Complete genome sequences of Aeromonas and Pseudomonas phages as a supportive tool for development of antibacterial treatment in aquaculture

Kazimierczak, Joanna; Wójcik, Ewelina; Witaszewska, Jolanta; Guziński, Arkadiusz; Górecka, E; Stańczyk, Małgorzata; Kaczorek, Edyta; Siwicki, Andrzej K.; Dastych, Jarosław

doi:10.1186/s12985-018-1113-5

Cited by 26 publications

(17 citation statements)

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“…These bacteria are usually resistant to first and second line antibiotic therapy involving beta-lactam drugs and third generation cephalosporins via mechanisms such as resistance genes and biofilm formation (Janda and Abbott, 2010). Bacteriophages, which have been suggested as an alternative to antibiotics, have been isolated against environmental and fish pathogen strains of A. hydrophila (Chow and Rouf, 1983;Merino et al, 1990a,b;Gibb and Edgell, 2007;Shen et al, 2012;Jun et al, 2013;Anand et al, 2016;Wang et al, 2016;Le et al, 2018;Yuan et al, 2018;Bai et al, 2019;Cao et al, 2019;Kazimierczak et al, 2019). The host range of these bacteriophages, however, was not reported to extend to clinical strains.…”

Section: Discussionmentioning

confidence: 99%

Novel Bacteriophages Capable of Disrupting Biofilms From Clinical Strains of Aeromonas hydrophila

et al. 2020

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The increase in global warming has favored growth of a range of opportunistic environmental bacteria and allowed some of these to become more pathogenic to humans. Aeromonas hydrophila is one such organism. Surviving in moist conditions in temperate climates, these bacteria have been associated with a range of diseases in humans, and in systemic infections can cause mortality in up to 46% of cases. Their capacity to form biofilms, carry antibiotic resistance mechanisms, and survive disinfection, has meant that they are not easily treated with traditional methods. Bacteriophage offer a possible alternative approach for controlling their growth. This study is the first to report the isolation and characterization of bacteriophages lytic against clinical strains of A. hydrophila which carry intrinsic antibiotic resistance genes. Functionally, these novel bacteriophages were shown to be capable of disrupting biofilms caused by clinical isolates of A. hydrophila. The potential exists for these to be tested in clinical and environmental settings.

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Section: Discussionmentioning

confidence: 99%

Novel Bacteriophages Capable of Disrupting Biofilms From Clinical Strains of Aeromonas hydrophila

et al. 2020

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“…As a phage therapy Le et al (2018) demonstrated that phages (Φ2 and Φ5) are considered as potential biocontrol agents to combat A. hydrophila infections in fish farms. In the same direction, Kazimierczak et al (2019) reported that, 6 new isolated phages could be used as a therapeutic cocktail giving the infected of 41% of the Aeromonas pathogenic environmental isolates. In this study, only 1.38 log CFU/g (P< 0.01) E. coli W102 viable count reduction was found with phage ΦECP8 treatment while 1.68 log CFU/g (P< 0.01) with phage ΦECP9 on tomato slices 30min of application at room temperature.…”

Section: Application Of Bacteriophages In Artificially Contaminated Fmentioning

confidence: 95%

Evaluation of Novel Virulent Phages Infecting the Aeromonas Hydrophila and Escherichia coli Isolated from Sewage Water Samples

Nasr-Eldin

Soliman

2020

Egypt. J. Bot.

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M ULTIDRUG-resistant bacteria are now emerging for almost all the present-day antibiotics. Aeromonas hydrophila D2007 and Escherichia coli W102 were isolated from fresh food and drinking water samples and they were resistant to 57.14% and 85.71% of tested common antibiotics respectively. Three bacteriophages (phages) were isolated from sewage samples. Morphological examinations suggested that phage ΦAHP7, which infects A. hydrophila D2007, belongs to the Myoviridae family and other phages ΦECP8 and ΦECP9 capable of lysing E. coil W102 belongs to Siphoviridae and Podoviridae families, respectively. For the three phages, the optimal multiplicity of infection (MOI) was calculated to be 0.001. Phages were characterized by determining their host range and stability in pHs, temperatures, and salinity. The latent periods of phages ΦAHP7, ΦECP8, and ΦECP9 were 10, 20 and 10min with average burst sizes of 53.5±0.5, 26.5±0.5 and 67.5±0.5 phages per infected cell, respectively. The three phages gradually reduced OD 600 and are able to stop the growth of A. hydrophila D2007 and E. coli W102 in vitro at a low MOI of 0.001. Phages ΦAHP7, ΦECP8, and ΦECP9 treatments achieved 1.55, 1.68 and 2.28 log CFU/g (P< 0.01) reduction of viable bacterial number in red cabbage and 1.48, 1.38 and 1.68 log CFU/g (P< 0.01) reduction in tomato after 30 min at room temperature (28°C) respectively. Applications of lytic ΦAHP7, ΦECP8, and ΦECP9 bacteriophages lead to a rapid reduction of A. hydrophila D2007 and E. coli W102 counts in fresh food for human consumption.

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“…Therefore, there are various approaches to define a phage life cycle [6,7]. It often starts with a search of reference sequences in Basic Local Alignment Search Tool (BLAST) and both automatic and manual annotation of genomes (e.g.in DNAMaster, University of Pittsburgh).…”

Section: Introductionmentioning

confidence: 99%

PhageAI - Bacteriophage Life Cycle Recognition with Machine Learning and Natural Language Processing

Tynecki

Guziński²,

Kazimierczak³

et al. 2020

Preprint

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As antibiotic resistance is becoming a major problem nowadays in a treatment of infections, bacteriophages (also known as phages) seem to be an alternative. However, to be used in a therapy, their life cycle should be strictly lytic. With the growing popularity of Next Generation Sequencing (NGS) technology, it is possible to gain such information from the genome sequence. A number of tools are available which help to define phage life cycle. However, there is still no unanimous way to deal with this problem, especially in the absence of well-defined open reading frames. To overcome this limitation, a new tool is definitely needed. We developed a novel tool, called PhageAI, that allows to access more than 10 000 publicly available bacteriophages and differentiate between their major types of life cycles: lytic and lysogenic. The tool included life cycle classifier which achieved 98.90% accuracy on a validation set and 97.18% average accuracy on a test set. We adopted nucleotide sequences embedding based on the Word2Vec with Ship-gram model and linear Support Vector Machine with 10-fold cross-validation for supervised classification. PhageAI is free of charge and it is available at https://phage.ai/. PhageAI is a REST web service and available as Python package. Machine learning and Natural Language Processing allows to extract information from bacteriophages nucleotide sequences for lifecycle prediction tasks. The PhageAI tool classifies phages into either virulent or temperate with a higher accuracy than any existing methods and shares interactive 3D visualization to help interpreting model classification results.

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Complete genome sequences of Aeromonas and Pseudomonas phages as a supportive tool for development of antibacterial treatment in aquaculture

Cited by 26 publications

References 50 publications

Novel Bacteriophages Capable of Disrupting Biofilms From Clinical Strains of Aeromonas hydrophila

Novel Bacteriophages Capable of Disrupting Biofilms From Clinical Strains of Aeromonas hydrophila

Evaluation of Novel Virulent Phages Infecting the Aeromonas Hydrophila and Escherichia coli Isolated from Sewage Water Samples

PhageAI - Bacteriophage Life Cycle Recognition with Machine Learning and Natural Language Processing

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