scholarly journals Phages from Genus Bruynoghevirus and Phage Therapy: Pseudomonas Phage Delta Case

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1965
Author(s):  
Petar Knezevic ◽  
Aleksandra Petrovic Fabijan ◽  
Damir Gavric ◽  
Jovana Pejic ◽  
Zsolt Doffkay ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Phage Therapy ◽  
In Silico Analysis ◽  
Bacterial Toxin ◽  
Broad Host Range ◽  
Multiplicity Of Infection ◽  
Promising Candidate ◽  
A Genome ◽  
Silico Analysis

The applicability and safety of bacteriophage Delta as a potential anti-Pseudomonas aeruginosa agent belonging to genus Bruynoghevirus (family Podoviridae) was characterised. Phage Delta belongs to the species Pseudomonas virus PaP3, which has been described as a temperate, with cos sites at the end of the genome. The phage Delta possesses a genome of 45,970 bp that encodes tRNA for proline (Pro), aspartic acid (Asp) and asparagine (Asn) and does not encode any known protein involved in lysogeny formation or persistence. Analysis showed that phage Delta has 182 bp direct terminal repeats at the end of genome and lysogeny was confirmed, neither upon infection at low nor at high multiplicity of infection (MOI). The turbid plaques that appear on certain host lawns can result from bacteriophage insensitive mutants that occur with higher frequency (10−4). In silico analysis showed that the genome of Delta phage does not encode any known bacterial toxin or virulence factor, determinants of antibiotic resistance and known human allergens. Based on the broad host range and high lytic activity against planktonic and biofilm cells, phage Delta represents a promising candidate for phage therapy.

Insights into the interaction of key biofilm proteins in Pseudomonas aeruginosa PAO1 with TiO2 nanoparticle: An in silico analysis

2019 ◽  
Vol 462 ◽  
pp. 12-25
Author(s):  
Rani Anupama ◽  
Sajitha Lulu ◽  
Rout Madhusmita ◽  
Sundararajan Vino ◽  
Amitava Mukherjee ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
In Silico ◽  
In Silico Analysis ◽  
Tio2 Nanoparticle ◽  
Pseudomonas Aeruginosa Pao1 ◽  
Silico Analysis

scholarly journals Co-existence of virulence factors and antibiotic resistance in new Klebsiella pneumoniae clones emerging in south of Italy

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Teresa Fasciana ◽  
Bernardina Gentile ◽  
Maria Aquilina ◽  
Andrea Ciammaruconi ◽  
Chiara Mascarella ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Klebsiella Pneumoniae ◽  
Virulence Factors ◽  
In Silico ◽  
Geographical Area ◽  
In Silico Analysis ◽  
University Hospital ◽  
Uptake System ◽  
Genes Encoding ◽  
Silico Analysis

Abstract Background Endemic presence of Klebsiella pneumoniae resistant to carbapenem in Italy has been due principally to the clonal expansion of CC258 isolates; however, recent studies suggest an ongoing epidemiological change in this geographical area. Methods 50 K. pneumoniae strains, 25 carbapenem-resistant (CR-Kp) and 25 susceptible (CS-Kp), collected from march 2014 to march 2016 at the Laboratory of Bacteriology of the Paolo Giaccone Polyclinic University hospital of Palermo, Italy, were characterized for antibiotic susceptibility and fully sequenced by next generation sequencing (NGS) for the in silico analysis of resistome, virulome, multi-locus sequence typing (MLST) and core single nucleotide polymorphism (SNP) genotypes Results MLST in silico analysis of CR-Kp showed that 52% of isolates belonged to CC258, followed by ST395 (12%), ST307 (12%), ST392 (8%), ST348 (8%), ST405 (4%) and ST101 (4%). In the CS-Kp group, the most represented isolate was ST405 (20%), followed by ST392 and ST15 (12%), ST395, ST307 and ST1727 (8%). The in silico β-lactamase analysis of the CR-Kp group showed that the most detected gene was blaSHV (100%), followed by blaTEM (92%), blaKPC (88%), blaOXA (88%) and blaCTX-M (32%). The virulome analysis detected mrk operon in all studied isolates, and wzi-2 was found in three CR-Kp isolates (12%). Furthermore, the distribution of virulence genes encoding for the yersiniabactin system, its receptor fyuA and the aerobactin system did not show significant distribution differences between CR-Kp and CS-Kp, whereas the Klebsiella ferrous iron uptake system (kfuA, kfuB and kfuC genes), the two-component system kvgAS and the microcin E495 were significantly (p < 0.05) prevalent in the CS-Kp group compared to the CR-Kp group. Core SNP genotyping, correlating with the MLST data, allowed greater strain tracking and discrimination than MLST analysis. Conclusions Our data support the idea that an epidemiological change is ongoing in the Palermo area (Sicily, Italy). In addition, our analysis revealed the co-existence of antibiotic resistance and virulence factors in CR-Kp isolates; this characteristic should be considered for future genomic surveillance studies.

scholarly journals In Silico Analysis of Antibiotic Resistance Genes in the Gut Microflora of Individuals from Diverse Geographies and Age-Groups

