Bacteriophage-mediated spread of bacterial virulence genes

Interaction between gut virome and microbiota on inflammatory bowel disease

Inflammatory bowel disease (IBD), encompassing Crohn's disease and ulcerative colitis, is a chronic condition marked by recurring gastrointestinal inflammation. While immune, genetic, and environmental factors are well-studied, the gut virome has received less attention. This editorial highlights the work which investigates the gut virome’s role in IBD and its interactions with the bacterial microbiome and host immune system. The gut virome consists of bacteriophages, eukaryotic viruses, and endogenous retroviruses. Among these, Caudovirales bacteriophages are predominant and influence bacterial communities via lysogenic and lytic cycles. Eukaryotic viruses infect host cells directly, while endogenous retroviruses impact gene regulation and immune responses. In IBD, the virome shows distinct alterations, including an increased abundance of Caudovirales phages and reduced Microviridae diversity, suggesting a pro-inflammatory viral environment. Dysbiosis, chronic inflammation, and aberrant immune responses contribute to these changes by disrupting microbial communities and modifying virome composition. Phages affect bacterial dynamics through lysis, lysogeny, and horizontal gene transfer, shaping microbial adaptability and resilience. Understanding these interactions is crucial for identifying novel therapeutic targets and restoring microbial balance in IBD.

Genomic analysis of prophages in 44 clinical strains of Pseudomonas aeruginosa isolated in Saudi Arabia

Prophages are bacteriophages that integrate their genomes into the bacterial chromosome. This research aimed to analyze and characterize prophages integrated into 44 Pseudomonas aeruginosa strains isolated from tertiary hospitals in Saudi Arabia. A total of 97 intact prophages were identified among clinical strains, with 16 prophages found present in more than one strain simultaneously. All prophages were found to have lengths ranging from 7.7 kb to 74.1 kb, and their GC content was found to be between 49.91% and 64.9%. Our findings show that prophages are present in the majority of the isolated P. aeruginosa strains (41 out of 44). Additionally, several proteins related to viral defense (toxin/antitoxin modules and proteins against restriction-modification enzymes) were identified, supporting the idea that prophages influence bacterial pathogenesis and anti-phage defenses.

House dust microbiome differentiation and phage-mediated antibiotic resistance and virulence dissemination in the presence of endocrine-disrupting chemicals and pharmaceuticals

BACKGROUND

House dust serves as a reservoir of a diverse array of microbial life and anthropogenic chemicals, both of which can potentially influence the health of occupants, particularly those who spend significant amounts of time at home. However, the effects of anthropogenic chemicals on dust microbiomes remain poorly understood. This study investigated the presence of anthropogenic chemicals in the dust of homes occupied by elderly occupants and explored those chemicals' relationships with dust microbiomes.

RESULTS

We detected 69 out of 76 analyzed anthropogenic chemicals, including endocrine-disrupting chemicals, non-antibiotic pharmaceuticals, and antibiotics, in at least one house dust sample from 32 residential homes, with concentrations ranging from 2720 to 89,300 ng/g. Some of these detected compounds were pharmaceuticals regularly consumed by the occupants. The dust microbiomes were associated with varying levels of anthropogenic chemicals, forming two distinct clusters, each with unique diversity, taxonomy, metabolic functions, and resistome profiles. Higher concentrations and a greater variety of these chemicals were associated with an increased co-occurrence of antibiotic resistance and virulence genes, as well as an enhanced potential for their transfer through mobile genetic elements. Under these conditions, phages, especially phage-plasmids, facilitated the dissemination of antibiotic resistance and virulence among bacterial populations.

CONCLUSIONS

The findings indicate that everyday anthropogenic chemicals are important factors associated with the microbes in indoor environments. This underscores the importance of improving household chemical stewardship to reduce the health risks associated with exposure to these chemicals and their effects on indoor microbiomes. Video Abstract.

Monitoring phage infection and lysis of surface-immobilized bacteria by QCM-D

While being a promising approach for the treatment of infections caused by drug-resistant, pathogenic bacteria, the clinical implementation of phage therapy still faces several challenges. One of these challenges lies in the high strain-specificity of most bacteriophages, which makes it necessary to screen large phage collections against the target pathogens in order to identify suitable candidates for the formulations of personalized therapeutic phage cocktails. In this work, we evaluate the potential of quartz crystal microbalance with dissipation monitoring (QCM-D) to identify and detect phage infection and subsequent lysis of bacteria immobilized on the surfaces of the QCM-D sensors. Using lytic Escherichia coli phage T7 as a model, we show that phage infection of E. coli cells results in various unique alterations in the behaviors of the frequency (Δf) and dissipation (ΔD) signals, which are not observed during exposure of the E. coli strain to non-infectious Bacillus subtilis phage phi29 at similar concentration. To aid future phage screening campaigns, we furthermore identify a single measurement parameter, i.e., the spread between the different overtones of ΔD, that can be used to detect phage-induced lysis. For T7 infection of E. coli, this is achieved within 4 h after inoculation, including immobilization and growth of the bacteria on the sensor surface, as well as the completed phage propagation cycle. Given the commercial availability of highly automated multichannel systems and the fact that this approach does not require any sensor modifications, QCM-D has the potential to become a valuable tool for screening medium-sized phage collections against target pathogens.

Carbapenem-Resistant Pseudomonas aeruginosa's Resistome: Pan-Genomic Plasticity, the Impact of Transposable Elements and Jumping Genes

Pseudomonas aeruginosa, a Gram-negative, motile bacterium, may cause significant infections in both community and hospital settings, leading to substantial morbidity and mortality. This opportunistic pathogen can thrive in various environments, making it a public health concern worldwide. P. aeruginosa's genomic pool is highly dynamic and diverse, with a pan-genome size ranging from 5.5 to 7.76 Mbp. This versatility arises from its ability to acquire genes through horizontal gene transfer (HGT) via different genetic elements (GEs), such as mobile genetic elements (MGEs). These MGEs, collectively known as the mobilome, facilitate the spread of genes encoding resistance to antimicrobials (ARGs), resistance to heavy metals (HMRGs), virulence (VGs), and metabolic functions (MGs). Of particular concern are the acquired carbapenemase genes (ACGs) and other β-lactamase genes, such as classes A, B [metallo-β-lactamases (MBLs)], and D carbapenemases, which can lead to increased antimicrobial resistance. This review emphasizes the importance of the mobilome in understanding antimicrobial resistance in P. aeruginosa.

