Comprehensive Evaluation of Complex Polymicrobial Specimens Using Next Generation Sequencing and Standard Microbiological Culture Lisa A
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Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. -
Biofire Blood Culture Identification System (BCID) Fact Sheet
BioFire Blood Culture Identification System (BCID) Fact Sheet What is BioFire BioFire BCID is a multiplex polymerase chain reaction (PCR) test designed to BCID? identify 24 different microorganism targets and three antibiotic resistance genes from positive blood culture bottles. What is the purpose The purpose of BCID is to rapidly identify common microorganisms and of BCID? antibiotic resistance genes from positive blood cultures so that antimicrobial therapy can be quickly optimized by the physician and the antibiotic stewardship pharmacist. It is anticipated that this will result in improved patient outcomes, decreased length of stay, improved antibiotic stewardship, and decreased costs. When will BCID be BCID is performed on all initially positive blood cultures after the gram stain is routinely performed and reported. performed? When will BCID not For blood cultures on the same patient that subsequently become positive with be routinely a microorganism showing the same morphology as the initial positive blood performed? culture, BCID will not be performed. BCID will not be performed on positive blood cultures with gram positive bacilli unless Listeria is suspected. BCID will not be performed on blood culture bottles > 8 hours after becoming positive. BCID will not be performed between 10PM-7AM on weekdays and 2PM-7AM on weekends. BCID will not be performed for clinics that have specifically opted out of testing. How soon will BCID After the blood culture becomes positive and the gram stain is performed and results be available? reported, the bottle will be sent to the core Microbiology lab by routine courier. BCID testing will then be performed. It is anticipated that total turnaround time will generally be 2-3 hours after the gram stain is reported. -
Goals of This Review Testable Concepts Fundamentals: Host
41a –Infections in the Neutropenic Cancer Patient and Hematopoietic Stem Cell Recipients Speaker: Kieren Marr, MD Disclosures of Financial Relationships with Relevant Commercial Interests • Consultant – Amplyx, Cidara, Merck and Company, Infections in the Neutropenic Cancer Patient and Sfunga Therapeutics Hematopoietic Stem Cell Recipients • Ownership Interests – MycoMed Technologies Kieren Marr, MD Professor of Medicine and Oncology John Hopkins University School of Medicine Director, Transplant and Oncology Infectious Diseases John Hopkins University School of Medicine Goals of This Review Testable Concepts • Immune compromised people develop “typical” • Think about the patient infections and those specific to their underlying risks – How does underlying disease impact risks? • Focus here on testable complications specific to the • Think about the treatment received host – What type of immune suppression? – Types of immune – suppressing drugs and diseases • Think about infections breaking through preventative – Recognition of specific “neutropenic syndromes” therapies • Skin lesions – A good context to test resistance and differentials • Invasive fungal infections • Think about common non‐infectious syndromes • Neutropenic colitis Fundamentals: Host Immune Risks Classic Immunologic risks • Immune defects associated with underlying • Neutropenia malignancy (and prior therapies) – Prolonged (>10 days) and profound (< 500 cells / mm3) – AML and myelodysplastic syndromes (MDS) associated with high risks for severe bacterial and fungal • -
Abstract: Introduction: Investigation Into The
C-109 ASM 106th General Convention - Orlando, Florida - May 22-24, 2006 INVESTIGATION INTO THE EFFECT OF TEMPERATURE ON THE ViaBILITY OF FaSTIDIOUS AND NON-FaSTIDIOUS BaCTERia IN TWO COMMERCiaL AMIES GEL TRANSPORT SYSTEMS: BD CULTURESWAB MaX V(+) AND REMEL BaCTiSWAB. C. BIGGS, THE CHESTER COUNTY HOSPITAL THE CHESTER COUNTY HOSPITAL West Chester, Pennsylvania ABSTRACT: At The Chester County Hospital we use basic insulated cooler boxes with Downingtown, Exton, Kennett Square, and Lionville, Pennsylvania that ice packs for transport of bacteriology swabs from outreach clinics and include various out-patient labs and drawing stations that collect throat physicians offices. During July 2005 we monitored the internal tempera- cultures and urine samples. In addition to this we collect samples from ture of these coolers using digital temperature recorders. Average daily various physicians’ offices. The microbiology lab utilizes a contract cou- temperatures ranged between 11.4 - 19.8º C with peaks as high as 24.3º rier service that