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In the time of antimicrobial resistance, phage therapy is frequently suggested as a possible solution for such difficult-to-treat infections. Vancomycin-intermediate Staphylococcus aureus (VISA) remains a relatively rare yet increasing occurrence in the clinic for which phage therapy may be an option. However, the data presented herein suggest a potential cross-resistance mechanism to phage following vancomycin exposure in VISA strains. When comparing genetically similar strains differing in their susceptibility to vancomycin, those with intermediate levels of vancomycin resistance displayed decreased sensitivity to phage in solid and liquid assays. Serial passaging with vancomycin induced both reduced vancomycin susceptibility and phage sensitivity. As a consequence, the process of phage infection was shown to be interrupted after DNA ejection from adsorbed phage but prior to phage DNA replication, as demonstrated through adsorption assays, lysostaphin sensitivity assays, electron microscopy, and quantitative PCR (qPCR). At a time when phage products are being used for experimental treatments and tested in clinical trials, it is important to understand possible interference between mechanisms underlying antibiotic and phage resistance in order to design effective therapeutic regimens.

Objectives Bacteraemia can be caused by Acinetobacter baumannii (A. baumannii), with clinical manifestations ranging from transient bacteraemia to septic shock. Extensively drug-resistant A. baumannii (XDRAB) strains producing the New Delhi metallo-s-lactamase, which confers resistance to all s-lactams including carbapenems, have emerged. Infected patients suffer increased mortality, morbidity and length of hospitalisation. The lack of new antimicrobials has led to a renewed interest in phage therapy, the so-called forgotten cure. Accordingly, we tested new lytic bacteriophages in a Galleria mellonella and a mouse model of XDRAB-induced bacteraemia. Methods Galleria mellonella were challenged with 5.105 CFU of the XDRAB strain FER. Phages vB_AbaM_3054 and vB_AbaM_3090 were administrated alone or in combination 30 min after bacterial challenge. Saline and imipenem were injected as controls. Mice were intraperitoneally (i.p.) challenged with 6.107 CFU of A. baumannii FER. vB_AbaM_3054 and vB_AbaM_3090 were administrated i.p. alone or in combination 2 h after bacterial challenge. Saline and imipenem were injected as controls. Larvae and mice survival were followed for 7 days and compared with Log-Rank (Mantel-Cox) and Gehan-Breslow-Wilcoxon tests. Results Phage-based treatments showed high efficacy in larvae (ca. 100% survival at 80 h) and mice (ca. 100% survival at day 7) compared with the untreated controls (0% survival at 48 h and 24 h in larvae and mice, respectively). Conclusions The present data reporting efficacy of phage therapy in a mouse model of bacteraemia support the development of phage-based drugs to manage infection due to multi-drug resistant A. baumannii and particularly XDRAB.

Endolysins are peptidoglycan hydrolases produced at the end of the bacteriophage (phage) replication cycle to lyse the host cell. Gram-positive phages endolysins come in a variety of multi-modular forms that combine different catalytic domains and may have evolved to adapt to their bacterial hosts. However, the reason why phage can adopt endolysin with such complex multidomain architecture is for the moment not well understood.We used theStreptococcus dysgalactiaephage endolysin PlySK1249 as a model to study the implication of multi-domain architecture in phage-induced bacterial lysis and lysis regulation. The activity of the enzyme relied on a bacteriolytic amidase (Ami), a non-bacteriolytic L-Ala-D-Ala endopeptidase (CHAP) acting as a de-chaining enzyme and central LysM cell wall binding domain (CBD).Ami and CHAP synergized for peptidoglycan digestion and bacteriolysis in the native enzyme or when expressed individually and reunifiedin vitro. This cooperation could be modulated by bacterial cell wall-associated proteases, which specifically cleaved the two linkers connecting the different domains. While both catalytic domains were observed to act coordinately to optimize bacterial lysis, the CBD is expected to delay diffusion of the enzyme until proteolytic inactivation is achieved.As for certain autolysins, PlySK1249 cleavage by bacterial cell wall associated proteases might be an example of dual phage-bacterial regulation and mutual coevolution. In addition, understanding more thoroughly the multidomain interplay of PlySK1249 opens new perspectives on the ideal architecture of therapeutic antibacterial endolysins.

