المؤلفون: Donald C. Hall, Phillip Palmer, Hai-Feng Ji, Garth D. Ehrlich, Jarosław E. Król

المصدر: Frontiers in Microbiology, Vol 12 (2021)
Frontiers in Microbiology

مصطلحات موضوعية: Microbiology (medical), 3d printed, antimicrobial properties, Coronavirus disease 2019 (COVID-19), PLA polymer, Nanotechnology, medicine.disease_cause, Microbiology, biofilm, Biofouling, 03 medical and health sciences, medicine, Biofilm growth, 030304 developmental biology, Original Research, 0303 health sciences, 3D structures, biology, 030306 microbiology, Chemistry, Pseudomonas aeruginosa, surface topology, Biofilm, 3D printing, Antimicrobial, biology.organism_classification, QR1-502, bacterial infections, Bacteria

الوصف: Recent advances in 3D printing have led to a rise in the use of 3D printed materials in prosthetics and external medical devices. These devices, while inexpensive, have not been adequately studied for their ability to resist biofouling and biofilm buildup. Bacterial biofilms are a major cause of biofouling in the medical field and, therefore, hospital-acquired, and medical device infections. These surface-attached bacteria are highly recalcitrant to conventional antimicrobial agents and result in chronic infections. During the COVID-19 pandemic, the U.S. Food and Drug Administration and medical officials have considered 3D printed medical devices as alternatives to conventional devices, due to manufacturing shortages. This abundant use of 3D printed devices in the medical fields warrants studies to assess the ability of different microorganisms to attach and colonize to such surfaces. In this study, we describe methods to determine bacterial biofouling and biofilm formation on 3D printed materials. We explored the biofilm-forming ability of multiple opportunistic pathogens commonly found on the human body including Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus to colonize eight commonly used polylactic acid (PLA) polymers. Biofilm quantification, surface topography, digital optical microscopy, and 3D projections were employed to better understand the bacterial attachment to 3D printed surfaces. We found that biofilm formation depends on surface structure, hydrophobicity, and that there was a wide range of antimicrobial properties among the tested polymers. We compared our tested materials with commercially available antimicrobial PLA polymers.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0461d123539e449ee440ddf9ec069aafTest
https://www.frontiersin.org/articles/10.3389/fmicb.2021.646303/fullTest

المؤلفون: Rachel L. Ehrlich, Jennifer McCaffrey, Jarosław E. Król, Justin Sibert, Ming Xiao, Joshua Chang Mell, Joshua P. Earl, Steven Pastor, Garth D. Ehrlich, Donald C. Hall, Sergey Balashov, Steven Lang

المصدر: BMC Genomics, Vol 20, Iss 1, Pp 1-18 (2019)
BMC Genomics

مصطلحات موضوعية: lcsh:QH426-470, lcsh:Biotechnology, Biology, medicine.disease_cause, Sigma 70, Salt Stress, Genome, Bacterial Adhesion, Microbiology, Aggregation, Bacterial stress response, 03 medical and health sciences, Start codon, lcsh:TP248.13-248.65, Genes, Regulator, Salt concentration, Genetics, Escherichia coli, medicine, Complete genome sequence, Insertion sequence, Promoter Regions, Genetic, Curli synthesis, Gene, 030304 developmental biology, 0303 health sciences, Sequence Inversion, 030306 microbiology, Escherichia coli Proteins, Temperature, Biofilm, Chromosome Mapping, Promoter, Gene Expression Regulation, Bacterial, Carbon storage regulator, Cell aggregation, E. coli biofilm formation, lcsh:Genetics, Biofilms, Temperature stress, Genome, Bacterial, Biotechnology, Research Article, Transcription Factors

الوصف: Escherichia coliC forms more robust biofilms than the other laboratory strains. Biofilm formation and cell aggregation under a high shear force depends on temperature and salt concentrations. It is the last of fiveE. colistrains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. Here we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43,waaSBOJYZULfor LPS synthesis, andcpsBfor curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulatorcsrAgene. This insertion is located 86 bp upstream of thecsrAstart codon inside the −35 region of P4 promoter and blocks the transcription from the sigma32and sigma70promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of thecsgDgene, which may drive its overexpression in biofilm. And finally,E. coliC encodes an additional sigma70subunit overexpressed in biofilm and driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions and total expression profiles using RNA-seq analyses comparing planktonic and biofilm envirovars provided insights into understanding this regulatory pathway inE. coli.IMPORTANCEBiofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains ofE. coligrown for decadesin vitrohave evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain ofE. coliC produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence as well as gene expression profiles of both the biofilm and planktonic envirovars of this classic strain, which provide for a base level of characterization and make it useful for many biofilm-based applications.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::730c14693a9e041ef5fcd576b08ff6cfTest
https://doi.org/10.1101/523134Test

المؤلفون: Jarosław E. Król, Hai-Feng Ji, John P. Cahill, Garth D. Ehrlich, Donald C. Hall

