract
BD Phoenix CPO Detect panels can identify and classify carbapenemase-producing organisms (CPOs) simultaneously with antimicrobial susceptibility testing (AST) for Gram-negative bacteria. Detection and classification of carbapenemase producers were performed using the BD Phoenix CPO Detect panels NMIC/ID-441 for Enterobacterales, NMIC/ID-442 for nonfermenting bacteria, and NMIC-440 for both. The results were compared with those obtained using comparator methods. A total of 133 strains (32 Klebsiella pneumoniae, 37 Enterobacter cloacae complex, 33 Pseudomonas aeruginosa, and 31 Acinetobacter baumannii complex strains), including 60 carbapenemase producers (54 imipenemases [IMPs] and 6 OXA type), were analyzed. Using panels NMIC-440 and NMIC/ID-441 or NMIC/ID-442, all 54 IMP producers were accurately identified as CPOs (positive percent agreement [PPA], 100.0%; 54/54). Among the 54 IMP producers identified as CPOs using panels NMIC-440 and NMIC/ID-441, 12 and 14 Enterobacterales were not resistant to carbapenem, respectively. Among all 54 IMP producers, 48 (88.9%; 48/54) were correctly classified as Ambler class B using panel NMIC-440. Using panels NMIC-440 and NMIC/ID-442, all four OXA-23-like carbapenemase-producing A. baumannii complex strains (100.0%, 4/4) were correctly identified as CPOs, and three (75.0%, 3/4) were precisely classified as class D using panel NMIC-440. Both carbapenemase producers harboring the blaISAba1-OXA-51-like gene were incorrectly identified as non-CPOs using panels NMIC-440 and NMIC/ID-442. For detecting carbapenemase producers, the overall PPA and negative percent agreement (NPA) between panel NMIC-440 and the comparator methods were 96.7% (58/60) and 71.2% (52/73), respectively, and the PPA and NPA between panels NMIC/ID-441 or NMIC/ID-442 and the comparator methods were 96.7% (58/60) and 74.0% (54/73), respectively. BD Phoenix CPO Detect panels can successfully screen carbapenemase producers, particularly IMP producers, regardless of the presence of carbapenem resistance and can be beneficial in routine AST workflows. IMPORTANCE Simple and efficient screening methods of detecting carbapenemase producers are required. BD Phoenix CPO Detect panels effectively screened carbapenemase producers, particularly IMP producers, with a high overall PPA. As the panels enable automatic screening for carbapenemase producers simultaneously with AST, the workflow from AST to confirmatory testing for carbapenemase production can be shortened. In addition, because carbapenem resistance varies among carbapenemase producers, the BD Phoenix CPO Detect panels, which can screen carbapenemase producers regardless of carbapenem susceptibility, can contribute to the accurate detection of carbapenemase producers. Our results report that these panels can help streamline the AST workflow before confirmatory testing for carbapenemase production in routine microbiological tests.
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Affiliation(s)
- Mika Murata
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Kosuke Kosai
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Norihiko Akamatsu
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | | | - Mitsuharu Oda
- Nippon Becton, Dickinson Company, Ltd., Minato, Tokyo, Japan
| | | | - Koichi Izumikawa
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
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6
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Levican A, Varela C, Porte L, Weitzel T, Briceño I, Guerra F, Mena B, Hinton A. Head-to-head comparison of CAMPYAIR aerobic culture medium versus standard microaerophilic culture for Campylobacter isolation from clinical samples. Front Cell Infect Microbiol 2023; 13:1153693. [PMID: 37384222 PMCID: PMC10293832 DOI: 10.3389/fcimb.2023.1153693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023] Open
Abstract
Campylobacter spp. are considered the most frequent cause of acute gastroenteritis worldwide. However, outside high-income countries, its burden is poorly understood. Limited published data suggest that Campylobacter prevalence in low- and middle-income countries is high, but their reservoirs and age distribution are different. Culturing Campylobacter is expensive due to laboratory equipment and supplies needed to grow the bacterium (e.g., selective culture media, microaerophilic atmosphere, and a 42°C incubator). These requirements limit the diagnostic capacity of clinical laboratories in many resource-poor regions, leading to significant underdiagnosis and underreporting of isolation of the pathogen. CAMPYAIR, a newly developed selective differential medium, permits Campylobacter isolation without the need for microaerophilic incubation. The medium is supplemented with antibiotics to allow Campylobacter isolation in complex matrices such as human feces. The present study aims to evaluate the ability of the medium to recover Campylobacter from routine clinical samples. A total of 191 human stool samples were used to compare the ability of CAMPYAIR (aerobic incubation) and a commercial Campylobacter medium (CASA, microaerophilic incubation) to recover Campylobacter. All Campylobacter isolates were then identified by MALDI-TOF MS. CAMPYAIR showed sensitivity and specificity values of 87.5% (95% CI 47.4%-99.7%) and 100% (95% CI 98%-100%), respectively. The positive predictive value of CAMPYAIR was 100% and its negative predictive value was 99.5% (95% CI 96.7%-99.9%); Kappa Cohen coefficient was 0.93 (95% CI 0.79-1.0). The high diagnostic performance and low technical requirements of the CAMPYAIR medium could permit Campylobacter culture in countries with limited resources.
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Affiliation(s)
- Arturo Levican
- Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Carmen Varela
- Laboratorio Clínico, Clínica Alemana, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Lorena Porte
- Laboratorio Clínico, Clínica Alemana, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Thomas Weitzel
- Laboratorio Clínico, Clínica Alemana, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Isabel Briceño
- Laboratorio Clínico, Hospital Naval Almirante Nef, Viña del Mar, Chile
| | - Francisco Guerra
- Laboratorio Clínico, Hospital Naval Almirante Nef, Viña del Mar, Chile
| | - Benjamín Mena
- Laboratorio Clínico, Hospital Naval Almirante Nef, Viña del Mar, Chile
| | - Arthur Hinton
- Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Athens, GA, United States
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Lee H, Kim SI. Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases. Int J Mol Sci 2022; 23:ijms23042187. [PMID: 35216306 PMCID: PMC8878692 DOI: 10.3390/ijms23042187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography-mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.
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Affiliation(s)
- Hayoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seung Il Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence:
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Zhang X, Li C, Xue B, Ji P, Li Y, Sun L, Wang S. Development of a Rapid Sporulation Method of Fusarium graminearum Using Liquid Cultivation. Plant Dis 2022; 106:34-38. [PMID: 34282928 DOI: 10.1094/pdis-05-21-0911-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fusarium graminearum is an important fungus causing a variety of maize diseases, including stalk rot, ear rot, and sheath rot. However, conidia of F. graminearum are not easily obtained under normal culture conditions, which seriously affects the identification and pathogenicity assessment of the isolates and screening of resistance sources. This study was undertaken to develop and utilize a rapid sporulation technique of F. graminearum using liquid cultivation, which could meet the needs of various tests. The results show that the optimum conditions for sporulation of F. graminearum were as follows: culture medium, 0.154 mol/liter of saline; temperature, 28 to 30°C; incubation time, 96 h; initial pH, 9 to 10; illumination, continuous ultraviolet light; and shaking speed, 150 rpm. Using this culture method, conidial concentration of tested F. graminearum strains can reach >1.5 × 105 conidia/ml. Compared with the existing methods using mung bean and carboxylmethyl cellulose as matrix, saline is relatively inexpensive, and the culture process, relatively quick. Overall, this study provided a systematic, rapid, and simple method to obtain a large number of conidia of F. graminearum.
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Affiliation(s)
- Xue Zhang
- Agricultural College, Northeast Agricultural University, Harbin, Heilongjiang 150030, P. R. China
| | - Chunjie Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang 150081, P. R. China
| | - Baiyan Xue
- Agricultural College, Northeast Agricultural University, Harbin, Heilongjiang 150030, P. R. China
| | - Pingsheng Ji
- Department of Plant Pathology, University of Georgia, Tifton, GA 31794, U.S.A
| | - Yonggang Li
- Agricultural College, Northeast Agricultural University, Harbin, Heilongjiang 150030, P. R. China
| | - Lei Sun
- Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang 150086, P. R. China
| | - Shuang Wang
- Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang 150086, P. R. China
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Abdolrasouli A, Fraser MA. Candida auris Identification and Profiling by MALDI-ToF Mass Spectrometry. Methods Mol Biol 2022; 2517:21-32. [PMID: 35674942 DOI: 10.1007/978-1-0716-2417-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
MALDI-ToF MS has become the standard method for routine identification of most medically important yeasts in clinical and public health laboratories and has largely replaced phenotypic identification methods as a first-line identification tool. Fungal identification is based on extensive and well-curated mass spectra libraries usually provided by the manufacturer of the MALDI-ToF MS platform; however, many centers do create specialized or in-house database collections to aid analysis. Most MALDI-ToF MS systems offer simple and standardized workflows for the identification of clinically relevant yeasts to species level with a high throughput, high accuracy, and a low overall cost per test. This makes MALDI-ToF MS an ideal platform for use in routine clinical, diagnostic, and research microbiology laboratories which may lack experience or expertise in the identification of pathogenic fungi.In this chapter we review three standard protocols for the proteomic-based identification of Candida auris isolated from cultures of clinical or environmental surveillance samples in diagnostic and research laboratories.
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Affiliation(s)
- Alireza Abdolrasouli
- Department of Medical Microbiology, King's College Hospital , London, UK.
- Department of Infectious Diseases, Imperial College London, London, UK.
| | - Mark A Fraser
- National Mycology Reference Laboratory, UK Health Security Agency, Bristol, UK
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Twaddell SH, Gibson PG, Grainge C, Baines KJ. Parapneumonic Effusions Are Characterized by Elevated Levels of Neutrophil Extracellular Traps. Chest 2021; 160:1645-1655. [PMID: 34293318 DOI: 10.1016/j.chest.2021.07.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 07/05/2021] [Accepted: 07/11/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Neutrophil extracellular traps (NETs) increasingly are implicated in acute and chronic conditions involving multiple organ systems. RESEARCH QUESTION Are NET concentrations higher in parapneumonic effusions compared with effusions of other origin and does this reflect the inflammatory nature of these effusions? STUDY DESIGN AND METHODS Patients (N = 101) seeking hospital treatment for undifferentiated pleural effusion underwent pleural fluid classification based on cytologic analysis results, biochemical findings, microbiological characteristics, and clinical judgement. Concentrations of NET markers (extracellular DNA [eDNA], citrullinated histone H3 [citH3]), neutrophils (α-defensins), and inflammation (IL-1β)-related proteins were quantified by enzyme-linked immunosorbent assay. Differences between groups were analyzed using the Kruskal-Wallis one-way analysis of variance. Correlations used Spearman coefficient. Receiver operating characteristic (ROC) curves were calculated. RESULTS Effusions were classified into four groups: parapneumonic (n = 18), malignant (n = 35), transudative (n = 22), and unclassifiable (n = 26). Concentrations of NETs markers were significantly higher in the parapneumonic group compared with malignant, transudative, and unclassifiable groups (median eDNA, 12.8 ng/mL vs 0.77 ng/mL, 0.44 ng/mL, and 0.86 ng/mL [P < .001]; and median citH3, 127.1 ng/mL vs 0.44 ng/mL, 0.34 ng/mL, and 0.49 ng/mL [P < .001]). citH3 and eDNA were correlated highly with lactate dehydrogenase (LDH; Spearman r = 0.66 and r = 0.73, respectively; P < .001) and moderately negatively correlated with pH (r = -0.55 and r = -0.62, respectively; P < .001). α-Defensins and IL-1β were higher in the parapneumonic group than in other groups (median α-defensins, 124.4 ng/mL vs 4.7 ng/mL,7 ng/mL, and 6.9 ng/mL [P < .001]; and median IL-1β, 145 pg/mL vs 1.87 pg/mL, 1.39 pg/mL, and 2.6 pg/mL [P < .001]) and moderately correlated with LDH (r = 0.60 and r = 0.57; P < .001). ROC curves showed high sensitivity and specificity for NET markers for prediction of parapneumonic effusion. INTERPRETATION High levels of some NET-related mediators in parapneumonic effusions correlate with inflammation. Effusions of other causes do not show high levels of NETs. These results may have treatment implications because NETs may be an important contributor to the inflammation and viscosity of parapneumonic effusions and may help us to understand the therapeutic benefit of deoxyribonuclease in empyema.