Role of Lysogenic Phages in the Dissemination of Antibiotic Resistance Genes Applied in the Food Chain

Bacteriophages, first discovered in 1915, have re-emerged as critical players in microbial ecosystems, particularly in food production. Their ability to lysogenize bacterial hosts raises concerns about their role in the horizontal transfer of antibiotic resistance genes (ARGs) and virulence factors, contributing to the global challenge of antimicrobial resistance. Key studies reveal that ARG-carrying phages are prevalent across various stages of the food chain, including soil, vegetables, meat, dairy, and wastewater associated with food production. These findings demonstrate the potential for lysogenic phages to act as vectors for resistance gene dissemination, posing risks to public health. The review also explores emerging genetic elements, such as phage-inducible chromosomal islands and gene transfer agents, that further enhance the mobility of resistance and virulence genes. Advancements in metagenomic tools have improved our understanding of phage-mediated gene transfer, but significant knowledge gaps remain. Future research should aim to quantify these processes in real-world settings and develop strategies to mitigate the risks associated with lysogenic phages in food systems.

Environmental hygiene strategies to combat antimicrobial resistance in healthcare settings

In this manuscript, we highlight current literature on environmental hygiene techniques to combat reservoirs of antibiotic resistant organisms in the healthcare environment. We discuss several topics for each strategy, including mechanism of action, assessment of effectiveness based on studies, cost, and real-world translatability. The techniques and topics summarized here are not inclusive of all available environmental hygiene techniques but highlight some of the more popular and investigated strategies. We focus on the following: Ultraviolet radiation, hydrogen peroxide vapor, copper-coated surfaces, phages, interventions involving sinks, and educational initiatives.

Comparative Genomic Analysis of 66 Bacteriophages Infecting Morganella morganii Strains

Bacteriophages are viruses that specifically target bacteria and play a crucial role in influencing bacterial evolution and the transmission of antibiotic resistance. In this study, we explored the genomic profiles of 66 bacteriophages that infect Morganella morganii, an opportunistic pathogen associated with difficult-to-treat nosocomial and urinary tract infections. Our findings highlight the extraordinary diversity within this phage population, reflected in their genomic features, evolutionary relationships, and potential contributions to bacterial pathogenicity. The 66 phage genomes exhibited diversity in size, spanning from 6 to 115 kilobase pairs, reflecting a heterogeneous genetic material and coding potential. Their guanine-cytosine (G+C) content varied widely, from 43.3% to 64.6%, suggesting diverse evolutionary origins and adaptive strategies. Phylogenetic analysis identified ten distinct evolutionary clusters, some classified as singletons, highlighting unique evolutionary pathways. Several clusters included phages capable of infecting multiple M. morganii strains, indicating a broader host range and the potential for horizontal gene transfer. Genomic analysis also determined a substantial number of hypothetical proteins, underscoring the need for further investigation to clarify their functions. Importantly, we identified a wide array of antibiotic resistance and virulence-associated genes within these phage genomes, illuminating their potential to impact the treatment of M. morganii infections and develop new, more virulent strains. These findings highlight the critical role of phage-mediated gene transfer in shaping bacterial evolution and facilitating the transmission of antibiotic resistance.

A novel roseosiphovirus infecting dinoroseobacter shibae DFL12T represents a new genus

Bacteria belonging to the Roseobacter clade are key players in marine ecosystems, contributing significantly to carbon and sulfur cycles. Marine viruses, particularly those targeting Roseobacter, play crucial roles in regulating microbial communities and biogeochemical processes. Despite their importance, phages infecting organisms of the Roseobacter clade remain poorly understood. In this study, a novel roseophage, vB_DshS-R26L (R26L), infecting Dinoroseobacter shibae DFL12T, was isolated and characterized in terms of physiological and genomic properties. R26L has siphovirus morphology with an elongated head and a long, non-flexible tail. The phage has a narrow host range and demonstrates a long infection cycle with a latent period of 3.5 h and a burst size of 22 plaque-forming units (PFU cell- 1). R26L possesses a circular, double-stranded DNA genome of 79,534 bp with a G + C content of 62.6%, encoding a total of 116 open reading frames. Notably, seven auxiliary metabolic genes (AMGs), including those related to phosphate metabolism and queuosine biosynthesis, were identified. Phylogenetic and taxonomic analyses revealed that R26L represents a new genus, with its highest intergenomic similarities being 54.7% to another roseophage (R5C). By elucidating the unique characteristics of R26L, this study highlights the complexity of phage infections and the genomic diversity of roseophages, offering valuable insights into the ecological significance of Roseobacter-phage interactions in marine environments.

Identification of Diverse Bacteriophages Associated with Bees and Hoverflies

Bacteriophages are the most numerous, ubiquitous, and diverse biological entities on the planet. Prior studies have identified bacteriophages associated with pathogenic and commensal microbiota of honeybees. In this study we expand on what is known about bacteriophages from the lineages Caudoviricetes, Inoviridae, and Microviridae, which are associated with honeybees (Apidae, Apis mellifera), solitary bees of the genus Nomia (Halictidae, Nomia), and hoverflies (Syrphidae). The complete genomes of seven caudoviruses, seven inoviruses, and 288 microviruses were assembled from honeybees (n = 286) and hoverflies in Arizona (n = 2). We used bacterial host predictive software and sequence read mapping programs to infer the commensal and transient bacterial hosts of pollinating insects. Lastly, this study explores the phylogenetic relationships of microviruses sampled from bees, opportunistically sampled pollinating insects such as hoverflies, and blackflies.

A sequencing-based method for quantifying gene-deletion mutants of bacteria in the intracellular environment

Advancements in next-generation sequencing (NGS) have significantly accelerated the development of innovative methodologies in microbiological research. In this study, we present a novel method to quantify the net survival of gene-deletion mutants within the intracellular environment. Based on standardized Illumina short-read sequencing of genomic DNA, the method eliminates the need for specific selective markers on each deletion mutant. For validation, the method was shown to accurately quantify mutants in spiked pools of mixed mutants, showing no statistically significant differences compared to the expected values based on CFU determination (p > 0.05). Further, the method was used to quantify mutants of S. Gallinarum in macrophages. Six mutants and one control strain were mixed in a pool and allowed to infect HD11 cells for 2 h. The results align with prior research results, providing evidence of the feasibility of mixed mutant infections in functional gene identification. Notably, the simplicity and standardization of the method, rooted in standard whole-genome sequencing protocols, make it easily implementable across various laboratories.

