Lytic bacteriophages facilitate antibiotic sensitization ofEnterococcus faecium

Abstract

Enterococcus faecium, a commensal of the human intestine, has emerged as a hospital-adapted, multi-drug resistant (MDR) pathogen. Bacteriophages (phages), natural predators of bacteria, have regained attention as therapeutics to stem the rise of MDR bacteria. Despite their potential to curtail MDR E. faecium infections, the molecular events governing E. faecium-phage interactions remain largely unknown. Such interactions are important to delineate because phage selective pressure imposed on E. faecium will undoubtedly result in phage resistance phenotypes that could threaten the efficacy of phage therapy. In an effort to understand the emergence of phage resistance in E. faecium, three newly isolated lytic phages were used to demonstrate that E. faecium phage resistance is conferred through an array of cell wall-associated molecules, including secreted antigen A (SagA), enterococcal polysaccharide antigen (Epa), wall teichoic acids, capsule, and an arginine-arginine-aspartate (RDD) protein of unknown function. We find that capsule and Epa are important for robust phage adsorption and that phage resistance mutations in sagA, epaR, and epaX enhance E. faecium susceptibility to ceftriaxone, an antibiotic normally ineffective due to its low affinity for enterococcal penicillin binding proteins. Consistent with these findings, we provide evidence that phages potently synergize with cell wall (ceftriaxone and ampicillin) and membrane-acting (daptomycin) antimicrobials to slow or completely inhibit the growth of E. faecium. Our work demonstrates that the evolution of phage resistance comes with fitness defects resulting in drug sensitization and that lytic phages could potentially serve as antimicrobial adjuvants in treating E. faecium infections.

Genetically distant bacteriophages select for unique genomic changes in Enterococcus faecalis

“…SNPs in pip EF and epa indicate that phage receptor and coreceptor mutations are common to prevent phage infection. Additionally, many enterococcal phages rely on Epa for adsorption to cells (Al‐Zubidi et al, 2019; Canfield et al, 2021; Chatterjee et al, 2019, 2020; Ho et al, 2018). In this study, we show that epa mutations are abundant when the bacteria are challenged with phi47.…”

The Age of Phage: Friend or Foe in the New Dawn of Therapeutic and Biocontrol Applications?

“…The application of phage LUZ7 in combination with streptomycin against Pseudomonas aeruginosa resulted in reductions in bacterial cell densities significantly greater than each individual treatment [265]. Interestingly, findings have also displayed that mutations associated with developing phage resistance such as sagA, epaR, and epaX may enhance the susceptibility of Enterococcus faecium to ceftriaxone, an antibiotic which is normally ineffective against E. faecium [266]. Nonetheless, further considerations are needed regarding the combined use of bacteriophages and antibiotics against bacterial infections regarding the choice of phage and antibiotic, and the ratios of each agent used [262].…”

A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens

“…Genome-wide genetic screens are performed to uncover phage infection determinants including phage receptor discovery ( Rousset et al., 2018 ; Adler et al., 2020 ; Chatterjee et al., 2020 ; Kortright et al., 2020 ; Mutalik et al., 2020 ). These phage-host bacteria characterization platforms are further used to map out cross-resistance (CR) and collateral sensitivity (CS) trait profiles of phages in addition to antibiotics, biocides, ionophores, metals, drugs, preservatives, and pesticides ( Chan et al., 2016 ; Allen et al., 2017 ; Price et al., 2018 ; Barbosa et al., 2019 ; Mutalik et al., 2019 ; Burmeister et al., 2020 ; Chatterjee et al., 2020 ; Gurney et al., 2020 ; Jiang et al., 2020 ; Mangalea and Duerkop, 2020 ; Altamirano et al., 2021 ; Canfield et al., 2021 ; Kever et al., 2021 ). The HT genetic tools developed for target bacterial hosts should also be able to support mapping of gene essentiality in select phages in the phage banks ( Marinelli et al., 2012 ; Dedrick et al., 2013 ; Thomas et al., 2016 ; Shen et al., 2018 ; Meeske et al., 2019 ; Mageeney et al., 2020 ; Marino et al., 2020 ; Vo et al., 2020 ; Rubin et al., 2021 ).…”

“…The HT genetic tools developed for target bacterial hosts should also be able to support mapping of gene essentiality in select phages in the phage banks ( Marinelli et al., 2012 ; Dedrick et al., 2013 ; Thomas et al., 2016 ; Shen et al., 2018 ; Meeske et al., 2019 ; Mageeney et al., 2020 ; Marino et al., 2020 ; Vo et al., 2020 ; Rubin et al., 2021 ). Infection efficiency of phages or combination of phages is assessed by designing rational formulations using genome-wide phage-host interaction datasets including knowledge of probable phage receptors ( Wright et al., 2018 , 2019 , 2021 ; Chatterjee et al., 2020 ; Altamirano et al., 2021 ; Canfield et al., 2021 ). Deeper assessment of phage stability, efficacy, competition, and evolutionary changes within phage cocktails and costs of delaying resistance are carried out ( Tanji et al., 2004 ; Chan and Abedon, 2012 ; Chan et al., 2013 ; Reyes et al., 2013 ; Schmerer et al., 2014 ; Wright et al., 2019 ).…”

“…As these omics approaches can get cost-prohibitive and unscalable to hundreds of samples, specific criteria should be established for assessing the need for such datasets in a specific application. The adaptive landscape of a phage is mapped via low-throughput ALE experiments ( Scanlan et al., 2015a ; Lenski, 2017a ; Akusobi et al., 2018 ; Sandberg et al., 2019 ; Favor et al., 2020 ; Kering et al., 2020 ), and new functions such as altered receptor identification ( Meyer et al., 2012 ) or evolutionary trade-off traits such as antibiotic sensitivity to phage resistance are evolved ( Chan et al., 2016 ; Chatterjee et al., 2020 ; Gurney et al., 2020 ; Mangalea and Duerkop, 2020 ; Canfield et al., 2021 ; Gordillo Altamirano et al., 2021 ).…”