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Affiliation(s)
- Scott H Twaddell
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW, Australia; School of Medicine and Public Health, Faculty of Health and Medicine and Priority Research Centre for Healthy Lungs, The University of Newcastle, and Hunter Medical Research Institute, Newcastle, NSW, Australia.
| | - Peter G Gibson
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW, Australia; School of Medicine and Public Health, Faculty of Health and Medicine and Priority Research Centre for Healthy Lungs, The University of Newcastle, and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Christopher Grainge
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW, Australia; School of Medicine and Public Health, Faculty of Health and Medicine and Priority Research Centre for Healthy Lungs, The University of Newcastle, and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Katherine J Baines
- School of Medicine and Public Health, Faculty of Health and Medicine and Priority Research Centre for Healthy Lungs, The University of Newcastle, and Hunter Medical Research Institute, Newcastle, NSW, Australia
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11
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Chimhini G, Olaru ID, Fitzgerald F, Chisenga M, Ferreyra C, Malou N, Piton J, Chimhuya S, Yeung S, De S, Mujuru HA, Kranzer K. Evaluation of a Novel Culture System for Rapid Pathogen Identification and Detection of Cephalosporin Resistance in Neonatal Gram-negative Sepsis at a Tertiary Referral Unit in Harare, Zimbabwe. Pediatr Infect Dis J 2021; 40:785-791. [PMID: 33941744 PMCID: PMC8677569 DOI: 10.1097/inf.0000000000003155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Neonatal sepsis accounts for a large proportion of neonatal deaths in sub-Saharan Africa. The lack of access to diagnostic testing and excessively long turnaround times to result contributes to delays in sepsis identification and initiation of appropriate treatment. This study aims to evaluate the novel InTrays COLOREX Screen and extended-spectrum beta-lactamase for rapid identification of bacterial pathogens causing sepsis and detection of resistance. METHODS Neonates with suspected sepsis admitted to the Harare Central Hospital were prospectively enrolled. One blood culture was collected and incubated using the BacT/ALERT automated system. Positive blood cultures with potential pathogens identified by Gram stain were inoculated on the InTray COLOREX Screen and extended-spectrum beta-lactamase culture plates. RESULTS A total of 216 neonates with suspected sepsis were recruited. Pathogens were isolated from blood cultures in 56 (25.9%) neonates of which 54 were Klebsiella pneumoniae. All K. pneumoniae were resistant to ceftriaxone and 53 (98%) were resistant to gentamicin. Sensitivity and specificity for ceftriaxone-resistant K. pneumoniae detection using InTrays were 100%. InTrays results were interpretable as early as 5-10 hours (median 7 hours, interquartile range 7-7) post blood culture positivity enabling rapid identification and notification of result and leading to a 60% reduction in time to result from blood culture collection. CONCLUSIONS This study shows that the implementation of a novel culture method was feasible and reduced turnaround times for results by 60% compared with standard microbiologic techniques. An impact on patient outcomes and cost-effectiveness of this method needs to be demonstrated.
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Affiliation(s)
- Gwendoline Chimhini
- Child and Adolescent Health Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe
| | - Ioana Diana Olaru
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Felicity Fitzgerald
- Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | | | - Cecilia Ferreyra
- FIND (Foundation for Innovative New Diagnostics), Geneva, Switzerland
| | - Nada Malou
- FIND (Foundation for Innovative New Diagnostics), Geneva, Switzerland
| | - Jeremie Piton
- FIND (Foundation for Innovative New Diagnostics), Geneva, Switzerland
| | - Simbarashe Chimhuya
- Child and Adolescent Health Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe
| | - Shunmay Yeung
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Paediatric Infectious Disease, St Mary’s Imperial College Hospital
| | - Surjo De
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Hilda A. Mujuru
- Child and Adolescent Health Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe
| | - Katharina Kranzer
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Biomedical Research and Training Institute, Harare, Zimbabwe
- Division of Infectious and Tropical Medicine, Medical Centre of the University of Munich, Munich, Germany
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Steele E, Alebous HD, Vickers M, Harris ME, Johnson MD. Co-culturing experiments reveal the uptake of myo-inositol phosphate synthase (EC 5.5.1.4) in an inositol auxotroph of Saccharomyces cerevisiae. Microb Cell Fact 2021; 20:138. [PMID: 34281557 PMCID: PMC8287684 DOI: 10.1186/s12934-021-01610-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 06/08/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Myo-Inositol Phosphate Synthase (MIP) catalyzes the conversion of glucose 6- phosphate into inositol phosphate, an essential nutrient and cell signaling molecule. Data obtained, first in bovine brain and later in plants, established MIP expression in organelles and in extracellular environments. A physiological role for secreted MIP has remained elusive since its first detection in intercellular space. To provide further insight into the role of MIP in intercellular milieus, we tested the hypothesis that MIP may function as a growth factor, synthesizing inositol phosphate in intercellular locations requiring, but lacking ability to produce or transport adequate quantities of the cell-cell communicator. This idea was experimentally challenged, utilizing a Saccharomyces cerevisiae inositol auxotroph with no MIP enzyme, permeable membranes with a 0.4 µm pore size, and cellular supernatants as external sources of inositol isolated from S. cerevisiae cells containing either wild-type enzyme (Wt-MIP), no MIP enzyme, auxotroph (Aux), or a green fluorescent protein (GFP) tagged reporter enzyme (MIP- GFP) in co- culturing experiments. RESULTS Resulting cell densities and microscopic studies with corroborating biochemical and molecular analyses, documented sustained growth of Aux cells in cellular supernatant, concomitant with the uptakeof MIP, detected as MIP-GFP reporter enzyme. These findings revealed previously unknown functions, suggesting that the enzyme can: (1) move into and out of intercellular space, (2) traverse cell walls, and (3) act as a growth factor to promote cellular proliferation of an inositol requiring cell. CONCLUSIONS Co-culturing experiments, designed to test a probable function for MIP secreted in extracellular vesicles, uncovered previously unknown functions for the enzyme and advanced current knowledge concerning spatial control of inositol phosphate biosynthesis. Most importantly, resulting data identified an extracellular vesicle (a non-viral vector) that is capable of synthesizing and transporting inositol phosphate, a biological activity that can be used to enhance specificity of current inositol phosphate therapeutics.
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Affiliation(s)
- Erika Steele
- The University of Alabama, The Institute of Social Science Research, PO Box 8702161, Tuscaloosa, AL 35487 USA
| | - Hana D. Alebous
- Department of Biological Sciences, School of Science, The University of Jordan, PO Box 11942, Amman-Jordan, Jordan
| | - Macy Vickers
- Department of Biological Sciences, The University of Alabama, PO Box 870344, Tuscaloosa, AL 35487 USA
| | - Mary E. Harris
- Department of Biological Sciences, The University of Alabama, PO Box 870344, Tuscaloosa, AL 35487 USA
| | - Margaret D. Johnson
- Department of Biological Sciences, The University of Alabama, PO Box 870344, Tuscaloosa, AL 35487 USA
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Behl T, Kaur I, Sehgal A, Singh S, Bhatia S, Al-Harrasi A, Zengin G, Babes EE, Brisc C, Stoicescu M, Toma MM, Sava C, Bungau SG. Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry. Int J Mol Sci 2021; 22:6184. [PMID: 34201152 PMCID: PMC8227524 DOI: 10.3390/ijms22126184] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/03/2021] [Accepted: 06/05/2021] [Indexed: 02/01/2023] Open
Abstract
With advanced technology and its development, bioinformatics is one of the avant-garde fields that has managed to make amazing progress in the pharmaceutical-medical field by modeling the infrastructural dimensions of healthcare and integrating computing tools in drug innovation, facilitating prevention, detection/more accurate diagnosis, and treatment of disorders, while saving time and money. By association, bioinformatics and pharmacovigilance promoted both sample analyzes and interpretation of drug side effects, also focusing on drug discovery and development (DDD), in which systems biology, a personalized approach, and drug repositioning were considered together with translational medicine. The role of bioinformatics has been highlighted in DDD, proteomics, genetics, modeling, miRNA discovery and assessment, and clinical genome sequencing. The authors have collated significant data from the most known online databases and publishers, also narrowing the diversified applications, in order to target four major areas (tetrad): DDD, anti-microbial research, genomic sequencing, and miRNA research and its significance in the management of current pandemic context. Our analysis aims to provide optimal data in the field by stratification of the information related to the published data in key sectors and to capture the attention of researchers interested in bioinformatics, a field that has succeeded in advancing the healthcare paradigm by introducing developing techniques and multiple database platforms, addressed in the manuscript.
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Affiliation(s)
- Tapan Behl
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India; (I.K.); (A.S.); (S.S.)
| | - Ishnoor Kaur
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India; (I.K.); (A.S.); (S.S.)
| | - Aayush Sehgal
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India; (I.K.); (A.S.); (S.S.)
| | - Sukhbir Singh
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India; (I.K.); (A.S.); (S.S.)
| | - Saurabh Bhatia
- Amity Institute of Pharmacy, Amity University, Gurugram 122413, India;
- Natural & Medical Sciences Research Centre, University of Nizwa, Birkat Al Mauz, Nizwa 616, Oman;
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Centre, University of Nizwa, Birkat Al Mauz, Nizwa 616, Oman;
| | - Gokhan Zengin
- Department of Biology, Faculty of Science, Selcuk University Campus, 42130 Konya, Turkey;
| | - Elena Emilia Babes
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (C.B.); (M.S.); (C.S.)
| | - Ciprian Brisc
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (C.B.); (M.S.); (C.S.)
| | - Manuela Stoicescu
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (C.B.); (M.S.); (C.S.)
| | - Mirela Marioara Toma
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania;
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania
| | - Cristian Sava
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (C.B.); (M.S.); (C.S.)
| | - Simona Gabriela Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania;
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania
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Cameron SJS, Perdones-Montero A, Van Meulebroek L, Burke A, Alexander-Hardiman K, Simon D, Schaffer R, Balog J, Karancsi T, Rickards T, Rebec M, Stead S, Vanhaecke L, Takáts Z. Sample Preparation Free Mass Spectrometry Using Laser-Assisted Rapid Evaporative Ionization Mass Spectrometry: Applications to Microbiology, Metabolic Biofluid Phenotyping, and Food Authenticity. J Am Soc Mass Spectrom 2021; 32:1393-1401. [PMID: 33980015 DOI: 10.1021/jasms.0c00452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Mass spectrometry has established itself as a powerful tool in the chemical, biological, medical, environmental, and agricultural fields. However, experimental approaches and potential application areas have been limited by a traditional reliance on sample preparation, extraction, and chromatographic separation. Ambient ionization mass spectrometry methods have addressed this challenge but are still somewhat restricted in requirements for sample manipulation to make it suitable for analysis. These limitations are particularly restrictive in view of the move toward high-throughput and automated analytical workflows. To address this, we present what we consider to be the first automated sample-preparation-free mass spectrometry platform utilizing a carbon dioxide (CO2) laser for sample thermal desorption linked to the rapid evaporative ionization mass spectrometry (LA-REIMS) methodology. We show that the pulsatile operation of the CO2 laser is the primary factor in achieving high signal-to-noise ratios. We further show that the LA-REIMS automated platform is suited to the analysis of three diverse biological materials within different application areas. First, clinical microbiology isolates were classified to species level with an accuracy of 97.2%, the highest accuracy reported in current literature. Second, fecal samples from a type 2 diabetes mellitus cohort were analyzed with LA-REIMS, which allowed tentative identification of biomarkers which are potentially associated with disease pathogenesis and a disease classification accuracy of 94%. Finally, we showed the ability of the LA-REIMS system to detect instances of adulteration of cooking oil and determine the geographical area of production of three protected olive oil products with 100% classification accuracy.
