scholarly journals AFM in cellular and molecular microbiology

2021 ◽  
Author(s):  
Yves F. Dufrêne ◽  
Albertus Viljoen ◽  
Johann Mignolet ◽  
Marion Mathelié‐Guinlet
Keyword(s):  
Molecular Microbiology

scholarly journals Next-generation microbiology: from comparative genomics to gene function

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Carolin M. Kobras ◽  
Andrew K. Fenton ◽  
Samuel K. Sheppard
Keyword(s):  
Data Science ◽  
Genetic Basis ◽  
Turning Point ◽  
Functional Genomic ◽  
Bacterial Cells ◽  
Next Generation ◽  
New Techniques ◽  
Molecular Microbiology ◽  
Genetic Complexity ◽  
Generation Sequencing

AbstractMicrobiology is at a turning point in its 120-year history. Widespread next-generation sequencing has revealed genetic complexity among bacteria that could hardly have been imagined by pioneers such as Pasteur, Escherich and Koch. This data cascade brings enormous potential to improve our understanding of individual bacterial cells and the genetic basis of phenotype variation. However, this revolution in data science cannot replace established microbiology practices, presenting the challenge of how to integrate these new techniques. Contrasting comparative and functional genomic approaches, we evoke molecular microbiology theory and established practice to present a conceptual framework and practical roadmap for next-generation microbiology.

scholarly journals Understanding decisions about antibiotic prescribing in ICU: an application of the Necessity Concerns Framework

2021 ◽  
pp. bmjqs-2020-012479
Author(s):  
Alyssa M Pandolfo ◽  
Robert Horne ◽  
Yogini Jani ◽  
Tom W Reader ◽  
Natalie Bidad ◽  
...  
Keyword(s):  
Focus Groups ◽  
Antibiotic Prescribing ◽  
Negative Consequences ◽  
Out Of Hours ◽  
Team Members ◽  
Clinical Vignettes ◽  
Molecular Microbiology ◽  
Semistructured Interviews ◽  
Decision Making Processes ◽  
The Individual

BackgroundAntibiotics are extensively prescribed in intensive care units (ICUs), yet little is known about how antibiotic-related decisions are made in this setting. We explored how beliefs, perceptions and contextual factors influenced ICU clinicians’ antibiotic prescribing.MethodsWe conducted 4 focus groups and 34 semistructured interviews with clinicians involved in antibiotic prescribing in four English ICUs. Focus groups explored factors influencing prescribing, whereas interviews examined decision-making processes using two clinical vignettes. Data were analysed using thematic analysis, applying the Necessity Concerns Framework.ResultsClinicians’ antibiotic decisions were influenced by their judgement of the necessity for prescribing/not prescribing, relative to their concerns about potential adverse consequences. Antibiotic necessity perceptions were strongly influenced by beliefs that antibiotics would protect patients from deterioration and themselves from the ethical and legal consequences of undertreatment. Clinicians also reported concerns about prescribing antibiotics. These generally centred on antimicrobial resistance; however, protecting the individual patient was prioritised over these societal concerns. Few participants identified antibiotic toxicity concerns as a key influencer. Clinical uncertainty often complicated balancing antibiotic necessity against concerns. Decisions to start or continue antibiotics often represented ‘erring on the side of caution’ as a protective response in uncertainty. This approach was reinforced by previous experiences of negative consequences (‘being burnt’) which motivated prescribing ‘just in case’ of an infection. Prescribing decisions were also context-dependent, exemplified by a lower perceived threshold to prescribe antibiotics out-of-hours, input from external team members and local prescribing norms.ConclusionEfforts to improve antibiotic stewardship should consider clinicians’ desire to protect with a prescription. Rapid molecular microbiology, with appropriate communication, may diminish clinicians’ fears of not prescribing or of using narrower-spectrum antibiotics.

scholarly journals Nitrification–denitrification in waste stabilisation ponds: a mechanism for permanent nitrogen removal in maturation ponds

2010 ◽  
Vol 61 (5) ◽  
pp. 1137-1146 ◽  
Author(s):  
M. A. Camargo Valero ◽  
L. F. Read ◽  
D. D. Mara ◽  
R. J. Newton ◽  
T. P. Curtis ◽  
...  
Keyword(s):  
Nitrogen Removal ◽  
Inorganic Nitrogen ◽  
Isotope Analysis ◽  
Pilot Scale ◽  
Intermediate Step ◽  
Nitrogen Transformations ◽  
Waste Stabilisation Ponds ◽  
Molecular Microbiology ◽  
Denitrification Process ◽  
Ammonia Oxidising Bacteria