is shared with other hospital departments which manages C. We decided to evaluate viability of fastidious bacteria in two Amies Gel the collection of patient samples throughout the day within the network. swab transports; Becton Dickinson CultureSwab Max V(+) (BD) and Transit times for microbiology specimens can vary from 15 minutes Remel BactiSwab (RE) held at room temperature (RT) 20 – 25º C and to several hours depending on timing and courier routing. Before the refrigerator temperature (RF) 4 – 8º C to understand if upgrading our summer of 2005 we had followed guidelines that appear in microbiology coolers to units with electrical refrigeration might improve recovery of reference manuals which advocate the shipment of microbiology swab organisms from swabs. -
Pdfs/ Ommended That Initial Cultures Focus on Common Pathogens, Pscmanual/9Pscssicurrent.Pdf)
Clinical Infectious Diseases IDSA GUIDELINE A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiologya J. Michael Miller,1 Matthew J. Binnicker,2 Sheldon Campbell,3 Karen C. Carroll,4 Kimberle C. Chapin,5 Peter H. Gilligan,6 Mark D. Gonzalez,7 Robert C. Jerris,7 Sue C. Kehl,8 Robin Patel,2 Bobbi S. Pritt,2 Sandra S. Richter,9 Barbara Robinson-Dunn,10 Joseph D. Schwartzman,11 James W. Snyder,12 Sam Telford III,13 Elitza S. Theel,2 Richard B. Thomson Jr,14 Melvin P. Weinstein,15 and Joseph D. Yao2 1Microbiology Technical Services, LLC, Dunwoody, Georgia; 2Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; 3Yale University School of Medicine, New Haven, Connecticut; 4Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland; 5Department of Pathology, Rhode Island Hospital, Providence; 6Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill; 7Department of Pathology, Children’s Healthcare of Atlanta, Georgia; 8Medical College of Wisconsin, Milwaukee; 9Department of Laboratory Medicine, Cleveland Clinic, Ohio; 10Department of Pathology and Laboratory Medicine, Beaumont Health, Royal Oak, Michigan; 11Dartmouth- Hitchcock Medical Center, Lebanon, New Hampshire; 12Department of Pathology and Laboratory Medicine, University of Louisville, Kentucky; 13Department of Infectious Disease and Global Health, Tufts University, North Grafton, Massachusetts; 14Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, Illinois; and 15Departments of Medicine and Pathology & Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey Contents Introduction and Executive Summary I. -
Comparison of the Versatrek® and the Bact/ALERT® Blood Culture Systems for the Growth of Fastidious Microorganisms
VersaTREK Fastidious Organism Recovery 1 American Society of Microbiology Orlando, Florida - 2005 Poster C-214 Comparison of the VersaTREK® and the BacT/ALERT® Blood Culture Systems for the Growth of Fastidious Microorganisms Fastidious organism recovery in automated blood culture systems is poorly documented. For this reason, in-vitro simulations were performed at Duke University Medical Center comparing the VersaTREK Automated Microbial Detection System (VT) (TREK Diagnostic Systems, Cleveland, OH) to the BacT/ALERT system (3D) (bioMeriéux, Inc., Durham, NC). Thirty seven strains of organisms grown from frozen stocks were used in the study. Organisms were diluted in sterile saline and were targeted to achieve a concentration of 10- 100 CFU/ml. REDOX 1® and REDOX 2® bottles from TREK Diagnostic Systems and BacT/ALERT standard aerobic and anaerobic bottles from bioMeriéux were inoculated with the organisms. The bottles were supplemented with fresh human blood prior to incubation in their respective instrument. To further assess media performance, identical bottles were inoculated with the same organism set and were not supplemented with blood. Parameters assessed in the analysis included recovery of the organisms and mean time to detection in hours for both systems in bottles with and without blood. Results demonstrated the VT REDOX 1 bottle was the most productive bottle in the study. The REDOX 1 bottle (with blood) yielded faster time to detection compared to bioMeriéux standard aerobic bottles for 100% of all aerobic organisms tested. Overall detection for VT was 100% (37/37) compared to 97.0% (36/37) for the 3D system with blood supplementation. The VT system had an overall recovery rate of 94.6% (35/37) compared to 86.5% (32/37) for the 3D system without blood supplementation. -
Tenggerimyces Flavus Sp. Nov., Isolated from Soil in a Karst Cave, and Emended Description of the Genus Tenggerimyces