Methicillin-resistant Staphylococcus pseudintermedius: epidemiological changes, antibiotic resistance, and alternative therapeutic strategies

Staphylococcus pseudintermedius is a major opportunistic bacterial pathogen that belongs to the skin and mucosal microbiota of the dog. Since its global emergence around 2006, multidrug - methicillin-resistant S. pseudintermedius (MRSP) clones have become endemic worldwide. MRSP strains pose a significant threat to animal health and make antimicrobial therapy difficult due to their typical multidrug resistance phenotypes. The difficulty to treat MRSP infections using the current antimicrobials licensed for veterinary use has intensified research efforts to develop new treatment strategies and alternative anti-infective approaches to conventional antimicrobial therapy. The present narrative review outlines the latest changes in the epidemiology of MRSP with focus on the geographical distribution variability and antimicrobial resistance profiles in the main MRSP lineages. It also provides an overview of the effectiveness of currently available antimicrobials and the status of anti-infective alternatives to conventional antimicrobials.Recent studies have reported notable changes in the population structure of MRSP, with the emergence of new epidemic lineages, such as ST258, ST123, ST496, and ST551 in European countries and ST45, ST181, ST258, ST496 in non-European countries, which partly or totally replaced those that were initially prevalent, such as ST71 in Europe and ST68 in the US. Due to methicillin resistance often associated with the resistance to a broader number of antimicrobials, treating canine MRSP skin infection is challenging. Several alternative or supplementary treatment options to conventional antibiotics, especially for topical treatment, such as a novel water-soluble hydroxypyridinone-containing iron-chelating 9 kDa polymer (DIBI), antimicrobial peptides (AMPs), nanoparticles, and bacteriophages seem to be particularly interesting from a clinical perspective.

Another piece of puzzle for the human microbiome: the gut virome under dietary modulation

The virome is the most abundant and highly variable microbial consortium in the gut. Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes, the virome has remained a relatively elusive aspect of the human microbiome. In recent years, studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health. Here, we review the responses of the gut virome to dietary intake and the potential health implications, presenting changes in the gut viral community and preferences of viral members to particular diets. We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota. We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer, as well as the import of new viral members along with the diet. Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary interventions and health maintenance strategies targeting the gut microbiota.

Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments

The spread of antibiotic resistance genes (ARGs) poses a substantial threat to human health. Phage-mediated transduction could exacerbate ARG transmission. While several case studies exist, it is yet unclear to what extent phages encode and mobilize ARGs at the global scale and whether human impacts play a role in this across different habitats. Here, we combine 38,605 bacterial genomes, 1432 metagenomes, and 1186 metatranscriptomes across 12 contrasting habitats to explore the distribution of prophages and their cargo ARGs in natural and human-impacted environments. Worldwide, we observe a significant increase in the abundance, diversity, and activity of prophage-encoded ARGs in human-impacted habitats linked with relatively higher risk of past antibiotic exposure. This effect was driven by phage-encoded cargo ARGs that could be mobilized to provide increased resistance in heterologous E. coli host for a subset of analyzed strains. Our findings suggest that human activities have altered bacteria-phage interactions, enriching ARGs in prophages and making ARGs more mobile across habitats globally.

Virome and metagenomic sequencing reveal the impact of microbial inoculants on suppressions of antibiotic resistome and viruses during co-composting

Co-composting with exogenous microbial inoculant, presents an effective approach for the harmless utilization of livestock manure and agroforestry wastes. However, the impact of inoculant application on the variations of viral and antibiotic resistance genes (ARGs) remains poorly understood, particularly under varying manure quantity (low 10 % vs. high 20 % w/w). Thus, employing virome and metagenomic sequencing, we examined the influence of Streptomyces-Bacillus Inoculants (SBI) on viral communities, phytopathogen, ARGs, mobile genetic elements, and their interrelations. Our results indicate that SBI shifted dominant bacterial species from Phenylobacterium to thermotropic Bordetella, and the quantity of manure mediates the effect of SBI on whole bacterial community. Major ARGs and genetic elements experienced substantial changes with SBI addition. There was a higher ARGs elimination rate in the composts with low (∼76 %) than those with high manure (∼70 %) application. Virus emerged as a critical factor influencing ARG dynamics. We observed a significant variation in virus community, transitioning from Gemycircularvirus- (∼95 %) to Chlamydiamicrovirus-dominance. RDA analysis revealed that Gemycircularvirus was the most influential taxon in shaping ARGs, with its abundance decreased approximately 80 % after composting. Collectively, these findings underscore the role of microbial inoculants in modulating virus communities and ARGs during biowaste co-composting.

Phagemid-based capsid system for CRISPR-Cas13a antimicrobials targeting methicillin-resistant Staphylococcus aureus

In response to the escalating antibiotic resistance in multidrug-resistant pathogens, we propose an innovative phagemid-based capsid system to generate CRISPR-Cas13a-loaded antibacterial capsids (AB-capsids) for targeted therapy against multidrug-resistant Staphylococcus aureus. Our optimized phagemid system maximizes AB-capsid yield and purity, showing a positive correlation with phagemid copy number. Notably, an 8.65-fold increase in copy number results in a 2.54-fold rise in AB-capsid generation. Phagemids carrying terL-terS-rinA-rinB (prophage-encoded packaging site genes) consistently exhibit high packaging efficiency, and the generation of AB-capsids using lysogenized hosts with terL-terS deletion resulted in comparatively lower level of wild-type phage contamination, with minimal compromise on AB-capsid yield. These generated AB-capsids selectively eliminate S. aureus strains carrying the target gene while sparing non-target strains. In conclusion, our phagemid-based capsid system stands as a promising avenue for developing sequence-specific bactericidal agents, offering a streamlined approach to combat antibiotic-resistant pathogens within the constraints of efficient production and targeted efficacy.

Antimicrobial resistance: use of phage therapy in the management of resistant infections

The emergence and increase in antimicrobial resistance (AMR) is now widely recognized as a major public health challenge. Traditional antimicrobial drugs are becoming increasingly ineffective, while the development of new antibiotics is waning. As a result, alternative treatments for infections are garnering increased interest. Among these alternatives, bacteriophages, also known as phages, are gaining renewed attention and are reported to offer a promising solution to alleviate the burden of bacterial infections. This review discusses the current successes of phage therapy (PT) against multidrug-resistant organisms (MDROs), such as Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter spp. The review also compares the efficacy of PT with that of chemical antibiotics, reporting on its benefits and limitations, while highlighting its impact on the human gut microbiome and immune system. Despite its potential, phage therapy is reported to face challenges such as the narrow antibacterial range, the complexity of developing phage cocktails, and the need for precise dosing and duration protocols. Nevertheless, continued research, improved regulatory frameworks, and increased public awareness are essential to realize its full potential and integration into standard medical practice, paving the way for innovative treatments that can effectively manage infections in an era of rising antimicrobial resistance.

