Systematic exploration ofEscherichia coliphage-host interactions with the BASEL phage collection

Abstract

Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 66 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL collection (BActeriophage SElection for your Laboratory). This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside ten well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to eleven defense systems across different layers of bacterial immunity, and matched these results to the phages' host range across a panel of pathogenic enterobacterial strains. Our results reveal clear patterns in the distribution of phage phenotypes and genomic features that highlight systematic differences in the potency of different immunity systems and point towards the molecular basis of receptor specificity in several phage groups. Strong trade-offs were detected between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.

A new sugar for an old phage: A c-di-GMP dependent polysaccharide pathway sensitizes E. coli for bacteriophage infection

“…Understanding how bacteria maintain the expression of highly conserved surface glycans, despite of phage predation, is not only relevant for phage ecology and evolution but could also have great value for the therapeutic use of bacteriophages. Not unexpectedly, the bona fide ECAtargeting phages studied in previous work systematically displayed the broadest host recognition of all phages tested (Maffei et al, 2021) which is, intuitively, a key property when selecting phages for therapeutic purposes (Hyman, 2019).…”

“…While exposed glycan structures are often used as a first "primary" receptor for host recognition, irreversible adsorption and injection of the phage genome are triggered by subsequent binding to a terminal or "secondary" receptor directly on the cell surface (Nobrega et al, 2018). For Gram-negative bacteria like the model organism Escherichia coli, all known types of glycans including capsules, the highly variable O-antigen chains of LPS, and the conserved yet enigmatic enterobacterial common antigen (ECA) have been described as primary receptors for phage docking (Maffei et al, 2021;Broeker and Barbirz, 2017;Kim et al, 2015;Silva et al, 2016;Washizaki et al, 2016). However, surface exposed polysaccharides also play major roles in bacterial defense against phages as they can shield terminal receptors on the cell surface (Broeker and Barbirz, 2017;Kim et al, 2015;Porter and Martens, 2015;Rousset et al, 2018).…”

“…However, surface exposed polysaccharides also play major roles in bacterial defense against phages as they can shield terminal receptors on the cell surface (Broeker and Barbirz, 2017;Kim et al, 2015;Porter and Martens, 2015;Rousset et al, 2018). E.g., in E. coli K12 O-antigen expression was shown to eliminate the adsorption of a wide range of bacteriophages that could bind diverse terminal receptors and infect productively in the absence of this barrier (Maffei et al, 2021). Likewise, overproduction of capsules can effectively protect bacteria from phage adsorption (Chaudhry et al, 2020;Mutalik et al, 2020).…”

“…Previous genetic studies indicated that the ECA glycan chains are exploited as host receptor by diverse and very common bacteriophages like the well-studied podovirus N4 (Kiino and Rothman-Denes, 1989;Maffei et al, 2021). This is remarkable sinceunlike the almost 200 different types of O-antigens for E. coli alone (Liu et al, 2019) the ECA glycan is invariable across enterobacteria, possibly due to functional constraints in their interaction with their animal hosts (Rai and Mitchell, 2020a).…”

Digital control of c-di-GMP in E. coli balances population-wide developmental transitions and phage sensitivity

“…Specific members of these important bacterial predators use exopolysaccharides, capsules, or LPS as primary receptors and have evolved virionassociated polysaccharide depolymerases to gain access to secondary receptors on the cell surface (Nobrega et al, 2018). Screening a library of E. coli bacteriophages (Maffei et al, 2021) for agents that specifically prey on cells with high levels of c-di-GMP led to the identification of the podovirus N4 (Fig. 6e), which readily infects E. coli strain MG1655 (CGSC 6300) but does not kill an isogenic strain that constitutively expresses pdeL (Fig.…”