scholarly journals Characterization of vB_StuS_MMDA13, a Newly Discovered Bacteriophage Infecting the Agar-Degrading Species Sphingomonas turrisvirgatae

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 894
Author(s):  
Pasquale Marmo ◽  
Maria Cristina Thaller ◽  
Gustavo Di Lallo ◽  
Lucia Henrici De Angelis ◽  
Noemi Poerio ◽  
...  
Keyword(s):  
Burst Size ◽  
Latency Period ◽  
Biosynthetic Gene Cluster ◽  
Open Reading Frames ◽  
Lytic Bacteriophage ◽  
Coding Region ◽  
Narrow Host Range ◽  
Physiological Characterization ◽  
Wide Range ◽  
Valuable Compounds

Members of Sphingomonas genus have gained a notable interest for their use in a wide range of biotechnological applications, ranging from bioremediation to the production of valuable compounds of industrial interest. To date, knowledge on phages targeting Sphingomonas spp. are still scarce. Here, we describe and characterize a lytic bacteriophage, named vB_StuS_MMDA13, able to infect the Sphingomonas turrisvirgatae MCT13 type strain. Physiological characterization demonstrated that vB_StuS_MMDA13 has a narrow host range, a long latency period, a low burst size, and it is overall stable to both temperature and pH variations. The phage has a double-stranded DNA genome of 63,743 bp, with 89 open reading frames arranged in two opposite arms separated by a 1186 bp non-coding region and shows a very low global similarity to any other known phages. Interestingly, vB_StuS_MMDA13 is endowed with an original nucleotide modification biosynthetic gene cluster, which greatly differs from those of its most closely related phages of the Nipunavirus genus. vB_StuS_MMDA13 is the first characterized lytic bacteriophage of the Siphoviridae family infecting members of the Sphingomonas genus.

scholarly journals Characterization of vB_Kpn_F48, a Newly Discovered Lytic Bacteriophage for Klebsiella pneumoniae of Sequence Type 101

Viruses ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 482 ◽  
Author(s):  
Nagaia Ciacci ◽  
Marco D’Andrea ◽  
Pasquale Marmo ◽  
Elisa Demattè ◽  
Francesco Amisano ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Host Range ◽  
High Throughput Sequencing ◽  
Burst Size ◽  
Antibiotic Resistance Genes ◽  
Clinical Problem ◽  
Lytic Bacteriophage ◽  
Transmission Electron Microscopy Analysis ◽  
Narrow Host Range ◽  
Physiological Characterization

Resistance to carbapenems in Enterobacteriaceae, including Klebsiella pneumoniae, represents a major clinical problem given the lack of effective alternative antibiotics. Bacteriophages could provide a valuable tool to control the dissemination of antibiotic resistant isolates, for the decolonization of colonized individuals and for treatment purposes. In this work, we have characterized a lytic bacteriophage, named vB_Kpn_F48, specific for K. pneumoniae isolates belonging to clonal group 101. Phage vB_Kpn_F48 was classified as a member of Myoviridae, order Caudovirales, on the basis of transmission electron microscopy analysis. Physiological characterization demonstrated that vB_Kpn_F48 showed a narrow host range, a short latent period, a low burst size and it is highly stable to both temperature and pH variations. High throughput sequencing and bioinformatics analysis revealed that the phage is characterized by a 171 Kb dsDNA genome that lacks genes undesirable for a therapeutic perspective such integrases, antibiotic resistance genes and toxin encoding genes. Phylogenetic analysis suggests that vB_Kpn_F48 is a T4-like bacteriophage which belongs to a novel genus within the Tevenvirinae subfamily, which we tentatively named “F48virus”. Considering the narrow host range, the genomic features and overall physiological parameters phage vB_Kpn_F48 could be a promising candidate to be used alone or in cocktails for phage therapy applications.

scholarly journals Isolation of the Novel Phage PHB09 and Its Potential Use against the Plant Pathogen Pseudomonas syringae pv. actinidiae