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Affiliation(s)
- Simon J S Cameron
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, U.K
| | - Alvaro Perdones-Montero
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Ghent University, Ghent B-9820, Belgium
| | - Adam Burke
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Kate Alexander-Hardiman
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Daniel Simon
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- Waters Research Center, Budapest 1031, Hungary
| | | | - Julia Balog
- Waters Research Center, Budapest 1031, Hungary
| | | | - Tony Rickards
- Department of Microbiology, Imperial College Healthcare NHS Trust, London W6 8RD, U.K
| | - Monica Rebec
- Department of Microbiology, Imperial College Healthcare NHS Trust, London W6 8RD, U.K
| | - Sara Stead
- Waters Corporation, Wilmslow SK9 4AX, U.K
| | - Lynn Vanhaecke
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, U.K
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Ghent University, Ghent B-9820, Belgium
| | - Zoltán Takáts
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, U.K
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Moon J, Kim N, Lee HS, Lee ST, Jung KH, Park KI, Lee SK, Lee DO, Lee DY, Chu K. Nanopore 16S Amplicon Sequencing Enhances the Understanding of Pathogens in Medically Intractable Diabetic Foot Infections. Diabetes 2021; 70:1357-1371. [PMID: 34162681 DOI: 10.2337/db20-0907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 03/15/2021] [Indexed: 11/13/2022]
Abstract
Diabetic foot infections (DFIs) cause substantial morbidity and mortality. The mainstay of the treatment is empiric antibiotics and surgical debridement in severe cases. In this study, we performed nanopore 16S rDNA sequencing from the debridement specimens of DFIs. Fifty-four surgical debridement specimens obtained from 45 patients with medically intractable DFI were included. The 16S rDNA PCR was performed on each specimen, and Nanopore sequencing was performed for up to 3 h. The reads were aligned to the BLAST database, and the results were compared with conventional culture studies. The 16S sequencing results revealed that the majority of the DFIs (44 of 54, 81.5%) were polymicrobial infections. All bacteria isolated by conventional culture studies were detected by 16S sequencing. Several anaerobes (Prevotella, Finegoldia, Anaerococcus, Bacteroides) were commonly identified by 16S sequencing but were frequently missed by culture studies. In many cases, certain bacteria only revealed by the 16S sequencing were more abundant than the bacteria isolated by the culture studies. In conclusion, nanopore 16S sequencing was capable of pathogen identification in DFIs and has many advantages over conventional culture studies. Nanopore 16S sequencing enables a comprehensive understanding of the bacteria involved in DFIs.
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Affiliation(s)
- Jangsup Moon
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, South Korea
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Narae Kim
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, South Korea
| | - Han Sang Lee
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, South Korea
| | - Soon-Tae Lee
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, South Korea
| | - Keun-Hwa Jung
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, South Korea
| | - Kyung-Il Park
- Department of Neurology, Seoul National University Hospital Healthcare System Gangnam Center, College of Medicine, Seoul National University, Seoul, South Korea
| | - Sang Kun Lee
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, South Korea
| | - Dong-Oh Lee
- Department of Orthopedic Surgery, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, South Korea
| | - Dong Yeon Lee
- Department of Orthopedic Surgery, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, South Korea
| | - Kon Chu
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, South Korea
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16
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Lin H, Lee HJ, Tague N, Lugagne JB, Zong C, Deng F, Shin J, Tian L, Wong W, Dunlop MJ, Cheng JX. Microsecond fingerprint stimulated Raman spectroscopic imaging by ultrafast tuning and spatial-spectral learning. Nat Commun 2021; 12:3052. [PMID: 34031374 PMCID: PMC8144602 DOI: 10.1038/s41467-021-23202-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/29/2021] [Indexed: 12/21/2022] Open
Abstract
Label-free vibrational imaging by stimulated Raman scattering (SRS) provides unprecedented insight into real-time chemical distributions. Specifically, SRS in the fingerprint region (400-1800 cm-1) can resolve multiple chemicals in a complex bio-environment. However, due to the intrinsic weak Raman cross-sections and the lack of ultrafast spectral acquisition schemes with high spectral fidelity, SRS in the fingerprint region is not viable for studying living cells or large-scale tissue samples. Here, we report a fingerprint spectroscopic SRS platform that acquires a distortion-free SRS spectrum at 10 cm-1 spectral resolution within 20 µs using a polygon scanner. Meanwhile, we significantly improve the signal-to-noise ratio by employing a spatial-spectral residual learning network, reaching a level comparable to that with 100 times integration. Collectively, our system enables high-speed vibrational spectroscopic imaging of multiple biomolecules in samples ranging from a single live microbe to a tissue slice.
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Affiliation(s)
- Haonan Lin
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Photonics Center, Boston University, Boston, MA, USA
| | - Hyeon Jeong Lee
- Photonics Center, Boston University, Boston, MA, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- College of Biomedical Engineering and Instrument Sciences, Zhejiang University, Hangzhou, PR China
| | - Nathan Tague
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | - Cheng Zong
- Photonics Center, Boston University, Boston, MA, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Fengyuan Deng
- Photonics Center, Boston University, Boston, MA, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Jonghyeon Shin
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Lei Tian
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Wilson Wong
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Photonics Center, Boston University, Boston, MA, USA.
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA.
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Wang Z, Ji Y, Zhang J, Su K, Fan HB, Yang WW, Zhang Y, Yao XM. Investigation on Atypical Pathogens related with Community Acquired Pneumonia and the Factors Associated with Mycoplasma Pneumoniae Infection in Jiangsu, China. Clin Lab 2021; 66. [PMID: 32538063 DOI: 10.7754/clin.lab.2019.191036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Community acquired pneumonia remains a leading infectious cause of hospitalization with substantial morbidity and mortality in China. At present, the role of atypical pathogens in CAP arouses peoples' concern. Previous studies indicated that MP was the dominant pathogen of CAP, but the associated factors of MP infection were rarely reported. METHODS We retrospectively investigated the distribution of atypical pathogens related with CAP and compared their differences among various populations. Furthermore, we accessed the associated factors of MP infection in various population. RESULTS A total of 3,675 patients were enrolled and divided into three groups. One thousand and eighty-nine subjects (29.6%) were infected with at least one atypical pathogen. MP was the most predominant pathogen in these CAP patients. Our study found that infection rates of the atypical pathogens were significantly different among three groups. Our results also revealed, in a pediatric group, as the temperature increased, so did the infection rate of MP, while it was the opposite in adult and elderly groups. Furthermore, in preschool and school-age children, high temperature, female, PIVs, ADV, and INFB infection were independent risk factors for MP infection, INFA infection was a protection factor for MP infection. However, in adult and elderly groups, the associated factors might be different. CONCLUSIONS The infection of atypical pathogens related with CAP is quite serious, and MP infection plays a key role in CAP. Besides, the infection rates of the atypical pathogens are different in various populations, as are the associated factors for MP infection.
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[Sponsor On-demand Presentation]. Nihon Saikingaku Zasshi 2021; 76:127-8. [PMID: 33627527 DOI: 10.3412/jsb.76.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Patel A, Emerick M, Cabunoc MK, Williams MH, Preas MA, Schrank G, Rabinowitz R, Luethy P, Johnson JK, Leekha S. Rapid Spread and Control of Multidrug-Resistant Gram-Negative Bacteria in COVID-19 Patient Care Units. Emerg Infect Dis 2021; 27:1234-1237. [PMID: 33565961 PMCID: PMC8007317 DOI: 10.3201/eid2704.204036] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We describe rapid spread of multidrug-resistant gram-negative bacteria among patients in dedicated coronavirus disease care units in a hospital in Maryland, USA, during May–June 2020. Critical illness, high antibiotic use, double occupancy of single rooms, and modified infection prevention practices were key contributing factors. Surveillance culturing aided in outbreak recognition and control.
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Li HY, Jia WN, Li XY, Zhang L, Liu C, Wu J. Advances in detection of infectious agents by aptamer-based technologies. Emerg Microbes Infect 2020; 9:1671-1681. [PMID: 32623963 PMCID: PMC7473197 DOI: 10.1080/22221751.2020.1792352] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/01/2020] [Indexed: 02/07/2023]
Abstract
Infectious diseases still remain one of the biggest challenges for human health. Accurate and early detection of infectious pathogens are crucial for transmission control, clinical diagnosis, and therapy. For a traditional reason, most immunological and microbiological laboratories are equipped with instruments designated for antibody-based assays in detection of infectious pathogens or clinical diagnosis. Emerging aptamer-based technologies have pushed a shift from antibody-based to aptamer-based assays due to equal specificity, even better sensitivity, lower manufacturing cost and more flexibility in amending for chemiluminescent, electrochemical or fluorescent detection in a multifaceted and high throughput fashion in comparison of aptamer-based to antibody-based assays. The nature of aptamer-based technologies is particularly suitable for point-of-care testing in remote areas at warm or hot atmosphere, and mass screening for potential infection in pandemic of emerging infectious agents, such as SARS-CoV or SARS-CoV-2 in an epicentre or other regions. This review intends to summarize currently available aptamer-based technologies in detection of bacterial, viral, and protozoan pathogens for research and clinical application. It is anticipated that potential technologies will be further optimized and validated for clinical translation in meeting increasing demands for prompt, precise, and reliable detection of specific pathogens in various atmospheric conditions.