PLoS ONE ◽  
2013 ◽  
Vol 8 (12) ◽  
pp. e83823 ◽  
Author(s):  
Tarini Shankar Ghosh ◽  
Sourav Sen Gupta ◽  
Gopinath Balakrish Nair ◽  
Sharmila S. Mande
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
In Silico ◽  
Age Groups ◽  
Antibiotic Resistance Genes ◽  
In Silico Analysis ◽  
Gut Microflora ◽  
Silico Analysis

scholarly journals Identification and antibiotic resistance of Bacillus spp. isolates from natural samples

2018 ◽  
Vol 70 (3) ◽  
pp. 581-588
Author(s):  
Tanja Beric ◽  
Marjan Biocanin ◽  
Slavisa Stankovic ◽  
Ivica Dimkic ◽  
Tamara Janakiev ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Inhibitory Concentration ◽  
Antibiotic Resistance Genes ◽  
In Silico Analysis ◽  
Rrna Gene ◽  
Erythromycin Resistance ◽  
Phylogenetic Groups ◽  
Bacillus Spp ◽  
Silico Analysis

Identification of 33 Bacillus spp. isolates from different environmental samples collected from the territory of Serbia was performed by sequencing of the 5?-hypervariable section of 16S rRNA gene. Eight species were identified within four phylogenetic groups: B. pumilus, B. megaterium, B. subtilis and B. cereus. Determination of their antibiotic resistance was performed using the minimum inhibitory concentration (MIC) assay. We found that just one isolate was resistant to gentamicin, 9 were resistant to clindamycin and all were resistant to vancomycin. Based on the profile of resistance, the isolates were categorized into 4 categories. In silico analysis of the erythromycin-resistance (erm) gene for clindamycin resistance showed their distribution between related and nonrelated soil and human isolates including different species of Bacillus genera. This finding indicates that Bacillus spp. from the environment could be a source of resistance to clindamycin. The potential for the presence and spread of resistance determinants in the soil and similar ecosystems exists so that monitoring of antibiotic resistance genes in nonpathogenic Bacillus strains from the environment is advised.

scholarly journals Cloning, Sequencing and In Silico Analysis of Omp C of Salmonella Typhimurium

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Richa Jha ◽  
Anil Kumar ◽  
Anjani Saxena ◽  
Shantanu Tamuly ◽  
M. K. Saxena
Keyword(s):  
Dna Vaccine ◽  
Outer Membrane Proteins ◽  
In Silico Analysis ◽  
Broad Host Range ◽  
Coding Region ◽  
Bioinformatic Tools ◽  
Poultry Products ◽  
Histocompatibility Complex ◽  
Cell Mediated Immune Response ◽  
Silico Analysis

Salmonella Typhimurium is an important pathogen having a broad host range. In human population it causes mostly gastroenteritis but there are reports in which it was found to be responsible to cause several lethal diseases like endocarditis and meningitis. Poultry products are the major sources of this organism in India as these are consumed at various stages of cooking. The available vaccines have their own limitations such as short-term immunity. Outer membrane proteins have shown some promising potential, so in the present study Omp C of Salmonella Typhimurium was cloned and sequenced to explore the possibility of development of r-DNA vaccine against Salmonella Typhimurium for poultry. The sequence of Omp C was studied for antigenic indexing, epitope mapping, and MHC mapping using various bioinformatic tools. The ORF analysis revealed a complete coding region of approximately 1000 bp. Five major and 13 minor B-cell epitopes were identified having an antigenic index of 1.7. The sequences also showed major histocompatibility complex (MHC) class I and class II binding region indicating a potential of eliciting cell-mediated immune response. The findings indicate that Omp C may be proven as promising candidate for development of r-DNA vaccine against Salmonella Typhimurium.

scholarly journals Emerging Strains Of SARS-Cov2 And Their Inhibition by The Use of Phytochemicals: An In-Silico Analysis

2021 ◽  
Author(s):  
Mohammad Faheem Khan ◽  
Tanveer Ahamad ◽  
Waseem Ahmad Ansari ◽  
Mohsin Ali Khan ◽  
Zaw Ali Khan ◽  
...  
Keyword(s):  
Rna Virus ◽  
In Silico Analysis ◽  
Open Reading Frames ◽  
Host Cells ◽  
Structural Proteins ◽  
Angiotensin Converting Enzyme 2 ◽  
A Genome ◽  
Infectivity Rate ◽  
Silico Analysis ◽  
Prime Target

Abstract Recently identified coronavirus namely severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded positive-sense RNA virus with a genome of 29.9 kb in size encoding 14 open reading frames (ORFs) and 27 different structural and non-structural proteins. Among the structural proteins, trimeric-shaped spike glycoprotein is responsible for the entry of the SARS-CoV2 genome into host cells by interacting with human angiotensin-converting enzyme 2 (ACE2) receptors that are present on the cell surface with high affinity. Notably, inhibition of spike protein is considered a prime target for the development of drugs against COVID-19. Viruses can mutate, and SARS-CoV-2 is no exception. Since the first whole genome of SARS-CoV2 was published in February 2020, at least 4400 amino acid substitutions and several thousand mutations have been identified to date. As of today, more than 3500 new variants of SARS-CoV2 have been sequenced with a high spreading and infectivity rate which makes the virus more contagious. These new variants have been spread to several countries including United States (US), United Kingdom (UK), Brazil, South Africa, India, and other countries, etc. Therefore, herein, we analysed the new SARS-CoV2 strains, constructed the 3D homology models of Brazil P.1 and Indian B.1.617 variants, and screened them against 100 phytochemicals having previously identified anti-viral activity. Our study revealed that the top three phytochemicals for each of the new strains might serve as potential anti- SARS-CoV-2 agents for further drug discovery and development process to tackle COVID-19.