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2275
Author(s):  
Yanxi Liu ◽  
Mengjiao Liu ◽  
Ran Hu ◽  
Jun Bai ◽  
Xiaoqing He ◽  
...  
Keyword(s):  
Host Range ◽  
Pseudomonas Syringae ◽  
Management Strategies ◽  
Lytic Bacteriophage ◽  
Bacterial Canker ◽  
Isolation And Identification ◽  
Narrow Host Range ◽  
Development Of Resistance ◽  
Wide Range ◽  
Complete Genome Sequence Analysis

Bacteriophages are viruses that specifically infect target bacteria. Recently, bacteriophages have been considered potential biological control agents for bacterial pathogens due to their host specificity. Pseudomonas syringae pv. actinidiae (Psa) is a reemerging pathogen that causes bacterial canker of kiwifruit (Actinidia sp.). The economic impact of this pest and the development of resistance to antibiotics and copper sprays in Psa and other pathovars have led to investigation of alternative management strategies. Phage therapy may be a useful alternative to conventional treatments for controlling Psa infections. Although the efficacy of bacteriophage φ6 was evaluated for the control of Psa, the characteristics of other DNA bacteriophages infecting Psa remain unclear. In this study, the PHB09 lytic bacteriophage specific to Psa was isolated from kiwifruit orchard soil. Extensive host range testing using Psa isolated from kiwifruit orchards and other Pseudomonas strains showed PHB09 has a narrow host range. It remained stable over a wide range of temperatures (4–50 °C) and pH values (pH 3–11) and maintained stability for 50 min under ultraviolet irradiation. Complete genome sequence analysis indicated PHB09 might belong to a new myovirus genus in Caudoviricetes. Its genome contains a total of 94,844 bp and 186 predicted genes associated with phage structure, packaging, host lysis, DNA manipulation, transcription, and additional functions. The isolation and identification of PHB09 enrich the research on Pseudomonas phages and provide a promising biocontrol agent against kiwifruit bacterial canker.

scholarly journals Characterization of a Novel Bacteriophage Henu2 and Evaluation of the Synergistic Antibacterial Activity of Phage-Antibiotics

Antibiotics ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 174
Author(s):  
Xianghui Li ◽  
Tongxin Hu ◽  
Jiacun Wei ◽  
Yuhua He ◽  
Abualgasim Elgaili Abdalla ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Burst Size ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Sewage Sample ◽  
Bacterial Killing ◽  
Wide Range ◽  
The Family ◽  
Infected Cells

Staphylococcus aureus phage Henu2 was isolated from a sewage sample collected in Kaifeng, China, in 2017. In this study, Henu2, a linear double-stranded DNA virus, was sequenced and found to be 43,513 bp long with 35% G + C content and 63 putative open reading frames (ORFs). Phage Henu2 belongs to the family Siphoviridae and possesses an isometric head (63 nm in diameter). The latent time and burst size of Henu2 were approximately 20 min and 7.8 plaque forming unit (PFU)/infected cells. The Henu2 maintained infectivity over a wide range of temperature (10–60 °C) and pH values (4–12). Phylogenetic and comparative genomic analyses indicate that Staphylococcus aureus phage Henu2 should be a new member of the family of Siphoviridae class-II. In this paper, Phage Henu2 alone exhibited weak inhibitory activity on the growth of S. aureus. However, the combination of phage Henu2 and some antibiotics or oxides could effectively inhibit the growth of S. aureus, with a decrease of more than three logs within 24 h in vitro. These results provide useful information that phage Henu2 can be combined with antibiotics to increase the production of phage Henu2 and thus enhance the efficacy of bacterial killing.

scholarly journals Broad-Host-Range Yersinia Phage PY100: Genome Sequence, Proteome Analysis of Virions, and DNA Packaging Strategy

2007 ◽  
Vol 190 (1) ◽  
pp. 332-342 ◽  
Author(s):  
Dominik Schwudke ◽  
Asgar Ergin ◽  
Kathrin Michael ◽  
Sven Volkmar ◽  
Bernd Appel ◽  
...  
Keyword(s):  
Host Range ◽  
Proteome Analysis ◽  
Open Reading Frames ◽  
Broad Host Range ◽  
Lytic Bacteriophage ◽  
Coding Region ◽  
Putative Gene ◽  
Packaging Strategy ◽  
Virion Particles ◽  
Tail Proteins

