Complete genomic sequence of bacteriophage felix o1

Phage based magnetic capture method as an aid for real time RPA detection of Salmonella spp. in milk

Salmonella is a major cause of foodborne diseases worldwide. Conventional rapid assays for detecting Salmonella in real samples often encounter severe matrix interference or detect the limited number of species of a genus, resulting the inaccuracy of detection. In this study, we developed a method that combined phage-based magnetic capture with real time recombinase polymerase amplification (RPA) for the rapid, highly sensitive, and specific detection of Salmonella in milk with an ultra-low detection limit. The Felix O-1 phage-conjugated magnetic beads (O-1 pMBs) synthesized in this method showed excellent capture ability for Salmonella spp. and ideal specificity for non-Salmonella strains. After O-1 pMBs-based magnetic separation, the limit of detection (LOD) of the real time RPA assay was 50 cfu/mL in milk samples, which was significantly increased by a magnitude of 3-4 orders. The method exhibited a high sensitivity (compatibility) of 100% (14/14) for all tested Salmonella serotype strains and an ideal specificity (exclusivity) of 100% (7/7) for the tested non-Salmonella strains. The entire detection process including Salmonella capture, DNA extraction, and real time RPA detection was completed within 1.5 h. Furthermore, milk samples spiked with 10 cfu/25 mL of Salmonella were detected positive after cultured in buffered peptone water for only 3 h. Therefore, the proposed method could be an alternative for the rapid and accurate detection of Salmonella.

Cell-free synthesis of the Salmonella specific broad host range bacteriophage, felixO1

Phage-based biocontrol of foodborne Salmonella is limited by the requisite use of Salmonella to propagate the phages. This limitation can be circumvented by producing Salmonella phages using a cell-free gene expression system (CFE) with a non-pathogenic chassis. Here, we produce the Salmonella phage felixO1 using an E. coli-based CFE system.

Multireceptor phage cocktail against Salmonella enterica to circumvent phage resistance

Non-Typhoidal Salmonella (NTS) is one of the most common food-borne pathogens worldwide, with poultry products being the major vehicle for pathogenesis in humans. The use of bacteriophage (phage) cocktails has recently emerged as a novel approach to enhancing food safety. Here, a multireceptor Salmonella phage cocktail of five phages was developed and characterized. The cocktail targets four receptors: O-antigen, BtuB, OmpC, and rough Salmonella strains. Structural analysis indicated that all five phages belong to unique families or subfamilies. Genome analysis of four of the phages showed they were devoid of known virulence or antimicrobial resistance factors, indicating enhanced safety. The phage cocktail broad antimicrobial spectrum against Salmonella, significantly inhibiting the growth of all 66 strains from 20 serovars tested in vitro. The average bacteriophage insensitive mutant (BIM) frequency against the cocktail was 6.22 × 10-6 in S. Enteritidis, significantly lower than that of each of the individual phages. The phage cocktail reduced the load of Salmonella in inoculated chicken skin by 3.5 log10 CFU/cm2 after 48 h at 25°C and 15°C, and 2.5 log10 CFU/cm2 at 4°C. A genome-wide transduction assay was used to investigate the transduction efficiency of the selected phage in the cocktail. Only one of the four phages tested could transduce the kanamycin resistance cassette at a low frequency comparable to that of phage P22. Overall, the results support the potential of cocktails of phage that each target different host receptors to achieve complementary infection and reduce the emergence of phage resistance during biocontrol applications.

PHEIGES: all-cell-free phage synthesis and selection from engineered genomes

Bacteriophages constitute an invaluable biological reservoir for biotechnology and medicine. The ability to exploit such vast resources is hampered by the lack of methods to rapidly engineer, assemble, package genomes, and select phages. Cell-free transcription-translation (TXTL) offers experimental settings to address such a limitation. Here, we describe PHage Engineering by In vitro Gene Expression and Selection (PHEIGES) using T7 phage genome and Escherichia coli TXTL. Phage genomes are assembled in vitro from PCR-amplified fragments and directly expressed in batch TXTL reactions to produce up to 1011 PFU/ml engineered phages within one day. We further demonstrate a significant genotype-phenotype linkage of phage assembly in bulk TXTL. This enables rapid selection of phages with altered rough lipopolysaccharides specificity from phage genomes incorporating tail fiber mutant libraries. We establish the scalability of PHEIGES by one pot assembly of such mutants with fluorescent gene integration and 10% length-reduced genome.

