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Journal of Medical Microbiology Mar 2021
Topics: Anti-Infective Agents; COVID-19; Humans; Infections; Microbiological Techniques; Microbiology; Periodicals as Topic; SARS-CoV-2
PubMed: 33759740
DOI: 10.1099/jmm.0.001296 -
Clinical Chemistry and Laboratory... Feb 2013Recently, different bacteriological laboratory interventions that decrease reporting time have been developed. These promising new broad-based techniques have merit,... (Review)
Review
Recently, different bacteriological laboratory interventions that decrease reporting time have been developed. These promising new broad-based techniques have merit, based on their ability to identify rapidly many bacteria, organisms difficult to grow or newly emerging strains, as well as their capacity to track disease transmission. The benefit of rapid reporting of identification and/or resistance of bacteria can greatly impact patient outcomes, with an improvement in the use of antibiotics, in the reduction of the emergence of multidrug resistant bacteria and in mortality rates. Different techniques revolve around mass spectrometry (MS) technology: matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), PCR combined with electrospray ionization-mass spectrometry (PCR/ESIMS), iPLEX MassArray system and other new evolutions combining different techniques. This report emphasizes the (r)evolution of these technologies in clinical microbiology.
Topics: Bacteriological Techniques; Mass Spectrometry; Microbiology
PubMed: 23072853
DOI: 10.1515/cclm-2012-0291 -
FEMS Microbiology Reviews Nov 2017Microbial single cell analysis has led to discoveries that are beyond what can be resolved with population-based studies. It provides a pristine view of the mechanisms... (Review)
Review
Microbial single cell analysis has led to discoveries that are beyond what can be resolved with population-based studies. It provides a pristine view of the mechanisms that organize cellular physiology, unbiased by population heterogeneity or uncontrollable environmental impacts. A holistic description of cellular functions at the single cell level requires analytical concepts beyond the miniaturization of existing technologies, defined but uncontrolled by the biological system itself. This review provides an overview of the latest advances in single cell technologies and demonstrates their potential. Opportunities and limitations of single cell microbiology are discussed using selected application-related examples.
Topics: Bacterial Physiological Phenomena; Microbiological Techniques; Microbiology; Single-Cell Analysis
PubMed: 29029257
DOI: 10.1093/femsre/fux044 -
FEBS Letters Jun 2010The exploitation of microorganisms in industrial, medical, food and environmental biotechnology requires a comprehensive understanding of their physiology. The... (Review)
Review
The exploitation of microorganisms in industrial, medical, food and environmental biotechnology requires a comprehensive understanding of their physiology. The availability of genome sequences and accumulation of high-throughput data allows gaining understanding of microbial physiology at the systems level, and genome-scale metabolic models represent a valuable framework for integrative analysis of metabolism of microorganisms. Genome-scale metabolic models are reconstructed based on a combination of genome sequence information and detailed biochemical information, and these reconstructed models can be used for analyzing and simulating the operation of metabolism in response to different stimuli. Here we discuss the requirement for having detailed physiological insight in order to exploit microorganisms for production of fuels, chemicals and pharmaceuticals. We further describe the reconstruction process of genome-scale metabolic models and different algorithms that can be used to apply these models to gain improved insight into microbial physiology.
Topics: Algorithms; Biotechnology; Environmental Microbiology; Fermentation; Food Microbiology; Genomics; Industrial Microbiology; Microbiological Phenomena; Models, Biological; Systems Biology
PubMed: 20420838
DOI: 10.1016/j.febslet.2010.04.052 -
Clinical Microbiology and Infection :... Nov 2021The importance of defining and establishing professional standards for Clinical Microbiology (CM) in Europe has long been highlighted, starting with the development of a... (Review)
Review
BACKGROUND
The importance of defining and establishing professional standards for Clinical Microbiology (CM) in Europe has long been highlighted, starting with the development of a European curriculum. The first European Curriculum in Medical Microbiology (MM) was adopted by the European Union of Medical Specialists (UEMS) council in 2017.
OBJECTIVES
This paper assesses how training programmes in CM in Europe align with the European curriculum, just under 5 years after its introduction, and reviews what methods of assessment are in use to assess the CM trainees' progress during training programmes.
SOURCES
Using an internet-based platform, a questionnaire was circulated to the full, associate and observer members of the UEMS MM section. Information collected related to the structure, content and delivery of CM training in the participating countries, as well as methods of assessment used to evaluate training progress.
CONTENT
Twenty-one countries responded, from a total of 30 countries invited to participate. All had a structured CM training programme, with a curriculum, dedicated trainers and a record of training activities. Fifteen countries require trainees to pass an exit examination, and over 60% of countries participate in continuous workplace-based assessment. Of the participating countries, 57% meet the European Training Requirements recommendation that duration of specialist training is 60 months. Regarding core competencies, all trainees gain experience in laboratory skills and infection prevention and control, but the emphasis on clinical management and antimicrobial stewardship is more varied across countries.
IMPLICATIONS
The UEMS MM curriculum has been largely adopted by 21 countries within less than 5 years of ratification, which speaks optimistically to a future of standardized quality training across Europe. The introduction of a pilot European Examination in Clinical Microbiology in 2021 is the start of a pan-European assessment of the success of the implementation of this curriculum and the first step in quality assurance for CM training in Europe.
