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Bacteriophages

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Kimberley D Seed – One of the best experts on this subject based on the ideXlab platform.

  • analysis of 19 highly conserved vibrio cholerae Bacteriophages isolated from environmental and patient sources over a twelve year period
    Viruses, 2018
    Co-Authors: Angus Angermeye, Moon Moo Das, Durg V Singh, Kimberley D Seed

    Abstract:

    The Vibrio cholerae biotype “El Tor” is responsible for all of the current epidemic and endemic cholera outbreaks worldwide. These outbreaks are clonal, and it is hypothesized that they originate from the coastal areas near the Bay of Bengal, where the lytic bacteriophage ICP1 (International Centre for Diarrhoeal Disease Research, Bangladesh cholera phage 1) specifically preys upon these pathogenic outbreak strains. ICP1 has also been the dominant bacteriophage found in cholera patient stools since 2001. However, little is known about the genomic differences between the ICP1 strains that have been collected over time. Here, we elucidate the pan-genome and the phylogeny of the ICP1 strains by aligning, annotating, and analyzing the genomes of 19 distinct isolates that were collected between 2001 and 2012. Our results reveal that the ICP1 isolates are highly conserved and possess a large core-genome as well as a smaller, somewhat flexible accessory-genome. Despite its overall conservation, ICP1 strains have managed to acquire a number of unknown genes, as well as a CRISPR-Cas system which is known to be critical for its ongoing struggle for co-evolutionary dominance over its host. This study describes a foundation on which to construct future molecular and bioinformatic studies of these V. cholerae-associated Bacteriophages.

  • analysis of 19 highly conserved vibrio cholerae Bacteriophages isolated from environmental and patient sources over a twelve year period
    bioRxiv, 2018
    Co-Authors: Angus Angermeye, Moon Moo Das, Durg V Singh, Kimberley D Seed

    Abstract:

    The Vibrio cholerae biotype El Tor is responsible for all current epidemic and endemic cholera outbreaks worldwide. These outbreaks are clonal and are hypothesized to originate from the coastal areas near the Bay of Bengal where the lytic bacteriophage ICP1 specifically preys upon these pathogenic outbreak strains. ICP1 has also been the dominant bacteriophage found in cholera patient stool since 2001. However, little is known about its genomic differences between ICP1 strains collected over time. Here we elucidate the pan-genome and phylogeny of ICP1 strains by aligning, annotating and analyzing the genomes of 19 distinct isolates collected between 2001 and 2012. Our results reveal that ICP1 isolates are highly conserved and possess a large core-genome as well as a smaller, somewhat flexible accessory-genome. Despite its overall conservation, ICP1 strains have managed to acquire a number of unknown genes as well as a CRISPR-Cas system, which is known to be critical for its ongoing struggle for co-evolutionary dominance over its host. This study describes a foundation on which to construct future molecular and bioinformatic studies of this V. cholerae-associated Bacteriophages.

  • evidence of a dominant lineage of vibrio cholerae specific lytic Bacteriophages shed by cholera patients over a 10 year period in dhaka bangladesh
    Mbio, 2011
    Co-Authors: Kimberley D Seed, Kip L Odi, Andrew M Kropinski, Hanswolfgang Ackerma, Stephe Calderwood, Firdausi Qadri, Andrew Camilli

    Abstract:

    ABSTRACT Lytic Bacteriophages are hypothesized to contribute to the seasonality and duration of cholera epidemics in Bangladesh. However, the Bacteriophages contributing to this phenomenon have yet to be characterized at a molecular genetic level. In this study, we isolated and sequenced the genomes of 15 Bacteriophages from stool samples from cholera patients spanning a 10-year surveillance period in Dhaka, Bangladesh. Our results indicate that a single novel bacteriophage type, designated ICP1 (for the International Centre for Diarrhoeal Disease Research, Bangladesh cholera phage 1) is present in all stool samples from cholera patients, while two other bacteriophage types, one novel (ICP2) and one T7-like (ICP3), are transient. ICP1 is a member of the Myoviridae family and has a 126-kilobase genome comprising 230 open reading frames. Comparative sequence analysis of ICP1 and related isolates from this time period indicates a high level of genetic conservation. The ubiquitous presence of ICP1 in cholera patients and the finding that the O1 antigen of lipopolysaccharide (LPS) serves as the ICP1 receptor suggest that ICP1 is extremely well adapted to predation of human-pathogenic V. cholerae O1. IMPORTANCE The severe diarrheal disease cholera is caused by the bacterium Vibrio cholerae, which can be transmitted to humans from the aquatic environment. Factors that affect V. cholerae in the environment can impact the occurrence of cholera outbreaks; one of these factors is thought to be the presence of bacterial viruses, or Bacteriophages. Bacteriophages that prey on V. cholerae in the environment, and potentially in humans, have not been extensively genetically characterized. Here, we isolated and sequenced the genomes of Bacteriophages from cholera patient stool samples collected over a 10-year period in Dhaka, Bangladesh, a region that suffers from regular cholera outbreaks. We describe a unique bacteriophage present in all samples, infer its evolution by sequencing multiple isolates from different patients over time, and identify the host receptor that shows that the bacteriophage specifically predates the serogroup of V. cholerae responsible for the majority of disease occurrences.