ABSTRACT PY100 is a lytic bacteriophage with a broad host range within the genus Yersinia. The phage forms plaques on strains of the three human pathogenic species Yersinia enterocolitica, Y. pseudotuberculosis, and Y. pestis at 37°C. PY100 was isolated from farm manure and intended to be used in phage therapy trials. PY100 has an icosahedral capsid containing double-stranded DNA and a contractile tail. The genome consists of 50,291 bp and is predicted to contain 93 open reading frames (ORFs). PY100 gene products were found to be homologous to the capsid proteins and proteins involved in DNA metabolism of the enterobacterial phage T1; PY100 tail proteins possess homologies to putative tail proteins of phage AaΦ23 of Actinobacillus actinomycetemcomitans. In a proteome analysis of virion particles, 15 proteins of the head and tail structures were identified by mass spectrometry. The putative gene product of ORF2 of PY100 shows significant homology to the gene 3 product (small terminase subunit) of Salmonella phage P22 that is involved in packaging of the concatemeric phage DNA. The packaging mechanism of PY100 was analyzed by hybridization and sequence analysis of DNA isolated from virion particles. Newly replicated PY100 DNA is cut initially at a pac recognition site, which is located in the coding region of ORF2.

scholarly journals Isolation and Characterization of Six Vibrio parahaemolyticus Lytic Bacteriophages From Seafood Samples

2021 ◽  
Vol 12 ◽  
Author(s):  
Chia Wanq Tan ◽  
Yaya Rukayadi ◽  
Hanan Hasan ◽  
Noor-Azira Abdul-Mutalib ◽  
Nuzul Noorahya Jambari ◽  
...  
Keyword(s):  
Vibrio Parahaemolyticus ◽  
Burst Size ◽  
Foodborne Pathogen ◽  
Biological Properties ◽  
Promising Alternative ◽  
Narrow Host Range ◽  
Isolation And Characterization ◽  
Wide Range ◽  
The Stability

Vibrio parahaemolyticus is a foodborne pathogen that is frequently isolated from a variety of seafood. To control this pathogenic Vibrio spp., the implementation of bacteriophages in aquaculture and food industries have shown a promising alternative to antibiotics. In this study, six bacteriophages isolated from the seafood samples demonstrated a narrow host range specificity that infecting only the V. parahaemolyticus strains. Morphological analysis revealed that bacteriophages Vp33, Vp22, Vp21, and Vp02 belong to the Podoviridae family, while bacteriophages Vp08 and Vp11 were categorized into the Siphoviridae family. All bacteriophages were composed of DNA genome and showed distinctive restriction fragment length polymorphism. The optimal MOI for bacteriophage propagation was determined to be 0.001 to 1. One-step growth curve revealed that the latent period ranged from 10 to 20 min, and the burst size of bacteriophage was approximately 17 to 51 PFU/cell. The influence of temperature and pH levels on the stability of bacteriophages showed that all bacteriophages were optimally stable over a wide range of temperatures and pH levels. In vitro lytic activity of all bacteriophages demonstrated to have a significant effect against V. parahaemolyticus. Besides, the application of a bacteriophage cocktail instead of a single bacteriophage suspension was observed to have a better efficiency to control the growth of V. parahaemolyticus. Results from this study provided a basic understanding of the physiological and biological properties of the isolated bacteriophages before it can be readily used as a biocontrol agent against the growth of V. parahaemolyticus.

scholarly journals Isolation and Characterization of a Lytic Bacteriophage (vB_PmiS-TH) and Its Application in Combination with Ampicillin against Planktonic and Biofilm Forms of Proteus mirabilis Isolated from Urinary Tract Infection

2018 ◽  
Vol 28 (1) ◽  
pp. 37-46 ◽  
Author(s):  
Mahsa Yazdi ◽  
Majid Bouzari ◽  
Ezzat Allah Ghaemi
Keyword(s):  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Tract Infection ◽  
Proteus Mirabilis ◽  
Burst Size ◽  
High Dose ◽  
Lytic Bacteriophage ◽  
Isolation And Characterization ◽  
Biofilm Removal ◽  
Wide Range