Topics: Clinical Competence; Curriculum; Europe; European Union; Humans; Infectious Disease Medicine; Microbiology; Specialization; Surveys and Questionnaires
PubMed: 34197933
DOI: 10.1016/j.cmi.2021.06.027 -
Research in Microbiology 2010The issues of microbial taxonomy and potential interactions with a microbial commons are discussed, with emphasis on three components: characterization; classification;... (Review)
Review
The issues of microbial taxonomy and potential interactions with a microbial commons are discussed, with emphasis on three components: characterization; classification; and nomenclature. The current state of technology and the spectrum of methods that are used for phenotypic and genotypic characterization of prokaryotes, classification at different taxonomic levels and points of prokaryote nomenclature are reviewed. While all taxonomic ranks comprise a cohesive systematic framework for microorganisms, the prokaryotic genus and species provide the "working unit" of taxonomy. Since 2004, the number of validly published genera and species has increased by approximately 50%. Extensive development of technology will continue to enable ever higher resolution characterization and more refined classification of microorganisms. Characterization and classification at the species level may be most relevant for bacterial taxonomy, although reproducible differentiation at the strain level will probably prove to be more relevant for a microbial commons. A dynamic microbial taxonomy, albeit with well-founded and stable guidelines for defining microorganisms, provides an efficient organizational system for dealing with the enormous spectrum of microbial diversity.
Topics: Access to Information; Archaea; Bacteria; Bacterial Typing Techniques; Biological Specimen Banks; Classification; Information Dissemination; Microbiology; Sequence Analysis, DNA; Technology Transfer; Terminology as Topic
PubMed: 20670913
DOI: 10.1016/j.resmic.2010.05.007 -
Comptes Rendus Biologies Nov 2022I attempt in this essay to shed new light on the origins of Louis Pasteur's uniquely progressive mind and spirit and the various factors in his background and upbringing...
I attempt in this essay to shed new light on the origins of Louis Pasteur's uniquely progressive mind and spirit and the various factors in his background and upbringing that shaped them. There is, however, very limited documentation on the early period of Pasteur's life, apart from his son-in-law's (René Vallery-Radot) biographical account, and this is considered by many as more akin to a work of hagiography. We do have, on the other hand, Pasteur's correspondence with his parents and sisters as compiled and annotated by his grandson, Louis Pasteur Vallery-Radot. Using these limited sources, combined with what we know about Pasteur's home environment and early education, his cultural influences (like the books he read), and his drawings and etchings, I have attempted in this essay to hypothesize regarding the influences during Pasteur's childhood, adolescence, and very early adult years as a scientist and how they contributed to the formation of Pasteur's mind and spirit, while fully acknowledging the extent to which this is based on indirect evidence and, occasionally, outright speculation.
Topics: Humans; Famous Persons; Microbiology
PubMed: 36852596
DOI: 10.5802/crbiol.91 -
Environmental Microbiology Jan 2023
Topics: Ecology; Environmental Microbiology; Microbiology
PubMed: 36181387
DOI: 10.1111/1462-2920.16232 -
ELife Oct 2019Plant leaves constitute a huge microbial habitat of global importance. How microorganisms survive the dry daytime on leaves and avoid desiccation is not well understood....
Plant leaves constitute a huge microbial habitat of global importance. How microorganisms survive the dry daytime on leaves and avoid desiccation is not well understood. There is evidence that microscopic surface wetness in the form of thin films and micrometer-sized droplets, invisible to the naked eye, persists on leaves during daytime due to deliquescence - the absorption of water until dissolution - of hygroscopic aerosols. Here, we study how such microscopic wetness affects cell survival. We show that, on surfaces drying under moderate humidity, stable microdroplets form around bacterial aggregates due to capillary pinning and deliquescence. Notably, droplet-size increases with aggregate-size, and cell survival is higher the larger the droplet. This phenomenon was observed for 13 bacterial species, two of which - and - were studied in depth. Microdroplet formation around aggregates is likely key to bacterial survival in a variety of unsaturated microbial habitats, including leaf surfaces.
Topics: Microbial Viability; Plant Leaves; Water Microbiology
PubMed: 31610846
DOI: 10.7554/eLife.48508 -
Revista Espanola de Quimioterapia :... Oct 2016The various species included in the genus Clostridium are very heterogeneous, both from a phenotypic and a phylogenetic point of view. The advances in polyphasic... (Review)
Review
The various species included in the genus Clostridium are very heterogeneous, both from a phenotypic and a phylogenetic point of view. The advances in polyphasic taxonomy, particularly in phylogeny, are allowing to resolve this dysfunction reclassifying several species in other genres, although there is still work to be done. Changes in generic denominations are quite normal in taxonomy, but can turn into a problem when they affect species with strong clinical impact and that have been recognised for a long time, as in the case of some traditional Clostridium species. After knowing these changes clinical microbiologists, in whose work taxonomy is an essential tool, should evaluate what matters most, if the communication with other health professionals or the phylogeny, and think about the possibility of combining both things. This paper reviews some of the taxonomic changes that have took place in well-known Clostridium species that can be clinically interesting and evaluates, as far as possible, their significance in the scientific and medical communication.
Topics: Animals; Classification; Clostridium; Clostridium Infections; Humans; Microbiology; Phylogeny; Species Specificity; Terminology as Topic
PubMed: 27628950
DOI: No ID Found