Hasil untuk "Microbiology"

J. D. Elsas, J. Trevors, J. Jansson et al.

Soil Environment, D. Standing and K. Killham Microbial Phylogeny and Diversity in Soil, V. Torsvik and L. Ovreas Horizontal Gene Transfer and Microevolution in Soil, K.M. Nielsen, Pal Johnsen, and J.D. van Elsas Bacteria and Archaea in Soil, J. D. van Elsas, V. Torsvik, A. Hartmann, L. Ovreas, and J.K. Jansson Fungi in Soil, R.D. Finlay Protozoa and Other Protista in Soil, M. Clarholm, M. Bonkowsk, and B. Griffiths Microbial Interactions in Soil, J.D. van Elsas, L. Tam, R.D. Finlay, K. Killham, and J.T. Trevors Plant-Associated Bacteria-Lifestyle and Molecular Interactions, J. Sorensen and A. Sessitsch Microorganisms Cycling Soil Nutrients and Their Diversity, J.I. Prosser Soil Microbial Communities and Global Climate Change-Methanotrophic and Methanogenic Communities as Paradigms, R. Conrad Methods to Detect and Quantify Bacteria in Soil, O. Nybroe, K.K. Brandt, M.H. Nicolaisen, and J. Sorensen Analysis of Microbial Communities in Soil Microhabitats using Fluorescence In Situ Hybridization, M. Schmid, M. Rothballer, and A. Hartmann Functional Characterization of Soil Microbial Communities by Messenger RNA Analysis, S. Sharma, M.K. Anej, and M. Schloter Molecular Fingerprinting Techniques to Analyze Soil Microbial Communities, M. Oros-Sichler, R. Costa, H. Heuer, and K. Smalla Detection of Active Bacterial Populations in Soil, T.M. Timms-Wilson, R.I. Griffiths, A.S. Whiteley, J.I. Prosser, and M.J. Bailey Soil Metagenomics: Exploring and Exploiting the Soil Microbial Gene Pool, S. Sjoling, W. Stafford, and D.A. Cowan Biosensors to Monitor Soil Health or Toxicity, P.H.B. Poulsen, L. Hestbjerg Hansen, and S.J. Sorensen Soil Suppressiveness to Plant Diseases, C. Steinberg, V. Edel-Hermann, C. Alabouvette, and P. Lemanceau Biological Pesticides for Control of Seed- and Soil-Borne Plant Pathogens, J.M. Whipps and B. Gerhardson Plant Growth-Promoting Bacteria, S. Saleh and B.R. Glick Biodegradation and Bioremediation of Organic Pollutants in Soil, K.T. Leung, K. Nandakumar, K. Sreekumari, H. Lee, and J.T. Trevors Statistical Analyses of Microbiological and Environmental Data, B.B. McSpadden Gardener Glossary Modern Soil Microbiology Index