Bacteriophage P22 SieA-mediated superinfection exclusion

Many temperate phages encode prophage-expressed functions that interfere with superinfection of the host bacterium by external phages. Salmonella phage P22 has four such systems that are expressed from the prophage in a lysogen that are encoded by the c2 (repressor), gtrABC, sieA, and sieB genes. Here we report that the P22-encoded SieA protein is necessary and sufficient for exclusion by the SieA system and that it is an inner membrane protein that blocks DNA injection by P22 and its relatives, but has no effect on infection by other tailed phage types. The P22 virion injects its DNA through the host cell membranes and periplasm via a conduit assembled from three "ejection proteins" after their release from the virion. Phage P22 mutants that overcome the SieA block were isolated, and they have amino acid changes in the C-terminal regions of the gene 16 and 20 encoded ejection proteins. Three different single-amino acid changes in these proteins are required to obtain nearly full resistance to SieA. Hybrid P22 phages that have phage HK620 ejection protein genes are also partially resistant to SieA. There are three sequence types of extant phage-encoded SieA proteins that are less than 30% identical to one another, yet comparison of two of these types found no differences in phage target specificity. Our data strongly suggest a model in which the inner membrane protein SieA interferes with the assembly or function of the periplasmic gp20 and membrane-bound gp16 DNA delivery conduit.IMPORTANCEThe ongoing evolutionary battle between bacteria and the viruses that infect them is a critical feature of bacterial ecology on Earth. Viruses can kill bacteria by infecting them. However, when their chromosomes are integrated into a bacterial genome as a prophage, viruses can also protect the host bacterium by expressing genes whose products defend against infection by other viruses. This defense property is called "superinfection exclusion." A significant fraction of bacteria harbor prophages that encode such protective systems, and there are many different molecular strategies by which superinfection exclusion is mediated. This report is the first to describe the mechanism by which bacteriophage P22 SieA superinfection exclusion protein protects its host bacterium from infection by other P22-like phages. The P22 prophage-encoded inner membrane SieA protein prevents infection by blocking transport of superinfecting phage DNA across the inner membrane during injection.

A ToxIN homolog from Salmonella enterica serotype Enteritidis impairs bacteriophage infection

AIMS

To determine if the bacteriophage abortive infection system ToxIN is present in foodborne Salmonella and if it protects against infection by bacteriophages specific to enteric bacteria.

METHODS AND RESULTS

A set of foodborne Salmonella enteritidis isolates from a 2010 eggshell outbreak was identified via BLASTN (basic local alignment search tool nucleotide) queries as harboring a close homolog of ToxIN, carried on a plasmid with putative mobilization proteins. This homolog was cloned into a plasmid vector and transformed into the laboratory strain Salmonella typhimurium LT2 and tested against a set of Salmonella-specific phages (FelixO1, S16, Sp6, LPST153, and P22 HT105/1 int-201). ToxIN reduced infection by FelixO1, S16, and LPST153 by ∼1-4 log PFU ml-1 while reducing the plaque size of Sp6. When present in LT2 and Escherichia coli MG1655, ToxIN conferred cross-genus protection against phage isolates, which infect both bacteria. Finally, the putative ToxIN plasmid was found in whole-genome sequence contigs of several Salmonella serovars, pathogenic E. coli, and other pathogenic enterobacteria.

CONCLUSIONS

Salmonella and E. coli can resist infection by several phages via ToxIN under laboratory conditions; ToxIN is present in foodborne pathogens including Salmonella and Shiga-toxigenic E. coli.