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Affiliation(s)
- Hui-Yan Li
- Department of Medical Microbiology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Wan-Nan Jia
- Department of Medical Microbiology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Xin-Yi Li
- Department of Medical Microbiology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Li Zhang
- Department of Medical Microbiology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Chang Liu
- Department of Medical Microbiology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Jian Wu
- Department of Medical Microbiology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, People’s Republic of China
- Department of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai, People’s Republic of China
- Shanghai Institute of Liver Diseases, Fudan University Shanghai Medical College, Shanghai, People’s Republic of China
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Abstract
Dimorphic fungi in the genera Blastomyces, Histoplasma, Coccidioides, and Paracoccidioides are important human pathogens that affect human health in many countries throughout the world. Understanding the biology of these fungi is important for the development of effective treatments and vaccines. Gene editing is a critically important tool for research into these organisms. In recent years, gene targeting approaches employing RNA-guided DNA nucleases, such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9), have exploded in popularity. Here, we provide a detailed description of the steps involved in applying CRISPR/Cas9 technology to dimorphic fungi, with Blastomyces dermatitidis in particular as our model fungal pathogen. We discuss the design and construction of single guide RNA and Cas9-expressing targeting vectors (including multiplexed vectors) as well as introduction of these plasmids into Blastomyces using Agrobacterium-mediated transformation. Finally, we cover the outcomes that may be expected in terms of gene-editing efficiency and types of gene alterations produced. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Construction of CRISPR/Cas9 targeting vectors Support Protocol 1: Choosing protospacers in the target gene Basic Protocol 2: Agrobacterium-mediated transformation of Blastomyces Support Protocol 2: Preparation of electrocompetent Agrobacterium Support Protocol 3: Preparation and recovery of Blastomyces frozen stocks.
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Affiliation(s)
- Gregory C. Kujoth
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706
| | - Thomas D. Sullivan
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706
| | - Bruce S. Klein
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706
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22
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Abstract
The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.
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Affiliation(s)
- Alexander Cambré
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
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Bateman M, Oladele R, Kolls JK. Diagnosing Pneumocystis jirovecii pneumonia: A review of current methods and novel approaches. Med Mycol 2020; 58:1015-1028. [PMID: 32400869 PMCID: PMC7657095 DOI: 10.1093/mmy/myaa024] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 03/13/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022] Open
Abstract
Pneumocystis jirovecii can cause life-threatening pneumonia in immunocompromised patients. Traditional diagnostic testing has relied on staining and direct visualization of the life-forms in bronchoalveolar lavage fluid. This method has proven insensitive, and invasive procedures may be needed to obtain adequate samples. Molecular methods of detection such as polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and antibody-antigen assays have been developed in an effort to solve these problems. These techniques are very sensitive and have the potential to detect Pneumocystis life-forms in noninvasive samples such as sputum, oral washes, nasopharyngeal aspirates, and serum. This review evaluates 100 studies that compare use of various diagnostic tests for Pneumocystis jirovecii pneumonia (PCP) in patient samples. Novel diagnostic methods have been widely used in the research setting but have faced barriers to clinical implementation including: interpretation of low fungal burdens, standardization of techniques, integration into resource-poor settings, poor understanding of the impact of host factors, geographic variations in the organism, heterogeneity of studies, and limited clinician recognition of PCP. Addressing these barriers will require identification of phenotypes that progress to PCP and diagnostic cut-offs for colonization, generation of life-form specific markers, comparison of commercial PCR assays, investigation of cost-effective point of care options, evaluation of host factors such as HIV status that may impact diagnosis, and identification of markers of genetic diversity that may be useful in diagnostic panels. Performing high-quality studies and educating physicians will be crucial to improve the rates of diagnosis of PCP and ultimately to improve patient outcomes.
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Affiliation(s)
- Marjorie Bateman
- Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70122, USA
| | - Rita Oladele
- Department of Medical Microbiology and Parasitology, College of Medicine, University of Lagos, Nigeria
| | - Jay K Kolls
- Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70122, USA
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24
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Abstract
In resource-limited settings, point-of-care diagnostic devices have the potential to reduce diagnostic delays and improve epidemiologic surveillance of dermatologic conditions. We outline novel-point-of care diagnostics that have recently been developed for dermatologic conditions that primarily affect patients living in resource-limited settings, namely, Kaposi sarcoma, cutaneous leishmaniasis, leprosy, Buruli ulcer, yaws, onchocerciasis, and lymphatic filariasis. All of the technologies described in this article are prototypes, and some have undergone field testing. These devices still require validation in real-world settings and effective pricing to have a major impact on dermatologic care in resource-limited settings.
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Affiliation(s)
- Devon E McMahon
- Department of Dermatology, Harvard Medical School, Massachusetts General Hospital, 50 Staniford Street, Boston, MA 02114, USA
| | - Linda Oyesiku
- Department of Dermatology, Massachusetts General Hospital, 50 Staniford Street, Boston, MA 02114, USA; University of Miami Miller School of Medicine, Miami, FL, USA
| | | | | | - Esther E Freeman
- Department of Dermatology, Harvard Medical School, Massachusetts General Hospital, 50 Staniford Street, Boston, MA 02114, USA.
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Hira J, Uddin MJ, Haugland MM, Lentz CS. From Differential Stains to Next Generation Physiology: Chemical Probes to Visualize Bacterial Cell Structure and Physiology. Molecules 2020; 25:E4949. [PMID: 33114655 PMCID: PMC7663024 DOI: 10.3390/molecules25214949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022] Open
Abstract
Chemical probes have been instrumental in microbiology since its birth as a discipline in the 19th century when chemical dyes were used to visualize structural features of bacterial cells for the first time. In this review article we will illustrate the evolving design of chemical probes in modern chemical biology and their diverse applications in bacterial imaging and phenotypic analysis. We will introduce and discuss a variety of different probe types including fluorogenic substrates and activity-based probes that visualize metabolic and specific enzyme activities, metabolic labeling strategies to visualize structural features of bacterial cells, antibiotic-based probes as well as fluorescent conjugates to probe biomolecular uptake pathways.
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Affiliation(s)
- Jonathan Hira
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Md. Jalal Uddin
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Marius M. Haugland
- Department of Chemistry and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway;
| | - Christian S. Lentz
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
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26
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Affiliation(s)
- Joseph M Blondeau
- Division of Clinical Microbiology, Royal University Hospital & Saskatchewan Health Authority; Departments of Microbiology & Immunology, Pathology & Laboratory Medicine, Ophthalmology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Espina L. An approach to increase the success rate of cultivation of soil bacteria based on fluorescence-activated cell sorting. PLoS One 2020; 15:e0237748. [PMID: 32866195 PMCID: PMC7458294 DOI: 10.1371/journal.pone.0237748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/31/2020] [Indexed: 12/05/2022] Open
Abstract
Soil microbiota are considered a source of undiscovered bioactive compounds, yet cultivation of most bacteria within a sample remains generally unsuccessful. Two main reasons behind the unculturability of bacteria are the presence of cells in a viable but not culturable state (such as dormant cells) and the failure to provide the necessary growth requirements in vitro (leading to the classification of some bacterial taxa as yet-to-be-cultured). The present work focuses on the development of a single procedure that helps distinguish between both phenomena of unculturability based on viability staining coupled with flow cytometry and fluorescence-activated cell sorting. In the selected soil sample, the success rate of cultured bacteria was doubled by selecting viable and metabolically active bacteria. It was determined that most of the uncultured fraction was not dormant or dead but likely required different growth conditions. It was also determined that the staining process introduced changes in the taxonomic composition of the outgrown bacterial biomass, which should be considered for further developments. This research shows the potential of flow cytometry and fluorescence-activated cell sorting applied to soil samples to improve the success rate of bacterial cultivation by estimating the proportion of dormant and yet-to-be-cultured bacteria and by directly excluding dormant cells from being inoculated into growth media.
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Affiliation(s)
- Laura Espina
- Department of Medical Microbiology, Cardiff University, Cardiff, United Kingdom
- * E-mail:
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28
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Higgins TL, Deshpande A, Zilberberg MD, Lindenauer PK, Imrey PB, Yu PC, Haessler SD, Richter SS, Rothberg MB. Assessment of the Accuracy of Using ICD-9 Diagnosis Codes to Identify Pneumonia Etiology in Patients Hospitalized With Pneumonia. JAMA Netw Open 2020; 3:e207750. [PMID: 32697323 PMCID: PMC7376393 DOI: 10.1001/jamanetworkopen.2020.7750] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
IMPORTANCE Administrative databases may offer efficient clinical data collection for studying epidemiology, outcomes, and temporal trends in health care delivery. However, such data have seldom been validated against microbiological laboratory results. OBJECTIVE To assess the validity of International Classification of Diseases, Ninth Revision (ICD-9) organism-specific administrative codes for pneumonia using microbiological data (test results for blood or respiratory culture, urinary antigen, or polymerase chain reaction) as the criterion standard. DESIGN, SETTING, AND PARTICIPANTS Cross-sectional diagnostic accuracy study conducted between February 2017 and June 2019 using data from 178 US hospitals in the Premier Healthcare Database. Patients were aged 18 years or older admitted with pneumonia and discharged between July 1, 2010, and June 30, 2015. Data were analyzed from February 14, 2017, to June 27, 2019. EXPOSURES Organism-specific pneumonia identified from ICD-9 codes. MAIN OUTCOMES AND MEASURES Sensitivity, specificity, positive predictive value, and negative predictive value of ICD-9 codes using microbiological data as the criterion standard. RESULTS Of 161 529 patients meeting inclusion criteria (mean [SD] age, 69.5 [16.2] years; 51.2% women), 35 759 (22.1%) had an identified pathogen. ICD-9-coded organisms and laboratory findings differed notably: for example, ICD-9 codes identified only 14.2% and 17.3% of patients with laboratory-detected methicillin-sensitive Staphylococcus aureus and Escherichia coli, respectively. Although specificities and negative predictive values exceeded 95% for all codes, sensitivities ranged downward from 95.9% (95% CI, 95.3%-96.5%) for influenza virus to 14.0% (95% CI, 8.8%-20.8%) for parainfluenza virus, and positive predictive values ranged downward from 91.1% (95% CI, 89.5%-92.6%) for Staphylococcus aureus to 57.1% (95% CI, 39.4%-73.7%) for parainfluenza virus. CONCLUSIONS AND RELEVANCE In this study, ICD-9 codes did not reliably capture pneumonia etiology identified by laboratory testing; because of the high specificities of ICD-9 codes, however, administrative data may be useful in identifying risk factors for resistant organisms. The low sensitivities of the diagnosis codes may limit the validity of organism-specific pneumonia prevalence estimates derived from administrative data.
