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Escherichia coli

  • Open Access
    A High-Throughput Method for Screening for Genes Controlling Bacterial Conjugation of Antibiotic Resistance
    Editor's Pick Research Article | Novel Systems Biology Techniques
    A High-Throughput Method for Screening for Genes Controlling Bacterial Conjugation of Antibiotic Resistance

    The rapid transmission of antibiotic resistance genes on conjugative plasmids between bacterial host cells is a major cause of the accelerating antibiotic resistance crisis. There are currently no experimental platforms for fast and cost-efficient screening of genetic effects on antibiotic resistance transmission by conjugation, which prevents understanding and targeting conjugation.

    Hanna Alalam, Fabrice E. Graf, Martin Palm, Marie Abadikhah, Martin Zackrisson, Jonas Boström, Alfred Fransson, Chris Hadjineophytou, Linnéa Persson, Simon Stenberg, Matilda Mattsson, Payam Ghiaci, Per Sunnerhagen, Jonas Warringer, Anne Farewell
  • Open Access
    Struggle To Survive: the Choir of Target Alteration, Hydrolyzing Enzyme, and Plasmid Expression as a Novel Aztreonam-Avibactam Resistance Mechanism
    Research Article | Clinical Science and Epidemiology
    Struggle To Survive: the Choir of Target Alteration, Hydrolyzing Enzyme, and Plasmid Expression as a Novel Aztreonam-Avibactam Resistance Mechanism

    Carbapenemase-producing Enterobacterales (CPE) is a serious global challenge with limited therapeutic options. Aztreonam-avibactam is a promising antimicrobial combination with activity against CPE producing serine-based carbapenemases and metallo-β-lactamases and has the potential to be a major option for combatting CPE. Aztreonam-avibactam resistance has been found, but resistance mechanisms remain largely unknown....

    Ke Ma, Yu Feng, Alan McNally, Zhiyong Zong
  • Open Access
    Extreme Antibiotic Persistence via Heterogeneity-Generating Mutations Targeting Translation
    Research Article | Novel Systems Biology Techniques
    Extreme Antibiotic Persistence via Heterogeneity-Generating Mutations Targeting Translation

    Bacterial persistence is a fascinating phenomenon in which a small subpopulation of bacteria becomes phenotypically tolerant to lethal antibiotic exposure. There is growing evidence that populations of bacteria in chronic clinical infections develop a hyperpersistent phenotype, enabling a substantially larger subpopulation to survive repeated antibiotic treatment. The mechanisms of persistence and modes of increasing persistence rates...

    Anupama Khare, Saeed Tavazoie
  • Open Access
    Chemogenomic Screen for Imipenem Resistance in Gram-Negative Bacteria
    Research Article | Molecular Biology and Physiology
    Chemogenomic Screen for Imipenem Resistance in Gram-Negative Bacteria

    Gram-negative carbapenem-resistant bacteria are a major threat to global health. The use of genome-wide screening approaches to probe for genes or mutations enabling resistance can lead to identification of molecular markers for diagnostics applications. We describe an approach called Mut-Seq that couples chemical mutagenesis and next-generation sequencing for studying resistance to imipenem in the Gram-negative bacteria...

    Jessica Y. El Khoury, Alexandra Maure, Hélène Gingras, Philippe Leprohon, Marc Ouellette
  • Open Access
    Systems Analyses Reveal the Resilience of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate
    Research Article | Synthetic Biology
    Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate

    Citramalate is an attractive biotechnology target because it is a precursor of methylmethacrylate, which is used to manufacture Perspex and other high-value products. Engineered E. coli strains are able to produce high titers of citramalate, despite having to express a foreign enzyme and tolerate the presence of a nonnative biochemical. A systems analysis of the...