Endolysins are peptidoglycan hydrolases produced at the end of the bacteriophage (phage) replication cycle to lyse the host cell. Endolysins in Gram-positive phages come in a variety of multimodular forms that combine different catalytic and cell wall binding domains. However, the reason why phages adopt endolysins with such complex multidomain architecture is not well understood. In this study, we used the Streptococcus dysgalactiae phage endolysin PlySK1249 as a model to investigate the role of multidomain architecture in phage-induced bacterial lysis and lysis regulation. PlySK1249 consists of an amidase (Ami) domain that lyses bacterial cells, a nonbacteriolytic endopeptidase (CHAP) domain that acts as a dechaining enzyme, and a central LysM cell wall binding domain. We observed that the Ami and CHAP domains synergized for peptidoglycan digestion and bacteriolysis in the native enzyme or when expressed individually and reunified. The CHAP endopeptidase resolved complex polymers of stem-peptides to dimers and helped the Ami domain to digest peptidoglycan to completion. We also found that PlySK1249 was subject to proteolytic cleavage by host cell wall proteases both in vitro and after phage induction. Cleavage disconnected the different domains by hydrolyzing their linker regions, thus hindering their bacteriolytic cooperation and possibly modulating the lytic activity of the enzyme. PlySK1249 cleavage by cell-wall-associated proteases may represent another example of phage adaptation toward the use of existing bacterial regulation mechanism for their own advantage. In addition, understanding more thoroughly the multidomain interplay of PlySK1249 broadens our knowledge on the ideal architecture of therapeutic antibacterial endolysins.

Bacteriophage therapy is a commonly used treatment for Staphylococcus aureus infections in countries of the former Soviet Union, using both single phages and phage cocktails. The scarce data available on Eastern phage cocktails prompted an investigation into commercially-available Pyophage cocktails from two different manufacturers used to treat skin and wound infections. Comparison of the metagenomic composition of two Pyophage products from Georgia and Russia revealed substantial differences in phage-types targeting Escherichia, Enterococcus, Salmonella, Pseudomonas aeruginosa and Proteus, therefore indicating multiple strategies for composing phage cocktails against these bacterial pathogens. Closely-related Kayvirus-like Myoviruses were, however, a shared component against S. aureus within all products, except for the inclusion of a secondary S. aureus Podovirus in one Microgen cocktail. Metagenomic analysis also revealed the presence of several probable prophage sequences but detected no genetic safety risks in terms of virulence factors or antibiotic resistance genes. The safety of broad-spectrum cocktails was tested by comparing the effects of nasal and oral exposure to Eliava Pyophage, a monospecies counterpart and placebo in healthy human carriers of S. aureus. The lack of adverse effects in any treatment groups supports the clinical safety of S. aureus phages administered as a single phage or as phage cocktail.

Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Yet, despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. In this Review, we explore phage diversity at the structural, genomic and community levels as well as the complex evolutionary relationships between phages, moulded by the mosaicity of their genomes. Phages are tremendously abundant and are found in every environment where bacteria exist. In this Review, Dion, Oechslin and Moineau explore the diversity of phages at the structural, genomic and community levels as well as their complex evolutionary relationships.

Bacterial viruses, or phage, are key members of natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Here we explored how bacterial diversity affects the success of lytic phage in structured communities. We infected a sensitive Pseudomonas aeruginosa strain PAO1 with a lytic phage Pseudomonas 352 in the presence versus absence of an insensitive P. aeruginosa strain PA14, in liquid culture versus colonies on agar. We found that both in liquid and in colonies, inter-strain competition reduced resistance evolution in the susceptible strain and decreased phage population size. However, while all sensitive bacteria died in liquid, bacteria in colonies could remain sensitive yet escape phage infection, due mainly to reduced growth in colony centers. In sum, spatial structure can protect bacteria against phage infection, while the presence of competing strains reduces the evolution of resistance to phage., Testa et al. investigates the effect of strain diversity and spatial structure on success of lytic phage infecting Pseudomonas aeruginosa biofilms. They report that living in a spatially structured population can protect bacteria against phage infection, which is mainly due to slower growth at colony centre rather than any additional protection provided by presence of insensitive strain.

