scholarly journals Machine Learning Prediction of Resistance to Subinhibitory Antimicrobial Concentrations from Escherichia coli Genomes

mSystems ◽  
2021 ◽  
Vol 6 (4) ◽  
Author(s):  
Sam Benkwitz-Bedford ◽  
Martin Palm ◽  
Talip Yasir Demirtas ◽  
Ville Mustonen ◽  
Anne Farewell ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Growth ◽  
Predictive Power ◽  
Clinical Diagnostics ◽  
Genome Sequences ◽  
Novel Targets ◽  
Rapid Characterization ◽  
The Relationship ◽  
Natural Strains

Predicting bacterial growth from genome sequences is important for a rapid characterization of strains in clinical diagnostics and to disclose candidate novel targets for anti-infective drugs. Previous studies have dissected the relationship between bacterial growth and genotype in mutant libraries for laboratory strains, yet no study so far has examined the predictive power of genome sequence in natural strains.

scholarly journals Genomic characterization of 99 viruses from the bunyavirus families Nairoviridae, Peribunyaviridae, and Phenuiviridae, including 35 previously unsequenced viruses

2021 ◽  
Vol 17 (3) ◽  
pp. e1009315
Author(s):  
Marylee L. Kapuscinski ◽  
Nicholas A. Bergren ◽  
Brandy J. Russell ◽  
Justin S. Lee ◽  
Erin M. Borland ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Reference Sequence ◽  
Large Sample Size ◽  
Emerging Pathogens ◽  
Genome Sequences ◽  
Pathogenic Potential ◽  
Genomic Characterization ◽  
Response Decisions ◽  
Rapid Characterization

Bunyaviruses (Negarnaviricota: Bunyavirales) are a large and diverse group of viruses that include important human, veterinary, and plant pathogens. The rapid characterization of known and new emerging pathogens depends on the availability of comprehensive reference sequence databases that can be used to match unknowns, infer evolutionary and pathogenic potential, and make response decisions in an evidence-based manner. In this study, we determined the coding-complete genome sequences of 99 bunyaviruses in the Centers for Disease Control and Prevention’s Arbovirus Reference Collection, focusing on orthonairoviruses (family Nairoviridae), orthobunyaviruses (Peribunyaviridae), and phleboviruses (Phenuiviridae) that either completely or partially lacked genome sequences. These viruses had been collected over 66 years from 27 countries from vertebrates and arthropods representing 37 genera. Many of the viruses had been characterized serologically and through experimental infection of animals but were isolated in the pre-sequencing era. We took advantage of our unusually large sample size to systematically evaluate genomic characteristics of these viruses, including reassortment, and co-infection. We corroborated our findings using several independent molecular and virologic approaches, including Sanger sequencing of 197 genome segments, and plaque isolation of viruses from putative co-infected virus stocks. This study contributes to the described genetic diversity of bunyaviruses and will enhance the capacity to characterize emerging human pathogenic bunyaviruses.

scholarly journals Characterization of the β-lactamase specified by the resistance factor R-1818 in Escherichia coli K12 and other Gram-negative bacteria

1971 ◽  
Vol 123 (4) ◽  
pp. 501-505 ◽  
Author(s):  
J. W. Dale
Keyword(s):  
Escherichia Coli ◽  
Host Species ◽  
Host Bacterium ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
E Coli ◽  
R Factor ◽  
Relationship Of ◽  
The Relationship

1. The amino acid composition of the β-lactamase from E. coli (R-1818) was determined. 2. The R-1818 β-lactamase is inhibited by formaldehyde, hydroxylamine, sodium azide, iodoacetamide, iodine and sodium chloride. 3. The Km values for benzylpenicillin, ampicillin and oxacillin have been determined by using the R-factor enzyme from different host species. The same values were obtained, irrespective of the host bacterium. 4. The molecular weight of the enzyme was found to be 44600, and was the same for all host species. 5. The relationship of R-1818 and R-GN238 β-lactamases is discussed.

Influence of pyrolytic seeds on ZnO nanorod growth onto rigid substrates for photocatalytic abatement of Escherichia coli in water

2014 ◽  
Vol 14 (6) ◽  
pp. 1087-1094 ◽  
Author(s):  
Luis Sanchez ◽  
Lucas Guz ◽  
Pilar García ◽  
Silvia Ponce ◽  
Silvia Goyanes ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibacterial Activity ◽  
Zno Nanorods ◽  
Water Disinfection ◽  
Acetate Solution ◽  
Ethanol Mixture ◽  
E Coli ◽  
The Relationship ◽  
Nanorod Growth

ZnO nanorods (ZnO NRs) were grown on ZnO seeded fluorine doped tin oxide (FTO) substrates at low temperatures (90 °C) from Zn2+ precursors in alkaline aqueous solution. The ZnO seeds were deposited on the FTO substrate heated at 350 °C by spray pyrolysis of a zinc acetate solution in a water ethanol mixture. The structure of seeds was tuned by the ethanol water ratio, Γ, which controls the solvent evaporation rate of drops impinging the substrate. The relationship between the microstructure and optical properties of the ZnO NR films and the photocatalytic antibacterial activity for Escherichia coli abatement, was determined through a detailed characterization of the material. The higher photocatalytic antibacterial activity was performed by ZnO NR films grown on seeds deposited from solutions with Γ in the 0.0–0.03 range. With these films, the population of viable E. coli dropped more than six orders, from 8 × 108 to 4 × 102 CFU. These results show the potential of these materials in water disinfection.