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Affiliation(s)
- Thomas L. Higgins
- The Center for Case Management, Natick, Massachusetts
- Department of Critical Care Medicine, University of Massachusetts Medical School-Baystate, Springfield
| | - Abhishek Deshpande
- Center for Value-Based Care Research, Cleveland Clinic Community Care, Cleveland Clinic, Cleveland, Ohio
| | | | - Peter K. Lindenauer
- Institute for Healthcare Delivery and Population Science, Department of Medicine, University of Massachusetts Medical School-Baystate, Springfield
- Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester
| | - Peter B. Imrey
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Cleveland Clinic, Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Pei-Chun Yu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Sarah D. Haessler
- Division of Infectious Diseases, Department of Medicine, University of Massachusetts Medical School-Baystate, Springfield
| | - Sandra S. Richter
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Michael B. Rothberg
- Center for Value-Based Care Research, Cleveland Clinic Community Care, Cleveland Clinic, Cleveland, Ohio
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Benjamin-Chung J, Pilotte N, Ercumen A, Grant JR, Maasch JRMA, Gonzalez AM, Ester AC, Arnold BF, Rahman M, Haque R, Hubbard AE, Luby SP, Williams SA, Colford JM. Comparison of multi-parallel qPCR and double-slide Kato-Katz for detection of soil-transmitted helminth infection among children in rural Bangladesh. PLoS Negl Trop Dis 2020; 14:e0008087. [PMID: 32330127 PMCID: PMC7202662 DOI: 10.1371/journal.pntd.0008087] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/06/2020] [Accepted: 01/24/2020] [Indexed: 01/08/2023] Open
Abstract
There is growing interest in local elimination of soil-transmitted helminth (STH) infection in endemic settings. In such settings, highly sensitive diagnostics are needed to detect STH infection. We compared double-slide Kato-Katz, the most commonly used copromicroscopic detection method, to multi-parallel quantitative polymerase chain reaction (qPCR) in 2,799 stool samples from children aged 2–12 years in a setting in rural Bangladesh with predominantly low STH infection intensity. We estimated the sensitivity and specificity of each diagnostic using Bayesian latent class analysis. Compared to double-slide Kato-Katz, STH prevalence using qPCR was almost 3-fold higher for hookworm species and nearly 2-fold higher for Trichuris trichiura. Ascaris lumbricoides prevalence was lower using qPCR, and 26% of samples classified as A. lumbricoides positive by Kato-Katz were negative by qPCR. Amplicon sequencing of the 18S rDNA from 10 samples confirmed that A. lumbricoides was absent in samples classified as positive by Kato-Katz and negative by qPCR. The sensitivity of Kato-Katz was 49% for A. lumbricoides, 32% for hookworm, and 52% for T. trichiura; the sensitivity of qPCR was 79% for A. lumbricoides, 93% for hookworm, and 90% for T. trichiura. Specificity was ≥ 97% for both tests for all STH except for Kato-Katz for A. lumbricoides (specificity = 68%). There were moderate negative, monotonic correlations between qPCR cycle quantification values and eggs per gram quantified by Kato-Katz. While it is widely assumed that double-slide Kato-Katz has few false positives, our results indicate otherwise and highlight inherent limitations of the Kato-Katz technique. qPCR had higher sensitivity than Kato-Katz in this low intensity infection setting. Soil-transmitted helminth infections (STH) (e.g., Ascaris, hookworm, Trichuris) contribute to a large burden of disease among children in low- and middle-income countries. There is increasing interest in implementing large-scale deworming programs to eliminate STH in certain settings. Efforts to monitor whether local elimination has occurred require sensitive diagnostic tests that will not miss positive cases. Kato-Katz, a microscopy-based diagnostic test, has commonly been used to identify STH eggs in stool, but in settings where infection intensity is low, this method frequently misses positive samples because it requires visual identification of small numbers of eggs, and hookworm eggs may degrade prior to visualization. Quantitative polymerase chain reaction (qPCR) is a molecular diagnostic method for detecting STH. It may detect more low intensity infections than Kato-Katz because it identifies STH DNA in stool; DNA can be detected in very small quantities and is less likely to degrade than STH ova. Thus, qPCR is likely to be more accurate than Kato-Katz. This study compared the performance of double-slide Kato-Katz and qPCR using 2,799 stool samples from children aged 2–12 years in a setting in rural Bangladesh with predominantly low STH infection intensity. qPCR was more sensitive than Kato-Katz for hookworm and Trichuris infections. 26% of samples were classified as Ascaris positive by Kato-Katz and negative by qPCR. DNA sequencing of 10 samples confirmed that Ascaris was absent in samples classified as positive by Kato-Katz and negative by qPCR. We conclude that Kato-Katz likely produced false positive results for Ascaris and that qPCR had a higher sensitivity than double-slide Kato-Katz in this low infection intensity setting.
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Affiliation(s)
- Jade Benjamin-Chung
- Division of Epidemiology & Biostatistics, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - Nils Pilotte
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Ayse Ercumen
- Division of Epidemiology & Biostatistics, University of California, Berkeley, Berkeley, California, United States of America
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jessica R. Grant
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | | | - Andrew M. Gonzalez
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Ashanta C. Ester
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Benjamin F. Arnold
- Division of Epidemiology & Biostatistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Mahbubur Rahman
- Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Rashidul Haque
- Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Alan E. Hubbard
- Division of Epidemiology & Biostatistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Stephen P. Luby
- Infectious Diseases & Geographic Medicine, Stanford University, Stanford, California, United States of America
| | - Steven A. Williams
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - John M. Colford
- Division of Epidemiology & Biostatistics, University of California, Berkeley, Berkeley, California, United States of America
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30
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Hong S, Grande G, Yu C, Chapla DG, Reigh N, Yang JY, Yang Y, Izumori K, Moremen KW, Xie J, Wu P. hFUT1-Based Live-Cell Assay To Profile α1-2-Fucoside-Enhanced Influenza Virus A Infection. ACS Chem Biol 2020; 15:819-823. [PMID: 32271008 PMCID: PMC7521629 DOI: 10.1021/acschembio.9b00869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Host cell surface glycans play critical roles in influenza virus A (IVA) infection ranging from modulation of IVA attachment to membrane fusion and host tropism. Approaches for quick and sensitive profile of viral avidity toward a specific type of host cell glycan can contribute to the understanding of tropism switching among different IVA strains. Here, we developed a method based on chemoenzymatic glycan engineering to investigate the possible involvement of α1-2-fucosides in IVA infections. Using a truncated human fucosyltransferase 1 (hFUT1), we created α1-2-fucosides in situ on host cells to assess their influence on the host cell binding to IVA hemagglutinin and the susceptibility of host cells toward IVA-induced killing. We discovered that the newly created α1-2-fucosides on host cells enhanced the infection of several human pandemic IVA subtypes either directly or indirectly. These findings suggest that glycan epitopes other than sialic acid should also be considered for assessing the human pandemic risk of this viral pathogen.
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Affiliation(s)
- Senlian Hong
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Geramie Grande
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Chenhua Yu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Digantkumar G Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Natalie Reigh
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Yi Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Ken Izumori
- International Institute of Rare Sugar Research and Education, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Jia Xie
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Peng Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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31
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Moura RD, de Castro LAM, Culik MP, Fernandes AAR, Fernandes PMB, Ventura JA. Culture medium for improved production of conidia for identification and systematic studies of Fusarium pathogens. J Microbiol Methods 2020; 173:105915. [PMID: 32259530 DOI: 10.1016/j.mimet.2020.105915] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 11/17/2022]
Abstract
Fusarium guttiforme and Fusarium ananatum are the etiological agents of fusariosis and fruitlet core rot in pineapple, respectively, producing mycotoxins that are harmful to the health of consumers. These two fungi are morphologically similar and difficulty in obtaining macroconidia of the species limits their identification. Different types of media are available for the culture of these pathogens, but not all of them favor F. ananatum and F. guttiforme macroconidia production. Therefore, the objective of this study was to develop a simple culture medium to improve rapid macro- and microconidia formation in both F. guttiforme and F. ananatum to facilitate taxonomic, pathogenicity and mycotoxin studies. In vitro analysis showed that basal medium with carboxymethyl cellulose (CMC) was better than other media tested with the highest macroconidia production at 7 days of incubation. The highest production of microconidia was with synthetic nutrient medium (SN) at 7 days. F. ananatum produced a relatively high number of microconidia with one septum in comparison to F. guttiforme when cultured in CMC, which suggests an additional character useful for Fusarium taxonomy. CMC medium may serve as an improved alternative to culture media currently used in Fusarium research and contribute to further knowledge of the taxonomy and mycotoxins of Fusarium species.
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Affiliation(s)
- Raíssa Debacker Moura
- Biotechnology Core, Federal University of Espirito Santo, Av. Marechal Campos, 1468, Maruípe, 29043-910 Vitória, ES, Brazil.
| | - Luiza Adami Monteiro de Castro
- Biotechnology Core, Federal University of Espirito Santo, Av. Marechal Campos, 1468, Maruípe, 29043-910 Vitória, ES, Brazil
| | - Mark Paul Culik
- Capixaba Institute of Research, Technical Assistance and Rural Extension, INCAPER, Vitória, Espírito Santo, Brazil
| | | | | | - José Aires Ventura
- Capixaba Institute of Research, Technical Assistance and Rural Extension, INCAPER, Vitória, Espírito Santo, Brazil
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Russell GC, Zadoks RN, Willoughby K, Bachofen C. Bovine viral diarrhoea virus loses quasispecies diversity rapidly in culture. Microb Genom 2020; 6:e000343. [PMID: 32160141 PMCID: PMC7276709 DOI: 10.1099/mgen.0.000343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/07/2020] [Indexed: 12/25/2022] Open
Abstract
Bovine viral diarrhoea (BVD) is an important disease of cattle, with significant impacts on animal health and welfare. The wide host range of the causative pestiviruses may lead to formation of virus reservoirs in other ruminant or wildlife species, presenting a concern for the long-term success of BVD eradication campaigns. It is likely that the quasispecies nature of these RNA viruses contributes to their interspecies transmission by providing genetic plasticity. Understanding the spectrum of sequence variants present in persistently infected (PI) animals is, therefore, essential for studies of virus transmission. To analyse quasispecies diversity without amplification bias, we extracted viral RNA from the serum of a PI cow, and from cell culture fluid after three passages of the same virus in culture, to produce cDNA without amplification. Sequencing of this material using Illumina 250 bp paired-read technology produced full-length virus consensus sequences from both sources and demonstrated the quasispecies diversity of this pestivirus A genotype 1a field strain within serum and after culture. We report the distribution and diversity of over 800 SNPs and provide evidence for a loss of diversity after only three passages in cell culture, implying that cultured viruses cannot be used to understand quasispecies diversity and may not provide reliable molecular markers for source tracing or transmission studies. Additionally, both serum and cultured viruses could be sequenced as a set of 25 overlapping PCR amplicons that demonstrated the same consensus sequences and the presence of many of the same quasispecies variants. The observation that aspects of the quasispecies structure revealed by massively parallel sequencing are also detected after PCR and Sanger sequencing suggests that this approach may be useful for small or difficult to analyse samples.
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Affiliation(s)
- George C. Russell
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
| | - Ruth N. Zadoks
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
- Present address: Sydney School of Veterinary Science, University of Sydney, Camden, NSW, Australia
| | - Kim Willoughby
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
| | - Claudia Bachofen
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
- Present address: Institute of Virology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, CH-8057 Zürich, Switzerland
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De Angelis G, Menchinelli G, Torelli R, De Carolis E, Posteraro P, Sanguinetti M, Posteraro B. Different detection capabilities by mycological media for Candida isolates from mono- or dual-species cultures. PLoS One 2020; 15:e0226467. [PMID: 32203515 PMCID: PMC7089522 DOI: 10.1371/journal.pone.0226467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/04/2020] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to compare the Candida bromcresol green (BCG) medium with the chromogenic (CHROM) Brilliance Candida agar and Sabouraud dextrose agar (SDA) media in regard to their capability of detecting Candida isolates from mono- or dual-species cultures. We prepared Candida isolates' suspensions to obtain mono-species (n = 18) or dual-species (n = 153) culture plates per each medium, and three readers independently observed 513 plates at 24-h, 48-h and 72-h incubation time. We scored reading results as correct, over or under detection compared to the expected species number(s). BCG showed significantly higher correct-detection and lower under-detection rates for all Candida species when observed by at least one reader. At 24-h reading, 12 mono-species cultures had correct (or over) detections in all media, whereas 106, 60 and 78 dual-species cultures had correct (or over) detections in BCG, CHROM or SDA, respectively. BCG provides the basis for an accurate laboratory diagnosis of Candida infections.
