A Quest of Great Importance-Developing a Broad Spectrum Escherichia coli Phage Collection

Abstract

Shigella ssp. and enterotoxigenic Escherichia coli are the most common etiological agents of diarrheal diseases in malnourished children under five years of age in developing countries. The ever-growing issue of antibiotic resistance and the potential negative impact of antibiotic use on infant commensal microbiota are significant challenges to current therapeutic approaches. Bacteriophages (or phages) represent an alternative treatment that can be used to treat specific bacterial infections. In the present study, we screened water samples from both environmental and industrial sources for phages capable of infecting E. coli laboratory strains within our collection. Nineteen phages were isolatedand tested for their ability to infect strains within the ECOR collection and E. coli O157:H7 Δstx. Furthermore, since coliphages have been reported to cross-infect certain Shigella spp., we also evaluated the ability of the nineteen phages to infect a representative Shigella sonnei strain from our collection. Based on having distinct (although overlapping in some cases) host ranges, ten phage isolates were selected for genome sequence and morphological characterization. Together, these ten selected phages were shown to infect most of the ECOR library, with 61 of the 72 strains infected by at least one phage from our collection. Genome analysis of the ten phages allowed classification into five previously described genetic subgroups plus one previously underrepresented subgroup.

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

“…The Felixounavirus genus in the Ounavirinae subfamily of Myoviridae comprises a group of phages with genomes of 84-91 kb and characteristically straight lateral tail fibers of which Salmonella phage Felix O1 has been most well studied [30,90] (Figs 11A and 11B). Previous work aimed at the isolation of E. coli phages differed greatly in the reported abundance of Felixounavirus phages, ranging from no detection [23] over a moderate number of isolates in most studies [25,91] to around one fourth of all [24]. Across our phage sampling experiments we found a single Felixounavirus phage, JohannRWettstein (Bas61), which is rather distantly related to Felix O1 within the eponymous genus ( Fig 11B).…”

Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future

“…It should efficiently lyse the target bacteria, have the widest possible strain range within a pathogenic species, be sufficiently stable under storage conditions and at the sites of infection by the bacteria, be able to overcome at least some bacterial phage-resistance mechanisms, and cause no undesired immune reactions. Although hundreds of phages targeting bacterial pathogens have been isolated (e.g., [ 80 – 91 ]), none of them fulfills all these criteria, and in fact, none has been characterized with respect to all of them. First, many if not most DNA phages are temperate (Fig.…”

“…Although such a strategy fits the current trend to personalize medicine and has not only been widely discussed but also successfully used [ 28 ], it is commercially unattractive, as custom-made phage preparations cannot be currently approved for medical use [ 21 , 125 , 126 ]. Moreover, even mixtures of phages of different specificity usually do not exhibit a universal strain range [ 21 , 91 , 127 – 129 ], and searching for natural phages of the missing specificity is tedious, time consuming, and often either fails or leads to the isolation of only temperate phages [ 21 , 90 ]. Even the so called adaptation of phages to infect resistant strains by selection of natural phage mutants has limited potential in the acquisition of phages of new specificities [ 76 , 120 , 130 – 133 ].…”

“…Several of them are related to model phages. Related phages differ mostly in genome regions required for the host-specific interaction [ 80 , 81 , 87 , 91 , 119 , 127 , 137 – 139 ] The phage that infects a bacterium of a given species should be metabolically compatible with all strains of this species. Thus, if well characterized, it could serve as a universal scaffold to construct its derivatives differing, e.g., in strain specificity, stability, or other properties The core genomes of diverse bacterial strains of a given species, which determine their basic metabolic functions, are conserved [ 140 – 142 ] The Earth phageome, even if incompletely characterized, can serve as a source of genes or gene modules that can be analyzed functionally when incorporated to the genomes of well characterized phages and provide a much broader repertoire of functions than that encoded by the few well characterized phages The enormous diversity of phages, reflected, e.g., by their genome size range and differences in morphological and physiological properties, limits the possibility of a phage pan-genome functional analysis.…”

In Vitro and In Vivo Assessment of the Potential of Escherichia coli Phages to Treat Infections and Survive Gastric Conditions

“…In the prophylactic treatment model, the phages were injected 2 h before the bacterial suspension (PC + ECOR/strain pool), while in the remedial treatment model, the bacteria were injected 2 and 5 h before the phages (ECOR/strain pool + PC). Host range data for JK16, JK36, and JK38 is adapted from [27]. Strains highlighted in a red box represent those selected for the infection model assays.…”