Bacteriophage P22 SieA mediated superinfection exclusion

Many temperate phages encode prophage-expressed functions that interfere with superinfection of the host bacterium by external phages. Salmonella phage P22 has four such systems that are expressed from the prophage in a lysogen that are encoded by the c2 (repressor), gtrABC, sieA, and sieB genes. Here we report that the P22-encoded SieA protein is the only phage protein required for exclusion by the SieA system, and that it is an inner membrane protein that blocks DNA injection by P22 and its relatives, but has no effect on infection by other tailed phage types. The P22 virion injects its DNA through the host cell membranes and periplasm via a conduit assembled from three "ejection proteins" after their release from the virion. Phage P22 mutants were isolated that overcome the SieA block, and they have amino acid changes in the C-terminal regions of the gene 16 and 20 encoded ejection proteins. Three different single amino acid changes in these proteins are required to obtain nearly full resistance to SieA. Hybrid P22 phages that have phage HK620 ejection protein genes are also partially resistant to SieA. There are three sequence types of extant phage-encoded SieA proteins that are less than 30% identical to one another, yet comparison of two of these types found no differences in target specificity. Our data are consistent with a model in which the inner membrane protein SieA interferes with the assembly or function of the periplasmic gp20 and membrane-bound gp16 DNA delivery conduit.

Phage resistance of Salmonella enterica obtained by transposon Tn5-mediated SefR gene silent mutation

Salmonella enterica contamination is a primary cause of global food poisoning. Using phages as bactericidal alternatives to antibiotics could confront the issue of drug resistance. However, the problem of phage resistance, especially mutant strains with multiple phage resistance, is a critical barrier to the practical application of phages. In this study, a library of EZ-Tn5 transposable mutants of susceptible host S. enterica B3-6 was constructed. After the infestation pressure of a broad-spectrum phage TP1, a mutant strain with resistance to eight phages was obtained. Analysis of the genome resequencing results revealed that the SefR gene was disrupted in the mutant strain. The mutant strain displayed a reduced adsorption rate of 42% and a significant decrease in swimming and swarming motility, as well as a significantly reduced expression of the flagellar-related FliL and FliO genes to 17% and 36%, respectively. An uninterrupted form of the SefR gene was cloned into vector pET-21a (+) and used for complementation of the mutant strain. The complemented mutant exhibited similar adsorption and motility as the wild-type control. These results suggest that the disrupted flagellar-mediated SefR gene causes an adsorption inhibition, which is responsible for the phage-resistant phenotype of the S. enterica transposition mutant.

Characterization of Phage vB_SalM_SPJ41 and the Reduction of Risk of Antibiotic-Resistant Salmonella enterica Contamination in Two Ready-to-Eat Foods

Salmonella enterica is a major cause of foodborne illness, and the emergence of antibiotic-resistant bacteria has led to huge pressures on public health. Phage is a promising strategy for controlling foodborne pathogens. In this study, a novel Salmonella phage vB_SalM_SPJ41 was isolated from poultry farms in Shanghai, China. Phage vB_SalM_SPJ41 was able to lyse multiple serotypes of antibiotic-resistant S. enterica, including S. Enteritidis, S. Typhimurium, S. Shubra, S. Derby, and S. Nchanga. It had a short incubation period and was still active at a temperature <80 °C and in the pH range of 3~11. The phage can effectively inhibit the growth of S. enterica in liquid culture and has a significant inhibitory and destructive effect on the biofilm produced by antibiotic-resistant S. enterica. Moreover, the phage was able to reduce S. Enteritidis and MDR S. Derby in lettuce to below the detection limit at 4 °C. Furthermore, the phage could reduce S. Enteritidis and S. Derby in salmon below the limit of detection at 4 °C, and by 3.9 log₁₀ CFU/g and· 2.1 log₁₀ CFU/g at 15 °C, respectively. In addition, the genomic analysis revealed that the phages did not carry any virulence factor genes or antibiotic resistance genes. Therefore, it was found that vB_SalM_SPJ41 is a promising candidate phage for biocontrol against antibiotic-resistant Salmonella in ready-to-eat foods.