Laurent Debarbieux – One of the best experts on this subject based on the ideXlab platform.

  • phage therapy of pneumonia is not associated with an overstimulation of the inflammatory response compared to antibiotic treatment in mice
    Antimicrobial Agents and Chemotherapy, 2019
    Co-Authors: Nicolas Dufour, Jean Damien Ricard, Raphaelle Delattre, Anne Chevallereau, Laurent Debarbieux

    Abstract:

    : Supported by years of clinical use in some countries and more recently by literature on experimental models, as well as its compassionate use in Europe and in the United States, bacteriophage (phage) therapy is providing a solution for difficult-to-treat bacterial infections. However, studies of the impact of such treatments on the host remain scarce. Murine acute pneumonia initiated by intranasal instillation of two pathogenic strains of Escherichia coli (536 and LM33) was treated by two specific Bacteriophages (536_P1 and LM33_P1; intranasal) or antibiotics (ceftriaxone, cefoxitin, or imipenem-cilastatin; intraperitoneal). Healthy mice also received phages alone. The severity of pulmonary edema, acute inflammatory cytokine concentration (blood and lung homogenates), complete blood counts, and bacterial and bacteriophage counts were determined at early (≤12 h) and late (≥20 h) time points. The efficacy of bacteriophage to decrease bacterial load was faster than with antibiotics, but the two displayed similar endpoints. Bacteriophage treatment was not associated with overinflammation but in contrast tended to lower inflammation and provided a faster correction of blood cell count abnormalities than did antibiotics. In the absence of bacterial infection, bacteriophage 536_P1 promoted a weak increase in the production of antiviral cytokines (gamma interferon [IFN-γ] and interleukin-12 [IL-12]) and chemokines in the lungs but not in the blood. However, such variations were no longer observed when bacteriophage 536_P1 was administered to treat infected animals. The rapid lysis of bacteria by Bacteriophages in vivo does not increase the innate inflammatory response compared to that with antibiotic treatment.

  • treatment of highly virulent extraintestinal pathogenic escherichia coli pneumonia with Bacteriophages
    Critical Care Medicine, 2015
    Co-Authors: Nicolas Dufour, Laurent Debarbieux, Melanie Fromentin, Jean Damien Ricard

    Abstract:

    OBJECTIVE:
    To study the effect of bacteriophage treatment on highly virulent extraintestinal Escherichia coli pneumonia in mice and compare it with conventional antimicrobial treatment.

    DESIGN:
    Animal investigation.

    SETTING:
    University research laboratory.

    SUBJECTS:
    Pathogen-free 8-week-old Balb/cJRj male mice.

    INTERVENTIONS:
    Two Bacteriophages (536_P1 and 536_P7) were isolated from sewage using strain 536, a highly virulent extraintestinal E. coli. Their in vitro and in vivo efficacy against strain 536 and a ventilator-associated pneumonia E. coli were tested. The first group of mice were infected by intranasal instillation of bioluminescent strain 536 and received 536_P1 intranasally, ceftriaxone, or control. The second group of mice was infected with the ventilator-associated pneumonia strain and received 536_P7. Adaptation of 536_P7 to this clinical isolate was also evaluated in vitro and in vivo.

    MEASUREMENTS AND MAIN RESULTS:
    In vivo efficacy of bacteriophage and antibiotic treatment were assessed by recording bioluminescence for short-time periods and by recording body weight and survival of mice for longer periods. Both treatments improved survival compared with control (100% vs 0%), and in vivo bioluminescence recordings showed a similar rapid decrease of emitted light, suggesting prompt bacterial clearance. The majority of mice infected by the ventilator-associated pneumonia strain were not rescued by treatment with 536_P7; however, in vitro adaptation of this bacteriophage toward the ventilator-associated pneumonia strain led to isolate a variant which significantly improved in vivo treatment efficacy (animal survival increased from 20% to 75%).

    CONCLUSIONS:
    Bacteriophage treatment was as effective as antibiotherapy to provide 100% survival rate in a lethal model of highly virulent E. coli pneumonia. Adaptation of a bacteriophage is a rapid solution to improve its efficacy toward specific strains. These results suggest that phage therapy could be a promising therapeutic strategy for ventilator-associated pneumonia.