M. López-Siles, S. Duncan, L. Garcia-Gil et al.

P. Murray, E. Baron, J. Jorgensen et al.

E. Paul, F. Clark

J. M. Jay

A. Klainer

K. Alef, P. Nannipieri

P. Cotter, C. Hill, R. Ross

R. Amann, L. Krumholz, D. A. Stahl

C. Winn

A. Balows

J. van Prehn, E. Reigadas, E. Vogelzang et al.

SCOPE In 2009, the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) published the first treatment guidance document for Clostridioides difficile infection (CDI). This document was updated in 2014. The growing literature on CDI antimicrobial treatment and novel treatment approaches, such as fecal microbiota transplantation (FMT) and toxin-binding monoclonal antibodies, prompted the ESCMID study group on C. difficile (ESGCD) to update the 2014 treatment guidance document for CDI in adults. METHODS AND QUESTIONS Key questions on CDI treatment were formulated by the guideline committee and included: what is the best treatment for initial, severe, severe-complicated, refractory, recurrent and multiple recurrent CDI; what is the best treatment when no oral therapy is possible; can prognostic factors identify patients at risk for severe and recurrent CDI; and is there a place for CDI prophylaxis? Outcome measures for treatment strategy were: clinical cure, recurrence, and sustained cure. For studies on surgical interventions and severe-complicated CDI the outcome was mortality. Appraisal of available literature and drafting of recommendations was performed by the guideline drafting group. The total body of evidence for the recommendations on CDI treatment consists of the literature described in the previous guidelines, supplemented with a systematic literature search on randomized clinical trials and observational studies from 2012 and onwards. The Grades of Recommendation Assessment, Development and Evaluation (GRADE) system was used to grade the strength of our recommendations and the quality of the evidence. The guideline committee was invited to comment on the recommendations. The guideline draft was sent to external experts and a patients' representative for review. Full ESCMID endorsement was obtained after a public consultation procedure. RECOMMENDATIONS Important changes compared with previous guideline include but are not limited to: (1) metronidazole is no longer recommended for treatment of CDI when fidaxomicin or vancomycin are available, (2) fidaxomicin is the preferred agent for treatment of initial CDI and the first recurrence of CDI when available and feasible, (3) FMT or bezlotoxumab in addition to Standard of Care antibiotics (SoC) are preferred for treatment of a second or further recurrence of CDI, (4) bezlotoxumab in addition to SoC is recommended for the first recurrence of CDI when fidaxomicin was used to manage the initial CDI episode, and (5) bezlotoxumab is considered as an ancillary treatment to vancomycin for a CDI episode with high risk of recurrence when fidaxomicin is not available. Contrary to the previous guideline, in the current guideline emphasis is placed on risk for recurrence as a factor that determines treatment strategy for the individual patient, rather than the disease severity.

J. M. Miller, M. Binnicker, S. Campbell et al.

The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician/advanced practice provider and the microbiologists who provide enormous value to the healthcare team. This document, developed by experts in laboratory and adult and pediatric clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. This document presents a system-based approach rather than specimen-based approach, and includes bloodstream and cardiovascular system infections, central nervous system infections, ocular infections, soft tissue infections of the head and neck, upper and lower respiratory infections, infections of the gastrointestinal tract, intra-abdominal infections, bone and joint infections, urinary tract infections, genital infections, and other skin and soft tissue infections; or into etiologic agent groups, including arthropod-borne infections, viral syndromes, and blood and tissue parasite infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also emphasized. There is intentional redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a guidance for physicians in choosing tests that will aid them to quickly and accurately diagnose infectious diseases in their patients.

M. Laranjo, M. G. Córdoba, T. Semedo-Lemsaddek et al.

1 Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal 2Universitary Institute for Research in Agroalimentary Resources (INURA), Escuela de Ingenieŕıas Agrarias, University of Extremadura, Avda. Adolfo Suárez s/n, 06007 Badajoz, Spain 3CIISA – Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Pólo Universitário da Ajuda, 1300-477 Lisbon, Portugal 4Departamento de Medicina Veterinária, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal

J. F. Siqueira, I. N. Rôças

Apical periodontitis has a microbial aetiology and is one of the most common inflammatory diseases that affect humans. Fungi, archaea and viruses have been found in association with apical periodontitis, but bacteria are by far the most prevalent and dominant microorganisms in endodontic infections. Bacterial infection of the root canal system only occurs when the pulp is necrotic or was removed for previous treatment. In some specific cases, including acute and chronic abscesses, the bacterial infection may reach the periradicular tissues. Intracanal bacteria are usually observed as sessile multispecies communities (biofilms) attached to the dentinal root canal walls. Infection in the main root canal lumen can spread to other areas of the root canal system. Although more than 500 bacterial species have been detected in endodontic infections, a selected group of 20 to 30 species are most frequently detected and may be considered as the core microbiome. There is a high interindividual variability in the endodontic microbiome in terms of species composition and relative abundance. Obligate anaerobic species are more abundant in the intraradicular bacterial communities of teeth with primary apical periodontitis, while both anaerobes and facultatives dominate the communities in post-treatment apical periodontitis. Bacterial interactions play an essential role in determining the overall virulence of the community, which has been regarded as the unit of pathogenicity of apical periodontitis. This article reviews the microbiologic aspects of endodontic infections and provides perspectives for future research and directions in the field.

