PHAGE (New Rochelle, N.Y.)最新文献

{"title":"A March Mashup.","authors":"Martha R J Clokie","doi":"10.1089/phage.2022.29027.edi","DOIUrl":"https://doi.org/10.1089/phage.2022.29027.edi","url":null,"abstract":"","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"3 1","pages":"3-4"},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9436249/pdf/phage.2022.29027.edi.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10820875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>In Vitro</i> Evolution of Specific Phages Infecting the Fish Pathogen <i>Flavobacterium psychrophilum</i>.","authors":"Daniel Castillo,&nbsp;Alexander Ravndal Højsting,&nbsp;Andrea Roosvall,&nbsp;Giorgos Smyrlis,&nbsp;Johanna Jørgensen,&nbsp;Mathias Middelboe","doi":"10.1089/phage.2022.0006","DOIUrl":"https://doi.org/10.1089/phage.2022.0006","url":null,"abstract":"<p><strong>Background: </strong><i>Flavobacterium psychrophilum</i> is the causative agent of the bacterial cold-water disease and rainbow trout fry syndrome. Owing to the issues associated with increasing use of antibiotics to control the diseases, phage therapy has been proposed as an alternative method to control <i>Flavobacterium</i> infection within the industry.</p><p><strong>Materials and methods: </strong>We explored two simple and fast <i>in vitro</i> strategies for the isolation of evolved <i>F. psychrophilum</i> phages, using three well-characterized phages FpV4, FpV9, and FPSV-S20.</p><p><strong>Results: </strong>During <i>in vitro</i> serial transfer experiments, 12 evolved phages were selected 72-96 h after phage exposure in the first or second week. Phenotype analysis showed improvement of host range and efficiency of plating and adsorption constants. Comparative genomic analysis of the evolved phages identified 13 independent point mutations causing amino acid changes mostly in hypothetical proteins.</p><p><strong>Conclusions: </strong>These results confirmed the reliability and effectivity of two strategies to isolate evolved <i>F. psychrophilum</i> phages, which may be used to expand phage-host range and target phage-resistant pathogens in phage therapy applications against <i>Flavobacterium</i> infections.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"3 1","pages":"28-37"},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10071593/pdf/phage.2022.0006.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9325091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Call for Special Issue Papers:</i> Phage/Host Combat: Phage Strategies for Taking Over the Host and Host Strategies for Defense: Deadline for Manuscript Submission: July 1, 2022.","authors":"Deborah M Hinton,&nbsp;Paul E Turner","doi":"10.1089/phage.2022.29026.cfp","DOIUrl":"https://doi.org/10.1089/phage.2022.29026.cfp","url":null,"abstract":"","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"3 1","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9436253/pdf/phage.2022.29026.cfp.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10814642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Enterobacteria</i> Phage SV76 Host Range and Genomic Characterization.","authors":"Caitlin M Carmody,&nbsp;Emma L Farquharson,&nbsp;Sam R Nugen","doi":"10.1089/phage.2022.0005","DOIUrl":"https://doi.org/10.1089/phage.2022.0005","url":null,"abstract":"<p><strong>Background: </strong>Increasing the quantity and detail of bacteriophage genomic data is critical to broadening our understanding of how bacteriophages operate to allow us to harness their unique properties for biotechnology advancements. Here we present the complete sequence of phage SV76's assembled and annotated genome (Accession OM339528). SV76 has previously been classified as a T4-like bacteriophage belonging to the <i>Tequatrovirus</i> genus within the <i>Myoviridae</i> family of contractile tailed bacteriophages.</p><p><strong>Materials and methods: </strong>Whole genome sequencing, assembly, and annotation was performed on SV76. Double-agar spot assays were utilized to determine SV76's host range against a panel of 72 <i>Escherichia coli</i> isolates meant to represent the diversity of <i>E. coli</i>, as well as a series of knockouts designed to identify required receptor binding proteins. The genome and host range were compared to the closely related phage, T2.</p><p><strong>Results: </strong>Spot assays revealed that SV76 could plaque on 10 of the 72 strains (13.9 %) and nine of the nine <i>E. coli</i> K12 single gene knockout of known phage receptors (100%). SV76 did not plate on a <i>ΔfadL E. coli</i> indicating suggesting a requirement as a receptor binding protein.</p><p><strong>Conclusions: </strong>SV76 is closely related to T2 with similar host ranges within ECOR. This study presents novel host range and genomic data on SV76 phage, providing a foundation for future studies to further characterize SV76 to understand more about SV76 and other T4-like phages that can be applied to create novel biotechnologies.