Comparative Genomic Analysis of Prophages in Human Vaginal Isolates of Streptococcus agalactiae

Prophages, viral genomes integrated into bacterial genomes, are known to enhance bacterial colonization, adaptation, and ecological fitness, providing a better chance for pathogenic bacteria to disseminate and cause infection. Streptococcus agalactiae (Group B Streptococcus or GBS) is a common bacterium found colonizing the genitourinary tract of humans. However, GBS-colonized pregnant women are at risk of passing the organism to the neonate, where it can cause severe infections. GBS typically encode one or more prophages in their genomes, yet their role in pathogen fitness and virulence has not yet been described. Sequencing and bioinformatic analysis of the genomic content of GBS human isolates identified 42 complete prophages present in their genomes. Comparative genomic analyses of the prophage sequences revealed that the prophages could be classified into five distinct clusters based on their genomic content, indicating significant diversity in their genetic makeup. Prophage diversity was also identified across GBS capsule serotypes, sequence types (STs), and clonal clusters (CCs). Comprehensive genomic annotation revealed that all GBS strains encode paratox, a protein that prevents the uptake of DNA in Streptococcus, either on the chromosome, on the prophage, or both, and each prophage genome has at least one toxin-antitoxin system.

Phage-host co-evolution has led to distinct generalized transduction strategies

Generalized transduction is pivotal in bacterial evolution but lacks comprehensive understanding regarding the facilitating features and variations among phages. We addressed this gap by sequencing and comparing the transducing particle content of three different Salmonella Typhimurium phages (i.e. Det7, ES18 and P22) that share a headful packaging mechanism that is typically initiated from a cognate pac site within the phage chromosome. This revealed substantial disparities in both the extent and content of transducing particles among these phages. While Det7 outperformed ES18 in terms of relative number of transducing particles, both phages contrasted with P22 in terms of content. In fact, we found evidence for the presence of conserved P22 pac-like sequences in the host chromosome that direct tremendously increased packaging and transduction frequencies of downstream regions by P22. More specifically, a ca. 561 kb host region between oppositely oriented pac-like sequences in the purF and minE loci was identified as highly packaged and transduced during both P22 prophage induction and lytic infection. Our findings underscore the evolution of phage transducing capacity towards attenuation, promiscuity or directionality, and suggest that pac-like sequences in the host chromosome could become selected as sites directing high frequency of transduction.

The Streptococcus phage protein paratox is an intrinsically disordered protein

The bacteriophage protein paratox (Prx) blocks quorum sensing in its streptococcal host by directly binding the signal receptor and transcription factor ComR. This reduces the ability of Streptococcus to uptake environmental DNA and protects phage DNA from damage by recombination. Past work characterizing the Prx:ComR molecular interaction revealed that paratox adopts a well-ordered globular fold when bound to ComR. However, solution-state biophysical measurements suggested that Prx may be conformationally dynamic. To address this discrepancy, we investigated the stability and dynamic properties of Prx in solution using circular dichroism, nuclear magnetic resonance, and several fluorescence-based protein folding assays. Our work shows that under dilute buffer conditions Prx is intrinsically disordered. We also show that the addition of kosmotropic salts or protein stabilizing osmolytes induces Prx folding. However, the solute stabilized fold is different from the conformation Prx adopts when it is bound to ComR. Furthermore, we have characterized Prx folding thermodynamics and folding kinetics through steady-state fluorescence and stopped flow kinetic measurements. Our results show that Prx is a highly dynamic protein in dilute solution, folding and refolding within the 10 ms timescale. Overall, our results demonstrate that the streptococcal phage protein Prx is an intrinsically disordered protein in a two-state equilibrium with a solute-stabilized folded form. Furthermore, the solute-stabilized fold is likely the predominant form of Prx in a solute-crowded bacterial cell. Finally, our work suggests that Prx binds and inhibits ComR, and thus quorum sensing in Streptococcus, by a combination of conformational selection and induced-fit binding mechanisms.

Physicochemical Characterization of Novel Bacteriophages of Pseudomonas syringe from Northwest Iran

Bacterial canker, caused by Pseudomonas syringae, is a devastating disease of stone fruit trees worldwide. The bacterium has a broad host range and a high capacity for adaptation and dissemination, owing to its high mutation rate and horizontal gene transfer. Traditional control methods based on copper compounds and antibiotics have resulted in the development of resistance in the bacterial population. Thus, alternative approaches are needed, such as phage therapy. This study aimed to characterize the physicochemical and biological properties of novel Pseudomonas syringae pv. syringae (Pss)-specific phages isolated from the soils of northwestern Iran. Seventy-five phage isolates were obtained, and their host range was determined against various bacterial pathogens. Five phages exhibiting the highest lytic activity against Pss and a narrow host range were selected for subsequent analysis. The stability of the selected phages was assessed under different conditions such as ultraviolet irradiation, temperature, pH, NaCl concentration, and chloroform exposure. The selected phages demonstrated significant effectiveness in vivo, exerting substantial suppression on the population of Pss. This reduction was observed for both individual phages and when the phages were utilized as a mixture. The findings indicate that phages have the potential to be used as biocontrol agents in agriculture.

Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella

Salmonella enterica Serovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the Salmonella pseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains-LT2 and 14028S-for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the Salmonella pseudo-pac sites in this study could be applied to other phage-host systems.

An autonomous plasmid as an inovirus phage satellite

Bacterial viruses (phages) are potent agents of lateral gene transfer and thus are important drivers of evolution. A group of mobile genetic elements, referred to as phage satellites, exploits phages to disseminate their own genetic material. Here, we isolated a novel member of the family Inoviridae, Shewanella phage Dolos, along with an autonomously replicating plasmid, pDolos. Dolos causes a chronic infection in its host Shewanella oneidensis by phage production with only minor effects on the host cell proliferation. When present, plasmid pDolos hijacks Dolos functions to be predominantly packaged into phage virions and released into the environment and, thus, acts as a phage satellite. pDolos can disseminate further genetic material encoding, e.g., resistances or fluorophores to host cells sensitive to Dolos infection. Given the rather simple requirements of a plasmid for takeover of an inovirus and the wide distribution of phages of this group, we speculate that similar phage-satellite systems are common among bacteria.IMPORTANCEPhage satellites are mobile genetic elements, which hijack phages to be transferred to other host cells. The vast majority of these phage satellites integrate within the host's chromosome, and they all carry remaining phage genes. Here, we identified a novel phage satellite, pDolos, which uses an inovirus for dissemination. pDolos (i) remains as an autonomously replicating plasmid within its host, (ii) does not carry recognizable phage genes, and (iii) is smaller than any other phage satellites identified so far. Thus, pDolos is the first member of a new class of phage satellites, which resemble natural versions of phagemids.