المصدر: Microorganisms, Vol 8, Iss 1310, p 1310 (2020)
Microorganisms
Volume 8
Issue 9

مصطلحات موضوعية: Microbiology (medical), Multidrug tolerance, Stringent response, In silico, Microbiology, Article, chemistry.chemical_compound, 03 medical and health sciences, Transcription (biology), RNA polymerase, Virology, Gene expression, lcsh:QH301-705.5, in silico docking, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, drug resistance, biology, 030306 microbiology, Chemistry, fungi, Biofilm, food and beverages, stringent response, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Cell biology, antibiotic support, Enzyme, lcsh:Biology (General), persister cells, Stem cell, biofilms, Bacteria

الوصف: Biofilm infections have no approved effective medical treatments and can only be disrupted via physical means. This means that any biofilm infection that is not addressable surgically can never be eliminated and can only be managed as a chronic disease. Therefore, there is an urgent need for the development of new classes of drugs that can target the metabolic mechanisms within biofilms which render them recalcitrant to traditional antibiotics. Persister cells within the biofilm structure may play a large role in the enhanced antibiotic recalcitrance of bacteria biofilms. Biofilm persister cells can be resistant to up to 1000 times the minimal inhibitory concentrations of many antibiotics, as compared to their planktonic envirovars
they are thought to be the prokaryotic equivalent of metazoan stem cells. Their metabolic resistance has been demonstrated to be an active process induced by the stringent response that is triggered by the ribosomally-associated enzyme RelA in response to amino acid starvation. This 84-kD pyrophosphokinase produces the &ldquo
magic spot&rdquo
alarmones, collectively called (p)ppGpp. These alarmones act by directly regulating transcription by binding to RNA polymerase. These transcriptional changes lead to a major shift in cellular function to both upregulate oxidative stress-combating enzymes and down regulate major cellular functions associated with growth and replication. These changes in gene expression produce the quiescent persister cells. In this work, we describe a hybrid in silico laboratory pipeline for identifying and validating small-molecule inhibitors of RelA for use in the combinatorial treatment of bacterial biofilms as re-potentiators of classical antibiotics.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c3ee7e0474c2269b9f09564ae94c8012Test
https://doi.org/10.3390/microorganisms8091310Test

المؤلفون: Betsey Pitts, Aurélien J. Mazurie, James P. Folsom, Lee Richards, Albert E. Parker, Garth D. Ehrlich, Philip S. Stewart, Frank L. Roe

المصدر: BMC Microbiology, Vol 10, Iss 1, p 294 (2010)
BMC Microbiology

مصطلحات موضوعية: Microbiology (medical), Population, Homoserine, lcsh:QR1-502, Biology, medicine.disease_cause, Microbiology, Pilus, lcsh:Microbiology, Transcriptome, 03 medical and health sciences, chemistry.chemical_compound, medicine, education, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, 0303 health sciences, education.field_of_study, 030306 microbiology, Pseudomonas aeruginosa, Gene Expression Profiling, Biofilm, Gene Expression Regulation, Bacterial, biochemical phenomena, metabolism, and nutrition, Oxygen, Gene expression profiling, Quorum sensing, chemistry, Biofilms, Research Article

الوصف: Background Transcriptome analysis was applied to characterize the physiological activities of Pseudomonas aeruginosa grown for three days in drip-flow biofilm reactors. Conventional applications of transcriptional profiling often compare two paired data sets that differ in a single experimentally controlled variable. In contrast this study obtained the transcriptome of a single biofilm state, ranked transcript signals to make the priorities of the population manifest, and compared ranki ngs for a priori identified physiological marker genes between the biofilm and published data sets. Results Biofilms tolerated exposure to antibiotics, harbored steep oxygen concentration gradients, and exhibited stratified and heterogeneous spatial patterns of protein synthetic activity. Transcriptional profiling was performed and the signal intensity of each transcript was ranked to gain insight into the physiological state of the biofilm population. Similar rankings were obtained from data sets published in the GEO database http://www.ncbi.nlm.nih.gov/geoTest. By comparing the rank of genes selected as markers for particular physiological activities between the biofilm and comparator data sets, it was possible to infer qualitative features of the physiological state of the biofilm bacteria. These biofilms appeared, from their transcriptome, to be glucose nourished, iron replete, oxygen limited, and growing slowly or exhibiting stationary phase character. Genes associated with elaboration of type IV pili were strongly expressed in the biofilm. The biofilm population did not indicate oxidative stress, homoserine lactone mediated quorum sensing, or activation of efflux pumps. Using correlations with transcript ranks, the average specific growth rate of biofilm cells was estimated to be 0.08 h-1. Conclusions Collectively these data underscore the oxygen-limited, slow-growing nature of the biofilm population and are consistent with antimicrobial tolerance due to low metabolic activity.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::33b1336457e22e1f0ae4706633d98178Test
http://www.biomedcentral.com/1471-2180/10/294Test