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"3 1","pages":"59-63"},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041521/pdf/phage.2022.0005.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10810225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prophages Present in <i>Acinetobacter pittii</i> Influence Bacterial Virulence, Antibiotic Resistance, and Genomic Rearrangements.","authors":"Richard Zhu,&nbsp;Vinayak Mathur","doi":"10.1089/phage.2021.0014","DOIUrl":"https://doi.org/10.1089/phage.2021.0014","url":null,"abstract":"<p><p><b><i>Introduction:</i></b> Antibiotic resistance and virulence are common among bacterial populations, posing a global clinical challenge. The bacterial species <i>Acinetobacter pittii</i>, an infectious agent in clinical environments, has shown increasing rates of antibiotic resistance. Viruses that integrate as prophages into <i>A. pittii</i> could be a potential cause of this pathogenicity, as they often contain antibiotic resistance or virulence factor gene sequences. <b><i>Methods:</i></b> In this study, we analyzed 25 <i>A. pittii</i> strains for potential prophages. Using virulence factor databases, we identified many common and virulent prophages in <i>A. pittii</i>. <b><i>Results:</i></b> The analysis also included a specific catalogue of the virulence factors and antibiotic resistance genes contributed by <i>A. pittii</i> prophages. Finally, our results illustrate multiple similarities between <i>A. pittii</i> and its bacterial relatives with regard to prophage integration sites and prevalence. <b><i>Discussion:</i></b> These findings provide a broader insight into prophage behavior that can be applied to future studies on similar species in the <i>Acinetobacter calcoaceticus</i>-<i>baumannii</i> complex.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"3 1","pages":"38-49"},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041518/pdf/phage.2021.0014.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10814645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phage Therapies: Lessons (Not) Learned from the \"Antibiotic Era\".","authors":"Carlos F Amábile-Cuevas","doi":"10.1089/phage.2022.0001","DOIUrl":"10.1089/phage.2022.0001","url":null,"abstract":"<p><p>The use of phages as therapeutic or prophylactic approaches is gaining increased interest amid the growing menace of antibiotic resistance. Phages, along with other new anti-infective strategies, are certainly welcome as much needed additions to the medicinal arsenal. However, we can easily make with phages the same mistakes we made with antibiotics, which caused the current resistance crisis. The oversimplification of the ecological role of antibiotics, neglecting ancient resistance and the role of horizontal gene transfer; the active search for wide spectrum, and the massive agricultural abuse; and, most importantly, the financial greed behind the development and use of antibiotics; these are all trends that are now visible in phage research. Should we bring phages to the same track that wasted antibiotics, we could be looking at a \"postphage era\" in our near future.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"3 1","pages":"12-14"},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9436267/pdf/phage.2022.0001.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10820873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Special Issue on Phage Informatics and Artificial Intelligence.","authors":"Martha R J Clokie","doi":"10.1089/phage.2021.29022.edi","DOIUrl":"https://doi.org/10.1089/phage.2021.29022.edi","url":null,"abstract":"","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":" ","pages":"153-154"},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041507/pdf/phage.2021.29022.edi.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33485743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"inPhocus: \"State of Phage\" Survey Highlights Widespread Diverse Phage Isolation and Research in 40+ Countries.","authors":"Jessica C Sacher,&nbsp;Jan Zheng","doi":"10.1089/phage.2021.29023.jcs","DOIUrl":"https://doi.org/10.1089/phage.2021.29023.jcs","url":null,"abstract":"<p><p>The phage field is clearly growing around the world, but no one had compiled a bird's eye view of the phages being collected and the phage research and development work being done. To fill this gap, and help establish a baseline for the current state of phage research so we can track and cultivate its growth and evolution over time, we created the State of Phage 2020 Survey. We aimed to get a snapshot of the strains and phages being collected around the world, and to capture activities and opinions of phage laboratories, including go-to methods, definitions of what phage characterization looks like, level of characterization of phages, preferred phage sharing practices, and more. Here we present an overview of selected results from our State of Phage 2020 survey, along with our interpretations and perspective on where to go from here as a field to maximize the impact of phage work being done around the globe. We conclude that given the magnitude of the task at hand (developing a robust understanding of the phages we have, which span hundreds of phages targeting hundreds of species), and given the large yet diverse collective phage expertise around the world, the best way forward is to develop systems that allow the field to combine forces, including making room for domain experts to focus on their specific strengths and investing in phage and data sharing practices.