Bacterial viruses, or phage, play a key role in shaping natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Critically, phage often have a very narrow host range meaning they can only ever target a subset of strains in a community. Here we explore how strain diversity affects the success of lytic phage in structured communities. In particular, we infect a susceptiblePseudomonas aeruginosastrain PAO1 with lytic phage Pseudomonas 352 in the presence versus absence of an insensitiveP. aeruginosastrain PA14, in liquid culture versus colonies growing on agar. We find that competition between the two bacterial strains reduces the likelihood of the susceptible strain evolving resistance to the phage. This result holds in liquid culture and in colonies. However, while in liquid the phage eliminate the whole sensitive population, colonies contain refuges wherein bacteria can remain sensitive yet escape phage infection. These refuges form mainly due to reduced growth in colony centers. We find little evidence that the presence of the insensitive strain provides any additional protection against phage. Our study reveals that living in a spatially structured population can protect bacteria against phage infection, while the presence of competing strains may instead reduce the likelihood of evolving resistance to phage, if encountered.

Bacterial viruses, or phage, are key members of natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Here we explored how bacterial diversity affects the success of lytic phage in structured communities. We infected a sensitive Pseudomonas aeruginosa strain PAO1 with a lytic phage Pseudomonas 352 in the presence versus absence of an insensitive P. aeruginosa strain PA14, in liquid culture versus colonies on agar. We found that both in liquid and in colonies, inter-strain competition reduced resistance evolution in the susceptible strain and decreased phage population size. However, while all sensitive bacteria died in liquid, bacteria in colonies could remain sensitive yet escape phage infection, due mainly to reduced growth in colony centers. In sum, spatial structure can protect bacteria against phage infection, while the presence of competing strains reduces the evolution of resistance to phage.

Antibiotic resistance has incited a renewed interest in phage therapy as an alternative treatment option for bacterial infections. The potential risk of incurring a parallel situation of resistance to phage as to that observed with antibiotics is a veritable concern for evaluating the merits of this therapy. Bacterial resistance to phage is indeed a natural phenomenon but which requires a greater understanding of bacteria–phage interactions and treatment paradigms in order to determine its impact on therapeutic utility. This chapter aims to contextualize this knowledge within the available applied studies in animals and clinical medicine published to date. Options to use phage combinations or implement protocols that allow for phage substitution or combination with antibiotics may mitigate the risk of developing resistance to phage or even antibiotics themselves. While resistance can be anticipated with phage therapy, it is possible to circumvent its negative effects on clinical outcomes, or, in some situations, it may even be a silver lining that could contribute to effective treatment of bacterial infections.

Staphylococcus aureus is a highly contagious mastitis-causing pathogen infecting dairy cattle worldwide. Previous studies have shown the presence of different genotypes (GT) on farms. In Switzerland, Staph. aureus genotype B (GTB) is contagious, whereas GTC and other genotypes cause sporadic, noncontagious mastitis. In this study, we evaluated the epidemiological properties of Staph. aureus, together with its genotypes and spa types, on Swiss dairy farms. A total of 21 dairy farms were sampled throughout Switzerland; 10 farms were positive for the contagious Staph. aureus GTB and 11 farms were negative for GTB. Samples were taken from milk, body surfaces of dairy cattle and other animals, milkers, milking equipment, and environmental sites (e.g., parlor, washing room, stall floor, manger, and bedding). The epidemiology of Staph. aureus depended markedly on the genotype. Staphylococcus aureus GTB was associated with mammary gland, intramammary infections (IMI), and milking clusters, whereas GTC and other genotypes were related to cow and other animal surfaces and occasionally to environment. Genotype C was by far the most common subtype in cattle and was found on GTB-negative and GTB-positive farms. Each farm had a predominant genotype, such as GTB, GTC, GTA, or GTF, but a few farms were almost free from Staph. aureus. The genotypes and spa types of Staph. aureus detected in the noses of milkers clearly differed from those found in dairy cattle, other animals, milking equipment, and the environment. Exceptions were GTS (spa type t034) and GTF (t899), which crossed the species barrier. In most cases, however, the species barrier was maintained because Staph. aureus is adapted to a particular host and even to particular body sites. As biological properties differ among the genotypes, new guidelines to prevent IMI caused by different genotypes were established: classical measures to prevent IMI caused by contagious pathogens still hold for GTB but not for Staph. aureus genotypes that are opportunistic colonizers of bovine skin (e.g., GTC and GTA). For those genotypes, protection of the skin from minor lesions and wounds, particularly on the hocks, is essential.