<i>Proteus mirabilis</i> is one of the most common causes of urinary tract infection (UTI), particularly in patients undergoing long-term catheterization. Phage vB_PmiS-TH was isolated from wastewater with high lytic activity against <i>P. mirabilis</i> (TH) isolated from UTI. The phage had rapid adsorption, a large burst size (∼260 PFU per infected cell), and high stability at a wide range of temperatures and pH values. As analyzed by transmission electron microscopy, phage vB_PmiS-TH had an icosahedral head of ∼87 × 62 nm with a noncontractile tail about 137 nm in length and 11 nm in width. It belongs to the family <i>Siphoviridae</i>. Combination of the phage vB_PmiS-TH with ampicillin had a higher removal activity against planktonic cells of <i>P. mirabilis</i> (TH) than the phage or the antibiotic alone. Combination of the phage at a multiplicity of infection of 100 with a high dose of ampicillin (246 µg/mL) showed the highest biofilm removal activity after 24 h. This study demonstrates that using a combination of phage and antibiotic could be significantly more effective against planktonic and biofilm forms of <i>P. mirabilis</i> (TH).

scholarly journals Impacts of uORF codon identity and position on translation regulation

2019 ◽  
Vol 47 (17) ◽  
pp. 9358-9367 ◽  
Author(s):  
Yizhu Lin ◽  
Gemma E May ◽  
Hunter Kready ◽  
Lauren Nazzaro ◽  
Mao Mao ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Open Reading Frames ◽  
Translation Regulation ◽  
Coding Region ◽  
Wide Range ◽  
Range Of Functions ◽  
Functional Peptides ◽  
Regulatory Functions ◽  
The Impact ◽  
Reading Frames

Abstract Translation regulation plays an important role in eukaryotic gene expression. Upstream open reading frames (uORFs) are potent regulatory elements located in 5′ mRNA transcript leaders. Translation of uORFs usually inhibit the translation of downstream main open reading frames, but some enhance expression. While a minority of uORFs encode conserved functional peptides, the coding regions of most uORFs are not conserved. Thus, the importance of uORF coding sequences on their regulatory functions remains largely unknown. We investigated the impact of an uORF coding region on gene regulation by assaying the functions of thousands of variants in the yeast YAP1 uORF. Varying uORF codons resulted in a wide range of functions, including repressing and enhancing expression of the downstream ORF. The presence of rare codons resulted in the most inhibitory YAP1 uORF variants. Inhibitory functions of such uORFs were abrogated by overexpression of complementary tRNA. Finally, regression analysis of our results indicated that both codon identity and position impact uORF function. Our results support a model in which a uORF coding sequence impacts its regulatory functions by altering the speed of uORF translation.

scholarly journals Characterization of a Lytic Bacteriophage as an Antimicrobial Agent for Biocontrol of Shiga Toxin-Producing Escherichia coli O145 Strains

Antibiotics ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 74 ◽  
Author(s):  
Yen-Te Liao ◽  
Alexandra Salvador ◽  
Leslie A. Harden ◽  
Fang Liu ◽  
Valerie M. Lavenburg ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Agent ◽  
Shiga Toxin ◽  
Burst Size ◽  
Lytic Bacteriophage ◽  
E Coli ◽  
A Genome ◽  
Wide Range ◽  
Foodborne Outbreaks

Shiga toxin-producing Escherichia coli (STEC) O145 is one of the most prevalent non-O157 serogroups associated with foodborne outbreaks. Lytic phages are a potential alternative to antibiotics in combatting bacterial pathogens. In this study, we characterized a Siphoviridae phage lytic against STEC O145 strains as a novel antimicrobial agent. Escherichia phage vB_EcoS-Ro145clw (Ro145clw) was isolated and purified prior to physiological and genomic characterization. Then, in vitro antimicrobial activity against an outbreak strain, E. coli O145:H28, was evaluated. Ro145clw is a double-stranded DNA phage with a genome 42,031 bp in length. Of the 67 genes identified in the genome, 21 were annotated with functional proteins, none of which were stx genes. Ro145clw had a latent period of 21 min and a burst size of 192 phages per infected cell. The phage could sustain a wide range of pH (pH 3 to pH 10) and temperatures (−80 °C to −73 °C). Ro145clw was able to reduce E. coli O145:H28 in lysogeny broth by approximately 5 log at 37 °C in four hours. These findings indicate that the Ro145clw phage is a promising antimicrobial agent that can be used to control E. coli O145 in adverse pH and temperature conditions.