The Effect of Spray Parameters on the Survival of Bacteriophages

There have been numerous studies highlighting the efficacy of various bacteriophages (phages) and phage cocktails in the reduction of pathogens in food. Despite approval from legislative bodies permitting phage use in food processing environments, applied via spray or dip, there is still no information on which spray parameters should be used for successful implementation. The study here investigates phage survival diluted to 1% in distilled water (dH2O) and prepared bottled water (PBW), followed by a subsequent spray application through a fixed nozzle (530 μm) and strainer size (74 × 74 μm), with pressures of 3, 5, and 6 Bar. The survival of the phage was determined through sampling the outputs of the spray system and performing double agar overlay plaque assays. PBW decreased the phage concentration (p = 0.18) more than the dH2O (p = 0.73) prior to spray application. It was found that the PBW phage solution was less affected by the various spray parameters (p = 0.045) than the dH2O (p = 0.011). The study showed that unchlorinated water (dH2O), as well as a pressure of 3 Bar, had the highest output phage concentration through the nozzle and strainer, providing valuable information for industrial implementation.

Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection

Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of the molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 68 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL (BActeriophage SElection for your Laboratory) collection. This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside 10 well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to 11 defense systems across different layers of bacterial immunity, and matched these results to the phages' host range across a panel of pathogenic enterobacterial strains. Clear patterns in the distribution of phage phenotypes and genomic features highlighted systematic differences in the potency of different immunity systems and suggested the molecular basis of receptor specificity in several phage groups. Our results also indicate strong trade-offs between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific ecological niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.

Isolation and Characterization of a Virulent Bacteriophage for Controlling Salmonella Enteritidis Growth in Ready-to-Eat Mixed-Ingredient Salads

ABSTRACT

Ready-to-eat vegetable salads have gained popularity worldwide. However, the microbial safety of these salads is a health concern, primarily due to Salmonella Enteritidis contamination during the growing, harvesting, processing, and handling of produce. In this study, a bacteriophage-based strategy was developed to control Salmonella Enteritidis growth in mixed-ingredient salads. The lytic Salmonella-specific phage SapYZU01 was isolated from a soil sample from a suburban vegetable field in Yangzhou (People's Republic of China). SapYZU01 has a short latent period, a large burst size, and a lytic effect against 13 Salmonella Enteritidis strains isolated from various sources (human samples, pork, deli foods, chickens, and chicken meat). The SapYZU01 genome did not contain virulence or antibiotic resistance genes. SapYZU01 significantly decreased the viability of Salmonella Enteritidis cells in iceberg lettuce, chicken meat, and mixed-ingredient (lettuce plus chicken) salads at 37 and 25°C. Bacterial levels in the salad decreased significantly (by 4.0 log CFU/g) at 25°C after treatment of contaminated lettuce before salad preparation with SapYZU01 at a multiplicity of infection (MOI) of 100. Bacterial levels were decreased by 3.8 log CFU/g at 25°C in lettuce plus chicken salads treated after the salad preparation with SapYZU01 at an MOI of 100. In contrast, treating cooked chicken meat with SapYZU01 at an MOI of 100 before mixing it with contaminated lettuce decreased the bacterial level of the salad by 1.2 log CFU/g at 25°C. These findings indicate the potential application of SapYZU01 as a natural biocontrol agent against Salmonella Enteritidis in mixed-ingredient salads. However, both the treatment method and the bacteriophage MOI must be considered when using this lytic bacteriophage in mixed-ingredient salads.