المؤلفون: Duc Nguyen, Candice Johnson, Luanne Hall-Stoodley, Laura Nistico, Garth D. Ehrlich, Karthik Sambanthamoorthy, Bethany Dice, Fen Z. Hu, J. Christopher Post, Paul Stoodley, William J. Mershon

المصدر: BMC Microbiology, Vol 8, Iss 1, p 173 (2008)
BMC Microbiology

مصطلحات موضوعية: DNA, Bacterial, Microbiology (medical), Colony Count, Microbial, lcsh:QR1-502, Azithromycin, Biology, medicine.disease_cause, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Antibiotic resistance, Bacterial Proteins, Nasopharynx, Streptococcus pneumoniae, Extracellular, medicine, Deoxyribonuclease I, Humans, Child, 030304 developmental biology, 0303 health sciences, 030306 microbiology, Gene Expression Profiling, Biofilm, Biofilm matrix, Pathogenic bacteria, biochemical phenomena, metabolism, and nutrition, In vitro, Anti-Bacterial Agents, 3. Good health, Biofilms, Research Article, medicine.drug

الوصف: Background Streptococcus pneumoniae is a common respiratory pathogen and a major causative agent of respiratory infections, including otitis media (OM). Pneumococcal biofilms have been demonstrated on biopsies of the middle ear mucosa in children receiving tympanostomy tubes, supporting the hypothesis that chronic OM may involve biofilm development by pathogenic bacteria as part of the infectious process. To better understand pneumococcal biofilm formation six low-passage encapsulated nasopharyngeal isolates of S. pneumoniae were assessed over a six-eight day period in vitro. Results Multiparametric analysis divided the strains into two groups. Those with a high biofilm forming index (BFI) were structurally complex, exhibited greater lectin colocalization and were more resistant to azithromycin. Those with a low BFI developed less extensive biofilms and were more susceptible to azithromycin. dsDNA was present in the S. pneumoniae biofilm matrix in all strains and treatment with DNase I significantly reduced biofilm biomass. Since capsule expression has been hypothesized to be associated with decreased biofilm development, we also examined expression of cpsA, the first gene in the pneumococcal capsule operon. Interestingly, cpsA was downregulated in biofilms in both high and low BFI strains. Conclusion All pneumococcal strains developed biofilms that exhibited extracellular dsDNA in the biofilm matrix, however strains with a high BFI correlated with greater carbohydrate-associated structural complexity and antibiotic resistance. Furthermore, all strains of S. pneumoniae showed downregulation of the cpsA gene during biofilm growth compared to planktonic culture, regardless of BFI ranking, suggesting downregulation of capsule expression occurs generally during adherent growth.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cd3e2b96ea582231fa68fed021c62ce1Test
http://www.biomedcentral.com/1471-2180/8/173Test

المؤلفون: Richard Harold Veeh, Christopher Post, Garth D. Ehrlich, Stephan Zimmerli, Mark Quigley, Christoph A Fux, A. M. Worel

المصدر: Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. 12(4)

مصطلحات موضوعية: Microbiology (medical), Adult, DNA, Bacterial, Male, Pathology, medicine.medical_specialty, Adolescent, colonisation, Biology, DNA, Ribosomal, 03 medical and health sciences, 0302 clinical medicine, Cerebrospinal fluid, Extant taxon, RNA, Ribosomal, 16S, medicine, Humans, 0303 health sciences, Bacteria, 030306 microbiology, Biofilm, pathogenesis, Clinical course, General Medicine, Bacterial Infections, biology.organism_classification, Csf flow, Biological materials, Cerebrospinal Fluid Shunts, 3. Good health, Infectious Diseases, shunt infections, Biofilms, Microscopy, Electron, Scanning, Female, electron-microscopy, 030217 neurology & neurosurgery, Shunt (electrical)

الوصف: Cerebrospinal fluid (CSF) shunts carry a high risk of complications. Infections represent a major cause ofshunt failure. Diagnosis and therapy of such infections are complicated by the formation of bacterial biofilms attached to shunt surfaces. This study correlated the pathophysiology and clinical course of biofilm infections with microscopical findings on the respective shunts. Surface irregularities, an important risk-factor for shunt colonisation with bacteria, were found to increase over time because of silicone degradation. Scanning electron-microscopy (SEM) documented residual biological material (dead biofilm), which can further promote extant bacterial adhesion, on newly manufactured shunts. Clinical course and SEM both documented bacterial dissemination against CSF flow and the monodirectional valve. In all cases, biofilms grew on both the inner and outer surfaces of the shunts. Microscopy and conventional culture detected all bacterial shunt infections. Analyses of 16S rDNA sequences using conserved primers identified bacteria in only one of three cases, probably because of previous formalin fixation of the samples.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::abf49864e11c7b88b1789c839c3b6ae1Test
https://pubmed.ncbi.nlm.nih.gov/16524409Test