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":" ","pages":"156-169"},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041509/pdf/phage.2021.29023.jcs.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33485740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OnePetri: Accelerating Common Bacteriophage Petri Dish Assays with Computer Vision.","authors":"Michael Shamash,&nbsp;Corinne F Maurice","doi":"10.1089/phage.2021.0012","DOIUrl":"https://doi.org/10.1089/phage.2021.0012","url":null,"abstract":"<p><p><b><i>Introduction:</i></b> Bacteriophage plaque enumeration is a critical step in a wide array of protocols. The current gold standard for plaque enumeration on Petri dishes is through manual counting. However, this approach is not only time-consuming and prone to human error but also limited to Petri dishes with countable number of plaques resulting in low throughput. <b><i>Materials and Methods:</i></b> We present OnePetri, a collection of trained machine learning models and open-source mobile application for the rapid enumeration of bacteriophage plaques on circular Petri dishes. <b><i>Results:</i></b> When compared against the current gold standard of manual counting, OnePetri was ∼30 × faster. Compared against other similar tools, OnePetri had lower relative error (∼13%) than Plaque Size Tool (PST) (∼86%) and CFU.AI (∼19%), while also having significantly reduced detection times over PST (1.7 × faster). <b><i>Conclusions:</i></b> The OnePetri application is a user-friendly platform that can rapidly enumerate phage plaques on circular Petri dishes with high precision and recall.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":" ","pages":"224-231"},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041512/pdf/phage.2021.0012.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33485741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phage Commander, an Application for Rapid Gene Identification in Bacteriophage Genomes Using Multiple Programs.","authors":"Matt Lazeroff,&nbsp;Geordie Ryder,&nbsp;Sarah L Harris,&nbsp;Philippos K Tsourkas","doi":"10.1089/phage.2020.0044","DOIUrl":"https://doi.org/10.1089/phage.2020.0044","url":null,"abstract":"<p><p>The number of sequenced bacteriophage genomes is growing at an exponential rate. The majority of sequenced bacteriophage genomes are annotated by one or more of several freely available gene identification programs (Glimmer, GeneMark, RAST, Prodigal, etc.). No program has been shown to consistently outperform the others; thus, the choice of which program to use is not obvious. We present the Phage Commander application for rapid identification of bacteriophage genes using multiple gene identification programs. Phage Commander runs a bacteriophage genome sequence through nine gene identification programs (and an additional program for identification of tRNAs) and integrates the results within a single output table. Phage Commander also generates formatted output files for direct export to National Center for Biotechnology Information GenBank or genome visualization programs such as DNA Master. Users can select the threshold for which genes to export (genes identified by at least one program, genes identified by at least two programs, etc.). Phage Commander was benchmarked using eight high-quality bacteriophage genomes whose genes are backed by experimental data. Our results show that the most accurate annotations are obtained by exporting genes identified by at least two or three programs. Many groups opt to manually curate the annotations obtained from gene identification programs, and Phage Commander was designed to facilitate manual curation of genome annotations. Our benchmarking results show that manual curation does indeed produce more accurate annotations than any individual gene identification program. The authors thus recommend manually curating the output of Phage Commander to generate maximally accurate annotations. Phage Commander is currently being used in the corresponding author's bacteriophage genome annotation class and has reduced the labor cost and improved the quality of genome annotations.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":" ","pages":"204-213"},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/03/71/phage.2020.0044.PMC9041506.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33477956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}