HIGHLIGHTS

Phages and Enzybiotics in Food Biopreservation

Presently, biopreservation through protective bacterial cultures and their antimicrobial products or using antibacterial compounds derived from plants are proposed as feasible strategies to maintain the long shelf-life of products. Another emerging category of food biopreservatives are bacteriophages or their antibacterial enzymes called "phage lysins" or "enzybiotics", which can be used directly as antibacterial agents due to their ability to act on the membranes of bacteria and destroy them. Bacteriophages are an alternative to antimicrobials in the fight against bacteria, mainly because they have a practically unique host range that gives them great specificity. In addition to their potential ability to specifically control strains of pathogenic bacteria, their use does not generate a negative environmental impact as in the case of antibiotics. Both phages and their enzymes can favor a reduction in antibiotic use, which is desirable given the alarming increase in resistance to antibiotics used not only in human medicine but also in veterinary medicine, agriculture, and in general all processes of manufacturing, preservation, and distribution of food. We present here an overview of the scientific background of phages and enzybiotics in the food industry, as well as food applications of these biopreservatives.

Isolation, characterization and comparison of lytic Epseptimavirus phages targeting Salmonella

This study describes the characterization and genomic analysis of six lytic Salmonella phages. To examine the feasibility of using these phages as biocontrol agents, we analyzed their genomes and compared them to those of similar phages. These six phages belong to genus Epseptimavirus, family Demerecviridae. We identified the genes of these six phages by comparing their genomes with those of three type phages in subfamily Markadamsvirinae. All six phages examined in this study were obligately lytic and did not carry undesirable genes. Two phages (vB_SalS_1-23 and vB_SalS_3-29) were selected as the representative phages for general characterization and physiological tests. The biocontrol efficacy of the representative phages was determined by comparing the viable counts of recovered host Salmonella ser. Newlands ZC-S1 from treatment and phage-free control samples. The biocontrol experiment showed that the representative phages were able to reduce the counts of ZC-S1 to below 2 log₁₀ CFU/mL (~4.3 log₁₀ CFU/mL reduction) at 3 h post-infection at 37 °C. Furthermore, we investigated the application of these two phages in the control of ZC-S1 contamination in chicken products and on eggshells. When applied to the surfaces of the samples, the phage cocktail (MOI = 100) reduced the ZC-S1 count to below 2 log₁₀ CFU/mL on chicken skin and to undetectable levels (1 log₁₀ CFU/mL) in chicken breast meat, ground chicken meat and eggshell samples (p < 0.01). Compared to the initial experiment, the phage cocktail reduced the ZC-S1 count by 2-4.08 log₁₀ CFU/mL when applied at an MOI = 1 (except in the ground chicken meat group) and by 4.48-5.67 log₁₀ CFU/mL at an MOI = 100 after 7 h. In conclusion, these two phages with lytic effects show a high potential to inhibit the growth of Salmonella contaminants and can be used as candidate biocontrol agents.

Escherichia coli trxAgene as a molecular marker for genome engineering of felixounoviruses

BACKGROUND

Bacterial viruses (bacteriophages or phages) have a lot of uncharacterized genes, which hinders the progress of their applied research. Functional characterization of these genes is often hampered by a lack of suitable methods for engineering of phage genomes.

METHODS

Phages vB_EcoM_Alf5 (Alf5) and VB_EcoM_VpaE1 (VpaE1) were used as the model phages of Felixounovirus genus. The phage-coded properties were predicted by bioinformatics analysis. The 'pull-down' assay was used for detection of protein-protein interactions. Primer extension analysis was used for the DNA polymerase (DNAP) activity testing. Bacteriophage lambda Redγβα-assisted homologous recombination was used for construction of phage mutants.

RESULTS

Bioinformatics analysis showed that felixounoviruses encode DNA polymerase, which is homologous to the T7 DNAP. We found that the Escherichia coli thioredoxin A (TrxA) in vitro interacts with the predicted DNAP of Alf5 phage (gp096) and enhances its activity. Phages Alf5 and VpaE1 do not grow on E. coli strains lacking trxA gene unless it is provided in trans. This feature was used for construction of the deletion/insertion mutants of non-essential genes of felixounoviruses.

CONCLUSION

DNA replication of phages from Felixonuvirus genus depends on the host trxA, which therefore may be used as a molecular marker for their genome engineering.

GENERAL SIGNIFICANCE

We present a proof-of-principle of a strategy for targeted engineering of bacteriophages of Felixounovirus genus. The method developed here will facilitate the basic and applied research of this unexplored phage group. Furthermore, detected functional interactions between the phage and host proteins will be significant for basic research of DNA replication.