    Joseph Webb, Vicki Springthorpe, Luca Rossoni, David-Paul Minde, Swen Langer, Heather Walker, Amias Alstrom-Moore, Tony Larson, Kathryn Lilley, Graham Eastham, Gill Stephens, Gavin H. Thomas, David J. Kelly, Jeffrey Green
  • Open Access
    Genome and Functional Characterization of Colonization Factor Antigen I- and CS6-Encoding Heat-Stable Enterotoxin-Only Enterotoxigenic <em>Escherichia coli</em> Reveals Lineage and Geographic Variation
    Editor's Pick Research Article | Clinical Science and Epidemiology
    Genome and Functional Characterization of Colonization Factor Antigen I- and CS6-Encoding Heat-Stable Enterotoxin-Only Enterotoxigenic Escherichia coli Reveals Lineage and Geographic Variation

    Comparative genomics and functional characterization were used to analyze a global collection of CFA/I and CS6 ST-only ETEC isolates associated with human diarrhea, demonstrating differences in the genomic content of CFA/I and CS6 isolates related to CF type, lineage, and geographic location of isolation and also lineage-related differences in ST production. Complete genome sequencing of selected CFA/I and CS6 isolates enabled...

    Tracy H. Hazen, Sushma Nagaraj, Sunil Sen, Jasnehta Permala-Booth, Felipe Del Canto, Roberto Vidal, Eileen M. Barry, Jacob P. Bitoun, Wilbur H. Chen, Sharon M. Tennant, David A. Rasko
  • Open Access
    Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> to Stationary Phase
    Research Article | Molecular Biology and Physiology
    Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary Phase

    During the growth transition of E. coli from exponential phase to stationary, the genome expression pattern is altered markedly. For this alteration, the transcription apparatus is altered by binding of anti-sigma factor Rsd to the RpoD sigma factor for sigma factor replacement, while the translation machinery is modulated by binding of RMF to 70S ribosome to form...

    Hideji Yoshida, Tomohiro Shimada, Akira Ishihama
  • Open Access
    Responses of the Human Gut <em>Escherichia coli</em> Population to Pathogen and Antibiotic Disturbances
    Editor's Pick Research Article | Host-Microbe Biology
    Responses of the Human Gut Escherichia coli Population to Pathogen and Antibiotic Disturbances

    Research on human-associated E. coli tends to focus on pathogens, such as enterotoxigenic E. coli (ETEC) strains, which are a leading cause of diarrhea in developing countries. However, the severity of disease caused by these pathogens is thought to be influenced by the microbiome. The nonpathogenic...

    Taylor K. S. Richter, Jane M. Michalski, Luke Zanetti, Sharon M. Tennant, Wilbur H. Chen, David A. Rasko
  • Open Access
    Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> K-12 Genome
    Research Article | Molecular Biology and Physiology
    Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the Escherichia coli K-12 Genome

    The 91-amino-acid-residue small-subunit omega (the rpoZ gene product) of Escherichia coli RNA polymerase plays a structural role in the formation of RNA polymerase (RNAP) as a chaperone in folding the largest subunit (β′, of 1,407 residues in length), but except for binding of the stringent signal ppGpp, little is known of its role in the control of RNAP...

    Kaneyoshi Yamamoto, Yuki Yamanaka, Tomohiro Shimada, Paramita Sarkar, Myu Yoshida, Neerupma Bhardwaj, Hiroki Watanabe, Yuki Taira, Dipankar Chatterji, Akira Ishihama
  • Open Access
    Transcriptional Variation of Diverse Enteropathogenic <em>Escherichia coli</em> Isolates under Virulence-Inducing Conditions
    Editor's Pick Research Article | Novel Systems Biology Techniques
    Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence-Inducing Conditions

    Recent studies have demonstrated that there is considerable genomic diversity among EPEC isolates; however, it is unknown if this genomic diversity leads to differences in their global transcription. This study used RNA-Seq to compare the global transcriptomes of EPEC isolates from diverse phylogenomic lineages. We demonstrate that there are lineage- and isolate-specific differences in the transcriptomes of genomically diverse EPEC...

    Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, James P. Nataro, David A. Rasko
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