scholarly journals Complete Genome Sequence of vB_EcoP_SU7, a Podoviridae Coliphage with the Rare C3 Morphotype

2021 ◽  
Vol 9 (8) ◽  
pp. 1576
Author(s):  
Shazeeda Koonjan ◽  
Callum J. Cooper ◽  
Anders S. Nilsson
Keyword(s):  
Host Range ◽  
Burst Size ◽  
Phylogenetic Analyses ◽  
Treatment Plant ◽  
Latency Period ◽  
Enterotoxigenic Escherichia Coli ◽  
Therapeutic Success ◽  
Significant Similarity ◽  
Narrow Host Range ◽  
E Coli

Enterotoxigenic Escherichia coli (ETEC) strains are an important cause of bacterial diarrheal illness in humans and animals. Infections arising from ETEC could potentially be treated through the use of bacteriophage (phage) therapy, as phages encode for enzymes capable of bacterial cell lysis. vB_EcoP_SU7 was isolated from the Käppala wastewater treatment plant in Stockholm, Sweden, and propagated on an ETEC strain exhibiting the O:139 serovar. Transmission electron microscopy confirmed that vB_EcoP_SU7 belongs to the Podoviridae family and has the rare C3 morphotype of an elongated head. Bioinformatic analyses showed that the genome was 76,626 base pairs long and contained 35 genes with predicted functions. A total of 81 open reading frames encoding proteins with hypothetical function and two encoding proteins of no significant similarity were also found. A putative tRNA gene, which may aid in vB_EcoP_SU7’s translation, was also identified. Phylogenetic analyses showed that compared to other Podoviridae, vB_EcoP_SU7 is a rare Kuravirus and is closely related to E. coli phages with the uncommon C3 morphotype, such as ECBP2, EK010, vB_EcoP_EcoN5, and vB_EcoP_SU10. Phage vB_EcoP_SU7 has a narrow host range, infecting 11 out of the 137 E. coli strains tested, a latency period of 30 min, a burst size of 12 PFU/cell, and an adsorption rate of 8.78 × 10−9 mL/min five minutes post infection. With a limited host range and poor infection kinetics, it is unlikely that SU7 can be a standalone phage used for therapeutic purposes; rather, it must be used in combination with other phages for broad-spectrum therapeutic success.

scholarly journals Isolation of a Novel Lytic Bacteriophage against a Nosocomial Methicillin-Resistant Staphylococcus aureus Belonging to ST45

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Botond Zsombor Pertics ◽  
Dalma Szénásy ◽  
Dániel Dunai ◽  
Yannick Born ◽  
Lars Fieseler ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Lytic Bacteriophage ◽  
Lytic Enzymes ◽  
Methicillin Resistant ◽  
Narrow Host Range ◽  
Wide Range ◽  
Life Threatening ◽  
Amidase Gene ◽  
Phage Lysin

Methicillin-resistant Staphylococcus aureus (MRSA) can cause a wide range of infections from mild to life-threatening conditions. Its enhanced antibiotic resistance often leads to therapeutic failures and therefore alternative eradication methods must be considered. Potential candidates to control MRSA infections are bacteriophages and their lytic enzymes, lysins. In this study, we isolated a bacteriophage against a nosocomial MRSA strain belonging to the ST45 epidemiologic group. The phage belonging to Caudovirales, Siphoviridae, showed a narrow host range and stable lytic activity without the emergence of resistant MRSA clones. Phylogenetic analysis showed that the newly isolated Staphylococcus phage R4 belongs to the Triavirus genus in Siphoviridae family. Genetic analysis of the 45 kb sequence of R4 revealed 69 ORFs. No remnants of mobile genetic elements and traces of truncated genes were observed. We have localized the lysin (N-acetylmuramoyl-L-alanine amidase) gene of the new phage that was amplified, cloned, expressed, and purified. Its activity was verified by zymogram analysis. Our findings could potentially be used to develop specific anti-MRSA bacteriophage- and phage lysin-based therapeutic strategies against major clonal lineages and serotypes.

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