Molecular mechanisms of enterococcal-bacteriophage interactions and implications for human health

Insertion sequence-mediated phage resistance contributes to attenuated colonization of cytolytic Enterococcus faecalis variants in the gut

Specific elimination of cytolytic Enterococcus faecalis from the intestinal microbiota by bacteriophages (phages) attenuates ethanol-induced liver disease in pre-clinical studies; however, other clinical phage therapy studies have reported the occurrence of phage-resistant variants. Here, we assessed phage resistance using a cytolytic E. faecalis clinical isolate, EF01. After infecting EF01 with ΦEf2.1 (Myoviridae) or ΦEf2.2 (Podoviridae), four host variants (R-EF01ΦEf2.1-A and R-EF01ΦEf2.1-B from infection with ΦEf2.1, and R-EF01ΦEf2.2-A and R-EF01ΦEf2.2-B from infection with ΦEf2.2) were isolated. Although isolate R-EF01ΦEf2.2 exhibited resistance to both phages, isolate R-EF01ΦEf2.1 demonstrated partial resistance only to ΦEf2.1. Whole-genome sequencing of these four isolates revealed an insertion sequence, IS256, -mediated disruption of xylA in R-EF01ΦEf2.1-A and R-EF01ΦEf2.1-B. In addition, a non-synonymous mutation in epaR, essential for the complete Enterococcus polysaccharide antigen (Epa), was identified in the R-EF01ΦEf2.2-A isolate. Furthermore, R-EF01ΦEf2.2 isolates exhibited IS256-associated chromosomal deletions and lacked galE, a gene involved in Epa biosynthesis. After gavaging mice with EF01 WT, R-EF01ΦEf2.1-A, R-EF01ΦEf2.2-A, and R-EF01ΦEf2.2-B isolates, colonization of R-EF01ΦEf2.2 isolates was significantly attenuated. R-EF01ΦEf2.2 isolates exhibited less resistance to the bile salt sodium deoxycholate and showed reduced adherence to intestinal cell monolayers, suggesting that phage-resistant variants with alterations in bacterial surface molecules, potentially including those involved in Epa biosynthesis, reduced pathogen fitness by attenuating gut colonization. In summary, IS256 is involved in phage resistance of a cytolytic E. faecalis clinical isolate, and certain phage resistance mechanisms could contribute to favorable clinical outcomes by promoting the swift elimination of phage-resistant variants in the treatment of alcohol-associated hepatitis.

IMPORTANCE

Phage therapy is a promising approach for precise editing of the gut microbiota. Notably, the specific elimination of cytolytic E. faecalis from the intestinal microbiota by phages attenuates ethanol-induced liver disease in pre-clinical studies. Despite the great promise of phage therapy, the occurrence of phage-resistant variants represents a concern for the successful development of phage-based therapies. In this context, we assessed phage resistance using a cytolytic E. faecalis clinical isolate. Isolated phage-resistant variants acquired mutations or deletions of Epa biosynthesis-related genes and exhibited attenuated colonization in the gut. These phage-resistant variants showed less resistance to bile salts and reduced adherence to intestinal cell monolayers. These results suggest that even if phage-resistant variants arise during phage therapy, certain mechanisms of phage resistance may contribute to the rapid elimination of phage-resistant variants promoting favorable clinical outcomes in the treatment of alcohol-associated hepatitis.

Formulation of three tailed bacteriophages by spray-drying and atomic layer deposition for thermal stability and controlled release

Deep infection is the second most common complication of arthroplasty following loosening of the implant. Antibiotic-loaded bone cements (ALBCs) and high concentrations of systemic broad-spectrum antibiotics are commonly used to prevent infections following injury and surgery. However, clinical data fails to show that ALBCs are effective against deep infection, and negative side effects can result following prolonged administration of antibiotics. Additionally, the rise of multidrug resistant (MDR) bacteria provides an urgent need for alternatives to broad-spectrum antibiotics. Phage therapy, or the use of bacteriophages (viruses that infect bacteria) to target pathogenic bacteria, might offer a safe alternative to combat MDR bacteria. Application of phage therapy in the setting of deep infections requires formulation strategies that would stabilize bacteriophage against chemical and thermal stress during bone-cement polymerization, that maintain bacteriophage activity for weeks or months at physiological temperatures, and that allow for sustained release of phage to combat slow-growing, persistent bacteria. Here, we demonstrate the formulation of three phages that target diverse bacterial pathogens, which includes spray-drying of the particles for enhanced thermal stability at 37 °C and above. Additionally, we use atomic layer deposition (ALD) to coat spray-dried powders with alumina to allow for delayed release of phage from the dry formulations, and potentially protect phage against chemical damage during bone cement polymerization. Together, these findings present a strategy to formulate phages that possess thermal stability and sustained release properties for use in deep infections.