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 1499–1505 DOI 10.1099/ijsem.0.000908 Tenggerimyces flavus sp. nov., isolated from soil in a karst cave, and emended description of the genus Tenggerimyces Xiao-Jun Li,1,2 Su-Juan Dai,1 Shao-Wei Liu,1 Jia-Meng Liu,1 Li Chen,3 Lin Hu3 and Cheng-Hang Sun1 Correspondence 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Cheng-Hang Sun Medical College, Beijing 100050, PR China [email protected] or 2College of laboratory Medical Science, Hebei North University, Zhangjiakou 075000, PR China [email protected] 3Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China A novel actinomycete, designated strain S6R2A4-9T, was isolated from a soil sample collected from a karst cave in Henan Province, China, and subjected to a polyphasic taxonomic study. This isolate grew optimally at 25–28 8C, pH 6.5–8.0 and in the absence of NaCl. The substrate mycelium of the isolate was well developed with irregular branches. Aerial mycelium fragmented into long, rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain S6R2A4-9T resided in the cluster of the genus Tenggerimyces within the family Nocardioidaceae and shared the highest 16S rRNA gene sequence similarity (98.98 %) with Tenggerimyces mesophilus I12A-02601T. The G+C content of the genomic DNA was 67.0 mol%. The strain contained glucose, ribose and xylose in its whole-cell hydrolysates. Strain S6R2A4-9T possessed a novel variation of peptidoglycan derived from the type A1c meso-Dpm-direct. -
Rhizosphere Soil Microbial Properties on Tetraena Mongolica in the Arid and Semi-Arid Regions, China
International Journal of Environmental Research and Public Health Article Rhizosphere Soil Microbial Properties on Tetraena mongolica in the Arid and Semi-Arid Regions, China Mengying Ruan 1, Yuxiu Zhang 1,* and Tuanyao Chai 2 1 School of Chemical and Environmental Engineering, China University of Mining & Technology-Beijing, Beijing 100083, China; [email protected] 2 College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China; [email protected] * Correspondence: [email protected]; Tel.: +86-010-62331792 Received: 26 June 2020; Accepted: 13 July 2020; Published: 16 July 2020 Abstract: Tetraena mongolica is a rare and endangered species unique to China. The total number and density of Tetraena mongolica shrubs in desertification areas have experienced a sharp decrease with increases in coal mining activities. However, available information on the T. mongolica rhizosphere soil quality and microbial properties is scarce. Here, we investigated the effect of coal mining on the soil bacterial community and its response to the soil environment in the T. mongolica region. The results showed that the closer to the coal mining area, the lower the vegetation coverage and species diversity. The electrical conductivity (EC) in the contaminated area increased, while the total nitrogen (TN), available phosphorus (AP), available potassium (AK), and soil organic carbon (SOC) decreased. The activity of NAG, sucrose, β-glucosidase, and alkaline phosphatase further decreased. In addition, the mining area could alter the soil’s bacterial abundance and diversity. The organic pollutant degradation bacteria such as Sphingomonas, Gemmatimonas, Nocardioides, and Gaiella were enriched in the soil, and the carbon-nitrogen cycle was changed. -
Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergol
applied sciences Article Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland Magdalena Dyda 1,2,* , Agnieszka Laudy 3, Przemyslaw Decewicz 4 , Krzysztof Romaniuk 4, Martyna Ciezkowska 4, Anna Szajewska 5 , Danuta Solecka 6, Lukasz Dziewit 4 , Lukasz Drewniak 4 and Aleksandra Skłodowska 1 1 Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] 2 Research and Development for Life Sciences Ltd. (RDLS Ltd.), Miecznikowa 1/5a, 02-096 Warsaw, Poland 3 Laboratory of Environmental Analysis, Museum of King John III’s Palace at Wilanow, Stanislawa Kostki Potockiego 10/16, 02-958 Warsaw, Poland; [email protected] 4 Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] (P.D.); [email protected] (K.R.); [email protected] (M.C.); [email protected] (L.D.); [email protected] (L.D.) 5 The Main School of Fire Service, Slowackiego 52/54, 01-629 Warsaw, Poland; [email protected] 6 Department of Plant Molecular Ecophysiology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] * Correspondence: [email protected] or [email protected]; Tel.: +48-786-28-44-96 Citation: Dyda, M.; Laudy, A.; Abstract: The aim of the presented investigation was to describe seasonal changes of microbial com- Decewicz, P.; Romaniuk, K.; munity composition in situ in different biocenoses on historical sandstone of the Northern Pergola in Ciezkowska, M.; Szajewska, A.; the Museum of King John III’s Palace at Wilanow (Poland). -
Fis-His-2020-Abstract-Supplement-Free-Paper.Pdf
