The disparate effects of bacteriophages on antibiotic-resistant bacteria

Antimicrobial Peptides and Cationic Nanoparticles: A Broad-Spectrum Weapon to Fight Multi-Drug Resistance Not Only in Bacteria

In the last few years, antibiotic resistance and, analogously, anticancer drug resistance have increased considerably, becoming one of the main public health problems. For this reason, it is crucial to find therapeutic strategies able to counteract the onset of multi-drug resistance (MDR). In this review, a critical overview of the innovative tools available today to fight MDR is reported. In this direction, the use of membrane-disruptive peptides/peptidomimetics (MDPs), such as antimicrobial peptides (AMPs), has received particular attention, due to their high selectivity and to their limited side effects. Moreover, similarities between bacteria and cancer cells are herein reported and the hypothesis of the possible use of AMPs also in anticancer therapies is discussed. However, it is important to take into account the limitations that could negatively impact clinical application and, in particular, the need for an efficient delivery system. In this regard, the use of nanoparticles (NPs) is proposed as a potential strategy to improve therapy; moreover, among polymeric NPs, cationic ones are emerging as promising tools able to fight the onset of MDR both in bacteria and in cancer cells.

Tackling antimicrobial stewardship through synergy and antimicrobial peptides

The unrestricted use of antibiotics has led to rapid development of antibiotic resistance (AR) and renewed calls to address this serious problem. This review summarizes the most common mechanisms of antibiotic action, and in turn antibiotic resistance, as well as pathways to mitigate the harm. Focus is then turned to emerging antibiotic strategies, including antimicrobial peptides (AMPs), with a discussion of their modes of action, biochemical features, and potential challenges for their use as antibiotics. The role of synergy in antimicrobials is also examined, with a focus on the synergy of AMPs and other emerging interactions with synergistic potential.

The Oral Microbiota: Community Composition, Influencing Factors, Pathogenesis, and Interventions

The human oral cavity provides a habitat for oral microbial communities. The complexity of its anatomical structure, its connectivity to the outside, and its moist environment contribute to the complexity and ecological site specificity of the microbiome colonized therein. Complex endogenous and exogenous factors affect the occurrence and development of the oral microbiota, and maintain it in a dynamic balance. The dysbiotic state, in which the microbial composition is altered and the microecological balance between host and microorganisms is disturbed, can lead to oral and even systemic diseases. In this review, we discuss the current research on the composition of the oral microbiota, the factors influencing it, and its relationships with common oral diseases. We focus on the specificity of the microbiota at different niches in the oral cavity, the communities of the oral microbiome, the mycobiome, and the virome within oral biofilms, and interventions targeting oral pathogens associated with disease. With these data, we aim to extend our understanding of oral microorganisms and provide new ideas for the clinical management of infectious oral diseases.

Treatment of Wound Infections in a Mouse Model Using Zn2+-Releasing Phage Bound to Gold Nanorods

Infections caused by drug-resistant bacteria, particularly Gram-negative organisms, are increasingly difficult to treat using antibiotics. A potential alternative is "phage therapy", in which phages infect and lyse the bacterial host. However, phage therapy poses serious drawbacks and safety concerns, such as the risk of genetic transduction of antibiotic resistance genes, inconsistent pharmacokinetics, and unknown evolutionary potential. In contrast, metallic nanoparticles possess precise, tunable properties, including efficient conversion of electronic excitation into heat. In this work, we demonstrate that engineered phage-nanomaterial conjugates that target the Gram-negative pathogen Pseudomonas aeruginosa are highly effective as a treatment of infected wounds in mice. Photothermal heating, performed as a single treatment (15 min) or as two treatments on consecutive days, rapidly reduced the bacterial load and released Zn²⁺ to promote wound healing. The phage-nanomaterial treatment was significantly more effective than systemic standard-of-care antibiotics, with a >10× greater reduction in bacterial load and ∼3× faster healing as measured by wound size reduction when compared to fluoroquinolone treatment. Notably, the phage-nanomaterial was also effective against a P. aeruginosa strain resistant to polymyxins, a last-line antibiotic therapy. Unlike these antibiotics, the phage-nanomaterial showed no detectable toxicity or systemic effects in mice, consistent with the short duration and localized nature of phage-nanomaterial treatment. Our results demonstrate that phage therapy controlled by inorganic nanomaterials can be a safe and effective antimicrobial strategy in vivo.

Considerations for the Use of Phage Therapy in Clinical Practice

Increasing antimicrobial resistance and medical device-related infections have led to a renewed interest in phage therapy as an alternative or adjunct to conventional antimicrobials. Expanded access and compassionate use cases have risen exponentially but have varied widely in approach, methodology, and clinical situations in which phage therapy might be considered. Large gaps in knowledge contribute to heterogeneity in approach and lack of consensus in many important clinical areas. The Antibacterial Resistance Leadership Group (ARLG) has convened a panel of experts in phage therapy, clinical microbiology, infectious diseases, and pharmacology, who worked with regulatory experts and a funding agency to identify questions based on a clinical framework and divided them into three themes: potential clinical situations in which phage therapy might be considered, laboratory testing, and pharmacokinetic considerations. Suggestions are provided as answers to a series of questions intended to inform clinicians considering experimental phage therapy for patients in their clinical practices.

T7 Phage as an Emerging Nanobiomaterial with Genetically Tunable Target Specificity

Bacteriophages, also known as phages, are specific antagonists against bacteria. T7 phage has drawn massive attention in precision medicine owing to its distinctive advantages, such as short replication cycle, ease in displaying peptides and proteins, high stability and cloning efficiency, facile manipulation, and convenient storage. By introducing foreign gene into phage DNA, T7 phage can present foreign peptides or proteins site-specifically on its capsid, enabling it to become a nanoparticle that can be genetically engineered to screen and display a peptide or protein capable of recognizing a specific target with high affinity. This review critically introduces the biomedical use of T7 phage, ranging from the detection of serological biomarkers and bacterial pathogens, recognition of cells or tissues with high affinity, design of gene vectors or vaccines, to targeted therapy of different challenging diseases (e.g., bacterial infection, cancer, neurodegenerative disease, inflammatory disease, and foot-mouth disease). It also discusses perspectives and challenges in exploring T7 phage, including the understanding of its interactions with human body, assembly into scaffolds for tissue regeneration, integration with genome editing, and theranostic use in clinics. As a genetically modifiable biological nanoparticle, T7 phage holds promise as biomedical imaging probes, therapeutic agents, drug and gene carriers, and detection tools.

Phage Revolution Against Multidrug-Resistant Clinical Pathogens in Southeast Asia

Southeast Asia (SEA) can be considered a hotspot of antimicrobial resistance (AMR) worldwide. As recent surveillance efforts in the region reported the emergence of multidrug-resistant (MDR) pathogens, the pursuit of therapeutic alternatives against AMR becomes a matter of utmost importance. Phage therapy, or the use of bacterial viruses called bacteriophages to kill bacterial pathogens, is among the standout therapeutic prospects. This narrative review highlights the current understanding of phages and strategies for a phage revolution in SEA. We define phage revolution as the radical use of phage therapy in infectious disease treatment against MDR infections, considering the scientific and regulatory standpoints of the region. We present a three-phase strategy to encourage a phage revolution in the SEA clinical setting, which involves: (1) enhancing phage discovery and characterization efforts, (2) creating and implementing laboratory protocols and clinical guidelines for the evaluation of phage activity, and (3) adapting regulatory standards for therapeutic phage formulations. We hope that this review will open avenues for scientific and policy-based discussions on phage therapy in SEA and eventually lead the way to its fullest potential in countering the threat of MDR pathogens in the region and worldwide.