A novel Enterococcus faecium phage EF-M80: unveiling the effects of hydrogel-encapsulated phage on wound infection healing

Background

Enterococcus faecium is one of the members of ESKAPE pathogens. Due to its resistance to antimicrobial agents, treating this bacterium has become challenging. The development of innovative approaches to combat antibiotic resistance is necessary. Phage therapy has emerged as a promising method for curing antibiotic-resistant bacteria.

Methods

In this study, E. faecium phages were isolated from wastewater. Phage properties were characterized through in vitro assays (e.g. morphological studies, and physicochemical properties). In addition, whole genome sequencing was performed. A hydrogel-based encapsulated phage was obtained and its structure characteristics were evaluated. Wound healing activity of the hydrogel-based phage was assessed in a wound mice model.

Results

The purified phage showed remarkable properties including broad host range, tolerance to high temperature and pH and biofilm degradation feature as a stable and reliable therapeutic agent. Whole genome sequencing revealed that the genome of the EF-M80 phage had a length of 40,434 bp and harbored 65 open reading frames (ORFs) with a GC content of 34.9% (GenBank accession number is OR767211). Hydrogel-based encapsulated phage represented an optimized structure. Phage-loaded hydrogel-treated mice showed that the counting of neutrophils, fibroblasts, blood vessels, hair follicles and percentage of collagen growth were in favor of the wound healing process in the mice model.

Conclusion

These findings collectively suggest the promising capability of this phage-based therapeutic strategy for the treatment of infections associated with the antibiotic-resistant E. faecium. In the near future, we hope to expect the presence of bacteriophages in the list of antibacterial compounds used in the clinical settings.

Phage therapy: Targeting intestinal bacterial microbiota for the treatment of liver diseases

Phage therapy has been overshadowed by antibiotics for decades. However, it is being revisited as a powerful approach against antimicrobial-resistant bacteria. As bacterial microbiota have been mechanistically linked to gastrointestinal and liver diseases, precise editing of the gut microbiota via the selective bactericidal action of phages has prompted renewed interest in phage therapy. In this review, we summarise the basic virological properties of phages and the latest findings on the composition of the intestinal phageome and the changes associated with liver diseases. We also review preclinical and clinical studies assessing phage therapy for the treatment of gastrointestinal and liver diseases, as well as future prospects and challenges.

Fitness Trade-Offs between Phage and Antibiotic Sensitivity in Phage-Resistant Variants: Molecular Action and Insights into Clinical Applications for Phage Therapy

In recent decades, phage therapy has been overshadowed by the widespread use of antibiotics in Western countries. However, it has been revitalized as a powerful approach due to the increasing prevalence of antimicrobial-resistant bacteria. Although bacterial resistance to phages has been reported in clinical cases, recent studies on the fitness trade-offs between phage and antibiotic resistance have revealed new avenues in the field of phage therapy. This strategy aims to restore the antibiotic susceptibility of antimicrobial-resistant bacteria, even if phage-resistant variants develop. Here, we summarize the basic virological properties of phages and their applications within the context of antimicrobial resistance. In addition, we review the occurrence of phage resistance in clinical cases, and examine fitness trade-offs between phage and antibiotic sensitivity, exploring the potential of an evolutionary fitness cost as a countermeasure against phage resistance in therapy. Finally, we discuss future strategies and directions for phage-based therapy from the aspect of fitness trade-offs. This approach is expected to provide robust options when combined with antibiotics in this era of phage 're'-discovery.

Enterococcal Phages: Food and Health Applications

Enterococcus is a diverse genus of Gram-positive bacteria belonging to the lactic acid bacteria (LAB) group. It is found in many environments, including the human gut and fermented foods. This microbial genus is at a crossroad between its beneficial effects and the concerns regarding its safety. It plays an important role in the production of fermented foods, and some strains have even been proposed as probiotics. However, they have been identified as responsible for the accumulation of toxic compounds-biogenic amines-in foods, and over the last 20 years, they have emerged as important hospital-acquired pathogens through the acquisition of antimicrobial resistance (AMR). In food, there is a need for targeted measures to prevent their growth without disturbing other LAB members that participate in the fermentation process. Furthermore, the increase in AMR has resulted in the need for the development of new therapeutic options to treat AMR enterococcal infections. Bacteriophages have re-emerged in recent years as a precision tool for the control of bacterial populations, including the treatment of AMR microorganism infections, being a promising weapon as new antimicrobials. In this review, we focus on the problems caused by Enterococcus faecium and Enterococcus faecalis in food and health and on the recent advances in the discovery and applications of enterococcus-infecting bacteriophages against these bacteria, with special attention paid to applications against AMR enterococci.