A pilot-scale primary maturation pond was spiked with 15N-labelled ammonia (15NH4Cl) and 15N-labelled nitrite (Na15NO2), in order to improve current understanding of the dynamics of inorganic nitrogen transformations and removal in WSP systems. Stable isotope analysis of δ15N showed that nitrification could be considered as an intermediate step in WSP, which is masked by simultaneous denitrification, under conditions of low algal activity. Molecular microbiology analysis showed that denitrification can be considered a feasible mechanism for permanent nitrogen removal in WSP, which may be supported either by ammonia-oxidising bacteria (AOB) or by methanotrophs, in addition to nitrite-oxidising bacteria (NOB). However, the relative supremacy of the denitrification process over other nitrogen removal mechanisms (e.g., biological uptake) depends upon phytoplanktonic activity.

scholarly journals The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo-attB sites in the genus Nocardia

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4784 ◽  
Author(s):  
Marion Herisse ◽  
Jessica L. Porter ◽  
Romain Guerillot ◽  
Takehiro Tomita ◽  
Anders Goncalves Da Silva ◽  
...  
Keyword(s):  
Genetic Manipulation ◽  
Bacterial Species ◽  
Bacterial Attachment ◽  
Single Strain ◽  
Molecular Microbiology ◽  
Attachment Sites ◽  
Phage Integrase ◽  
Foreign Dna ◽  
Stable Vectors ◽  
Target Effects

Plasmid vectors based on bacteriophage integrases are important tools in molecular microbiology for the introduction of foreign DNA, especially into bacterial species where other systems for genetic manipulation are limited. Site specific integrases catalyze recombination between phage and bacterial attachment sites (attP and attB, respectively) and the best studied integrases in the actinomycetes are the serine integrases from the Streptomyces bacteriophages ΦC31 and ΦBT1. As this reaction is unidirectional and highly stable, vectors containing phage integrase systems have been used in a number of genetic engineering applications. Plasmids bearing the ΦBT1 integrase have been used to introduce DNA into Streptomyces and Amycolatopsis strains; however, they have not been widely studied in other actinobacterial genera. Here, we show that vectors based on ΦBT1 integrase can stably integrate into the chromosomes of a range of Nocardia species, and that this integration occurs despite the absence of canonical attB sites in these genomes. Furthermore, we show that a ΦBT1 integrase-based vector can insert at multiple pseudo-attB sites within a single strain and we determine the sequence of a pseudo-attB motif. These data suggest that ΦBT1 integrase-based vectors can be used to readily and semi-randomly introduce foreign DNA into the genomes of a range of Nocardia species. However, the precise site of insertion will likely require empirical determination in each species to avoid unexpected off-target effects.

scholarly journals Amniotic Fluid Infection in Preterm Pregnancies with Intact Membranes

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Tarja Myntti ◽  
Leena Rahkonen ◽  
Irmeli Nupponen ◽  
Anu Pätäri-Sampo ◽  
Minna Tikkanen ◽  
...  
Keyword(s):  
Amniotic Fluid ◽  
Preterm Labor ◽  
Molar Ratio ◽  
Amniotic Cavity ◽  
Culture Techniques ◽  
Reactive Protein ◽  
Molecular Microbiology ◽  
Microbial Invasion ◽  
Proteolytic Cascade ◽  
Singleton Pregnancies

Introduction. Intra-amniotic infection (IAI) is a major cause of preterm labor and adverse neonatal outcome. We evaluated amniotic fluid (AF) proteolytic cascade forming biomarkers in relation to microbial invasion of the amniotic cavity (MIAC) and IAI in preterm pregnancies with intact membranes. Material and Methods. Amniocentesis was made to 73 women with singleton pregnancies; 27 with suspected IAI; and 46 controls. AF biomarkers were divided into three cascades: Cascade 1: matrix metalloproteinase-8 (MMP-8), MMP-9, myeloperoxidase (MPO), and interleukin-6; Cascade 2: neutrophil elastase (HNE), elafin, and MMP-9; Cascade 3: MMP-2, tissue inhibitor of matrix metalloproteinases-1 (TIMP-1), MMP-8/TIMP-1 molar ratio, and C-reactive protein (CRP). MMP-8 was measured by an immunoenzymometric assay and the others were measured by ELISA. Standard biochemical methods, molecular microbiology, and culture techniques were used. Results. MMP-8, MMP-9, MPO, elafin, and TIMP-1 concentrations were higher in IAI suspected cases compared to controls and also in IAI suspected cases with MIAC compared to those without MIAC when adjusted by gestational age at amniocentesis. All biomarkers except elafin and MMP-2 had the sensitivity of 100% with thresholds based on ROC-curve. Odd ratios of biomarkers for MIAC were 1.2-38 and 95% confidential intervals 1.0-353.6. Conclusions. Neutrophil based AF biomarkers were associated with IAI and MIAC.

Sign in / Sign up

Export Citation Format

Share Document