Pelzer B, Khodamoradi Y, Vehreschild MJGT. The role of the human gut microbiota in colonization and infection with multidrug-resistant bacteria

About 100 years ago, the first antibiotic drug was introduced into health care. Since then, antibiotics have made an outstanding impact on human medicine. However, our society increasingly suffers from collateral damage exerted by these highly effective drugs. The rise of resistant pathogen strains, combined with a reduction of microbiota diversity upon antibiotic treatment, has become a significant obstacle in the fight against invasive infections worldwide.Alternative and complementary strategies to classical "Fleming antibiotics" comprise microbiota-based treatments such as fecal microbiota transfer and administration of probiotics, live-biotherapeutics, prebiotics, and postbiotics. Other promising interventions, whose efficacy may also be influenced by the human microbiota, are phages and vaccines. They will facilitate antimicrobial stewardship, to date the only globally applied antibiotic resistance mitigation strategy.In this review, we present the available evidence on these nontraditional interventions, highlight their interaction with the human microbiota, and discuss their clinical applicability.

Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance

Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.

Past and Future of Phage Therapy and Phage-Derived Proteins in Patients with Bone and Joint Infection

Phage-derived therapies comprise phage therapy and the use of phage-derived proteins as anti-bacterial therapy. Bacteriophages are natural viruses that target specific bacteria. They were proposed to be used to treat bacterial infections in the 1920s, before the discovery and widespread over-commercialized use of antibiotics. Phage therapy was totally abandoned in Western countries, whereas it is still used in Poland, Georgia and Russia. We review here the history of phage therapy by focusing on bone and joint infection, and on the development of phage therapy in France in this indication. We discuss the rationale of its use in bacterial infection and show the feasibility of phage therapy in the 2020s, based on several patients with complex bone and joint infection who recently received phages as compassionate therapy. Although the status of phage therapy remains to be clarified by health care authorities, obtaining pharmaceutical-grade therapeutic phages (i.e., following good manufacturing practice guidelines or being “GMP-like”) targeting bacterial species of concern is essential. Moreover, multidisciplinary clinical expertise has to determine what could be the relevant indications to perform clinical trials. Finally “phage therapy 2.0” has to integrate the following steps: (i) follow the status of phage therapy, that is not settled and defined; (ii) develop in each country a close relationship with the national health care authority; (iii) develop industrial–academic partnerships; (iv) create academic reference centers; (v) identify relevant clinical indications; (vi) use GMP/GMP-like phages with guaranteed quality bioproduction; (vii) start as salvage therapy; (vii) combine with antibiotics and adequate surgery; and (viii) perform clinical trials, to finally (ix) demonstrate in which clinical settings phage therapy provides benefit. Phage-derived proteins such as peptidoglycan hydrolases, polysaccharide depolymerases or lysins are enzymes that also have anti-biofilm activity. In contrast to phages, their development has to follow the classical process of medicinal products. Phage therapy and phage-derived products also have a huge potential to treat biofilm-associated bacterial diseases, and this is of crucial importance in the worldwide spread of antimicrobial resistance.

The bacteriophage decides own tracks: When they are with or against the bacteria

Bacteriophages, bacteria-infecting viruses, are considered by many researchers a promising solution for antimicrobial resistance. On the other hand, some phages have shown contribution to bacterial resistance phenomenon by transducing antimicrobial resistance genes to their bacterial hosts. Contradictory consequences of infections are correlated to different phage lifecycles. Out of four known lifecycles, lysogenic and lytic pathways have been riddles since the uncontrolled conversion between them could negatively affect the intended use of phages. However, phages still can be engineered for applications against bacterial and viral infections to ensure high efficiency. This review highlights two main aspects: (1) the different lifecycles as well as the different factors that affect lytic-lysogenic switch are discussed, including the intracellular and molecular factors control this decision. In addition, different models which describe the effect of phages on the ecosystem are compared, besides the approaches to study the switch. (2) An overview on the contribution of the phage in the evolution of the bacteria, instead of eating them, as a consequence of different mode of actions. As well, how phage display has helped in restricting phage cheating and how it could open new gates for immunization and pandemics control will be tacked.

Effects of the Newly Isolated T4-like Phage on Transmission of Plasmid-Borne Antibiotic Resistance Genes via Generalized Transduction

Bacteriophages are the most abundant biological entities on earth and may play an important role in the transmission of antibiotic resistance genes (ARG) from host bacteria. Although the specialized transduction mediated by the temperate phage targeting a specific insertion site is widely explored, the carrying characteristics of “transducing particles” for different ARG subtypes in the process of generalized transduction remains largely unclear. Here, we isolated a new T4-like lytic phage targeting transconjugant Escherichia coli C600 that contained plasmid pHNAH67 (KX246266) and encoded 11 different ARG subtypes. We found that phage AH67C600_Q9 can misload plasmid-borne ARGs and package host DNA randomly. Moreover, for any specific ARG subtype, the carrying frequency was negatively correlated with the multiplicity of infection (MOI). Further, whole genome sequencing (WGS) identified that only 0.338% (4/1183) of the contigs of an entire purified phage population contained ARG sequences; these were floR, sul2, aph(4)-Ia, and fosA. The low coverage indicated that long-read sequencing methods are needed to explore the mechanism of ARG transmission during generalized transduction.

Distribution and genomic characterization of tigecycline-resistant tet(X4)-positive Escherichia coli of swine farm origin

Abstract

The emergence of plasmid-mediated tigecycline-resistant strains is posing a serious threat to food safety and human health, which has attracted worldwide attention. The tigecycline resistance gene tet (X4) has been found in diverse sources, but the distribution of tet (X4) and its genetic background in the animal farming environment is not fully understood. Thirty-two tet (X)-positive Escherichia coli strains isolated from 159 samples collected from swine farms showed resistance to tigecycline. The tet (X)-positive strains were characterized by antimicrobial susceptibility testing, conjugation assay, PCR, Illumina and long-read Nanopore sequencing, and bioinformatics analysis. A total of 11 different sequence types (STs) were identified and most of them belonged to phylogroup A, except ST641. In total, 196 possible prophage sequences were identified and some of the prophage regions were found to carry resistance genes, including tet (X4). Furthermore, our results showed possible correlations between CRISPR spacer sequences and serotypes or STs. The co-existence of tigecycline-resistant tet (A) variants and tet (X4) complicates the evolution of vital resistance genes in farming environments. Further, four reorganization plasmids carrying tet (X4) were observed, and the formation mechanism mainly involved homologous recombination. These findings contribute significantly to a better understanding of the diversity and complexity of tet (X4)-bearing plasmids, an emerging novel public health concern.

Metagenomics of wastewater phageome identifies an extensively cored antibiotic resistome in a swine feedlot water treatment environment

Huge number of antibiotic resistance genes (ARGs) have been widely detected in phage genomes from anthropogenic environment or animal farms, whereas little is known about the dynamic changes of phage contribution to resistance under a feedlot wastewater treatment facility (WTF) pressure. Here, a metagenomics method was used to characterize the sewage phageome and identifies the antibiotic resistome. The results showed that the phage families of Siphoviridae, Myoviridae, and Podoviridae were always the most dominant. Analysis of ARGs carried by bacterial and phages showed that MLS and tetracycline resistance genes always had the highest abundances and the other ARG types also have a fixed hierarchy, showing that there is no significant change in overall ARGs abundance distribution. However, an extensively cored antibiotic resistome were specifically identified in aerobic environment. ARGs encoding ribosomal protection proteins, especially for the ARG subtypes lsaE, tet44, tetM, tetP, macB, MdlB and rpoB2, were more inclined to be selected by phages, suggesting that a more refined mechanism, such as specialized transduction and lateral transduction, was probably involved. In all, these results suggest that monitoring of dynamic changes of phage contribution to resistance should be given more attention and ARGs-carrying phage management should focus on using technologies for controlling cored ARGs rather than only the overall distribution of ARGs in phages.

