Wildy Prize Lecture, 2020-2021: Who wouldn't want to discover a new virus?

Harnessing the Activity of Lytic Bacteriophages to Foster the Sustainable Development Goals and the "One Health" Strategy

As bacteriophages (phages) are viruses that infect and destroy bacterial cells, they can be considered natural bactericides that can either directly or indirectly contribute to the achievement of the United Nations Sustainable Development Goals (UN SDGs) on health and well-being, food production and food security, as well as environmental protection and climate change mitigation, thus contributing to the success of the European "One Health" strategy to combat antimicrobial resistance in humans, animals, plants, and the environment. The biological activity of lytic bacteriophages can operate in the fields of microbiology and biotechnology for clinical, veterinary, agricultural, and industrial applications, among others, to achieve the proposed goals, mainly because the phages can help increase crop productivity by reducing bacterial diseases; constitute alternative therapies against infections caused by multidrug-resistant bacteria; can reduce populations of pathogenic bacteria that contaminate soil and water, therefore ensuring healthier and safer food production; and they can help reduce environmental pollution caused by the presence of agrochemicals and antibiotics. Phage-based therapies developed through research and innovation have the potential to promote greater global food security and health in a more environmentally friendly and eco-sustainable way.

A Bioinformatic Ecosystem for Bacteriophage Genomics: PhaMMSeqs, Phamerator, pdm_utils, PhagesDB, DEPhT, and PhamClust

The last thirty years have seen a meteoric rise in the number of sequenced bacteriophage genomes, spurred on by both the rise and success of groups working to isolate and characterize phages, and the rapid and significant technological improvements and reduced costs associated with sequencing their genomes. Over the course of these decades, the tools used to glean evolutionary insights from these sequences have grown more complex and sophisticated, and we describe here the suite of computational and bioinformatic tools used extensively by the integrated research-education communities such as SEA-PHAGES and PHIRE, which are jointly responsible for 25% of all complete phage genomes in the RefSeq database. These tools are used to integrate and analyze phage genome data from different sources, for identification and precise extraction of prophages from bacterial genomes, computing "phamilies" of related genes, and displaying the complex nucleotide and amino acid level mosaicism of these genomes. While over 50,000 SEA-PHAGES students have primarily benefitted from these tools, they are freely available for the phage community at large.

Introducing Casbah, Kronus, and MmasiCarm, Members of the Mycobacteriophage Subcluster B3

Background

As part of a large science education effort, bacteriophages that lyse Mycobacterium smegmatis mc2155 continue to be discovered.

Materials and Methods

Phages were isolated from soil samples from urban sites in the Northeastern United States. Their genomes were sequenced, assembled, and bioinformatically compared.

Results

Three lytic siphoviruses belonging to subcluster B3 with high similarity to each other and other B3 mycobacteriophages were isolated. These phages contain double-stranded DNA genomes (68,754 to 69,495 bp) with high GC content (67.4-67.5%) and 102-104 putative protein coding genes. Notable features include a HicA-like toxin and 33 genes exclusive to subcluster B3. One phage had an intein in its terminase sequence.

Conclusions

Genomic analyses of these phages provide insights into genome evolution and horizontal gene transfer (HGT). The networks for HGT are apparently vast and gene specific. Interestingly, a number of genes are found in both B3 and Gordonia DR phages.

Unusual prophages in Mycobacterium abscessus genomes and strain variations in phage susceptibilities

Mycobacterium abscessus infections are relatively common in patients with cystic fibrosis and are clinically challenging, with frequent intrinsic resistance to antibiotics. Therapeutic treatment with bacteriophages offers some promise but faces many challenges including substantial variation in phage susceptibilities among clinical isolates, and the need to personalize therapies for individual patients. Many strains are not susceptible to any phages or are not efficiently killed by lytic phages, including all smooth colony morphotype strains tested to-date. Here, we analyze a set of new M. abscessus isolates for the genomic relationships, prophage content, spontaneous phage release, and phage susceptibilities. We find that prophages are common in these M. abscessus genomes, but some have unusual arrangements, including tandemly integrated prophages, internal duplications, and they participate in active exchange of polymorphic toxin-immunity cassettes secreted by ESX systems. Relatively few strains are efficiently infected by any mycobacteriophages, and the infection patterns do not reflect the overall phylogenetic relationships of the strains. Characterization of these strains and their phage susceptibility profiles will help to advance the broader application of phage therapies for NTM infections.

PhaMMseqs: a new pipeline for constructing phage gene phamilies using MMseqs2

The diversity and mosaic architecture of phage genomes present challenges for whole-genome phylogenies and comparative genomics. There are no universally conserved core genes, ∼70% of phage genes are of unknown function, and phage genomes are replete with small (<500 bp) open reading frames. Assembling sequence-related genes into "phamilies" ("phams") based on amino acid sequence similarity simplifies comparative phage genomics and facilitates representations of phage genome mosaicism. With the rapid and substantial increase in the numbers of sequenced phage genomes, computationally efficient pham assembly is needed, together with strategies for including newly sequenced phage genomes. Here, we describe the Python package PhaMMseqs, which uses MMseqs2 for pham assembly, and we evaluate the key parameters for optimal pham assembly of sequence- and functionally related proteins. PhaMMseqs runs efficiently with only modest hardware requirements and integrates with the pdm_utils package for simple genome entry and export of datasets for evolutionary analyses and phage genome map construction.

Complete Genome Sequences of Cluster A Mycobacteriophages Kenmech and Peterson and Cluster F Mycobacteriophage Rockne

Kenmech, Peterson, and Rockne are bacteriophages that infect Mycobacterium smegmatis mc² 155. Both Kenmech and Peterson genomes are ~52 kbp long and contain 1 tRNA as well as 92 and 89 protein-coding genes, respectively. Rockne has a 56,704-bp genome with 108 protein-coding genes and no tRNA.

Mycobacteriophages: From Petri dish to patient

Mycobacteriophages-bacteriophages infecting Mycobacterium hosts-contribute substantially to our understanding of viral diversity and evolution, provide resources for advancing Mycobacterium genetics, are the basis of high-impact science education programs, and show considerable therapeutic potential. Over 10,000 individual mycobacteriophages have been isolated by high school and undergraduate students using the model organism Mycobacterium smegmatis mc2155 and 2,100 have been completely sequenced, giving a high-resolution view of the phages that infect a single common host strain. The phage genomes are revealed to be highly diverse and architecturally mosaic and are replete with genes of unknown function. Mycobacteriophages have provided many widely used tools for Mycobacterium genetics including integration-proficient vectors and recombineering systems, as well as systems for efficient delivery of reporter genes, transposons, and allelic exchange substrates. The genomic insights and engineering tools have facilitated exploration of phages for treatment of Mycobacterium infections, although their full therapeutic potential has yet to be realized.