Environmental Microbiology: Advanced Research and Multidisciplinary Applications focus on the current research on microorganisms in the environment. Contributions in the volume cover several aspects of applied microbial research, basic research on microbial ecology and molecular genetics. The reader will find a collection of topics with theoretical and practical value, allowing them to connect environmental microbiology to a variety of subjects in life sciences, ecology, and environmental science topics. Advanced topics including biogeochemical cycling, microbial biosensors, bioremediation, application of microbial biofilms in bioremediation, application of microbial surfactants, microbes for mining and metallurgical operations, valorization of waste, and biodegradation of aromatic waste, microbial communication, nutrient cycling and biotransformation are also covered. The content is designed for advanced undergraduate students, graduate students, and environmental professionals, with a comprehensive and up-to-date discussion of environmental microbiology as a discipline that has greatly expanded in scope and interest over the past several decades.

Amin Kassem, Lana Abbas, Oliver Coutinho et al.

Microorganisms play pivotal roles in shaping ecosystems and biogeochemical cycles. Their intricate interactions involve complex biochemical processes. Fourier Transform-Infrared (FT-IR) spectroscopy is a powerful tool for monitoring these interactions, revealing microorganism composition and responses to the environment. This review explores the diversity of applications of FT-IR spectroscopy within the field of microbiology, highlighting its specific utility in microbial cell biology and environmental microbiology. It emphasizes key applications such as microbial identification, process monitoring, cell wall analysis, biofilm examination, stress response assessment, and environmental interaction investigation, showcasing the crucial role of FT-IR in advancing our understanding of microbial systems. Furthermore, we address challenges including sample complexity, data interpretation nuances, and the need for integration with complementary techniques. Future prospects for FT-IR in environmental microbiology include a wide range of transformative applications and advancements. These include the development of comprehensive and standardized FT-IR libraries for precise microbial identification, the integration of advanced analytical techniques, the adoption of high-throughput and single-cell analysis, real-time environmental monitoring using portable FT-IR systems and the incorporation of FT-IR data into ecological modeling for predictive insights into microbial responses to environmental changes. These innovative avenues promise to significantly advance our understanding of microorganisms and their complex interactions within various ecosystems.

M. Borchardt, A. Boehm, M. Salit et al.

Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding quantitative organism-specific data of nucleic acid targets in the environment. Such data are essential for characterizing interactions and processes of microbial communities, assessing microbial contaminants in the environment (water, air, fomites), and developing interventions (water treatment, surface disinfection, air purification) to curb infectious disease transmission. However, our review of recent qPCR and dPCR literature in our field of health-related environmental microbiology showed that many researchers are not reporting necessary and sufficient controls and methods, which would serve to strengthen their study results and conclusions. Here, we describe the application, utility, and interpretation of the suite of controls needed to make high quality qPCR and dPCR measurements of microorganisms in the environment. Our presentation is organized by the discrete steps and operations typical of this measurement process. We propose systematic terminology to minimize ambiguity and aid comparisons among studies. Example schemes for batching and combining controls for efficient work flow are demonstrated. We describe critical reporting elements for enhancing data credibility, and we provide an element checklist in the Supporting Information. Additionally, we present several key principles in metrology as context for laboratories to devise their own quality assurance and quality control reporting framework. Following the EMMI guidelines will improve comparability and reproducibility among qPCR and dPCR studies in environmental microbiology, better inform engineering and public health actions for preventing disease transmission through environmental pathways, and for the most pressing issues in the discipline, focus the weight of evidence in the direction toward solutions.

G. Belibasakis, D. Belstrøm, S. Eick et al.

This narrative review summarizes the collective knowledge on periodontal microbiology, through a historical timeline that highlights the European contribution in the global field. The etiological concepts on periodontal disease culminate to the ecological plaque hypothesis and its dysbiosis-centered interpretation. Reference is made to anerobic microbiology and to the discovery of select periodontal pathogens and their virulence factors, as well as to biofilms. The evolution of contemporary molecular methods and high-throughput platforms is highlighted in appreciating the breadth and depth of the periodontal microbiome. Finally clinical microbiology is brought into perspective with the contribution of different microbial species in periodontal diagnosis, the combination of microbial and host biomarkers for this purpose, and the use of antimicrobials in the treatment of the disease.