Biosynthesis of a Novel Antibacterial Dipeptide, Using Proteases From South American Native Fruits, Useful as a Food Preservative

Antiacanthain and granulosain are the partially purified proteolytic extracts from the South American native fruits of Bromelia antiacantha (Bertol. ) and Solanum granuloso leprosum, respectively. The aim of this work was to compare the ability of both soluble and immobilized antiacanthain and granulosain f or the synthesis of Z-Tyr-Val-OH, a novel antibacterial dipeptide, in different reaction systems formed by almost anhydrous organic solvents (X_w: 1 × 10⁻⁵) and several percentages of immiscible organic solvents in 100 mM Tris(hydroxymethyl)aminomethane hydrochloride buffer pH 8.0. Soluble antiacanthain in half of the 24 different organic biphasic media showed higher catalytic potential than in 100 mM Tris(hydroxymethyl)aminomethane hydrolchloride buffer pH 8.0. Soluble granulosain showed lower catalytic potential in all liquid-liquid biphasic media than in the same buffer. However, 50% (v/v) ethyl ethanoate in 100 mM Tris(hydroxymethyl)aminomethane hydrolchloride buffer pH 8.0 allowed to express the highest catalytic potential of both soluble enzymes. In 50% v/v ethyl ethanoate, soluble antiacanthain and granulosain catalyzed the synthesis of Z-Tyr-Val-OH with 72 ± 0.15 and 60 ± 0.10% maximal peptide yields, respectively. Multi-point immobilization in glyoxyl-silica did not lead to better peptide yields than soluble enzymes, in that liquid-liquid biphasic medium under the same reaction conditions. Soluble and glyoxyl-silica immobilized antiacanthain in almost anhydrous ethyl ethanoate (X_w: 1 × 10⁻⁵) were able to retain 17.3 and 45% of the initial proteolytic activity of antiacanthain in 100 mM Tris hydrolchloride buffer pH 8.0, respectively, at 40°C under agitation (200 rpm). Soluble and glyoxyl-silica immobilized granulosain were inactivated under the same reaction conditions. Glyoxyl-silica immobilized antiacanthain showed to be a robust biocatalyst in almost anhydrous ethyl ethanoate (X_w: 1 × 10⁻⁵), eliciting the best peptide yield (75 ± 0.13%). The synthesis reaction of Z-Tyr-Val-OH could not proceed when soluble antiacanthain was used under the same conditions. Both peptidases only catalyzed the synthesis reaction under kinetic control, using activated acyl donor substrates. Finally, this work reports a novel broad-spectrum antibacterial peptide that significantly decreased (p ≤ 0.05) the specific growth rates of Gram positive and Gram negative microorganisms at very low concentrations (≥15 and 35 μg/ml, respectively); contributing with a new safe food preservative of applying for different food systems.

Bacteriophage-Mediated Control of Phytopathogenic Xanthomonads: A Promising Green Solution for the Future

Xanthomonads, members of the family Xanthomonadaceae, are economically important plant pathogenic bacteria responsible for infections of over 400 plant species. Bacteriophage-based biopesticides can provide an environmentally friendly, effective solution to control these bacteria. Bacteriophage-based biocontrol has important advantages over chemical pesticides, and treatment with these biopesticides is a minor intervention into the microflora. However, bacteriophages’ agricultural application has limitations rooted in these viruses’ biological properties as active substances. These disadvantageous features, together with the complicated registration process of bacteriophage-based biopesticides, means that there are few products available on the market. This review summarizes our knowledge of the Xanthomonas-host plant and bacteriophage-host bacterium interaction’s possible influence on bacteriophage-based biocontrol strategies and provides examples of greenhouse and field trials and products readily available in the EU and the USA. It also details the most important advantages and limitations of the agricultural application of bacteriophages. This paper also investigates the legal background and industrial property right issues of bacteriophage-based biopesticides. When appropriately applied, bacteriophages can provide a promising tool against xanthomonads, a possibility that is untapped. Information presented in this review aims to explore the potential of bacteriophage-based biopesticides in the control of xanthomonads in the future.

Synergistic action of phage phiIPLA-RODI and lytic protein CHAPSH3b: a combination strategy to target Staphylococcus aureus biofilms

Staphylococcus aureus is considered a priority pathogen due to its increasing acquisition of antibiotic resistance determinants. Additionally, this microbe has the ability to form recalcitrant biofilms on different biotic and inert surfaces. In this context, bacteriophages and their derived lytic proteins may be a forward-looking strategy to help combat staphylococcal biofilms. However, these antimicrobials exhibit individual limitations that may be overcome by combining them with other compounds. This work investigates the combination of a phage-derived lytic protein, CHAPSH3b, and the virulent bacteriophage phiIPLA-RODI. The obtained results show the synergy between both antimicrobials for the treatment of 24-h-old S. aureus biofilms, with greater reductions in viable cell counts observed when phage and lysin are applied together compared to the individual treatments. Time-kill curves and confocal microscopy revealed that the fast antibacterial action of CHAPSH3b reduces the population up to 7 hours after initial exposure, which is subsequently followed by phage predation, limiting regrowth of the bacterial population. Moreover, at least 90% of bacteriophage insensitive mutants are susceptible to the lytic protein. Therefore, CHAPSH3b might help curtail the development of phage resistance during treatment. The combination of the lysin and phiIPLA-RODI also showed promising results in an ex vivo pig skin model of wound infection. Overall, the results of this study demonstrate that the combination of phage-derived lytic proteins and bacteriophages can be a viable strategy to develop improved antibiofilm products.

Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future

The current problems with increasing bacterial resistance to antibacterial therapies, resulting in a growing frequency of incurable bacterial infections, necessitates the acceleration of studies on antibacterials of a new generation that could offer an alternative to antibiotics or support their action. Bacteriophages (phages) can kill antibiotic-sensitive as well as antibiotic-resistant bacteria, and thus are a major subject of such studies. Their efficacy in curing bacterial infections has been demonstrated in in vivo experiments and in the clinic. Unlike antibiotics, phages have a narrow range of specificity, which makes them safe for commensal microbiota. However, targeting even only the most clinically relevant strains of pathogenic bacteria requires large collections of well characterized phages, whose specificity would cover all such strains. The environment is a rich source of diverse phages, but due to their complex relationships with bacteria and safety concerns, only some naturally occurring phages can be considered for therapeutic applications. Still, their number and diversity make a detailed characterization of all potentially promising phages virtually impossible. Moreover, no single phage combines all the features required of an ideal therapeutic agent. Additionally, the rapid acquisition of phage resistance by bacteria may make phages already approved for therapy ineffective and turn the search for environmental phages of better efficacy and new specificity into an endless race. An alternative strategy for acquiring phages with desired properties in a short time with minimal cost regarding their acquisition, characterization, and approval for therapy could be based on targeted genome modifications of phage isolates with known properties. The first example demonstrating the potential of this strategy in curing bacterial diseases resistant to traditional therapy is the recent successful treatment of a progressing disseminated Mycobacterium abscessus infection in a teenage patient with the use of an engineered phage. In this review, we briefly present current methods of phage genetic engineering, highlighting their advantages and disadvantages, and provide examples of genetically engineered phages with a modified host range, improved safety or antibacterial activity, and proven therapeutic efficacy. We also summarize novel uses of engineered phages not only for killing pathogenic bacteria, but also for in situ modification of human microbiota to attenuate symptoms of certain bacterial diseases and metabolic, immune, or mental disorders.

Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life

Caesarean section delivery (CSD) disrupts mother-to-neonate transmission of specific microbial strains and functional repertoires as well as linked immune system priming. Here we investigate whether differences in microbiome composition and impacts on host physiology persist at 1 year of age. We perform high-resolution, quantitative metagenomic analyses of the gut microbiomes of infants born by vaginal delivery (VD) or by CSD, from immediately after birth through to 1 year of life. Several microbial populations show distinct enrichments in CSD-born infants at 1 year of age including strains of Bacteroides caccae, Bifidobacterium bifidum and Ruminococcus gnavus, whereas others are present at higher levels in the VD group including Faecalibacterium prausnitizii, Bifidobacterium breve and Bifidobacterium kashiwanohense. The stimulation of healthy donor-derived primary human immune cells with LPS isolated from neonatal stool samples results in higher levels of tumour necrosis factor alpha (TNF-α) in the case of CSD extracts over time, compared to extracts from VD infants for which no such changes were observed during the first year of life. Functional analyses of the VD metagenomes at 1 year of age demonstrate a significant increase in the biosynthesis of the natural antibiotics, carbapenem and phenazine. Concurrently, we find antimicrobial resistance (AMR) genes against several classes of antibiotics in both VD and CSD. The abundance of AMR genes against synthetic (including semi-synthetic) agents such as phenicol, pleuromutilin and diaminopyrimidine are increased in CSD children at day 5 after birth. In addition, we find that mobile genetic elements, including phages, encode AMR genes such as glycopeptide, diaminopyrimidine and multidrug resistance genes. Our results demonstrate persistent effects at 1 year of life resulting from birth mode-dependent differences in earliest gut microbiome colonisation.

Analysis of microorganisms with nonlinear electrokinetic microsystems

Nonlinear electrokinetics (EK), specifically electrophoresis of the second kind, dielectrophoresis (DEP) and electrorotation (EROT), have gained significant interest recently for their flexibility and labeless discriminant manner of operation. The current applications of these technologies are a clear advancement from what they were when first discovered, but also still show strong signs of future growth. The present review article presents a discussion of the current uses of microscale nonlinear EK technologies as analytical, sensing, and purification tools for microorganisms. The discussion is focused on some of the latest discoveries with various nonlinear EK microfluidic techniques, such as DEP particle trapping and EROT for particle assessments, for the analysis of microorganisms ranging from viruses to parasites. Along the way, special focus was given to key research articles from within the past two years to provide the most up-to-date knowledge on the current state-of-the-art within the field of microscale EK, and from there, an outlook on where the future of the field is headed is also included.

Phage therapy as strategy to face post-antibiotic era: a guide to beginners and experts

Interest in the therapeutic use of bacteriophages (phages) has emerged in recent years, driven mainly by the antimicrobial resistance crisis. This review aimed to summarize some important studies addressing the use of phages as a therapeutic alternative for multiresistant bacterial infections. To this end, a literature search was conducted to address the efficacy and versatility of phage therapy, the advantages and disadvantages of its use, and potential limitations for the application of phage therapy that need to be overcome, especially in Western countries. Thus, this review highlights that phage therapy may be a promising route in the treatment of infections caused by multidrug-resistant pathogens and that a combined approach has the potential to prolong the life of the current available antimicrobials. In addition, standardized clinical trials using monoclonal or polyclonal phages, alone or in combination with antimicrobials, are crucial to determine the real potential of these treatments in clinical practice.

Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage

Bacteriophages, or phages, are ubiquitous bacterial and archaeal viruses with an estimated total global population of 10³¹. It is well-known that wherever there are bacteria, their phage counterparts will be found, aiding in shaping the bacterial population. The present study used metagenomic data from global influent sewage in 79 cities in 60 countries to identify phages associated with bacteria and to explore their potential role in antimicrobial resistance gene (ARG) dissemination. The reads were mapped to known databases for bacteriophages and their abundances determined and correlated to geographic origin and the countries socio-economic status, as well as the abundances of bacterial species and ARG. We found that some phages were not equally distributed on a global scale, but their distribution was rather dictated by region and the socioeconomic status of the specific countries. This study provides a preliminary insight into the global and regional distribution of phages and their potential impact on the transmission of ARGs between bacteria. Moreover, the findings may indicate that phages in sewage could have adopted a lytic lifestyle, meaning that most may not be associated with bacteria and instead may be widely distributed as free-living phages, which are known to persist longer in the environment than their hosts. In addition, a significant correlation between phages and ARGs was obtained, indicating that phages may play a role in ARG dissemination. However, further analyses are needed to establish the true relationship between phages and ARGs due to a low abundance of the phages identified.

Changes of Gut-Microbiota-Liver Axis in Hepatitis C Virus Infection

Simple Summary

Gut microbiota alteration is linked to many health disorders including hepatitis C virus (HCV) infection. This dysbiosis in turn impacts the coordination between the gut and the liver that is known as the gut–liver-axis. Here, we discuss the latest findings regarding the changes in gut microbiota structure and functionality post HCV infection and its treatment regimens. In addition, we underline the contribution of the microbiota alterations to HCV associated liver complications.

Abstract

The gut–liver-axis is a bidirectional coordination between the gut, including microbial residents, the gut microbiota, from one side and the liver on the other side. Any disturbance in this crosstalk may lead to a disease status that impacts the functionality of both the gut and the liver. A major cause of liver disorders is hepatitis C virus (HCV) infection that has been illustrated to be associated with gut microbiota dysbiosis at different stages of the disease progression. This dysbiosis may start a cycle of inflammation and metabolic disturbance that impacts the gut and liver health and contributes to the disease progression. This review discusses the latest literature addressing this interplay between the gut microbiota and the liver in HCV infection from both directions. Additionally, we highlight the contribution of gut microbiota to the metabolism of antivirals used in HCV treatment regimens and the impact of these medications on the microbiota composition. This review sheds light on the potential of the gut microbiota manipulation as an alternative therapeutic approach to control the liver complications post HCV infection.

The Acquisition of Colistin Resistance Is Associated to the Amplification of a Large Chromosomal Region in Klebsiella pneumoniae kp52145

The appearance of carbapenem-resistant Klebsiella pneumoniae has increased the use of colistin as a last-resort antibiotic for treating infections by this pathogen. A consequence of its use has been the spread of colistin-resistant strains, in several cases carrying colistin resistance genes. In addition, when susceptible strains are confronted with colistin during treatment, mutation is a major cause of the acquisition of resistance. To analyze the mechanisms of resistance that might be selected during colistin treatment, an experimental evolution assay for 30 days using as a model the clinical K. pneumoniae kp52145 isolate in the presence of increasing amounts of colistin was performed. All evolved populations presented a decreased susceptibility to colistin, without showing cross-resistance to antibiotics belonging to other structural families. We did not find any common mutation in the evolved mutants, neither in already known genes, previously known to be associated with the resistance phenotype, nor in new ones. The only common genetic change observed in the strains that evolved in the presence of colistin was the amplification of a 34 Kb sequence, homologous to a prophage (Enterobacteria phage Fels-2). Our data support that gene amplification can be a driving force in the acquisition of colistin resistance by K. pneumoniae.