  • Predicting In Vivo Efficacy of Therapeutic Bacteriophages Used To Treat Pulmonary Infections
    Antimicrobial Agents and Chemotherapy, 2013
    Co-Authors: Marine Henry, Rob Lavigne, Laurent Debarbieux

    Abstract:

    The potential of bacteriophage therapy to treat infections caused by antibiotic-resistant bacteria has now been well established using various animal models. While numerous newly isolated Bacteriophages have been claimed to be potential therapeutic candidates on the basis of in vitro observations, the parameters used to guide their choice among billions of available Bacteriophages are still not clearly defined. We made use of a mouse lung infection model and a bioluminescent strain of Pseudomonas aeruginosa to compare the activities in vitro and in vivo of a set of nine different Bacteriophages (PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5, CHA_P1, LBL3, LUZ19, and PhiKZ). For seven Bacteriophages, a good correlation was found between in vitro and in vivo activity. While the remaining two Bacteriophages were active in vitro , they were not sufficiently active in vivo under similar conditions to rescue infected animals. Based on the bioluminescence recorded at 2 and 8 h postinfection, we also define for the first time a reliable index to predict treatment efficacy. Our results showed that the Bacteriophages isolated directly on the targeted host were the most efficient in vivo , supporting a personalized approach favoring an optimal treatment.

Hakdong Shin – One of the best experts on this subject based on the ideXlab platform.

  • exogenous lytic activity of spn9cc endolysin against gram negative bacteria
    Journal of Microbiology and Biotechnology, 2014
    Co-Authors: Hakdong Shin

    Abstract:

    Over the last decade, a dramatic increase in the prevalence of antibiotic resistance has occurred in several significant pathogens [11]. It is difficult to develop new classes of antibiotics to control antibiotic-resistant bacteria, and alternative therapeutic reagents or methods are required [3, 21]. Bacteriophage endolysin is an enzyme that targets bacterial peptidoglycan. Generally, Bacteriophages, which have double-stranded DNA, encode two proteins for host lysis, holin and endolysin. In the last step of the lytic bacteriophage life cycle, endolysin passes through a cytoplasmic membrane pore formed by holin to reach its target, peptidoglycan. Endolysin hydrolyzes peptidoglycan by cleaving a glycosidic bond, peptide bond, or amide bond, and host bacteria are then lysed by osmotic pressure. Finally, progeny virions can be released [1, 23, 27, 34]. In the case of gram-negative bacteria, additional supporting proteins (Rz/Rz1-like proteins) may be needed for full lysis [40]. Purified endolysins have the potential to serve as a new class of therapeutic agents against gram-positive bacteria by acting as exolysins because they make direct contact with the cell wall of gram-positive bacteria [2]. Endolysins have a number of advantages, including bactericidal activity, being made from a naturally occurring material, and effectiveness against antibiotic-resistant bacteria [8]. The target specificity of endolysin especially renders it a promising antibiotic substitute, because endolysin is not toxic to the eukaryotic cell and does not disrupt environmental microorganisms [8, 23]. In many studies, endolysins have been shown to have antimicrobial activity against pathogens such as Streptococcus pneumoniae, Bacillus anthracis, B. subtilis, Staphylococcus aureus, Lactobacillus fermentum, Received: March 13, 2014 Revised: March 24, 2014 Accepted: March 24, 2014

  • complete genome sequence of the pectobacterium carotovorum subsp carotovorum virulent bacteriophage pm1
    Archives of Virology, 2014
    Co-Authors: Hakdong Shin

    Abstract:

    PM1, a novel virulent bacteriophage that infects Pectobacterium carotovorum subsp. carotovorum, was isolated. Its morphological features were examined by electron microscopy, which indicated that this phage belongs to the family Myoviridae. It has a 55,098-bp genome, including a 2,665-bp terminal repeat. A total of 63 open reading frames (ORFs) were predicted, but only 20 ORFs possessed homology with functional proteins. There is one tRNA coding region, and the GC-content of the genome is 44.9 %. Most ORFs in bacteriophage PM1 showed high homology to enterobacteria phage ΦEcoM-GJ1 and Erwinia phage νB EamM-Y2. Like these Bacteriophages, PM1 encodes an RNA polymerase, which is a hallmark of T7-like phages. There is no integrase or repressor, suggesting that PM1 is a virulent bacteriophage.

  • complete genome sequence of phytopathogenic pectobacterium carotovorum subsp carotovorum bacteriophage pp1
    Journal of Virology, 2012
    Co-Authors: Hakdong Shin, Samnyu Ji, Shweta Malhotra, Mukesh Kumar

    Abstract:

    Pectobacterium carotovorum subsp. carotovorum is a phytopathogen causing soft rot disease on diverse plant species. To control this plant pathogen, P. carotovorum subsp. carotovorum-targeting bacteriophage PP1 was isolated and its genome was completely sequenced to develop a novel biocontrol agent. Interestingly, the 44,400-bp genome sequence does not encode any gene involved in the formation of lysogen, suggesting that this phage may be very useful as a biocontrol agent because it does not make lysogen after host infection. This is the first report on the complete genome sequence of the P. carotovorum subsp. carotovorum-targeting bacteriophage, and it will enhance our understanding of the interaction between phytopathogens and their targeting Bacteriophages.