Phages in sludge from the A/O wastewater treatment process play an important role in the transmission of ARGs

Phages can influence the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through transduction, but their profiles and effects on the transmission of ARGs are unclear, especially in complex swine sludge. In this study, we investigated the characterization of phage and ARG profiles in sludge generated from anoxic/oxic (A/O) wastewater treatment processes on swine farms using metagenomes and viromes. The results demonstrated that 205-221 subtypes of ARGs could be identified in swine sludge, among which sul1, tet(M), and floR were the dominant ARGs, indicating that sludge is an important reservoir of ARGs, especially in sludge (S) tanks. The greater abundance of mobile genetic elements (MGEs) in the S tank could significantly contribute to the greater abundance of ARGs there compared to the anoxic (A) and oxic (O) tanks (P < 0.05). However, when we compared the abundances of ARGs and MGEs in the A and O tanks, we observed opposite significant differences (P < 0.05), suggesting that MGEs are not the only factor influencing the abundance of ARGs. The high proportion of lysogenic phages in sludge from the S tank can also have a major impact on the ARG profile. Siphoviridae, Myoviridae, and Podoviridae were the dominant phage families in sludge, and a network diagram of bacteria-ARG-phages revealed that dominant phages and bacteria acted simultaneously as potential hosts for ARGs, which may have led to phage-mediated HGT of ARGs. Therefore, the risk of phage-mediated HGT of ARGs cannot be overlooked.

Short-, long-read metagenome and virome reveal the profile of phage-mediated ARGs in anoxic-oxic processes for swine wastewater treatment

Phages are among the most widely spread viruses, but their profiles and the antibiotic resistance genes (ARGs) they carry in swine wastewater remain underexplored. The present study investigated the distribution characteristics of phages and their ARG risk in anoxic/oxic (A/O) wastewater treatment processes of swine farms using short- and long-read metagenome and virome. The results demonstrated that the virome could extract more phage sequences than the total metagenome; thus, it was more suited for studying phages in wastewater settings. Intriguingly, phages had significantly lower abundance of ARG than ARGs harbored by total microorganisms (P < 0.01). Eleven ARGs co-occurred with phages and bacteria (R > 0.6 and P < 0.05), with Siphoviridae being the phage co-occurring with the most ARGs (5). Horizontal gene transfer (HGT) events were observed between Proteobacteria and the major phyla except for Bacteroidota. Furthermore, there were prophage sequences and ARGs on the same contig in bacterial MAGs. These data strongly demonstrate that phages promote horizontal transfer of ARG between bacterial hosts in A/O processes for swine wastewater treatment. Therefore, the risk of phage-mediated horizontal transfer of ARGs cannot be overlooked despite the low abundance of phage ARGs (pARG).

Current examining methods and mathematical models of horizontal transfer of antibiotic resistance genes in the environment

The increasing prevalence of antibiotic resistance genes (ARGs) in the environment has garnered significant attention due to their health risk to human beings. Horizontal gene transfer (HGT) is considered as an important way for ARG dissemination. There are four general routes of HGT, including conjugation, transformation, transduction and vesiduction. Selection of appropriate examining methods is crucial for comprehensively understanding characteristics and mechanisms of different HGT ways. Moreover, combined with the results obtained from different experimental methods, mathematical models could be established and serve as a powerful tool for predicting ARG transfer dynamics and frequencies. However, current reviews of HGT for ARG spread mainly focus on its influencing factors and mechanisms, overlooking the important roles of examining methods and models. This review, therefore, delineated four pathways of HGT, summarized the strengths and limitations of current examining methods, and provided a comprehensive summing-up of mathematical models pertaining to three main HGT ways of conjugation, transformation and transduction. Finally, deficiencies in current studies were discussed, and proposed the future perspectives to better understand and assess the risks of ARG dissemination through HGT.

Interdisciplinary-Inspired Smart Antibacterial Materials and Their Biomedical Applications

The discovery of antibiotics has saved millions of lives, but the emergence of antibiotic-resistant bacteria has become another problem in modern medicine. To avoid or reduce the overuse of antibiotics in antibacterial treatments, stimuli-responsive materials, pathogen-targeting nanoparticles, immunogenic nano-toxoids, and biomimetic materials are being developed to make sterilization better and smarter than conventional therapies. The common goal of smart antibacterial materials (SAMs) is to increase the antibiotic efficacy or function via an antibacterial mechanism different from that of antibiotics in order to increase the antibacterial and biological properties while reducing the risk of drug resistance. The research and development of SAMs are increasingly interdisciplinary because new designs require the knowledge of different fields and input/collaboration from scientists in different fields. A good understanding of energy conversion in materials, physiological characteristics in cells and bacteria, and bactericidal structures and components in nature are expected to promote the development of SAMs. In this review, the importance of multidisciplinary insights for SAMs is emphasized, and the latest advances in SAMs are categorized and discussed according to the pertinent disciplines including materials science, physiology, and biomimicry.

Phage susceptibility determinants of the opportunistic pathogen Staphylococcus epidermidis

Staphylococcus epidermidis is a common member of the human skin and nose microbiomes and a frequent cause of invasive infections. Transducing phages accomplish the horizontal transfer of resistance and virulence genes by mispackaging of mobile-genetic elements, contributing to severe, therapy-refractory S. epidermidis infections. Lytic phages on the other hand can be interesting candidates for new anti-S. epidermidis phage therapies. Despite the importance of phages, we are only beginning to unravel S. epidermidis phage interactions. Recent studies shed new light on S. epidermidis phage diversity, host range, and receptor specificities. Modulation of cell wall teichoic acids, the major phage receptor structures, along with other phage defense mechanisms, are crucial determinants for S. epidermidis susceptibility to different phage groups.

Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella

Salmonella enterica Serovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the Salmonella pseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains- LT2 and 14028S- for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the Salmonella pseudo-pac sites in this study could be applied to other phage-host systems.

Xanthomonas Phage PBR31: Classifying the Unclassifiable

The ability of bacteriophages to destroy bacteria has made them the subject of extensive research. Interest in bacteriophages has recently increased due to the spread of drug-resistant bacteria, although genomic research has not kept pace with the growth of genomic data. Genomic analysis and, especially, the taxonomic description of bacteriophages are often difficult due to the peculiarities of the evolution of bacteriophages, which often includes the horizontal transfer of genes and genomic modules. The latter is particularly pronounced for temperate bacteriophages, which are capable of integration into the bacterial chromosome. Xanthomonas phage PBR31 is a temperate bacteriophage, which has been neither described nor classified previously, that infects the plant pathogen Xanthomonas campestris pv. campestris. Genomic analysis, including phylogenetic studies, indicated the separation of phage PBR31 from known classified bacteriophages, as well as its distant relationship with other temperate bacteriophages, including the Lederbervirus group. Bioinformatic analysis of proteins revealed distinctive features of PBR31, including the presence of a protein similar to the small subunit of D-family DNA polymerase and advanced lysis machinery. Taxonomic analysis showed the possibility of assigning phage PBR31 to a new taxon, although the complete taxonomic description of Xanthomonas phage PBR31 and other related bacteriophages is complicated by the complex evolutionary history of the formation of its genome. The general biological features of the PBR31 phage were analysed for the first time. Due to its presumably temperate lifestyle, there is doubt as to whether the PBR31 phage is appropriate for phage control purposes. Bioinformatics analysis, however, revealed the presence of cell wall-degrading enzymes that can be utilised for the treatment of bacterial infections.