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Affiliation(s)
- Giulia De Angelis
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giulia Menchinelli
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Riccardo Torelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Elena De Carolis
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Patrizia Posteraro
- Laboratorio di Analisi Cliniche e Microbiologiche, GVM Ospedale San Carlo di Nancy, Rome, Italy
| | - Maurizio Sanguinetti
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- * E-mail:
| | - Brunella Posteraro
- Istituto di Patologia Medica e Semeiotica Medica, Università Cattolica del Sacro Cuore Rome, Rome, Italy
- Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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Yoon SH, Min IK, Ahn JG. Immunochromatography for the diagnosis of Mycoplasma pneumoniae infection: A systematic review and meta-analysis. PLoS One 2020; 15:e0230338. [PMID: 32182283 PMCID: PMC7077834 DOI: 10.1371/journal.pone.0230338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/26/2020] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was to evaluate the diagnostic performance of immunochromatographic tests (ICTs) for the detection of Mycoplasma pneumoniae. Medline/Pubmed, Embase, the Cochrane Library, and ISI Web of Science were searched through June 12, 2019 for relevant studies that used ICTs for the detection of M. pneumoniae infection with polymerase chain reaction (PCR) or microbial culturing as reference standards. Pooled diagnostic accuracy with 95% confidence interval (CI) was calculated using a bivariate random effects model. We also constructed summary receiver operating characteristic curves and calculated the area under the curve (AUC). Statistical heterogeneity was evaluated by χ2 test or Cochrane’s Q test. Thirteen studies including 2,235 samples were included in the meta-analysis. The pooled sensitivity and specificity for diagnosing M. pneumoniae infection were 0.70 (95% CI: 0.59–0.79) and 0.92 (95% CI: 0.87–0.95), respectively. The positive likelihood ratio (LR) was 8.94 (95% CI: 4.90–14.80), negative LR 0.33 (95% CI: 0.22–0.46), diagnostic odds ratio 29.20 (95% CI: 10.70–64.20), and AUC 0.904. In subgroup analysis, ICTs demonstrated similar pooled sensitivities and specificities in populations of children only and mixed populations (children + adults). Specimens obtained from oropharyngeal swabs exhibited a higher sensitivity and specificity than those of nasopharyngeal swab. Moreover, pooled estimates of sensitivity and accuracy for studies using PCR as a reference standard were higher than those using culture. The pooled sensitivity and specificity of Ribotest Mycoplasma®, the commercial kit most commonly used in the included studies, were 0.66 and 0.89, respectively. Overall, ICT is a rapid user-friendly method for diagnosing M. pneumoniae infection with moderate sensitivity, high specificity, and high accuracy. This suggests that ICT may be useful in the diagnostic workup of M. pneumoniae infection; however, additional studies are needed for evaluating the potential impact of ICT in clinical practice.
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Affiliation(s)
- Seo Hee Yoon
- Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - In Kyung Min
- Biostatistics Collaboration Unit, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea
| | - Jong Gyun Ahn
- Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Korea
- * E-mail:
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Tang Y, Dai T, Su Z, Hasegawa K, Tian J, Chen L, Wen D. A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology. Microb Ecol 2020; 79:342-356. [PMID: 31428833 DOI: 10.1007/s00248-019-01421-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Current technologies could identify the abundance and functions of specific microbes, and evaluate their individual effects on microbial ecology. However, these microbes interact with each other, as well as environmental factors, in the form of complex network. Determination of their combined ecological influences remains a challenge. In this study, we developed a tripartite microbial-environment network (TMEN) analysis method that integrates microbial abundance, metabolic function, and environmental data as a tripartite network to investigate the combined ecological effects of microbes. Applying TMEN to analyzing the microbial-environment community structure in the sediments of Hangzhou Bay, one of the most seriously polluted coastal areas in China, we found that microbes were well-organized into 4 bacterial communities and 9 archaeal communities. The total organic carbon, sulfate, chemical oxygen demand, salinity, and nitrogen-related indexes were detected as crucial environmental factors in the microbial-environmental network. With close interactions with these environmental factors, Nitrospirales and Methanimicrococcu were identified as hub microbes with connection advantage. Our TMEN method could close the gap between lack of efficient statistical and computational approaches and the booming of large-scale microbial genomic and environmental data. Based on TMEN, we discovered a potential microbial ecological mechanism that crucial species with significant influence on the microbial community ecology would possess one or two of the community advantages for enhancing their ecological status and essentiality, including abundance advantage and connection advantage.
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Affiliation(s)
- Yushi Tang
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Tianjiao Dai
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Zhiguo Su
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Kohei Hasegawa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Massachusetts General Hospital, Harvard Medical School, 125 Nashua Street, Boston, MA, 02115, USA
| | - Jinping Tian
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Lujun Chen
- School of Environment, Tsinghua University, Beijing, 100084, China
- Zhejiang Provincial Key Laboratory of Water Science and Technology, Department of Environmental Technology and Ecology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, 314050, Zhejiang, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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Abstract
Rapid and accurate identification of microorganisms and estimation of their biomasses are of extreme importance to public health. Mass spectrometry has become an important technique for these purposes. Previously we published a workflow named Microorganism Classification and Identification (MiCId v.12.26.2017) that was shown to perform no worse than other workflows. This manuscript presents MiCId v.12.13.2018 that, in comparison with the earlier version v.12.26.2017, allows for biomass estimates, provides more accurate microorganism identifications (better controls the number of false positives), and is robust against database size increase. This significant advance is made possible by several new ingredients introduced: first, we apply a modified expectation-maximization method to compute for each taxon considered a prior probability, which can be used for biomass estimate; second, we introduce a new concept called ownership, through which the participation ratio is computed and use it as the number of taxa to be kept within a cluster of closely related taxa; third, based on confidently identified peptides, we calculate for each taxon its degree of independence from the rest of taxa considered to determine whether or not to split this taxon off the cluster. Using 270 data files, each containing a large number of MS/MS spectra, we show that, in comparison with v.12.26.2017, version v.12.13.2018 yields superior retrieval results. We also show that MiCId v.12.13.2018 can estimate species biomass reasonably well. The new MiCId v.12.13.2018, designed to run in Linux environment, is freely available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.
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Affiliation(s)
- Gelio Alves
- National Center for Biotehnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Yi-Kuo Yu
- National Center for Biotehnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
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Fakhreddine M, Khalid K, Othman D, Idrissa D, Houria B, Khalid Z. Rapid detection of mycobacterium tuberculosis complex by real-time polymerase chain reaction (PCR) in pulmonary and extra-pulmonary samples in Casablanca, Morocco. Pan Afr Med J 2020; 36:134. [PMID: 32849989 PMCID: PMC7422747 DOI: 10.11604/pamj.2020.36.134.16652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 06/09/2020] [Indexed: 11/11/2022] Open
Affiliation(s)
- Maaloum Fakhreddine
- Laboratoire de Microbiologie, Faculté de Médecine et Pharmacie, Université Hassan II de Casablanca, Casablanca, Maroc
- Laboratoire de Bactériologie, Virologie et Hygiène Hospitalière du CHU Ibn Rochd de Casablanca, Casablanca, Maroc
- Corresponding author: Maaloum Fakhreddine, Laboratoire de Microbiologie, Faculté de Médecine et Pharmacie, Université Hassan II de Casablanca, Casablanca, Maroc.
| | - Katfy Khalid
- Laboratoire de Microbiologie, Faculté de Médecine et Pharmacie, Université Hassan II de Casablanca, Casablanca, Maroc
- Laboratoire de Bactériologie, Virologie et Hygiène Hospitalière du CHU Ibn Rochd de Casablanca, Casablanca, Maroc
| | - Diraa Othman
- Laboratoire de Bactériologie, Virologie et Hygiène Hospitalière du CHU Ibn Rochd de Casablanca, Casablanca, Maroc
| | - Diawara Idrissa
- Faculté des Sciences et Techniques de Santé, Université Mohammed VI des Sciences de la Santé, Casablanca, Maroc
| | - Belabbes Houria
- Laboratoire de Microbiologie, Faculté de Médecine et Pharmacie, Université Hassan II de Casablanca, Casablanca, Maroc
- Laboratoire de Bactériologie, Virologie et Hygiène Hospitalière du CHU Ibn Rochd de Casablanca, Casablanca, Maroc
| | - Zerouali Khalid
- Laboratoire de Microbiologie, Faculté de Médecine et Pharmacie, Université Hassan II de Casablanca, Casablanca, Maroc
- Laboratoire de Bactériologie, Virologie et Hygiène Hospitalière du CHU Ibn Rochd de Casablanca, Casablanca, Maroc
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Doern GV, Carroll KC, Diekema DJ, Garey KW, Rupp ME, Weinstein MP, Sexton DJ. Practical Guidance for Clinical Microbiology Laboratories: A Comprehensive Update on the Problem of Blood Culture Contamination and a Discussion of Methods for Addressing the Problem. Clin Microbiol Rev 2019; 33:e00009-19. [PMID: 31666280 PMCID: PMC6822992 DOI: 10.1128/cmr.00009-19] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this review, we present a comprehensive discussion of matters related to the problem of blood culture contamination. Issues addressed include the scope and magnitude of the problem, the bacteria most often recognized as contaminants, the impact of blood culture contamination on clinical microbiology laboratory function, the economic and clinical ramifications of contamination, and, perhaps most importantly, a systematic discussion of solutions to the problem. We conclude by providing a series of unanswered questions that pertain to this important issue.
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Affiliation(s)
- Gary V Doern
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, John Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel J Diekema
- Division of Infectious Diseases, Department of Medicine and Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Mark E Rupp
- Division of Infectious Diseases, Department of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Melvin P Weinstein
- Department of Pathology and Laboratory Medicine, Department of Medicine, Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Daniel J Sexton
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
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Kwan JR, Lim M, Ng F, Shelat V. Fungal Isolates in Peritoneal Fluid Culture Do Not Impact Peri-Operative Outcomes of Peptic Ulcer Perforation. Surg Infect (Larchmt) 2019; 20:619-624. [PMID: 31099700 DOI: 10.1089/sur.2019.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Background: Fungal isolates from peritoneal fluid sampling in patients with perforated peptic ulcer (PPU) is not uncommon and its management unclear. This study aims to evaluate whether the presence of fungus in peritoneal fluid cultures is a predictor of morbidity and mortality after laparotomy for PPU. Method: This is a single-center retrospective study including adult patients with perforated gastric and duodenal ulcers over a 10-year period (January 2004 to January 2014). Evaluation of predictors contributing to fungal growth was conducted using multiple logistic regression analysis. Operative factors and 30-day mortality and morbidity outcomes were compared against fungal growth using a multivariable generalized linear mixed model analysis. Results: The median age was 58 (interquartile range [IQR] 44-70) years with 110 (20.3%) females. In addition to hypertension and hyperlipidemia, diabetes mellitus (13.5%), ischemic heart disease (2.6%), and heart failure (2.4%) were common. Fungus was cultured from peritoneal fluid in 209 (38.6%) patients. Median American Society of Anesthesiology (ASA) score was 2 (IQR 2-3) and median Mannheim peritonitis index (MPI) score was 15 (IQR 10-20). Free air was detected in 323 (59.6%) patients and 52 (9.6%) patients had gastrectomy. Median length of stay was 7 (IQR 6-11) days. All-cause complications were seen in 53 (9.8%) patients, of whom 37 patients (6.8%) developed intra-abdominal collection, 20 patients (3.7%) had anastomotic leakage, and 12 patients (2.2%) required repeat operation. Thirty-day mortality was seen in 47 (8.7%) patients. Multivariable analysis showed age (median age, 64; IQR 53-74) as a predictor of fungal growth (p < 0.001) but fungal growth not a predictor of adverse peri-operative outcomes. Conclusion: Fungal isolates in peritoneal fluid cultures are more likely to occur in older patients who have PPU. Presence of fungal isolates does not impact peri-operative outcomes.