Nanomechanical sensors for direct and rapid characterization of sperm motility based on nanoscale vibrations

Nanoscale ◽  
2017 ◽  
Vol 9 (46) ◽  
pp. 18258-18267 ◽  
Author(s):  
Shangquan Wu ◽  
Zhiguo Zhang ◽  
Xiarong Zhou ◽  
Hong Liu ◽  
Changguo Xue ◽  
...  
Keyword(s):  
Sperm Motility ◽  
Sperm Viability ◽  
Rapid Characterization ◽  
The Relationship ◽  
Insight Into ◽  
Gaining Insight ◽  
Nanomechanical Sensors

A nanomechanical biosensor was developed for gaining insight into the relationship between the sperm viability and nanomechanical fluctuation.

scholarly journals Rapid Genomic-Scale Analysis of Escherichia coli O104:H4 by Using High-Resolution Alternative Methods to Next-Generation Sequencing

2011 ◽  
Vol 78 (5) ◽  
pp. 1601-1605 ◽  
Author(s):  
Scott A. Jackson ◽  
Michael L. Kotewicz ◽  
Isha R. Patel ◽  
David W. Lacher ◽  
Jayanthi Gangiredla ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Strain Differences ◽  
Alternative Methods ◽  
Scale Analysis ◽  
Content Type ◽  
Outbreak Investigations ◽  
Genomic Scale ◽  
Rapid Characterization ◽  
Generation Sequencing

ABSTRACTTwo technologies, involving DNA microarray and optical mapping, were used to quickly assess gene content and genomic architecture of recent emergentEscherichia coliO104:H4 and related strains. In real-time outbreak investigations, these technologies can provide congruent perspectives on strain, serotype, and pathotype relationships. Our data demonstrated clear discrimination between clinically, temporally, and geographically distinct O104:H4 isolates and rapid characterization of strain differences.

scholarly journals Genetic Characterization of Escherichia coli Populations from Host Sources of Fecal Pollution by Using DNA Fingerprinting

2003 ◽  
Vol 69 (5) ◽  
pp. 2587-2594 ◽  
Author(s):  
Sandra L. McLellan ◽  
Annette D. Daniels ◽  
Alissa K. Salmore
Keyword(s):  
Escherichia Coli ◽  
Pairwise Comparison ◽  
Fecal Pollution ◽  
Host Animal ◽  
Host Group ◽  
E Coli ◽  
Single Host ◽  
Relationship Of ◽  
The Relationship

ABSTRACT Escherichia coli isolates were obtained from common host sources of fecal pollution and characterized by using repetitive extragenic palindromic (REP) PCR fingerprinting. The genetic relationship of strains within each host group was assessed as was the relationship of strains among different host groups. Multiple isolates from a single host animal (gull, human, or dog) were found to be identical; however, in some of the animals, additional strains occurred at a lower frequency. REP PCR fingerprint patterns of isolates from sewage (n = 180), gulls (n = 133), and dairy cattle (n = 121) were diverse; within a host group, pairwise comparison similarity indices ranged from 98% to as low as 15%. A composite dendrogram of E. coli fingerprint patterns did not cluster the isolates into distinct host groups but rather produced numerous subclusters (approximately >80% similarity scores calculated with the cosine coefficient) that were nearly exclusive for a host group. Approximately 65% of the isolates analyzed were arranged into host-specific groups. Comparable results were obtained by using enterobacterial repetitive intergenic consensus PCR and pulsed-field gel electrophoresis (PFGE), where PFGE gave a higher differentiation of closely related strains than both PCR techniques. These results demonstrate that environmental studies with genetic comparisons to detect sources of E. coli contamination will require extensive isolation of strains to encompass E. coli strain diversity found in host sources of contamination. These findings will assist in the development of approaches to determine sources of fecal pollution, an effort important for protecting water resources and public health.

Development of a Method for the Detection of Verotoxin-Producing Escherichia coli in Food

2012 ◽  
Vol 75 (5) ◽  
pp. 827-837 ◽  
Author(s):  
ALEXANDER GILL ◽  
AMALIA MARTINEZ-PEREZ ◽  
SARAH McILWHAM ◽  
BURTON BLAIS
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Agents ◽  
Selective Enrichment ◽  
Apple Cider ◽  
Isolation And Characterization ◽  
Wide Range ◽  
Rapid Characterization ◽  
Similar Combination

The growing recognition of the role of non-O157 verotoxigenic Escherichia coli (VTEC) in foodborne illness underscores the importance of developing methods to detect it in the food supply. We describe here the development of a protocol for the detection, isolation, and characterization of VTEC from foods, designed for the serotype-independent enrichment, detection, and isolation of VTEC, in combination with rapid characterization of VTEC O157, O26, O103, O111, and O145. This study examined the inhibitory concentration of six antimicrobial agents used either singly or in combination for the optimal enrichment of a panel of 18 different O serogroups of VTEC in modified tryptic soy broth. Considerable variability in resistance to the different antimicrobials tested was noted among different VTEC strains. The combination enabling growth of strains of all 18 different O serogroups was vancomycin (10 μg/ml) and cefsulodin (3 μg/ml). A similar combination of antimicrobials formulated in agar plates was found beneficial in the recovery of VTEC strains from enrichment broth cultures. The efficacy of these media in the recovery of selected VTEC (O26, O103, O111, O145, and O157) from ground beef and O157 VTEC from lettuce, spinach, and apple cider was demonstrated. The selective enrichment media described herein would appear suitable for incorporation in methods for the recovery and detection of a wide range of VTEC serogroups.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

Sign in / Sign up

Export Citation Format

Share Document