Complete Genome Sequence of Streptomyces Phage Shady

Streptomyces spp. are saprophytic soil bacteria that produce secondary metabolites with therapeutic potential. This announcement describes the isolation and genome annotation of Streptomyces sp. strain Mg1 siphophage Shady. Learning more about Shady’s novel 45-kb genome, containing 76 predicted protein-coding genes, could be industrially advantageous when using streptomycetes for their products.

Streptomyces spp. are saprophytic soil bacteria that produce secondary metabolites with therapeutic potential. This announcement describes the isolation and genome annotation of Streptomyces sp. strain Mg1 siphophage Shady. Learning more about Shady’s novel 45-kb genome, containing 76 predicted protein-coding genes, could be industrially advantageous when using streptomycetes for their products.

Protective Effect of Zuojin Fang on Lung Injury Induced by Sepsis through Downregulating the JAK1/STAT3 Signaling Pathway

Lung injury was the common and serious complication of sepsis, a systemic inflammatory response syndrome caused by severe infections. Chinese medicine had unique advantages in attenuating inflammatory response, such as Zuojinfang (ZJF). ZJF was a classical compound herb formula composed of Coptidis Rhizoma and Euodiae Fructus in a ratio of 6 : 1. In this paper, 15 ingredients in ZJF were identified and 8 of them absorbed into rat's serum were quantified by HPLC-MS/MS. Subsequently, sepsis-induced lung injury model was replicated in rats by cecal ligation and puncture. 60 SD rats were randomly divided into 6 groups (n = 10): control group (CON), sham group (Sham), model group (MOD), ZJF low-dose group (ZJF-L), ZJF high-dose group (ZJF-H), and prednisolone group (PNSL). Within the next 24 h, the levels of inflammatory factors, correlation between active ingredients and inflammatory cytokines, the pathological changes of lung tissue, and protein expression of the JAK1/STAT3 signaling pathways were analyzed one by one. Finally, the concentration order of components absorbed in rat serum was berberine > palmatine > jatrorrhizine > coptisine > evodin > chlorogenic acid > evodiamine. Compared with the MOD group, the TNF-α, IL-6, and IFN-γ in the ZJF-H group were significantly reduced (p < 0.05). Moreover, the TNF-α decreased significantly accompanied by the increase of berberine, chlorogenic acid, jatrorrhizine, palmatine, evodin, and evodiamine in serum (negative correlation, p < 0.05). Compared with the MOD, the area of lung injury, the expressions of JAK1, p-JAK1, STAT3, and p-STAT3 were significantly decreased under the treatment of ZJF (p < 0.05). Therefore, downregulating the JAK1/STAT3 signaling pathways was a potential avenue of ZJF in reversing lung injury induced by sepsis.

Phages versus Antibiotics To Treat Infected Diabetic Wounds in a Mouse Model: a Microbiological and Microbiotic Evaluation

The management of diabetic foot infections is frequently a dead end for surgeons and infectious disease specialists. When the pathogen to be treated is not resistant to conventional antibiotics, the latter tend to unbalance the intestinal microbiota, which is linked to multiple pathologies. A local treatment with bacteriophages, in addition to being as much or even more effective than antibiotics from a clinical and microbiological point of view, makes it possible to respect the patient’s microbiota. These results suggest that the use of this therapeutic alternative is a major avenue and that the introduction of recommendations for their use is now necessary.

Diabetes is marked by a range of complications, including chronic infections that can lead to limb amputation. The treatment of infected wounds is disrupted by arteriopathies that reduce tissue perfusion as well as by the critical development of bacterial resistance. We evaluated the impact of a local application of bacteriophages compared to that of a per os administration of amoxicillin-clavulanic acid in a mouse model of Staphylococcus aureus wound infection. We found that phage treatment resulted in improved clinical healing and a reduction in local bacterial load at 7 and 14 days postinfection. Unlike antibiotics, phage therapy did not deplete the intestinal microbiota of treated animals. Amoxicillin resulted in a reduction of alpha and beta diversities of the murine microbiota and disturbed architecture even 7 days after the end of treatment, whereas phage treatment did not impinge on the microbiota.

IMPORTANCE The management of diabetic foot infections is frequently a dead end for surgeons and infectious disease specialists. When the pathogen to be treated is not resistant to conventional antibiotics, the latter tend to unbalance the intestinal microbiota, which is linked to multiple pathologies. A local treatment with bacteriophages, in addition to being as much or even more effective than antibiotics from a clinical and microbiological point of view, makes it possible to respect the patient’s microbiota. These results suggest that the use of this therapeutic alternative is a major avenue and that the introduction of recommendations for their use is now necessary.

Evaluation of Potential ARG Packaging by Two Environmental T7-Like Phage during Phage-Host Interaction

The increase in antimicrobial resistance is a threat to both human and animal health. The transfer of antibiotic resistance genes (ARG) via plasmids has been studied in detail whereas the contribution of bacteriophage-mediated ARG transmission is relatively little explored. We isolated and characterized two T7-like lytic bacteriophages that infected multidrug-resistant Escherichia coli hosts. The morphology and genomic analysis indicated that both phage HZP2 and HZ2R8 were evolutionarily related and their genomes did not encode ARGs. However, ARG-like raw reads were detected in offspring sequencing data with a different abundance level implying that potential ARG packaging had occurred. PCR results demonstrated that six fragments of genes (qnrS, cmlA, tetM, bla_TEM, sul3, mcr-1) were potentially packaged by phage HZP2 and four (qnrS, cmlA, bla_TEM, mcr-1) by phage HZ2R8. Further quantitative results showed that ARG abundance hierarchies were similar. The gene bla_TEM was the most abundant (up to 1.38 × 10⁷ copies/mL) whereas cmlA and qnrS were the least. Moreover, the clinically important mcr-1 gene was the second most abundant ARG indicating a possibility for spread through generalized transduction. Together, our results indicated that these structurally similar phage possessed similar characteristics and potential packaging during phage-host interaction displayed an ARG preference rather than occurring randomly.

Lessons Learned From the First 10 Consecutive Cases of Intravenous Bacteriophage Therapy to Treat Multidrug-Resistant Bacterial Infections at a Single Center in the United States

Background

Due to increasing multidrug-resistant (MDR) infections, there is an interest in assessing the use of bacteriophage therapy (BT) as an antibiotic alternative. After the first successful case of intravenous BT to treat a systemic MDR infection at our institution in 2017, the Center for Innovative Phage Applications and Therapeutics (IPATH) was created at the University of California, San Diego, in June 2018.

Methods

We reviewed IPATH consult requests from June 1, 2018, to April 30, 2020, and reviewed the regulatory process of initiating BT on a compassionate basis in the United States. We also reviewed outcomes of the first 10 cases at our center treated with intravenous BT (from April 1, 2017, onwards).

Results

Among 785 BT requests to IPATH, BT was administered to 17 of 119 patients in whom it was recommended. One-third of requests were for Pseudomonas aeruginosa, Staphylococcus aureus, and Mycobacterium abscessus. Intravenous BT was safe with a successful outcome in 7/10 antibiotic-recalcitrant infections at our center (6 were before IPATH). BT may be safely self-administered by outpatients, used for infection suppression/prophylaxis, and combined successfully with antibiotics despite antibiotic resistance, and phage resistance may be overcome with new phage(s). Failure occurred in 2 cases despite in vitro phage susceptibility.