Horizontal gene transfer in activated sludge enhances microbial antimicrobial resistance and virulence

Activated sludge (AS) plays a vital role in removing organic pollutants and nutrients from wastewater. However, the risks posed by horizontal gene transfer (HGT) between bacteria in AS are still unclear. Here, a total of 478 high-quality non-redundant metagenome-assembled genomes (MAGs) were obtained. >50 % and 5 % of MAGs were involved in at least one HGT and recent HGT, respectively. Most of the transfers (82.4 %) of antimicrobial resistance genes (ARGs) occurred among the classes of Alphaproteobacteria and Gammaproteobacteria. The bacteria involved in the transfers of virulence factor genes (VFGs) mainly include Alphaproteobacteria (42.3 %), Bacteroidia (19.2 %), and Gammaproteobacteria (11.5 %). Moreover, the number of ARGs and VFGs in the classes of Alphaproteobacteria and Gammaproteobacteria was higher than that in other bacteria (P < 0.001). Mobile genetic elements were important contributors to ARGs and VFGs in AS bacteria. These results have implications for the management of antimicrobial resistance and virulence in activated sludge microorganisms.

Diversity and conservation of the genome architecture of phages infecting the Alphaproteobacteria

IMPORTANCE

This study reports the results of the largest analysis of genome sequences from phages that infect the Alphaproteobacteria class of bacterial hosts. We analyzed over 100 whole genome sequences of phages to construct dotplots, categorize them into genetically distinct clusters, generate a bootstrapped phylogenetic tree, compute protein orthologs, and predict packaging strategies. We determined that the phage sequences primarily cluster by the bacterial host family, phage morphotype, and genome size. We expect that the findings reported in this seminal study will facilitate future analyses that will improve our knowledge of the phages that infect these hosts.

Analysis of the life cycle of Helicobacter pylori bacteriophage KHP40 belonging to the genus Schmidvirus

Bacteriophage (phage) KHP40 was previously isolated from the supernatant of a culture of Helicobacter pylori KMT83 cells. In this study, we analysed the infection characteristics of KHP40, phage release pattern from KMT83 cells, and state of KHP40 DNA in KMT83 cells. The findings revealed that KHP40 phage showed varied adsorption efficiencies for different strains, long latent periods, and small burst sizes. Additionally, KHP40 activity was maintained at pH 2.5-12. KHP40 phages were released during the vegetative growth phase of the KMT83 cells. PCR analysis demonstrated that KHP40 DNA was stably maintained in KMT83 clones. Next-generation sequencing analysis revealed the presence of two distinct types of circular double-stranded DNA in H. pylori KMT83 cells. One was an H. pylori-specific DNA consisting of 1 578 403 bp, and the other was a 26 412-bp sequence that represented the episomal form of phage KHP40 DNA. Furthermore, defective KHP40-lysogenic DNA was detected in the H. pylori-specific DNA, the deleted portion of which appeared to have been transferred to another location in the bacterial genome. These findings indicate that KHP40 DNA exists in both episomal and defectively lysogenized states in KMT83 cells, and active phages are produced from KHP40-episomal DNA.

Genetic diversity of RNA viruses infecting invertebrate pests of rice

Invertebrate species are a natural reservoir of viral genetic diversity, and invertebrate pests are widely distributed in crop fields. However, information on viruses infecting invertebrate pests of crops is limited. In this report, we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields. We identified 296 new RNA viruses and 13 known RNA viruses. These viruses clustered within 31 families, with many highly divergent viruses constituting potentially new families and genera. Of the identified viruses, 13 RNA viruses clustered within the Fiersviridae family of bacteriophages, and 48 RNA viruses clustered within families and genera of mycoviruses. We detected known rice viruses in novel invertebrate hosts at high abundances. Furthermore, some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus species. Forty-five potential insect pathogenic RNA viruses were detected in invertebrate species. Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity. Cross-species transmission of RNA viruses was detected between invertebrate hosts. Newly identified viral genomes showed extensive variation for invertebrate viral families or genera. Together, the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species, the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.

Bacillus subtilis Phages Related to SIOphi from Desert Soils of the Southwest United States

Background

Phages impact Bacillus subtilis microbial dynamics, but our understanding of the diversity of phages that can lyse this model organism is limited.

Materials and Methods

Phages were isolated from soil collected from two Southwest United States desert sites on wild B. subtilis strains. Phage genomes were assembled and bioinformatically characterized, and phage host range was assessed.

Results

Four myoviruses with high nucleotide and amino acid similarity to each other (>97%) and to three phages in GenBank (>82%), including SIOphi, were isolated. These phages have double-stranded DNA genomes (153,882-156,577 bp), low GC content, and 256-270 putative protein coding genes (28-30% with predicted functions). Comparative genomics revealed differences in putative lysis and replication genes.

Conclusions

Comparative approaches provide insight into phage evolution, identifying unique genes shared within phage clusters. Better characterization of Bacillus phages will aid in linking genetic differences among phages (e.g., lysin genes) to phenotype (e.g., host range).

A modular phage vector platform for targeted photodynamic therapy of Gram-negative bacterial pathogens

Growing antibiotic resistance has encouraged the revival of phage-inspired antimicrobial approaches. On the other hand, photodynamic therapy (PDT) is considered a very promising research domain for the protection against infectious diseases. Yet, very few efforts have been made to combine the advantages of both approaches in a modular, retargetable platform. Here, we foster the M13 bacteriophage as a multifunctional scaffold, enabling the selective photodynamic killing of bacteria. We took advantage of the well-defined molecular biology of M13 to functionalize its capsid with hundreds of photo-activable Rose Bengal sensitizers and contemporarily target this light-triggerable nanobot to specific bacterial species by phage display of peptide targeting moieties fused to the minor coat protein pIII of the phage. Upon light irradiation of the specimen, the targeted killing of diverse Gram(-) pathogens occurred at subnanomolar concentrations of the phage vector. Our findings contribute to the development of antimicrobials based on targeted and triggerable phage-based nanobiotherapeutics.

Conjugative transfer of streptococcal prophages harboring antibiotic resistance and virulence genes

Prophages play important roles in the transduction of various functional traits, including virulence factors, but remain debatable in harboring and transmitting antimicrobial resistance genes (ARGs). Herein we characterize a prevalent family of prophages in Streptococcus, designated SMphages, which harbor twenty-five ARGs that collectively confer resistance to ten antimicrobial classes, including vanG-type vancomycin resistance locus and oxazolidinone resistance gene optrA. SMphages integrate into four chromosome attachment sites by utilizing three types of integration modules and undergo excision in response to phage induction. Moreover, we characterize four subtypes of Alp-related surface proteins within SMphages, the lethal effects of which are extensively validated in cell and animal models. SMphages transfer via high-frequency conjugation that is facilitated by integrative and conjugative elements from either donors or recipients. Our findings explain the widespread of SMphages and the rapid dissemination of ARGs observed in members of the Streptococcus genus.