Abstract supplement (free paper abstracts) FIS/HIS International 2020 cannot be held responsible for errors or inconsistencies contained within the abstract supplement. Only major formatting alterations have been made and abstract content remains consistent with what was entered at time of submission by the author/s. How to search this document Laptop, PC or similar: ‘Ctrl’ + ‘F’ or ‘Edit’ then ‘Find’ Smart device: Open this PDF in either the 'iBooks' app (Apple) or 'My Files' app (Android). Both are built in apps and have a magnifying glass search icon. Contents A quick reference guide by topic, paper number and presentation type can be found at the end of the document or click here. (Click paper title to take you straight there) Free paper oral presentations 11: Investigations, actions and learning from an outbreak of SARS-CoV-2 infection among health care workers in the United Kingdom ........................................................................................................................ 13 12: Procalcitonin as an antibiotic stewardship tool in COVID-19 patients in the intensive care ...................... 14 20: Impact of antibiotic timing on mortality from Gram negative Bacteraemia in an English District General Hospital: the importance of getting it right every time .................................................................................... 15 35: Case report: A fall in the forest ................................................................................................................... 16 65: Not -
Use of the Diagnostic Bacteriology Laboratory: a Practical Review for the Clinician
148 Postgrad Med J 2001;77:148–156 REVIEWS Postgrad Med J: first published as 10.1136/pmj.77.905.148 on 1 March 2001. Downloaded from Use of the diagnostic bacteriology laboratory: a practical review for the clinician W J Steinbach, A K Shetty Lucile Salter Packard Children’s Hospital at EVective utilisation and understanding of the Stanford, Stanford Box 1: Gram stain technique University School of clinical bacteriology laboratory can greatly aid Medicine, 725 Welch in the diagnosis of infectious diseases. Al- (1) Air dry specimen and fix with Road, Palo Alto, though described more than a century ago, the methanol or heat. California, USA 94304, Gram stain remains the most frequently used (2) Add crystal violet stain. USA rapid diagnostic test, and in conjunction with W J Steinbach various biochemical tests is the cornerstone of (3) Rinse with water to wash unbound A K Shetty the clinical laboratory. First described by Dan- dye, add mordant (for example, iodine: 12 potassium iodide). Correspondence to: ish pathologist Christian Gram in 1884 and Dr Steinbach later slightly modified, the Gram stain easily (4) After waiting 30–60 seconds, rinse with [email protected] divides bacteria into two groups, Gram positive water. Submitted 27 March 2000 and Gram negative, on the basis of their cell (5) Add decolorising solvent (ethanol or Accepted 5 June 2000 wall and cell membrane permeability to acetone) to remove unbound dye. Growth on artificial medium Obligate intracellular (6) Counterstain with safranin. Chlamydia Legionella Gram positive bacteria stain blue Coxiella Ehrlichia Rickettsia (retained crystal violet). -
Detection of Neonatal Bacteremia Using 16S Rrna Gene Amplification by Polymerase Chain Reaction
Egyptian Journal of Medical Microbiology, January 2009 Vol. 18, No. 1 Detection of Neonatal Bacteremia Using 16S rRNA Gene Amplification by Polymerase Chain Reaction Sahar M. Fayed, Azza Abo Senna and Hesham Kamel* Department of Pediatric٭ Department of Clinical Pathology, Banha Faculty of Medicine and Emergencies and Critical Care Children Hospital – Cairo University. ABSTRACT The purpose of this study was to evaluate the potential of a broad diagnostic approach based on 16S rRNA gene amplification and sequencing for rapid detection of neonatal bacteremia. Subjects and Methods: Blood samples were collected from fifty neonates admitted to the neonatal intensive care units with suspected sepsis, for paired analysis of bacterial growth using the BACTEC 9050 instrument and for bacterial 16S rRNA gene using a PCR assay with subsequent DNA sequencing for bacterial species identification. Results: The specimens were positive for bacteria in 43 cases (86%) by blood culture and 44 cases (88%) by PCR out of a total of 50 specimens analysed. There was very good agreement between the results of PCR and blood culture for detection of neonatal bacteremia (kappa ═ 0.8). Taking blood culture as a reference method, the sensitivity, specificity, positive and negative predictive values for PCR were 100%, 75%, 95.5% and 100% respectively after exclusion of candida isolate which was detected by blood culture only and not by PCR( the primer being used was 16S r RNA not 18S r RNA needed to identify fungal sepsis). Concerning the time consumed to detect sepsis, blood culture method took more time (up to 5 days) while PCR took less time <4 hour.