Bacteriophage therapy is a commonly used treatment for Staphylococcus aureus infections in countries of the former Soviet Union, using both single phages and phage cocktails. The scarce data available on Eastern phage cocktails prompted an investigation into commercially-available Pyophage cocktails from two different manufacturers used to treat skin and wound infections. Comparison of the metagenomic composition of two Pyophage products from Georgia and Russia revealed substantial differences in phage-types targeting Escherichia, Enterococcus, Salmonella, Pseudomonas aeruginosa and Proteus, therefore indicating multiple strategies for composing phage cocktails against these bacterial pathogens. Closely-related Kayvirus-like Myoviruses were, however, a shared component against S. aureus within all products, except for the inclusion of a secondary S. aureus Podovirus in one Microgen cocktail. Metagenomic analysis also revealed the presence of several probable prophage sequences but detected no genetic safety risks in terms of virulence factors or antibiotic resistance genes. The safety of broad-spectrum cocktails was tested by comparing the effects of nasal and oral exposure to Eliava Pyophage, a monospecies counterpart and placebo in healthy human carriers of S. aureus. The lack of adverse effects in any treatment groups supports the clinical safety of S. aureus phages administered as a single phage or as phage cocktail.

Staphylococcus aureus is the leading cause of infective endocarditis (IE). While the role of S. aureus cell-wall associated protein clumping factor A (ClfA) in promoting IE has been already demonstrated, that of the secreted plasma-clotting factors staphylocoagulase (Coa) and von Willebrand factor-binding protein (vWbp) has not yet been elucidated. We investigated the role of Coa and vWbp in IE initiation in rats with catheter-induced aortic vegetations, using Lactococcus lactis expressing coa, vWbp, clfA or vWbp/clfA, and S. aureus Newman Δcoa, ΔvWbp, ΔclfA or Δcoa/ΔvWbp/ΔclfA mutants. vWbp-expression increased L. lactis valve infection compared to parent and coa-expressing strains (incidence: 62%, versus 0% and 13%, respectively; P< 0.01). Likewise, expression of clfA increased L. lactis infectivity (incidence: 80%), which was not further affected by co-expression of vWbp. In symmetry, deletion of the coa or vWbp genes in S. aureus did not decrease infectivity (incidence: 68 and 64%, respectively) whereas deletion of clfA did decrease valve infection (incidence: 45%; P= 0.03 versus parent), which was not further affected by the triple deletion Δcoa/ΔvWbp/ΔclfA (incidence: 36%; P> 0.05 versus ΔclfA mutant). Coa does not support the initial colonization of IE (in L. lactis) without other key virulence factors and vWbp contributes to initiation of IE (in L. lactis) but is marginal in the present of ClfA.

Streptococcus gordonii and related species of oral viridans group streptococci (VGS) are common etiological agents of infective endocarditis (IE). We explored vaccination as a strategy to prevent VGS-IE, using a novel antigen-presenting system based on non-genetically modified Lactococcus lactis displaying vaccinogens on its surface. Hsa and PadA are surface-located S. gordonii proteins implicated in platelet adhesion and aggregation, which are key steps in the pathogenesis of IE. This function makes them ideal targets for vaccination against VGS-IE. In the present study, we report the use of nonliving L. lactis displaying at its surface the N-terminal region of Hsa or PadA by means of the cell wall binding domain of Lactobacillus casei A2 phage lysine LysA2 (Hsa-LysA2 and PadA-LysA2, respectively) and investigation of their ability to elicit antibodies in rats and to protect them from S. gordonii experimental IE. Immunized and control animals with catheter-induced sterile aortic valve vegetations were inoculated with 10 6 CFU of S. gordonii . The presence of IE was evaluated 24 h later. Immunization of rats with L. lactis Hsa-LysA2, L. lactis PadA-LysA2, or both protected 6/11 (55%), 6/11 (55%), and 11/12 (91%) animals, respectively, from S. gordonii IE ( P < 0.05 versus controls). Protection correlated with the induction of high levels of functional antibodies against both Hsa and PadA that delayed or totally inhibited platelet aggregation by S. gordonii . These results support the value of L. lactis as a system for antigen delivery and of Hsa and PadA as promising candidates for a vaccine against VGS-IE.