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Affiliation(s)
- Jia Rui Kwan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Melvin Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Felicia Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Vishal Shelat
- Department of General Surgery, Tan Tock Seng Hospital, Singapore, Singapore
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Wang QW, Zhang CQ. q-LAMP Assays for the Detection of Botryosphaeria dothidea Causing Chinese Hickory Canker in Trunk, Water, and Air Samples. Plant Dis 2019; 103:3142-3149. [PMID: 31560617 DOI: 10.1094/pdis-04-19-0773-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trunk canker disease caused by Botryosphaeria dothidea with a prolonged latent infection phase poses a serious threat to Chinese hickory production. To further understand the epidemiological characteristics and develop reasonable management techniques, a quantitative loop-mediated isothermal amplification (q-LAMP) assay was developed to quantitatively monitor B. dothidea in hickory plants, water, and air samples. Specific primers were designed based on the different sites of the β-tubulin sequence between B. dothidea and other fungi commonly found on Chinese hickory. At the optimum reaction temperature of 65.9°C, this loop-mediated isothermal amplification (LAMP) assay can specifically distinguish B. dothidea from other tested fungi. The limit of detection of LAMP assays for B. dothidea was 0.001 ng/µl of pure genomic DNA and 10 spores per 1 ml of water. The q-LAMP assay enables rapid detection of B. dothidea within 60 min in hickory trunk, water in hickory forests, and spores captured on tapes. These results provide a powerful and convenient tool for monitoring B. dothidea, which could be applied widely in epidemiology, forecast, and management of tree canker disease.
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Affiliation(s)
- Q W Wang
- College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, Zhejiang 311300, People's Republic of China
| | - C Q Zhang
- College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, Zhejiang 311300, People's Republic of China
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Saika A, Fukuoka T, Mikome S, Kondo Y, Habe H, Morita T. Screening and isolation of the liamocin-producing yeast Aureobasidium melanogenum using xylose as the sole carbon source. J Biosci Bioeng 2019; 129:428-434. [PMID: 31732259 DOI: 10.1016/j.jbiosc.2019.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/02/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022]
Abstract
Xylose, the main component of xylan, is the second most abundant sugar in nature after glucose. Consequently, xylose represents an attractive feedstock for the production of value-added compounds such as biosurfactants (BSs), which are produced by various bacteria and yeasts. In this study, we screened and isolated yeast strains that synthesize BSs using xylose as the sole carbon source. We applied matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to screen for BS-producing yeasts and isolated eight strains as the liamocin producers. Two of the eight strains, AS37 and SK25, were identified as Aureobasidium melanogenum, which is known as black yeasts, by based on 26S ribosomal RNA gene sequences. Both strains produced a wide variety of liamocin structures from not only xylose but also glucose and sucrose. According to the MALDI-TOF MS analysis, signals corresponding to sodium ion adducts of di-, tri-, tetra-, penta- and hexa-acylated C6-liamocins and di-, tri- and tetra-acylated C5-liamocins were detected. In addition, their mono-acetylated form was also detected. The dominant sugar component of liamocins produced by strains AS37 and SK25 is mannitol as estimated by HPLC analysis. This is the first report to describe the screening of liamocins-producing yeasts using xylose as the sole carbon source.
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Affiliation(s)
- Azusa Saika
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5-2, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Tokuma Fukuoka
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5-2, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Shuntaro Mikome
- Department of Industrial Chemistry, Faculty of Engineering, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 162-8601, Japan
| | - Yukishige Kondo
- Department of Industrial Chemistry, Faculty of Engineering, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 162-8601, Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Tomotake Morita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5-2, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.
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Shi XX, Qiu HP, Wang JY, Zhang Z, Wang YL, Sun GC. A handy method to remove bacterial contamination from fungal cultures. PLoS One 2019; 14:e0224635. [PMID: 31693673 PMCID: PMC6834272 DOI: 10.1371/journal.pone.0224635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/17/2019] [Indexed: 11/22/2022] Open
Abstract
Contamination control and removal are very important technical aspects of microbiological research. Bacterial contamination is very common in fungal cultures. Currently, the commonly used approach for inhibiting bacteria is antibiotic treatment; however, there are drawbacks to using antibiotics, including incomplete removal, limited antibacterial spectra, tendency toward recontamination, effects to fungal strains, and potential risks to the environment. Therefore, in the present work, we developed a new method for bacterial removal from fungi cultured on solid medium, the Cabin-Sequestering (CS) method, based on the different culture characteristics between fungi and bacteria. First, 3–5 mm round or square holes (the “cabin”) are excavated on a solid medium plate. The fungal strain containing possible bacterial contamination is inoculated into the cabin. The cabin is then covered with a sterilized coverslip, followed by incubation at the appropriate temperature. After 7–10 days of culturing, fungal hyphae grow out along the edge of the coverslip; however, the contaminating bacteria cannot pass through the space formed between the medium and the coverslip and, thus, remain in the cabin. The newly grown fungal hyphae around the coverslip are re-inoculated into fresh culture plates, where they form bacteria-free fungal colonies. The CS method is easy handling, with a short experimental cycle and rare recontamination. When necessary, it can also be used in combination with antibiotics in bacterial removal operations.
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Affiliation(s)
- Xiao-Xiao Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Hai-Ping Qiu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiao-yu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- * E-mail: (J.W.); (G.S.)
| | - Zhen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yan-Li Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guo-Chang Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- * E-mail: (J.W.); (G.S.)
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Owati A, Agindotan B, Burrows M. Development and Application of Real-Time and Conventional SSR-PCR Assays for Rapid and Sensitive Detection of Didymella pisi Associated with Ascochyta Blight of Dry Pea. Plant Dis 2019; 103:2751-2758. [PMID: 31509494 DOI: 10.1094/pdis-02-19-0381-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Didymella pisi is the primary causal pathogen of Ascochyta blight (AB) of dry pea in Montana. Diagnosis of AB is challenging because there are six different species that cause AB worldwide and that can co-occur. Additionally, agar plate identification of D. pisi is challenging due to its slow growth rate. Currently, there are no PCR-based assays developed for specific detection of D. pisi or any fungal pathogen in the AB complex of dry pea. In this study, we evaluated simple sequence repeat (SSR) primer pairs for their specificity and sensitivity in real-time and conventional SSR-PCR both in vitro and in planta. The specificity of the assay was determined by testing DNA of 10 dry pea varieties, fungal species in the AB complex, and fungal species associated with dry pea. To avoid false-negative results, plant and fungal DNA markers were included as controls in a conventional multiplex SSR-PCR, to amplify any plant or fungal DNA in the absence of the D. pisi SSR target. SYBR Green SSR-quantitative PCR (qPCR) detection was conducted using the same primer pairs but in a uniplex format. D. pisi was specifically amplified, whereas other fungi and host DNA were not. Also, sensitivity experiments showed that the detection limit was 0.01 ng of DNA of D. pisi for both assays and 100 conidia in SSR-qPCR. These assays are valuable diagnostic tools for the detection of D. pisi.
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Affiliation(s)
- Ayodeji Owati
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, U.S.A
| | - Bright Agindotan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, U.S.A
| | - Mary Burrows
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, U.S.A
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Mora D, Filardi R, Arioli S, Boeren S, Aalvink S, de Vos WM. Development of omics-based protocols for the microbiological characterization of multi-strain formulations marketed as probiotics: the case of VSL#3. Microb Biotechnol 2019; 12:1371-1386. [PMID: 31402586 PMCID: PMC6801179 DOI: 10.1111/1751-7915.13476] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/17/2022] Open
Abstract
The growing commercial interest in multi-strain formulations marketed as probiotics has not been accompanied by an equal increase in the evaluation of quality levels of these biotechnological products. The multi-strain product VSL#3 was used as a model to setup a microbiological characterization that could be extended to other formulations with high complexity. Shotgun metagenomics by deep Illumina sequencing was applied to DNA isolated from the commercial VSL#3 product to confirm strains identity safety and composition. Single-cell analysis was used to evaluate the cell viability, and β-galactosidase and urease activity have been used as marker to monitor the reproducibility of the production process. Similarly, these lots were characterized in detail by a metaproteomics approach for which a robust protein extraction protocol was combined with advanced mass spectrometry. The results identified over 1600 protein groups belonging to all strains present in the VSL#3 formulation. Of interest, only 3.2 % proteins showed significant differences mainly related to small variations in strain abundance. The protocols developed in this study addressed several quality criteria that are relevant for marketed multi-strain products and these represent the first efforts to define the quality of complex probiotic formulations such as VSL#3.
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Affiliation(s)
- Diego Mora
- Department of Food Environmental and Nutritional Sciences (DeFENS)University of MilanMilanItaly
| | - Rossella Filardi
- Department of Food Environmental and Nutritional Sciences (DeFENS)University of MilanMilanItaly
| | - Stefania Arioli
- Department of Food Environmental and Nutritional Sciences (DeFENS)University of MilanMilanItaly
| | - Sjef Boeren
- Laboratory of BiochemistryWageningen UniversityWageningenThe Netherlands
| | - Steven Aalvink
- Laboratory of MicrobiologyWageningen UniversityWageningenThe Netherlands
| | - Willem M. de Vos
- Laboratory of MicrobiologyWageningen UniversityWageningenThe Netherlands
- Human Microbiome Research Program Unit, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
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Raulo R, Heuson E, Siah A, Phalip V, Froidevaux R. Innovative microscale workflow from fungi cultures to Cell Wall-Degrading Enzyme screening. Microb Biotechnol 2019; 12:1286-1292. [PMID: 31006173 PMCID: PMC6801129 DOI: 10.1111/1751-7915.13405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/17/2019] [Indexed: 11/30/2022] Open
Abstract
This study aimed at developing a complete miniaturized high-throughput screening workflow for the evaluation of the Cell Wall-Degrading Enzyme (CWDE) activities produced by any fungal strain directly cultivated on raw feedstock in a submerged manner. In this study, wheat straw was selected as model substrate as it represents an important carbon source but yet poorly valorised to yield high added value products. Fungi were grown in a microbioreactor in a high-throughput (HT) way to replace the fastidious shaking flask cultivations. Both approaches were compared in order to validate our new methodology. The range of CWDE activities produced from the cultures was assayed using AZO-died and pNP-linked substrates in an SBS plate format using a Biomek FXp pipetting platform. As highlighted in this study, it was shown that the CWDE activities gathered from the microbioreactor cultivations were similar or higher to those obtained from shake flasks cultures, with a lower standard deviation on the measured values, making this new method much faster than the traditional one and suitable for HT CWDE production thanks to its pipetting platform compatibility. Also, the results showed that the enzymatic activities measured were the same when doing the assay manually or using the automated method.