Large-scale phage cultivation for commensal human gut bacteria

Phages are highly abundant in the human gut, yet most of them remain uncultured. Here, we present a gut phage isolate collection (GPIC) containing 209 phages for 42 commensal human gut bacterial species. Genome analysis of the phages identified 34 undescribed genera. We discovered 22 phages from the Salasmaviridae family that have small genomes (∼10-20 kbp) and infect Gram-positive bacteria. Two phages from a candidate family, Paboviridae, with high prevalence in the human gut were also identified. Infection assays showed that Bacteroides and Parabacteroides phages are specific to a bacterial species, and strains of the same species also exhibit substantial variations in phage susceptibility. A cocktail of 8 phages with a broad host range for Bacteroides fragilis strains effectively reduced their abundance in complex host-derived communities in vitro. Our study expands the diversity of cultured human gut bacterial phages and provides a valuable resource for human microbiome engineering.

Vancomycin Resistance in Enterococcus and Staphylococcus aureus

Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus are both common commensals and major opportunistic human pathogens. In recent decades, these bacteria have acquired broad resistance to several major classes of antibiotics, including commonly employed glycopeptides. Exemplified by resistance to vancomycin, glycopeptide resistance is mediated through intrinsic gene mutations, and/or transferrable van resistance gene cassette-carrying mobile genetic elements. Here, this review will discuss the epidemiology of vancomycin-resistant Enterococcus and S. aureus in healthcare, community, and agricultural settings, explore vancomycin resistance in the context of van and non-van mediated resistance development and provide insights into alternative therapeutic approaches aimed at treating drug-resistant Enterococcus and S. aureus infections.

Current Status of Phage Therapy against Infectious Diseases and Potential Application beyond Infectious Diseases

Intestinal microbiota plays a key role in regulating the pathogenesis of human disease and maintaining health. Many diseases, mainly induced by bacteria, are on the rise due to the emergence of antibiotic-resistant strains. Intestinal microorganisms include organisms such as bacteria, viruses, and fungi. They play an important role in maintaining human health. Among these microorganisms, phages are the main members of intestinal viromes. In particular, the viral fraction, composed essentially of phages, affects homeostasis by exerting selective pressure on bacterial communities living in the intestinal tract. In recent years, with the widespread use and even abuse of antibacterial drugs, more and more drug-resistant bacteria have been found, and they show a trend of high drug resistance and multidrug resistance. Therefore, it has also become increasingly difficult to treat serious bacterial infections. Phages, a natural antibacterial agent with strong specificity and rapid proliferation, have come back to the field of vision of clinicians and scholars. In this study, the current state of research on intestinal phages was discussed, with an exploration of the impact of phage therapy against infectious diseases, as well as potential application beyond infectious diseases.

Barriers to genetic manipulation of Enterococci: Current Approaches and Future Directions

Enterococcus faecalis and Enterococcus faecium are Gram-positive commensal gut bacteria that can also cause fatal infections. To study clinically relevant multi-drug resistant E. faecalis and E. faecium strains, methods are needed to overcome physical (thick cell wall) and enzymatic barriers that limit the transfer of foreign DNA and thus prevent facile genetic manipulation. Enzymatic barriers to DNA uptake identified in E. faecalis and E. faecium include type I, II and IV restriction modification systems and CRISPR-Cas. This review examines E. faecalis and E. faecium DNA defence systems and the methods with potential to overcome these barriers. DNA defence system bypass will allow the application of innovative genetic techniques to expedite molecular-level understanding of these important, but somewhat neglected, pathogens.

Bacteriophage-Resistant Mutant of Enterococcus faecalis Is Impaired in Biofilm Formation

Enterococcus faecalis is a common gram-positive non-spore-forming bacterium in nature and is found in the upper respiratory tract, intestine, and mouth of healthy people. E. faecalis is also one of the common pathogens causing nosocomial infections and is resistant to several antibiotics commonly used in practice. Thus, treating drug-resistant E. faecalis with antibiotics is challenging, and new approaches are needed. In this study, we isolated a bacteriophage named EFap02 that targets E. faecalis strain EFa02 from sewage at Southwest Hospital. Phage EFap02 belongs to the Siphoviridae family with a long tail of approximately 210 nm, and EFap02 can tolerate a strong acid and alkali environment and high temperature. Its receptor was identified as the capsular polysaccharide. Phage-resistant mutants had loss-of-function mutations in glycosyltransferase (gtr2), which is responsible for capsular polysaccharide biosynthesis, and this caused the loss of capsular polysaccharide and interruption of phage adsorption. Although phage-resistant mutants against EFap02 can be selected, such mutants are impaired in biofilm formation due to the loss of capsular polysaccharide, which compromises its virulence. Therefore, this study provided a detailed description of the E. faecalis EFap02 phage with the potential for treating E. faecalis infection.