Conclusions

We demonstrate the safety and feasibility of intravenous BT for a variety of infections and discuss practical considerations that will be critical for informing future clinical trials.

Combined Bacteriophage and Antibiotic Treatment Prevents Pseudomonas aeruginosa Infection of Wild Type and cftr- Epithelial Cells

With the increase of infections due to multidrug resistant bacterial pathogens and the shortage of antimicrobial molecules with novel targets, interest in bacteriophages as a therapeutic option has regained much attraction. Before the launch of future clinical trials, in vitro studies are required to better evaluate the efficacies and potential pitfalls of such therapies. Here we studied in an ex vivo human airway epithelial cell line model the efficacy of phage and ciprofloxacin alone and in combination to treat infection by Pseudomonas aeruginosa. The Calu-3 cell line and the isogenic CFTR knock down cell line (cftr-) infected apically with P. aeruginosa strain PAO1 showed a progressive reduction in transepithelial resistance during 24 h. Administration at 6 h p.i. of single phage, phage cocktails or ciprofloxacin alone prevented epithelial layer destruction at 24 h p.i. Bacterial regrowth, due to phage resistant mutants harboring mutations in LPS synthesis genes, occurred thereafter both in vitro and ex vivo. However, co-administration of two phages combined with ciprofloxacin efficiently prevented PAO1 regrowth and maintained epithelial cell integrity at 72 p.i. The phage/ciprofloxacin treatment did not induce an inflammatory response in the tested cell lines as determined by nanoString® gene expression analysis. We conclude that combination of phage and ciprofloxacin efficiently protects wild type and cftr- epithelial cells from infection by P. aeruginosa and emergence of phage resistant mutants without inducing an inflammatory response. Hence, phage-antibiotic combination should be a safe and promising anti-Pseudomonas therapy for future clinical trials potentially including cystic fibrosis patients.

Bacteriophages and the One Health Approach to Combat Multidrug Resistance: Is This the Way?

Antimicrobial resistance necessitates action to reduce and eliminate infectious disease, ensure animal and human health, and combat emerging diseases. Species such as Acinetobacter baumanniii, vancomycin resistant Enterococcus, methicillin resistance Staphylococcus aureus, and Pseudomonas aeruginosa, as well as other WHO priority pathogens, are becoming extremely difficult to treat. In 2017, the EU adopted the “One Health” approach to combat antibiotic resistance in animal and human medicine and to prevent the transmission of zoonotic disease. As the current therapeutic agents become increasingly inadequate, there is a dire need to establish novel methods of treatment under this One Health Framework. Bacteriophages (phages), viruses infecting bacterial species, demonstrate clear antimicrobial activity against an array of resistant species, with high levels of specificity and potency. Bacteriophages play key roles in bacterial evolution and are essential components of all ecosystems, including the human microbiome. Factors such are their specificity, potency, biocompatibility, and bactericidal activity make them desirable options as therapeutics. Issues remain, however, relating to their large-scale production, formulation, stability, and bacterial resistance, limiting their implementation globally. Phages used in therapy must be virulent, purified, and well characterized before administration. Clinical studies are warranted to assess the in vivo pharmacokinetics and pharmacodynamic characteristics of phages to fully establish their therapeutic potential.

Phage steering of antibiotic-resistance evolution in the bacterial pathogen, Pseudomonas aeruginosa

Background and objectives

Antimicrobial resistance is a growing global concern and has spurred increasing efforts to find alternative therapeutics. Bacteriophage therapy has seen near constant use in Eastern Europe since its discovery over a century ago. One promising approach is to use phages that not only reduce bacterial pathogen loads but also select for phage resistance mechanisms that trade-off with antibiotic resistance-so called 'phage steering'.

Methodology

Recent work has shown that the phage OMKO1 can interact with efflux pumps and in so doing select for both phage resistance and antibiotic sensitivity of the pathogenic bacterium Pseudomonas aeruginosa. We tested the robustness of this approach to three different antibiotics in vitro (tetracycline, erythromycin and ciprofloxacin) and one in vivo (erythromycin).

Results

We show that in vitro OMKO1 can reduce antibiotic resistance of P. aeruginosa (Washington PAO1) even in the presence of antibiotics, an effect still detectable after ca.70 bacterial generations in continuous culture with phage. Our in vivo experiment showed that phage both increased the survival times of wax moth larvae (Galleria mellonella) and increased bacterial sensitivity to erythromycin. This increased antibiotic sensitivity occurred both in lines with and without the antibiotic.

Conclusions and implications

Our study supports a trade-off between antibiotic resistance and phage sensitivity. This trade-off was maintained over co-evolutionary time scales even under combined phage and antibiotic pressure. Similarly, OMKO1 maintained this trade-off in vivo, again under dual phage/antibiotic pressure. Our findings have implications for the future clinical use of steering in phage therapies. Lay Summary: Given the rise of antibiotic-resistant bacterial infection, new approaches to treatment are urgently needed. Bacteriophages (phages) are bacterial viruses. The use of such viruses to treat infections has been in near-continuous use in several countries since the early 1900s. Recent developments have shown that these viruses are not only effective against routine infections but can also target antibiotic resistant bacteria in a novel, unexpected way. Similar to other lytic phages, these so-called 'steering phages' kill the majority of bacteria directly. However, steering phages also leave behind bacterial variants that resist the phages, but are now sensitive to antibiotics. Treatment combinations of these phages and antibiotics can now be used to greater effect than either one independently. We evaluated the impact of steering using phage OMKO1 and a panel of three antibiotics on Pseudomonas aeruginosa, an important pathogen in hospital settings and in people with cystic fibrosis. Our findings indicate that OMKO1, either alone or in combination with antibiotics, maintains antibiotic sensitivity both in vitro and in vivo, giving hope that phage steering will be an effective treatment option against antibiotic-resistant bacteria.

Possible drugs for the treatment of bacterial infections in the future: anti-virulence drugs

Antibiotic resistance is a global threat that should be urgently resolved. Finding a new antibiotic is one way, whereas the repression of the dissemination of virulent pathogenic bacteria is another. From this point of view, this paper summarizes first the mechanisms of conjugation and transformation, two important processes of horizontal gene transfer, and then discusses the approaches for disarming virulent pathogenic bacteria, that is, virulence factor inhibitors. In contrast to antibiotics, anti-virulence drugs do not impose a high selective pressure on a bacterial population, and repress the dissemination of antibiotic resistance and virulence genes. Disarmed virulence factors make virulent pathogens avirulent bacteria or pathobionts, so that we human will be able to coexist with these disarmed bacteria peacefully.

Reduction of erythromycin resistance gene erm(F) and class 1 integron-integrase genes in wastewater by Bardenpho treatment

Wastewaters routinely contain antibiotic-resistant bacteria (ARB) and genes (ARG) that are removed to a varying degree during wastewater treatment. This study investigated the removal of the erythromycin ribosome methylase class F (erm(F)) and class 1 integron-integrase (intI1) genes at each stage from two water resource recovery facilities in southern Arizona. Although genes were significantly reduced by Bardenpho treatment, erm(F) and intI1 were still observed in ≥ 9 and 7 out of 12 secondary effluent samples. Primary processes via sedimentation or dissolved air flotation, as well as chlorine disinfection, did not significantly impact erm(F) and intI1 concentrations. Therefore, Bardenpho treatment was critical to reduce erm(F) and intI1. Concentrations of erm(F) and intI1 were compared with each other and other markers for anthropogenic pollution. Results from this study support intI1 as one suitable marker to measure erythromycin resistance genes in wastewater, as intI1 was found at higher concentrations, persisted more throughout treatment, and correlated with erm(F) at nearly every treatment stage. PRACTITIONER POINTS: Bardenpho treatment was the key process responsible for the reduction of intI1 and erm(F) genes during wastewater treatment. Primary treatment and chlorine disinfection did not impact erm(F) and intI1 gene concentrations. The intI1 gene is a suitable marker for measuring erm(F) genes in wastewater.

