Phylogenetic Incongruence in E. coli O104: Understanding the Evolutionary Relationships of Emerging Pathogens in the Face of Homologous Recombination

Vaccination remains one of the most successful medical interventions in history, significantly decreasing morbidity and mortality associated with, or even eradicating, numerous infectious diseases. Although traditional immunization strategies have recently proven insufficient in the face of many highly mutable and emerging pathogens, modern strategies aim to rationally engineer a single antigen or cocktail of antigens to generate a focused, protective immune response. However, the effect of cocktail vaccination (simultaneous immunization with multiple immunogens) on the antibody response to each individual antigen within the combination, remains largely unstudied. To investigate whether immunization with a cocktail of diverse antigens would result in decreased antibody titer against each unique antigen in the cocktail compared to immunization with each antigen alone, we immunized mice with surface proteins from uropathogenic Escherichia coli, Mycobacterium tuberculosis, and Neisseria meningitides, and monitored the development of antigen-specific IgG antibody responses. We found that antigen-specific endpoint antibody titers were comparable across immunization groups by study conclusion (day 70). Further, we discovered that although cocktail-immunized mice initially elicited more robust antibody responses, the rate of titer development decreases significantly over time compared to single antigen-immunized mice. Investigating the basic properties that govern the development of antigen-specific antibody responses will help inform the design of future combination immunization regimens.

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An efficient method for precise gene substitution in the AcMNPV genome by homologous recombination in E. coli

Journal of Virological Methods ◽

10.1016/s0166-0934(03)00225-8 ◽

2003 ◽

Vol 113 (2) ◽

pp. 95-101 ◽

Cited By ~ 4

Author(s):

Wuwei Wu ◽

Jinwen Wang ◽

Riqiang Deng ◽

Xunzhang Wang ◽

XiongLei He ◽

...

Keyword(s):

Homologous Recombination ◽

Efficient Method ◽

Gene Substitution ◽

E Coli

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Use of Recombination-Mediated Genetic Engineering for Construction of Rescue Human Cytomegalovirus Bacterial Artificial Chromosome Clones

Journal of Biomedicine and Biotechnology ◽

10.1155/2012/357147 ◽

2012 ◽

Vol 2012 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Kalpana Dulal ◽

Benjamin Silver ◽

Hua Zhu

Keyword(s):

Bacterial Artificial Chromosome ◽

Homologous Recombination ◽

Human Cytomegalovirus ◽

Artificial Chromosome ◽

Bac Clone ◽

Dna Viruses ◽

E Coli ◽

Recombination System ◽

Capture Method

Bacterial artificial chromosome (BAC) technology has contributed immensely to manipulation of larger genomes in many organisms including large DNA viruses like human cytomegalovirus (HCMV). The HCMV BAC clone propagated and maintained insideE. coliallows for accurate recombinant virus generation. Using this system, we have generated a panel of HCMV deletion mutants and their rescue clones. In this paper, we describe the construction of HCMV BAC mutants using a homologous recombination system. A gene capture method, or gap repair cloning, to seize large fragments of DNA from the virus BAC in order to generate rescue viruses, is described in detail. Construction of rescue clones using gap repair cloning is highly efficient and provides a novel use of the homologous recombination-based method inE. colifor molecular cloning, known colloquially as recombineering, when rescuing large BAC deletions. This method of excising large fragments of DNA provides important prospects forin vitrohomologous recombination for genetic cloning.

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DNA replication triggered by double-stranded breaks in E. coli: Dependence on homologous recombination functions

Cell ◽

10.1016/0092-8674(94)90279-8 ◽

1994 ◽

Vol 78 (6) ◽

pp. 1051-1061 ◽

Cited By ~ 64

Author(s):

Tsuneaki Asai ◽

David B. Bates ◽

Tokio Kogoma

Keyword(s):

Dna Replication ◽

Homologous Recombination ◽

E Coli

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Investigation of human infections with verocytotoxin-producing strains of Escherichia coli (VTEC) belonging to serogroup O118 with evidence for zoonotic transmission

Epidemiology and Infection ◽

10.1017/s0950268899004094 ◽

2000 ◽

Vol 125 (1) ◽

pp. 47-54 ◽

Cited By ~ 14

Author(s):

L. BEUTIN ◽

M. BÜLTE ◽

A. WEBER ◽

S. ZIMMERMANN ◽

K. GLEIER

Keyword(s):

Escherichia Coli ◽

Pulsed Field Gel Electrophoresis ◽

Zoonotic Transmission ◽

Rural Environment ◽

Emerging Pathogens ◽

E Coli ◽

Virulence Markers ◽

Young Infants ◽

Variant Gene ◽

Human Infections

Twenty verocytotoxigenic Escherichia coli (VTEC) O118 strains isolated between 1996 and 1998 from human patients in Germany were analysed for their serotypes, their virulence markers and their epidemiological relatedness. Three strains were typed as O118[ratio ]H12, these carried only the VT2d-Ount variant gene and were not associated with diarrhoea or haemolytic uraemic syndrome (HUS). Seventeen strains were serotyped as O118[ratio ]H16 or O118[ratio ]non-motile (NM). These carried all the genes for VT1, eae and EHEC-haemolysin. The O118[ratio ]H16/NM strains were from diarrhoea (13 cases) and HUS (2 cases). Sixteen of the patients were young infants and most infections were associated with a rural environment. Evidence for zoonotic transmission from cattle to humans was found in two cases. The epidemiological relationship between the human and bovine O118[ratio ]H16/NM isolates was indicated by homogeneous plasmid patterns and by very similar XbaI restriction patterns obtained by pulsed-field gel electrophoresis. VTEC O118[ratio ]H16/NM are emerging pathogens in Germany and should be classified as new enterohaemorrhagic E. coli (EHEC) types.