Increasing antibiotic resistance warrants therapeutic alternatives. Here we investigated the efficacy of bacteriophage-therapy (phage) alone or combined with antibiotics against experimental endocarditis (EE) due to Pseudomonas aeruginosa, an archetype of difficult-to-treat infection. In vitro fibrin clots and rats with aortic EE were treated with an antipseudomonas phage cocktail alone or combined with ciprofloxacin. Phage pharmacology, therapeutic efficacy, and resistance were determined. In vitro, single-dose phage therapy killed 7 log colony-forming units (CFUs)/g of fibrin clots in 6 hours. Phage-resistant mutants regrew after 24 hours but were prevented by combination with ciprofloxacin (2.5 × minimum inhibitory concentration). In vivo, single-dose phage therapy killed 2.5 log CFUs/g of vegetations in 6 hours (P < .001 vs untreated controls) and was comparable with ciprofloxacin monotherapy. Moreover, phage/ciprofloxacin combinations were highly synergistic, killing >6 log CFUs/g of vegetations in 6 hours and successfully treating 64% (n = 7/11) of rats. Phage-resistant mutants emerged in vitro but not in vivo, most likely because resistant mutations affected bacterial surface determinants important for infectivity (eg, the pilT and galU genes involved in pilus motility and LPS formation). Single-dose phage therapy was active against P. aeruginosa EE and highly synergistic with ciprofloxacin. Phage-resistant mutants had impaired infectivity. Phage-therapy alone or combined with antibiotics merits further clinical consideration.

Beta-hemolytic Streptococcus agalactiae is the leading cause of bacteremia and invasive infections. These diseases are treated with β-lactams or macrolides, but the emergence of less susceptible and even fully resistant strains is a cause for concern. New bacteriophage lysins could be promising alternatives against such organisms. They hydrolyze the bacterial peptidoglycan at the end of the phage cycle, in order to release the phage progeny. By using a bioinformatic approach to screen several beta-hemolytic streptococci, a gene coding for a lysin was identified on a prophage carried by Streptococcus dysgalactiae subsp. equisimilis SK1249. The gene product, named PlySK1249, harbored an original three-domain structure with a central cell wall-binding domain surrounded by an N-terminal amidase and a C-terminal CHAP domain. Purified PlySK1249 was highly lytic and bactericidal for S. dysgalactiae (2-log 10 CFU/ml decrease within 15 min). Moreover, it also efficiently killed S. agalactiae (1.5-log 10 CFU/ml decrease within 15 min) but not several streptococcal commensal species. We further investigated the activity of PlySK1249 in a mouse model of S. agalactiae bacteremia. Eighty percent of the animals ( n = 10) challenged intraperitoneally with 10 6 CFU of S. agalactiae died within 72 h, whereas repeated injections of PlySK1249 (45 mg/kg 3 times within 24 h) significantly protected the mice ( P < 0.01). Thus, PlySK1249, which was isolated from S. dysgalactiae , demonstrated high cross-lytic activity against S. agalactiae both in vitro and in vivo . These encouraging results indicated that PlySK1249 might represent a good candidate to be developed as a new enzybiotic for the treatment of systemic S. agalactiae infections.

Enterococcus faecalis and Streptococcus gallolyticus cause infective endocarditis (IE), which can originate from the continuous release or translocation of low bacterial numbers into the bloodstream. In this context, IE cannot be prevented with antibiotics. We previously demonstrated that aspirin plus ticlopidine protected rats from IE due to S. gordonii and Staphylococcus aureus. Here we showed that aspirin plus ticlopidine significantly reduced vegetation weight and protected 73 and 64% rats (P < 0.005) from IE due to E. faecalis and S. gallolyticus, respectively. These results further support the potential use of aspirin plus ticlopidine for a global prevention of IE in high-risk patients.