Characterization of Two New Shiga Toxin-Producing Escherichia coli O103-Infecting Phages Isolated from an Organic Farm

Shiga toxin-producing Escherichia coli (STEC) O103 strains have been recently attributed to various foodborne outbreaks in the United States. Due to the emergence of antibiotic-resistant strains, lytic phages are considered as alternative biocontrol agents. This study was to biologically and genomically characterize two STEC O103-infecting bacteriophages, vB_EcoP-Ro103C3lw (or Ro103C3lw) and vB_EcoM-Pr103Blw (or Pr103Blw), isolated from an organic farm. Based on genomic and morphological analyses, phages Ro103C3lw and Pr103Blw belonged to Autographiviridae and Myoviridae families, respectively. Ro103C3lw contained a 39,389-bp double-stranded DNA and encoded a unique tail fiber with depolymerase activity, resulting in huge plaques. Pr103Blw had an 88,421-bp double-stranded DNA with 26 predicted tRNAs associated with the enhancement of the phage fitness. Within each phage genome, no virulence, antibiotic-resistant, and lysogenic genes were detected. Additionally, Ro103C3lw had a short latent period (2 min) and a narrow host range, infecting only STEC O103 strains. By contrast, Pr103Blw had a large burst size (152 PFU/CFU) and a broad host range against STEC O103, O26, O111, O157:H7, and Salmonella Javiana strains. Furthermore, both phages showed strong antimicrobial activities against STEC O103:H2 strains. The findings provide valuable insight into these two phages’ genomic features with the potential antimicrobial activities against STEC O103.

Comparative Analysis of Felixounavirus Genomes Including Two New Members of the Genus That Infect Salmonella Infantis

Salmonella spp. is one of the most common foodborne pathogens worldwide; therefore, its control is highly relevant for the food industry. Phages of the Felixounavirus genus have the characteristic that one phage can infect a large number of different Salmonella serovars and, thus, are proposed as an alternative to antimicrobials in food production. Here, we describe two new members of the Felixounavirus genus named vB_Si_35FD and vB_Si_DR94, which can infect Salmonella Infantis. These new members were isolated and sequenced, and a subsequent comparative genomic analysis was conducted including 23 publicly available genomes of Felixounaviruses that infect Salmonella. The genomes of vB_Si_35FD and vB_Si_DR94 are 85,818 and 85,730 bp large and contain 129 and 125 coding sequences, respectively. The genomes did not show genes associated with virulence or antimicrobial resistance, which could be useful for candidates to use as biocontrol agents. Comparative genomics revealed that closely related Felixounavirus are found in distinct geographical locations and that this genus has a conserved genomic structure despite its worldwide distribution. Our study revealed a highly conserved structure of the phage genomes, and the two newly described phages could represent promising biocontrol candidates against Salmonella spp. from a genomic viewpoint.

Isolation and Characterization of a Novel Salmonella Phage vB_SalP_TR2

Salmonella is a widely distributed foodborne pathogen. The use of Salmonella phages as biocontrol agents has recently gained significant interest. Because the Salmonella genus has high diversity, efforts are necessary to identify lytic Salmonella phages focusing on different serovars. Here, five Salmonella phages were isolated from soil samples, and vB_SalP_TR2 was selected as a novel phage with high lytic potential against the host Salmonella serovar Albany, as well as other tested serovars, including Corvallis, Newport, Kottbus, and Istanbul. Morphological analyses demonstrated that phage vB_SalP_TR2 belongs to the Podoviridae family, with an icosahedral head (62 ± 0.5 nm in diameter and 60 ± 1 nm in length) and a short tail (35 ± 1 nm in length). The latent period and burst size of phage vB_SalP_TR2 was 15 min and 211 PFU/cell, respectively. It contained a linear dsDNA of 71,453 bp, and G + C content was 40.64%. Among 96 putative open reading frames detected, only 35 gene products were found in database searches, with no virulence or antibiotic resistance genes being identified. As a biological control agent, phage vB_SalP_TR2 exhibited a high temperature and pH tolerance. In vitro, it lysed most S. Albany after 24 h at 37°C with multiplicities of infection of 0.0001, 0.001, 0.01, 0.1, 1, 10, and 100. In food matrices (milk and chicken meat), treatment with phage vB_SalP_TR2 also reduced the number of S. Albany compared with that in controls. These findings highlighted phage vB_SalP_TR2 as a potential antibacterial agent for the control of Salmonella in food samples.