Secondary Bacterial Infections During Pulmonary Viral Disease: Phage Therapeutics as Alternatives to Antibiotics?

Secondary bacterial infections manifest during or after a viral infection(s) and can lead to negative outcomes and sometimes fatal clinical complications. Research and development of clinical interventions is largely focused on the primary pathogen, with research on any secondary infection(s) being neglected. Here we highlight the impact of secondary bacterial infections and in particular those caused by antibiotic-resistant strains, on disease outcomes. We describe possible non-antibiotic treatment options, when small molecule drugs have no effect on the bacterial pathogen and explore the potential of phage therapy and phage-derived therapeutic proteins and strategies in treating secondary bacterial infections, including their application in combination with chemical antibiotics.

Role of enterotoxigenic Escherichia coli prophage in spreading antibiotic resistance in a porcine-derived environment

Enterotoxigenic Escherichia coli (ETEC) cause acute secretory diarrhoea in pigs, posing a great economic loss to the swine industry. This study analysed the prevalence and genetic characteristics of prophages from 132 ETEC isolates from symptomatic pigs to determine their potential for spreading antibiotic resistance. A total of 1105 potential prophages were identified, and the distribution of the genome size showed three 'overlapping' trends. Similarity matrix comparison showed that prophages correlated with the ETEC lineage distribution, and further identification of these prophages corroborated the lineage specificity. In total, 1206 antibiotic resistance genes (ARGs) of 52 different categories were identified in 132 ETEC strains; among these, 2.65% (32/1206) of ARGs were found to be carried by prophages. Analysis of flanking sequences showed that almost all the ARGs could be grouped into two types: 'bla_TEM-1B ' and 'classic class 1 integron (IntI1)'. They co-occurred with a strictly conserved recombinase and transposon Tn3 family but with a difference: the 'bla_TEM-1B type' prophages exhibited a classic Tn2 transposon structure with 100% sequence identity, whereas the 'IntI1 type' co-occurred with the TnAs2 transposon with only 84% sequence identity. These results imply that ARGs might be pervasive in natural bacterial populations through transmission by transposable bacteriophages.

Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance

Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.

Associations between antibiotic resistance and bacteriophage resistance phenotypes in laboratory and clinical strains of Salmonella enterica subsp. enterica serovar Typhimurium

Bacteriophages have received great attention as an alternative over antibiotics due to the host specificity. Therefore, this study was designed to evaluate the associations between bacteriophage-insensitive (BI) and antibiotic-resistant mutants of Salmonella Typhimurium strains. Bacteriophage-sensitive (BS) Salmonella enterica serovar Typhimurium ATCC 19585 (BSST^WT), ciprofloxacin-induced S. Typhimurium ATCC 19585 (BSST^CIP), S. Typhimurium KCCM 40253 (BSST^LAB), and clinically isolated multidrug-resistant S. Typhimurium CCARM 8009 (BSST^MDR) were used to induce the bacteriophage-insensitive mutants (BIST^WT, BIST^CIP, BIST^LAB, and BIST^MDR), which were characterized by measuring mutant frequency lysogenic induction, phage adsorption, antibiotic susceptibility, and differential gene expression. The numbers of BSST^WT, BSST^CIP, and BSST^LAB were reduced by P22 (>3 log), while the least lytic activity was observed for BSST^MDR, suggesting alteration in bacteriophage-binding receptors on the surface of multidrug-resistant strain. BSST^WT treated with P22 showed the large variation in the cell state (CV>40%) and highest mutant frequency (62%), followed by 25% for BSST^CIP. The least similarities between BSST^WT and BIST^WT were observed for P22 and PBST-13 (<12%). The relative expression levels of bacteriophage-binding receptor-related genes (btuB, fhuA, fliK, fljB, ompC, ompF, rfaL, and tolC) were decreased in BIST^CIP and BIST^MDR. These results indicate that the bacteriophage resistance is highly associated with the antibiotic resistance. The findings in this study could pave the way for the application of bacteriophages as an alternative to control antibiotic-resistant bacteria.

Classical methods and perspectives for manipulating the human gut microbial ecosystem

A healthy Human Gut Microbial Ecosystem (HGME) is a necessary condition for maintaining the orderly function of the whole body. Major alterations in the normal gut microbial composition, activity and functionality (dysbiosis) by an environmental or host-related disruptive event, can compromise metabolic, inflammatory, and neurological processes, causing disorders such as obesity, inflammatory bowel disease, colorectal cancer, and depressive episodes. The restore or the maintaining of the homeostatic balance of Gut Microbiota (GM) populations (eubiosis) is possible through diet, the use of probiotics, prebiotics, antibiotics, and even Fecal Microbiota Transplantation (FMT). Although these "classic methods" represent an effective and accepted way to modulate GM, the complexity of HGME requires new approaches to control it in a more appropriate way. Among the most promising emergent strategies for modulating GM are the use of engineered nanomaterials (metallic nanoparticles (NP), polymeric-NP, quantum dots, micelles, dendrimers, and liposomes); phagotherapy (i.e., phages linked with the CRISPR/Cas9 system), and the use of antimicrobial peptides, non-antibiotic drugs, vaccines, and immunoglobulins. Here we review the current state of development, implications, advantages, disadvantages, and perspectives of the different approaches for manipulating HGME.

New insights into intestinal phages

The intestinal microbiota plays important roles in human health. This last decade, the viral fraction of the intestinal microbiota, composed essentially of phages that infect bacteria, received increasing attention. Numerous novel phage families have been discovered in parallel with the development of viral metagenomics. However, since the discovery of intestinal phages by d'Hérelle in 1917, our understanding of the impact of phages on gut microbiota structure remains scarce. Changes in viral community composition have been observed in several diseases. However, whether these changes reflect a direct involvement of phages in diseases etiology or simply result from modifications in bacterial composition is currently unknown. Here we present an overview of the current knowledge in intestinal phages, their identity, lifestyles, and their possible effects on the gut microbiota. We also gather the main data on phage interactions with the immune system, with a particular emphasis on recent findings.

Strategies to Combat Multidrug-Resistant and Persistent Infectious Diseases

Antibiotic failure is one of the most worrying health problems worldwide. We are currently facing an international crisis with several problematic facets: new antibiotics are no longer being discovered, resistance mechanisms are occurring in almost all clinical isolates of bacteria, and recurrent infections caused by persistent bacteria are hampering the successful treatment of infections. In this context, new anti-infectious strategies against multidrug-resistant (MDR) and persistent bacteria, as well as the rescue of Food and Drug Administration (FDA)-approved compounds (drug repurposing), are being explored. Among the highlighted new anti-infectious strategies, in this review, we focus on antimicrobial peptides, anti-virulence compounds, phage therapy, and new molecules. As drugs that are being repurposed, we highlight anti-inflammatory compounds, anti-psychotics, anti-helminthics, anti-cancerous drugs, and statins.