Transmission of livestock-associated methicillin-resistant Staphylococcus aureus between animals, environment, and humans in the farm

Staphylococcus aureus (S. aureus) is a fearsome bacterial pathogen that can colonize and infect humans and animals. Depending on the different sources, MRSA is classified as hospital-associated methicillin-resistant S. aureus (HA-MRSA), community-associated MRSA (CA-MRSA), and livestock-associated MRSA (LA-MRSA). LA-MRSA is initially associated with livestock, and clonal complexes (CCs) were almost always 398. However, the continued development of animal husbandry, globalization, and the widespread use of antibiotics have increased the spread of LA-MRSA among humans, livestock, and the environment, and other clonal complexes such as CC9, CC5, and CC8 have gradually emerged in various countries. This may be due to frequent host switching between humans and animals, as well as between animals. Host-switching is typically followed by subsequent adaptation through acquisition and/or loss of mobile genetic elements (MGEs) such as phages, pathogenicity islands, and plasmids as well as further host-specific mutations allowing it to expand into new host populations. This review aimed to provide an overview of the transmission characteristics of S. aureus in humans, animals, and farm environments, and also to describe the main prevalent clones of LA-MRSA and the changes in MGEs during host switching.

Phage-Inducible Chromosomal Islands as a Diagnostic Platform to Capture and Detect Bacterial Pathogens

Phage-inducible chromosomal islands (PICIs) are a family of phage satellites that hijack phage components to facilitate their mobility and spread. Recently, these genetic constructs are repurposed as antibacterial drones, enabling a new toolbox for unorthodox applications in biotechnology. To illustrate a new suite of functions, the authors have developed a user-friendly diagnostic system, based upon PICI transduction to selectively enrich bacteria, allowing the detection and sequential recovery of Escherichia coli and Staphylococcus aureus. The system enables high transfer rates and sensitivities in comparison with phages, with detection down to ≈50 CFU mL-1 . In contrast to conventional detection strategies, which often rely on nucleic acid molecular assays, and cannot differentiate between dead and live organisms, this approach enables visual sensing of viable pathogens only, through the expression of a reporter gene encoded in the PICI. The approach extends diagnostic sensing mechanisms beyond cell-free synthetic biology strategies, enabling new synthetic biology/biosensing toolkits.

Compounding Achromobacter Phages for Therapeutic Applications

Achromobacter species colonization of Cystic Fibrosis respiratory airways is an increasing concern. Two adult patients with Cystic Fibrosis colonized by Achromobacter xylosoxidans CF418 or Achromobacter ruhlandii CF116 experienced fatal exacerbations. Achromobacter spp. are naturally resistant to several antibiotics. Therefore, phages could be valuable as therapeutics for the control of Achromobacter. In this study, thirteen lytic phages were isolated and characterized at the morphological and genomic levels for potential future use in phage therapy. They are presented here as the Achromobacter Kumeyaay phage collection. Six distinct Achromobacter phage genome clusters were identified based on a comprehensive phylogenetic analysis of the Kumeyaay collection as well as the publicly available Achromobacter phages. The infectivity of all phages in the Kumeyaay collection was tested in 23 Achromobacter clinical isolates; 78% of these isolates were lysed by at least one phage. A cryptic prophage was induced in Achromobacter xylosoxidans CF418 when infected with some of the lytic phages. This prophage genome was characterized and is presented as Achromobacter phage CF418-P1. Prophage induction during lytic phage preparation for therapy interventions require further exploration. Large-scale production of phages and removal of endotoxins using an octanol-based procedure resulted in a phage concentrate of 1 × 109 plaque-forming units per milliliter with an endotoxin concentration of 65 endotoxin units per milliliter, which is below the Food and Drugs Administration recommended maximum threshold for human administration. This study provides a comprehensive framework for the isolation, bioinformatic characterization, and safe production of phages to kill Achromobacter spp. in order to potentially manage Cystic Fibrosis (CF) pulmonary infections.

CRISPR-Cas-Based Antimicrobials: Design, Challenges, and Bacterial Mechanisms of Resistance

The emergence of antibiotic-resistant bacterial strains is a source of public health concern across the globe. As the discovery of new conventional antibiotics has stalled significantly over the past decade, there is an urgency to develop novel approaches to address drug resistance in infectious diseases. The use of a CRISPR-Cas-based system for the precise elimination of targeted bacterial populations holds promise as an innovative approach for new antimicrobial agent design. The CRISPR-Cas targeting system is celebrated for its high versatility and specificity, offering an excellent opportunity to fight antibiotic resistance in pathogens by selectively inactivating genes involved in antibiotic resistance, biofilm formation, pathogenicity, virulence, or bacterial viability. The CRISPR-Cas strategy can enact antimicrobial effects by two approaches: inactivation of chromosomal genes or curing of plasmids encoding antibiotic resistance. In this Review, we provide an overview of the main CRISPR-Cas systems utilized for the creation of these antimicrobials, as well as highlighting promising studies in the field. We also offer a detailed discussion about the most commonly used mechanisms for CRISPR-Cas delivery: bacteriophages, nanoparticles, and conjugative plasmids. Lastly, we address possible mechanisms of interference that should be considered during the intelligent design of these novel approaches.

Phage Interactions with the Nervous System in Health and Disease

The central nervous system manages all of our activities (e.g., direct thinking and decision-making processes). It receives information from the environment and responds to environmental stimuli. Bacterial viruses (bacteriophages, phages) are the most numerous structures occurring in the biosphere and are also found in the human organism. Therefore, understanding how phages may influence this system is of great importance and is the purpose of this review. We have focused on the effect of natural bacteriophages in the central nervous system, linking them to those present in the gut microbiota, creating the gut-brain axis network, as well as their interdependence. Importantly, based on the current knowledge in the field of phage application (e.g., intranasal) in the treatment of bacterial diseases associated with the brain and nervous system, bacteriophages may have significant therapeutic potential. Moreover, it was indicated that bacteriophages may influence cognitive processing. In addition, phages (via phage display technology) appear promising as a targeted therapeutic tool in the treatment of, among other things, brain cancers. The information collected and reviewed in this work indicates that phages and their impact on the nervous system is a fascinating and, so far, underexplored field. Therefore, the aim of this review is not only to summarize currently available information on the association of phages with the nervous system, but also to stimulate future studies that could pave the way for novel therapeutic approaches potentially useful in treating bacterial and non-bacterial neural diseases.

Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land

Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a municipal wastewater treatment plant along the west coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARG mechanisms were observed between swine manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40-55 %), tetracyclines (30-45 %), beta-lactam-resistance (20-35 %), macrolides (18-30 %), and >50 % of the VFGs that the 24 microbiomes harbored were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. Metabolic reconstruction of metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with carbapenem resistance, multidrug resistance (MDR), and efflux pump. Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that the dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands, negatively impacting both soil and human health.

CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts

Viruses are the most abundant microbial guild on the planet, impacting microbial community structure and ecosystem services. Viruses are specifically understudied in engineered environments, including examinations of their host interactions. We examined host-virus interactions via host CRISPR spacer to viral protospacer mapping in a municipal landfill across two years. Viruses comprised ~ 4% of both the unassembled reads and assembled basepairs. A total of 458 unique virus-host connections captured hyper-targeted viral populations and host CRISPR array adaptation over time. Four viruses were predicted to infect across multiple phyla, suggesting that some viruses are far less host-specific than is currently understood. We detected 161 viral elements that encode CRISPR arrays, including one with 187 spacers, the longest virally-encoded CRISPR array described to date. Virally-encoded CRISPR arrays targeted other viral elements in interviral conflicts. CRISPR-encoding proviruses integrated into host chromosomes were latent examples of CRISPR-immunity-based superinfection exclusion. The bulk of the observed virus-host interactions fit the one-virus-one-host paradigm, but with limited geographic specificity. Our networks highlight rare and previously undescribed complex interactions influencing the ecology of this dynamic engineered system. Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for atypical virus-host dynamics.

Bacteriophages of the Order Crassvirales: What Do We Currently Know about This Keystone Component of the Human Gut Virome?

The order Crassvirales comprises dsDNA bacteriophages infecting bacteria in the phylum Bacteroidetes that are found in a variety of environments but are especially prevalent in the mammalian gut. This review summarises available information on the genomics, diversity, taxonomy, and ecology of this largely uncultured viral taxon. With experimental data available from a handful of cultured representatives, the review highlights key properties of virion morphology, infection, gene expression and replication processes, and phage-host dynamics.

How to Tackle Bacteriophages: The Review of Approaches with Mechanistic Insight

Bacteriophage-based applications have a renaissance today, increasingly marking their use in industry, medicine, food processing, biotechnology, and more. However, phages are considered resistant to various harsh environmental conditions; besides, they are characterized by high intra-group variability. Phage-related contaminations may therefore pose new challenges in the future due to the wider use of phages in industry and health care. Therefore, in this review, we summarize the current knowledge of bacteriophage disinfection methods, as well as highlight new technologies and approaches. We discuss the need for systematic solutions to improve bacteriophage control, taking into account their structural and environmental diversity.

In Vivo Gene Expression Profiling of Staphylococcus aureus during Infection Informs Design of Stemless Leukocidins LukE and -D as Detoxified Vaccine Candidates

Staphylococcus aureus is a clinically important bacterial pathogen that has become resistant to treatment with most routinely used antibiotics. Alternative strategies, such as vaccination and phage therapy, are therefore actively being investigated to prevent or combat staphylococcal infections. Vaccination requires that vaccine targets are expressed at sufficient quantities during infection so that they can be targeted by the host's immune system. While our knowledge of in vitro expression levels of putative vaccine candidates is comprehensive, crucial in vivo expression data are scarce and promising vaccine candidates during in vitro assessment often prove ineffective in preventing S. aureus infection. Here, we show how a newly developed high-throughput quantitative reverse transcription-PCR (qRT-PCR) assay monitoring the expression of 84 staphylococcal genes encoding mostly virulence factors can inform the selection and design of effective vaccine candidates against staphylococcal infections. We show that this assay can accurately quantify mRNA expression levels of these genes in several host organs relying only on very limited amounts of bacterial mRNA in each sample. We selected two highly expressed genes, lukE and lukD, encoding pore-forming leukotoxins, to inform the design of detoxified recombinant proteins and showed that immunization with recombinant genetically detoxified LukED antigens conferred protection against staphylococcal skin infection in mice. Consequently, knowledge of in vivo-expressed virulence determinants can be successfully deployed to identify and select promising candidates for optimized design of effective vaccine antigens against S. aureus. Notably, this approach should be broadly applicable to numerous other pathogens. IMPORTANCE Vaccination is an attractive strategy for preventing bacterial infections in an age of increased antimicrobial resistance. However, vaccine development frequently suffers significant setbacks when candidate antigens that show promising results in in vitro experimentation fail to protect from disease. An alluring strategy is to focus resources on developing bacterial virulence factors that are expressed during disease establishment or maintenance and are critical for bacterial in-host survival as vaccine targets. While expression profiles of many virulence factors have been characterized in detail in vitro, our knowledge of their in vivo expression profiles is still scarce. Here, using a high-throughput qRT-PCR approach, we identified two highly expressed leukotoxins in a murine infection model and showed that genetically detoxified derivatives of these elicited a protective immune response in a murine skin infection model. Therefore, in vivo gene expression can inform the selection of promising candidates for the design of effective vaccine antigens.

A Highly Effective Bacteriophage-1252 to Control Multiple Serovars of Salmonella enterica

Salmonella enterica (S. enterica) is the most common foodborne pathogen worldwide, leading to massive economic loss and a significant burden on the healthcare system. The primary source of S. enterica remains contaminated or undercooked poultry products. Considering the number of foodborne illnesses with multiple antibiotic resistant S. enterica, new controlling approaches are necessary. Bacteriophage (phage) therapies have emerged as a promising alternative to controlling bacterial pathogens. However, the limitation on the lysis ability of most phages is their species-specificity to the bacterium. S. enterica has various serovars, and several major serovars are involved in gastrointestinal diseases in the USA. In this study, Salmonella bacteriophage-1252 (phage-1252) was isolated and found to have the highest lytic activity against multiple serovars of S. enterica, including Typhimurium, Enteritidis, Newport, Heidelberg, Kentucky, and Gallinarum. Whole-genome sequencing analysis revealed phage-1252 is a novel phage strain that belongs to the genus Duplodnaviria in the Myoviridae family, and consists of a 244,421 bp dsDNA, with a G + C content of 48.51%. Its plaque diameters are approximately 2.5 mm to 0.5 mm on the agar plate. It inhibited Salmonella Enteritidis growth after 6 h. The growth curve showed that the latent and rise periods were approximately 40 min and 30 min, respectively. The burst size was estimated to be 56 PFU/cell. It can stabilize and maintain original activity between 4 °C and 55 °C for 1 h. These results indicate that phage-1252 is a promising candidate for controlling multiple S. enterica serovars in food production.

Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms

Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.