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Affiliation(s)
- Roxane Raulo
- EA 7394 – ICV – Institut Charles ViolletteUniv. Lille 1ISAINRAUniv. ArtoisUniv. Littoral Côte d'OpaleF‐59000LilleFrance
| | - Egon Heuson
- EA 7394 – ICV – Institut Charles ViolletteUniv. Lille 1ISAINRAUniv. ArtoisUniv. Littoral Côte d'OpaleF‐59000LilleFrance
| | - Ali Siah
- EA 7394 – ICV – Institut Charles ViolletteUniv. Lille 1ISAINRAUniv. ArtoisUniv. Littoral Côte d'OpaleF‐59000LilleFrance
| | - Vincent Phalip
- EA 7394 – ICV – Institut Charles ViolletteUniv. Lille 1ISAINRAUniv. ArtoisUniv. Littoral Côte d'OpaleF‐59000LilleFrance
| | - Renato Froidevaux
- EA 7394 – ICV – Institut Charles ViolletteUniv. Lille 1ISAINRAUniv. ArtoisUniv. Littoral Côte d'OpaleF‐59000LilleFrance
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Krych Ł, Castro-Mejía JL, Forero-Junco LM, Moesby DN, Mikkelsen MB, Rasmussen MA, Sykulski M, Nielsen DS. DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq. Commun Biol 2019; 2:369. [PMID: 31633060 PMCID: PMC6787052 DOI: 10.1038/s42003-019-0617-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 09/17/2019] [Indexed: 11/10/2022] Open
Abstract
Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.
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Affiliation(s)
- Łukasz Krych
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
- GenXone S.A., 60-476 Poznań, Poland
| | - Josué L. Castro-Mejía
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Laura M. Forero-Junco
- Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Daniel N. Moesby
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Morten B. Mikkelsen
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Morten A. Rasmussen
- Chemometrics and Analytical Technology, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Dennis S. Nielsen
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
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Roux G, Ravel C, Varlet-Marie E, Jendrowiak R, Bastien P, Sterkers Y. Inhibition of polymerase chain reaction: Pathogen-specific controls are better than human gene amplification. PLoS One 2019; 14:e0219276. [PMID: 31560697 PMCID: PMC6764677 DOI: 10.1371/journal.pone.0219276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/23/2019] [Indexed: 11/21/2022] Open
Abstract
PCR inhibition is frequent in medical microbiology routine practice and may lead to false-negative results; however there is no consensus on how to detect it. Pathogen-specific and human gene amplifications are widely used to detect PCR inhibition. We aimed at comparing the value of PCR inhibitor detection using these two methods. We analysed Cp shifts (ΔCp) obtained from qPCRs targeting either the albumin gene or the pathogen-specific sequence used in two laboratory-developed microbiological qPCR assays. 3152 samples including various matrixes were included. Pathogen-specific amplification and albumin qPCR identified 62/3152 samples (2.0%), and 409/3152 (13.0%) samples, respectively, as inhibited. Only 16 samples were detected using both methods. In addition, the use of the Youden's index failed to determine adequate Cp thresholds for albumin qPCR, even when we distinguished among the different sample matrixes. qPCR targeting the albumin gene therefore appears not adequate to identify the presence of PCR inhibitors in microbiological PCR assays. Our data may be extrapolated to other heterologous targets and should discourage their use to assess the presence of PCR inhibition in microbiological PCR assays.
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Affiliation(s)
- Guillaume Roux
- Univ. Montpellier, and Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU) of Nîmes, Nîmes, France
| | - Christophe Ravel
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
| | - Emmanuelle Varlet-Marie
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
| | - Rachel Jendrowiak
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
| | - Patrick Bastien
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
| | - Yvon Sterkers
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
- * E-mail:
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Navarro-Mtz AK, Martinez-Garcia R, Urzua-Valenzuela M, Roldan-Sabino C, Kakazey M, Juarez-Arellano EA. High-energy ball milling treatment of soybean for Bacillus thuringiensis culture media. J Biosci Bioeng 2019; 128:296-301. [PMID: 30962100 DOI: 10.1016/j.jbiosc.2019.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 11/16/2018] [Accepted: 02/20/2019] [Indexed: 11/29/2022]
Abstract
Soybean meal has been intensively used as a substrate in culture media for several microorganisms. However, the fermentable sugar containing the soybean needs to be released from the solid matrix through different processes. Against this backdrop, the present study explores the use of high-energy ball milling as a one-step treatment method for expedited production of fermentable sugars of textured soybean. The best result is observed after only 5 min of milling, obtaining 34.1 times more fermentable sugars than untreated textured soybean, and 2.5 times more than commercially used soybean meal. Notably, the textured soybean ball-milled has been used as a substrate for Bacillus thuringiensis var. kurstaki HD-73 fermentation. The cell and spore production is also compared with a standard Rowe media. The maximum cell concentration obtained in the entire fermentation process using ball-milled textured soybean media is found to be higher than the concentration obtained using the standard Rowe media. In addition, it is observed that there is a direct correlation between maximum cell production and reducing sugar concentration generated by the high-energy ball milling treatment. No fermentation inhibitors or by-products are generated during the physical treatment.
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Affiliation(s)
- Ana Karin Navarro-Mtz
- Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301 Tuxtepec, Oaxaca, Mexico
| | - Rigoberto Martinez-Garcia
- División de Estudios de Posgrado, Maestría en Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301 Tuxtepec, Oaxaca, Mexico
| | - Michell Urzua-Valenzuela
- División de Estudios de Posgrado, Maestría en Ciencias Químicas, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301 Tuxtepec, Oaxaca, Mexico
| | - Crisanto Roldan-Sabino
- División de Estudios de Posgrado, Maestría en Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301 Tuxtepec, Oaxaca, Mexico
| | - Mykola Kakazey
- CIICAp, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, 62209 Cuernavaca, Morelos, Mexico
| | - Erick Adrian Juarez-Arellano
- Instituto de Química Aplicada, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301 Tuxtepec, Oaxaca, Mexico.
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Bowling JD, O'Malley KJ, Klimstra WB, Hartman AL, Reed DS. A Vibrating Mesh Nebulizer as an Alternative to the Collison Three-Jet Nebulizer for Infectious Disease Aerobiology. Appl Environ Microbiol 2019; 85:e00747-19. [PMID: 31253680 PMCID: PMC6696971 DOI: 10.1128/aem.00747-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/23/2019] [Indexed: 11/20/2022] Open
Abstract
Experimental infection of animals with aerosols containing pathogenic agents is essential for an understanding of the natural history and pathogenesis of infectious disease as well as evaluation of potential treatments. We evaluated whether the Aeroneb nebulizer, a vibrating mesh nebulizer, would serve as an alternative to the Collison nebulizer, the "gold standard" for generating infectious bioaerosols. While the Collison possesses desirable properties that have contributed to its longevity in infectious disease aerobiology, concerns have lingered about the liquid volume and concentration of the infectious agent required to cause disease and the damage that jet nebulization causes to the agent. Fluorescein salt was added to the nebulizer contents to assess pathogen loss during aerosolization. Relative to fluorescein salt, loss of influenza virus during aerosolization was worse with the Collison than with the Aeroneb. Four other viruses also had superior aerosol performance with the Aeroneb. The Aeroneb did not improve the aerosol performance for a vegetative bacterium, Francisella tularensis Environmental parameters collected during the aerosol challenges indicated that the Aeroneb generated a higher relative humidity in exposure chambers while not affecting other environmental parameters. The aerosol mass median aerodynamic diameter (MMAD) was generally larger and more disperse for aerosols generated by the Aeroneb than what is seen with the Collison, but ≥80% of particles were within the range that would reach the lower respiratory tract and alveolar regions. The improved aerosol performance and generated particle size range suggest that for viral pathogens, the Aeroneb is a suitable alternative to the Collison three-jet nebulizer for use in experimental infection of animals.IMPORTANCE Respiratory infection by pathogens via aerosol remains a major concern for both natural disease transmission as well as intentional release of biological weapons. Critical to understanding the disease course and pathogenesis of inhaled pathogens are studies in animal models conducted under tightly controlled experimental settings, including the inhaled dose. The route of administration, particle size, and dose can affect disease progression and outcome. Damage to or loss of pathogens during aerosolization could increase the dose required to cause disease and could stimulate innate immune responses, altering outcome. Aerosol generators that reduce pathogen loss would be ideal. This study compares two aerosol generators to determine which is superior for animal studies. Aerosol research methods and equipment need to be well characterized to optimize the development of animal models for respiratory pathogens, including bioterrorism agents. This information will be critical for pivotal efficacy studies in animals to evaluate potential vaccines or treatments against these agents.
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Affiliation(s)
- Jennifer D Bowling
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Katherine J O'Malley
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - William B Klimstra
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Amy L Hartman
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Douglas S Reed
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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50
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Stolze N, Bader C, Henning C, Mastin J, Holmes AE, Sutlief AL. Automated image analysis with ImageJ of yeast colony forming units from cannabis flowers. J Microbiol Methods 2019; 164:105681. [PMID: 31381981 DOI: 10.1016/j.mimet.2019.105681] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 11/18/2022]
Abstract
Currently, in the state of Colorado and all other states within the United States of America with legalized marijuana programs, testing is required for bacteria, yeast, and mold on marijuana products. The Code of Colorado Regulations, 1 CCR 212-1, considers a passing result when a 1 g sample contains <104 colony forming units (CFU) for the total yeast and mold count (TYMC). These measurements are usually obtained by manually counting colonies on petri-dishes or 3 M™ Petrifilms™, which is a time consuming and user subjective process. Therefore, an automated counting method utilizing ImageJ has been developed for CFU analysis of TYMC on Petrifilms. The performance of this colony counting method was demonstrated by comparing manual and automated counts from marijuana flower samples containing spikes of Candida albicans as well as samples that tested positive for the presence of yeast and mold. Fifteen images of Petrifilms showing various concentrations of colonies were studied by fifteen users at two institutions using both the automated and manual counting methods. All counts from the automated ImageJ procedure were within 12% of those obtained manually. In twelve out of fifteen Petrifilms, the average count of the automated method was statistically similar to the manual counts. The statistical differences of the other three samples were observed to be random and caused by user errors. The automated counting method could be used to quickly count numbers that are as high as 400 CFUs, reducing time of analysis with improved documentation because the images and the electronic colony counts can be saved on a computer or cloud for long term storage and data access.
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Affiliation(s)
| | - Carly Bader
- AgriScience Labs, Denver, Colorado, United States of America
| | | | - Jared Mastin
- AgriScience Labs, Denver, Colorado, United States of America
| | - Andrea E Holmes
- Doane University, Crete, Nebraska, United States of America; AgriScience Labs, Denver, Colorado, United States of America
| | - Arin L Sutlief
- Doane University, Crete, Nebraska, United States of America.
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