Defeating Antibiotic-Resistant Bacteria: Exploring Alternative Therapies for a Post-Antibiotic Era

Antibiotics are one of the greatest medical advances of the 20th century, however, they are quickly becoming useless due to antibiotic resistance that has been augmented by poor antibiotic stewardship and a void in novel antibiotic discovery. Few novel classes of antibiotics have been discovered since 1960, and the pipeline of antibiotics under development is limited. We therefore are heading for a post-antibiotic era in which common infections become untreatable and once again deadly. There is thus an emergent need for both novel classes of antibiotics and novel approaches to treatment, including the repurposing of existing drugs or preclinical compounds and expanded implementation of combination therapies. In this review, we highlight to utilize alternative drug targets/therapies such as combinational therapy, anti-regulator, anti-signal transduction, anti-virulence, anti-toxin, engineered bacteriophages, and microbiome, to defeat antibiotic-resistant bacteria.

Anti-CRISPR proteins targeting the CRISPR-Cas system enrich the toolkit for genetic engineering

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas adaptive immune defense systems, which are widely distributed in bacteria and Archaea, can provide sequence-specific protection against foreign DNA or RNA in some cases. However, the evolution of defense systems in bacterial hosts did not lead to the elimination of phages, and some phages carry anti-CRISPR genes that encode products that bind to the components mediating the defense mechanism and thus antagonize CRISPR-Cas immune systems of bacteria. Given the extensive application of CRISPR-Cas9 technologies in gene editing, in this review, we focus on the anti-CRISPR proteins (Acrs) that inhibit CRISPR-Cas systems for gene editing. We describe the discovery of Acrs in immune systems involving type I, II, and V CRISPR-Cas immunity, discuss the potential function of Acrs in inactivating type II and V CRISPR-Cas systems for gene editing and gene modulation, and provide an outlook on the development of important biotechnology tools for genetic engineering using Acrs.

Implications of bacteriophages on the acquisition and spread of antibiotic resistance in the environment

Although bacteriophages (or simply phages) are the most abundant biological entities and have the potential to transfer genetic material between bacterial hosts, their contribution to the acquisition and spread of antibiotic resistance genes in the environment has not been extensively studied. The environment is continually exposed to a wide variety of pollutants from anthropogenic sources, which may promote horizontal gene transfer events, including those mediated by phages. Considering the significant and growing concern of antibiotic resistance, phages should be taken into consideration during the implementation of mitigation measures. This review is focused on the emergence and spread of antibiotic resistance in the environment, with a special emphasis on the role of phages.

The spinal cord-gut-immune axis as a master regulator of health and neurological function after spinal cord injury

Most spinal cord injury (SCI) research programs focus only on the injured spinal cord with the goal of restoring locomotor function by overcoming mechanisms of cell death or axon regeneration failure. Given the importance of the spinal cord as a locomotor control center and the public perception that paralysis is the defining feature of SCI, this "spinal-centric" focus is logical. Unfortunately, such a focus likely will not yield new discoveries that reverse other devastating consequences of SCI including cardiovascular and metabolic disease, bladder/bowel dysfunction and infection. The current review considers how SCI changes the physiological interplay between the spinal cord, the gut and the immune system. A suspected culprit in causing many of the pathological manifestations of impaired spinal cord-gut-immune axis homeostasis is the gut microbiota. After SCI, the composition of the gut microbiota changes, creating a chronic state of gut "dysbiosis". To date, much of what we know about gut dysbiosis was learned from 16S-based taxonomic profiling studies that reveal changes in the composition and abundance of various bacteria. However, this approach has limitations and creates taxonomic "blindspots". Notably, only bacteria can be analyzed. Thus, in this review we also discuss how the application of emerging sequencing technologies can improve our understanding of how the broader ecosystem in the gut is affected by SCI. Specifically, metagenomics will provide researchers with a more comprehensive look at post-injury changes in the gut virome (and mycome). Metagenomics also allows changes in microbe population dynamics to be linked to specific microbial functions that can affect the development and progression of metabolic disease, immune dysfunction and affective disorders after SCI. As these new tools become more readily available and used across the research community, the development of an "ecogenomic" toolbox will facilitate an Eco-Systems Biology approach to study the complex interplay along the spinal cord-gut-immune axis after SCI.

Considerations and Caveats in Combating ESKAPE Pathogens against Nosocomial Infections

ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are among the most common opportunistic pathogens in nosocomial infections. ESKAPE pathogens distinguish themselves from normal ones by developing a high level of antibiotic resistance that involves multiple mechanisms. Contemporary therapeutic strategies which are potential options in combating ESKAPE bacteria need further investigation. Herein, a broad overview of the antimicrobial research on ESKAPE pathogens over the past five years is provided with prospective clinical applications.

Antibacterial potential of Ni-doped zinc oxide nanostructure: comparatively more effective against Gram-negative bacteria including multi-drug resistant strains

Infections by multidrug-resistant (MDR) bacteria are one of the most threatening concerns for public health. For this purpose, nanomaterials have emerged with great potential for antibacterial activity. In this paper, we report the synthesis of new Ni²⁺-doped zinc oxide (Ni-ZnO or NZO) nanostructures as targeted antibacterial agents for Gram-negative bacteria. A one-pot low-temperature solution process was used with varying compositions containing 2 or 5% Ni²⁺ relative to Zn²⁺, resulting in 2NZO or 5NZO, respectively. X-ray diffractometry, transmission electron microscopy, and X-ray photoelectron spectroscopy were used for material characterization. Further, the antibacterial activity against both Gram-negative [Escherichia coli (E. coli) and Acinetobacter baumannii (A. baumannii) strains including standard, MDR, and clinical isolates associated with mcr-1 gene] and Gram-positive (Staphylococcus aureus and Staphylococcus epidermidis) bacteria were evaluated through analysis of zone of inhibition, minimum inhibitory concentration (MIC), and scanning electron microscopy images. Among the prepared nanostructures, the 5NZO sample showed excellent antibacterial activity against MDR strains of A. baumannii and E. coli. In addition, samples of NZO generated approximately 7 to 16 times more reactive oxygen species (ROS) in E. coli compared to ZnO. Our synthesized nanomaterials have the potential to fight MDR and colistin-resistant Gram-negative bacteria.

Synthesis of Ni²⁺-doped ZnO nanoparticles and their antibacterial activity.

Evolutionary Diversity of Prophage DNA in Klebsiella pneumoniae Chromosomes

Mobile gene elements play an important role in the continuous evolution of the prophage DNA of bacteria, promoting the emergence of new gene structures. This study explored the evolution of four strains of Klebsiella pneumoniae harboring prophages, 19051, 721005, 911021, and 675920, and 16 genomes of K. pneumoniae from GenBank. The results revealed a wide range of genetic variation in the prophage DNA inserted into the sap sites of K. pneumoniae chromosomes. From analysis and comparison of the sequences of the 20 prophage DNAs determined from the four strains and the 16 GenBank genomes of K. pneumoniae using high-throughput sequencing and antimicrobial susceptibility tests, we identified a novel transposon, Tn6556. We also identified at least nine large genetic structures with massive genetic acquisitions or losses and five hotspot sites showing a tendency to undergo insertion of gene elements such as IS1T, IS1R, IS26, ISKpn26, ISKpn28, Tn6556, MDR, and In27-related regions as variable regions; however, the only highly conserved core genes were int and umuCD among the 20 prophage DNAs. These findings provide important insights into the evolutionary diversity of bacteriophage DNA contained in K. pneumoniae.