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Homologous recombination in E. coli: Multiple pathways for multiple reasons

Cell ◽

10.1016/0092-8674(89)90929-x ◽

1989 ◽

Vol 58 (5) ◽

pp. 807-809 ◽

Cited By ~ 73

Author(s):

Gerald R. Smith

Keyword(s):

Homologous Recombination ◽

E Coli

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An N-Halamine/Graphene Oxide-Functionalized Electrospun Polymer Membrane That Inactivates Bacteria on Contact and by Releasing Active Chlorine

Polymers ◽

10.3390/polym13162784 ◽

2021 ◽

Vol 13 (16) ◽

pp. 2784

Author(s):

Shi Lan ◽

Jinghua Zhang ◽

Jie Li ◽

Yanan Guo ◽

Xianliang Sheng ◽

...

Keyword(s):

Graphene Oxide ◽

Antibacterial Properties ◽

Polymer Membrane ◽

Water Disinfection ◽

Fibrous Membrane ◽

Active Chlorine ◽

Public Health Issue ◽

Emerging Pathogens ◽

Electrospinning Technique ◽

E Coli

The emergence of antibiotic-resistant “superbugs” in recent decades has led to widespread illness and death and is a major ongoing public health issue. Since traditional antimicrobials and antibiotics are in many cases showing limited or no effectiveness in fighting some emerging pathogens, there is an urgent need to develop and explore novel antibacterial agents that are both powerful and reliable. Combining two or more antibiotics or antimicrobials has become a hot topic in antibacterial research. In this contribution, we report on using a simple electrospinning technique to create an N-halamine/graphene oxide-modified polymer membrane with excellent antibacterial activity. With the assistance of advanced techniques, the as-obtained membrane was characterized in terms of its chemical composition, morphology, size, and the presence of active chlorine. Its antibacterial properties were tested with Escherichia coli (E. coli) as the model bacteria, using the colony-counting method. Interestingly, the final N-halamine/graphene oxide-based antibacterial fibrous membrane inactivated E. coli both on contact and by releasing active chlorine. We believe that the synergistic antimicrobial action of our as-fabricated fibrous membrane should have great potential for utilization in water disinfection, air purification, medical and healthcare products, textile products, and other antibacterial-associated fields.

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Assembly of Radically Recoded E. coli Genome Segments

10.1101/070417 ◽

2016 ◽

Cited By ~ 1

Author(s):

Julie E. Norville ◽

Cameron L. Gardner ◽

Eduardo Aponte ◽

Conor K. Camplisson ◽

Alexandra Gonzales ◽

...

Keyword(s):

Homologous Recombination ◽

Genome Engineering ◽

Next Generation ◽

Selective Marker ◽

E Coli ◽

Cassette Exchange ◽

Large Potential ◽

Attachment Sites

AbstractThe large potential of radically recoded organisms (RROs) in medicine and industry depends on improved technologies for efficient assembly and testing of recoded genomes for biosafety and functionality. Here we describe a next generation platform for conjugative assembly genome engineering, termed CAGE 2.0, that enables the scarless integration of large synthetically recoded E. coli segments at isogenic and adjacent genomic loci. A stable tdk dual selective marker is employed to facilitate cyclical assembly and removal of attachment sites used for targeted segment delivery by sitespecific recombination. Bypassing the need for vector transformation harnesses the multi Mb capacity of CAGE, while minimizing artifacts associated with RecA-mediated homologous recombination. Our method expands the genome engineering toolkit for radical modification across many organisms and recombinase-mediated cassette exchange (RMCE).

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Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks

eLife ◽

10.7554/elife.02863 ◽

2014 ◽

Vol 3 ◽

Cited By ~ 20

Author(s):

Luca Albergante ◽

J Julian Blow ◽

Timothy J Newman

Keyword(s):

Large Scale ◽

Human Cancer ◽

Transcriptional Response ◽

Cancer Cell Line ◽

Transcriptional Networks ◽

E Coli ◽

Evolutionary Changes ◽

Cancer Initiation ◽

The Face ◽

Scale Properties

The gene regulatory network (GRN) is the central decision‐making module of the cell. We have developed a theory called Buffered Qualitative Stability (BQS) based on the hypothesis that GRNs are organised so that they remain robust in the face of unpredictable environmental and evolutionary changes. BQS makes strong and diverse predictions about the network features that allow stable responses under arbitrary perturbations, including the random addition of new connections. We show that the GRNs of E. coli, M. tuberculosis, P. aeruginosa, yeast, mouse, and human all verify the predictions of BQS. BQS explains many of the small- and large‐scale properties of GRNs, provides conditions for evolvable robustness, and highlights general features of transcriptional response. BQS is severely compromised in a human cancer cell line, suggesting that loss of BQS might underlie the phenotypic plasticity of cancer cells, and highlighting a possible sequence of GRN alterations concomitant with cancer initiation.

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