The power of unbiased phenotypic screens - cellulose as a first receptor for the Schitoviridae phage S6 of Erwinia amylovora

Bacteriophages, host‐dependent replicative non‐cellular entities which significantly shape the microbial genomes and consequently physiological and ecological properties of the microbial populations are exploited to restrict plant, animal and human pathogens. Unravelling of phage characteristics aids the understanding of the basic molecular mechanisms of phage infections which can subsequently lead to the development of rationalized strategies to combat microbial pathogens. In an unbiased screen to investigate the molecular basis of infectivity of the fire blight pathogen Erwinia amylovora by the lytic Schitoviridae phage S6, the biofilm extracellular matrix component cellulose has been identified as a cyclic di‐GMP dependent first receptor required for infection with the phage to possess beta‐1,4‐glucosidases to degrade the exopolysaccharide. This absolute receptor dependency allows maintenance of a phage‐microbe equilibrium with a low bacterial density.

Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps

Prophages affect bacterial fitness on multiple levels. These include bacterial infectivity, toxin secretion, virulence regulation, surface modification, immune stimulation and evasion and microbiome competition. Lysogenic conversion arms bacteria with novel accessory functions thereby increasing bacterial fitness, host adaptation and persistence, and antibiotic resistance. These properties allow the bacteria to occupy a niche long term and can contribute to chronic infections and inflammation such as chronic rhinosinusitis (CRS). In this study, we aimed to identify and characterize prophages present in Staphylococcus aureus from patients suffering from CRS in relation to CRS disease phenotype and severity. Prophage regions were identified using PHASTER. Various in silico tools like ResFinder and VF Analyzer were used to detect virulence genes and antibiotic resistance genes respectively. Progressive MAUVE and maximum likelihood were used for multiple sequence alignment and phylogenetics of prophages respectively. Disease severity of CRS patients was measured using computed tomography Lund-Mackay scores. Fifty-eight S. aureus clinical isolates (CIs) were obtained from 28 CRS patients without nasal polyp (CRSsNP) and 30 CRS patients with nasal polyp (CRSwNP). All CIs carried at least one prophage (average=3.6) and prophages contributed up to 7.7 % of the bacterial genome. Phage integrase genes were found in 55/58 (~95 %) S. aureus strains and 97/211 (~46 %) prophages. Prophages belonging to Sa3int integrase group (phiNM3, JS01, phiN315) (39/97, 40%) and Sa2int (phi2958PVL) (14/97, 14%) were the most prevalent prophages and harboured multiple virulence genes such as sak, scn, chp, lukE/D, sea. Intact prophages were more frequently identified in CRSwNP than in CRSsNP (P=0.0021). Intact prophages belonging to the Sa3int group were more frequent in CRSwNP than in CRSsNP (P=0.0008) and intact phiNM3 were exclusively found in CRSwNP patients (P=0.007). Our results expand the knowledge of prophages in S. aureus isolated from CRS patients and their possible role in disease development. These findings provide a platform for future investigations into potential tripartite associations between bacteria-prophage-human immune system, S. aureus evolution and CRS disease pathophysiology.

Mapping the functional landscape of the receptor binding domain of T7 bacteriophage by deep mutational scanning

The interaction between a bacteriophage and its host is mediated by the phage's receptor binding protein (RBP). Despite its fundamental role in governing phage activity and host range, molecular rules of RBP function remain a mystery. Here, we systematically dissect the functional role of every residue in the tip domain of T7 phage RBP (1660 variants) by developing a high-throughput, locus-specific, phage engineering method. This rich dataset allowed us to cross compare functional profiles across hosts to precisely identify regions of functional importance, many of which were previously unknown. Substitution patterns showed host-specific differences in position and physicochemical properties of mutations, revealing molecular adaptation to individual hosts. We discovered gain-of-function variants against resistant hosts and host-constricting variants that eliminated certain hosts. To demonstrate therapeutic utility, we engineered highly active T7 variants against a urinary tract pathogen. Our approach presents a generalized framework for characterizing sequence-function relationships in many phage-bacterial systems.