scholarly journals Phage Therapy Is Effective in a Mouse Model of Bacterial Equine Keratitis

2016 ◽  
Vol 82 (17) ◽  
pp. 5332-5339 ◽  
Author(s):  
Takaaki Furusawa ◽  
Hidetomo Iwano ◽  
Yutaro Hiyashimizu ◽  
Kazuki Matsubara ◽  
Hidetoshi Higuchi ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Mouse Model ◽  
Phage Therapy ◽  
Host Cells ◽  
Resistant Bacteria ◽  
Broad Host Range ◽  
Bacterial Keratitis ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant ◽  
Content Type

ABSTRACTBacterial keratitis of the horse is mainly caused by staphylococci, streptococci, and pseudomonads. Of these bacteria,Pseudomonas aeruginosasometimes causes rapid corneal corruption and, in some cases, blindness. Antimicrobial resistance can make treatment very difficult. Therefore, new strategies to control bacterial infection are required. A bacteriophage (phage) is a virus that specifically infects and kills bacteria. Since phage often can lyse antibiotic-resistant bacteria because the killing mechanism is different, we examined the use of phage to treat horse bacterial keratitis. We isolatedMyoviridaeorPodoviridaephages, which together have a broad host range. They adsorb efficiently to host bacteria; more than 80% of the ΦR18 phage were adsorbed to host cells after 30 s. In our keratitis mouse model, the administration of phage within 3 h also could kill bacteria and suppress keratitis. A phage multiplicity of infection of 100 times the host bacterial number could kill host bacteria effectively. A cocktail of two phages suppressed bacteria in the keratitis model mouse. These data demonstrated that the phages in this study could completely prevent the keratitis caused byP. aeruginosain a keratitis mouse model. Furthermore, these results suggest that phage may be a more effective prophylaxis for horse keratitis than the current preventive use of antibiotics. Such treatment may reduce the use of antibiotics and therefore antibiotic resistance. Further studies are required to assess phage therapy as a candidate for treatment of horse keratitis.IMPORTANCEAntibiotic-resistant bacteria are emerging all over the world. Bacteriophages have great potential for resolution of this problem. A bacteriophage, or phage, is a virus that infects bacteria specifically. As a novel therapeutic strategy against racehorse keratitis caused byPseudomonas aeruginosa, we propose the application of phages for treatment. Phages isolated in this work hadin vitroeffectiveness for a broad range ofP. aeruginosastrains. Indeed, a great reduction of bacterial proliferation was shown in phage therapy for mouse models ofP. aeruginosakeratitis. Therefore, to reduce antibiotic usage, phage therapy should be investigated and developed further.

scholarly journals Phage Cocktail Development against Aeromonas salmonicida subsp. salmonicida Strains Is Compromised by a Prophage

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2241
Author(s):  
Nava Hosseini ◽  
Valérie E. Paquet ◽  
Mahdi Chehreghani ◽  
Sylvain Moineau ◽  
Steve J. Charette
Keyword(s):  
Antibiotic Resistance ◽  
Food Production ◽  
Pathogenic Bacteria ◽  
Phage Therapy ◽  
Aeromonas Salmonicida ◽  
Multiplicity Of Infection ◽  
Production Sector ◽  
Phage Cocktail ◽  
Effective Use ◽  
The Impact

Aquaculture is a rapidly growing food production sector. Fish farmers are experiencing increasing problems with antibiotic resistance when fighting against pathogenic bacteria such as Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis. Phage therapy may provide an alternative, but effective use must be determined. Here, we studied the inhibition of A. salmonicida subsp. salmonicida strains by five phages (HER98 [44RR2.8t.2], HER110 [65.2], SW69-9, L9-6 and Riv-10) used individually or as combinations of two to five phages. A particular combination of four phages (HER98 [44RR2.8t.2], SW69-9, Riv-10, and HER110 [65.2]) was found to be the most effective when used at an initial multiplicity of infection (MOI) of 1 against the A. salmonicida subsp. salmonicida strain 01-B526. The same phage cocktail is effective against other strains except those bearing a prophage (named Prophage 3), which is present in 2/3 of the strains from the province of Quebec. To confirm the impact of this prophage, we tested the effectiveness of the same cocktail on strains that were either cured or lysogenized with Prophage 3. While the parental strains were sensitive to the phage cocktail, the lysogenized ones were much less sensitive. These data indicate that the prophage content of A. salmonicida subsp. salmonicida can affect the efficacy of a cocktail of virulent phages for phage therapy purposes.

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