Dear readers, we welcome you to the December edition of PHAGE. We hope that you have had a good year and are looking forward to 2023. Certainly, from a phage perspective, things have been incredibly exciting. Year 2022 saw the return of the much-awaited viruses of microbes (VoM) conference in Guimarães Portugal as well as the largely in-person Oxford Bacteriophage Conference in England, the former was so popular that a larger venue had to be found to accommodate the 700 delegates! Many group leaders brought their whole laboratory to VoM and this event felt like a much needed reunion of the phage community.
Oxford was also full at the seams with a strong international presence and all aspects of phages covered from fundamental to highly applied. Other well-attended in-person international phage meetings included the fifth phage therapy summit forum that was held online from Shanghai, China, and the second Latin American phage meeting that was held in Buenos Aires in Argentina.
Year 2022 has also seen important political and strategic moves within phage research. This includes the development of the Australian Initiative, Phage Australia—to progress phage therapy use—as previously described in PHAGE, and in a similar vein, the NIH announcing that it will fund Adaptive Phage Therapeutic to carry out a clinical trial on the use of phages to treat patients with Pseudomonas aeruginosa infections in cystic fibrosis. Belgium saw the launch of its Belgian Society for Viruses of Microbes that held its inaugural seminar in Leuven in September—aimed at exploiting the dense hub of interested physicians, academics, and bioinformatics—all of whom exist within a progressive regulatory framework to advance phage therapy.
Within the United Kingdom, there has been the establishment of the first U.K.-based Phage Centre—at Leicester and a phage network as part of Innovate U.K. research council, networks of clinicians interested in phages are also being formed and the first U.K. phage consultant was employed by the NHS, in a hospital in Scotland. Another significant milestone for interest in phage technology was the recent success of James Ebdon, a professor of environmental microbiology who pitched to the U.K. government the idea that research into phage technology was chronically underdeveloped, which seems short sighted within the context of antimicrobial resistance.
This pitch was part of a competition whereby scientists can inform the U.K. parliamentary committee of science and technology of underfunded research areas. Of an initial 90 proposals, this topic was chosen to be a subject of a government inquiry—responses to this are currently being invited.
Within PHAGE we are extremely pleased to have now been indexed on PubMed Central, Web of Science Emerging Sources Citation Index, Scopus, Biological Abstracts, BIOSIS Previews, CAB Abstracts, Global Health, and BenchSci. This is a key step for our future success, and we anticipate our first impact factor next year. Thank those of you who have published with us so far and warmly invite others to do so. We are delighted to see that the downloads for our previous issues are high—for example—with >20,000 downloads from our recent special issue on Phage Informatics and Artificial Intelligence.
Our InPhocus this issue comes from Africa and has been driven extensively by the founder and president of Phages for Global Health (PGH) (a nonprofit that aims to deliver phage knowledge to low–middle-income countries), Tobi Nagel who has spent a considerable about of time working with African academics to deliver a set of training to expand existing phage-based infrastructure and knowledge in Africa. Africa is of particular concern from an AMR perspective as it is predicted that more deaths will occur on this continent than any other unless action is taken.
The inPhocus summarizes the work that has been carried out in the African subcontinent and highlights the content and impact of the work delivered by PGH. It is great to watch the phage community start to flourish in Africa and it was particularly nice to be a part of the nicely organized World Phage week 2022 seminar series in November this year, organized by the Ibadan Bacteriophage Research Team, from University of Ibadan, Nigeria. We hope that you like the cartoon by Ellie Harrison that reflects the inPhocus article and African phage work as much as we do!
Fittingly with our inPhocus feature, the research article in this issue from Bumunang and colleagues from the University of Calgary and North-West University, Mmabatho, South Africa, who details work the Genomic profiling of non-O157 Shiga toxigenic Escherichia coli-infecting bacteriophages from South African feedlots and discuss their potential for use to decontaminate meat from this pernicious pathogen.
Having previously edited several volumes of methods books associated with working with phages, I am aware of the benefits to the community of clear protocols. Fittingly we are, therefore, happy to present three excellent and highly useful methods-focused articles in this issue that we hope will be of great interest to our readers. The first focuses on gene transfer agents or GTAs—phage like particles—which transfer genetic material between cells. It is important to be able to study them to establish their contribution to bacterial evolution both naturally and in the presence of bacteriophages; however, they are particularly difficult to purify.
Langille et al., from the Memorial University of Newfoundland in Canada, present an intriguing article that shows a quick and efficient way to purify these agents from bacterial cultures that may also have applications in phage therapy.
Determining phage hosts without experimental data is not easy but key to interpreting metagenomic and metaviromic sequencing data. Amgarten et al. from the University of São Paulo have developed the Viral Host UnveiLing Kit—a set of machine learning-based tools for predicting phage hosts based on genomic features. By transforming sequence similarity scores against the pVOG database into ∼10.000 features, they trained both a host species and a host genus predictor, which are able to identify 118 different bacterial host species and 77 different genera. The tool is freely available on github and is also easy to install. If you are curious about what is in your virome data, give it a try!
The power of building synthetic phages was brought into keen focus in 2018 by Samuel Kilchner from the ETH Zurich who synthesized Streptococcus and Bacillus phages then resuscitated or “rebooted” them in Listerial L-forms (bacteria lacking cell walls), thus removing multiple barriers to “regenerating” phages. Synthetic biology is an exciting tool for understanding phages that is likely to be increasingly used as any genome features can be studied free from the constraints of recombineering. Key to doing this at all is being able to correctly assemble the chunks of phage DNA in the first place.
The article by Vuong et al., from Sandia National Laboratories California, addresses the fact that no existing open-source overlap assembly design software explicitly facilitated the rebuilding steps of the large chunks of phage DNA. This article cleverly answers your phage DNA needs and will hopefully help to allow the testing of phages with payloads only limited by your imagination—well and their ability to be stable within capsids and with time when propagated!
Anyway, we hope you enjoy reading the articles in this issue and sincerely wish all readers our warmest wishes to this holiday season, and hope everyone has a nice break and exciting and phage-filled 2023!