Characterization of Salmonella Isolates from Various Geographical Regions of the Caucasus and Their Susceptibility to Bacteriophages

Non-typhoidal Salmonella present a major threat to animal and human health as food-borne infectious agents. We characterized 91 bacterial isolates from Armenia and Georgia in detail, using a suite of assays including conventional microbiological methods, determining antimicrobial susceptibility profiles, matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry, serotyping (using the White-Kauffmann-Le Minor scheme) and genotyping (repetitive element sequence-based PCR (rep-PCR)). No less than 61.5% of the isolates were shown to be multidrug-resistant. A new antimicrobial treatment strategy is urgently needed. Phage therapy, the therapeutic use of (bacterio-) phages, the bacterial viruses, to treat bacterial infections, is increasingly put forward as an additional tool for combatting antibiotic resistant infections. Therefore, we used this representative set of well-characterized Salmonella isolates to analyze the therapeutic potential of eleven single phages and selected phage cocktails from the bacteriophage collection of the Eliava Institute (Georgia). All isolates were shown to be susceptible to at least one of the tested phage clones or their combinations. In addition, genome sequencing of these phages revealed them as members of existing phage genera (Felixounavirus, Seunavirus, Viunavirus and Tequintavirus) and did not show genome-based counter indications towards their applicability against non-typhoidal Salmonella in a phage therapy or in an agro-food setting.

Alteromonas Myovirus V22 Represents a New Genus of Marine Bacteriophages Requiring a Tail Fiber Chaperone for Host Recognition

Marine phages play a variety of critical roles in regulating the microbial composition of our oceans. Despite constituting the majority of genetic diversity within these environments, there are relatively few isolates with complete genome sequences or in-depth analyses of their host interaction mechanisms, such as characterization of their receptor binding proteins (RBPs). Here, we present the 92,760-bp genome of the Alteromonas-targeting phage V22. Genomic and morphological analyses identify V22 as a myovirus; however, due to a lack of sequence similarity to any other known myoviruses, we propose that V22 be classified as the type phage of a new Myoalterovirus genus within the Myoviridae family. V22 shows gene homology and synteny with two different subfamilies of phages infecting enterobacteria, specifically within the structural region of its genome. To improve our understanding of the V22 adsorption process, we identified putative RBPs (gp23, gp24, and gp26) and tested their ability to decorate the V22 propagation strain, Alteromonas mediterranea PT11, as recombinant green fluorescent protein (GFP)-tagged constructs. Only GFP-gp26 was capable of bacterial recognition and identified as the V22 RBP. Interestingly, production of functional GFP-gp26 required coexpression with the downstream protein gp27. GFP-gp26 could be expressed alone but was incapable of host recognition. By combining size-exclusion chromatography with fluorescence microscopy, we reveal how gp27 is not a component of the final RBP complex but instead is identified as a new type of phage-encoded intermolecular chaperone that is essential for maturation of the gp26 RBP.IMPORTANCE Host recognition by phage-encoded receptor binding proteins (RBPs) constitutes the first step in all phage infections and the most critical determinant of host specificity. By characterizing new types of RBPs and identifying their essential chaperones, we hope to expand the repertoire of known phage-host recognition machineries. Due to their genetic plasticity, studying RBPs and their associated chaperones can shed new light onto viral evolution affecting phage-host interactions, which is essential for fields such as phage therapy or biotechnology. In addition, since marine phages constitute one of the most important reservoirs of noncharacterized genetic diversity on the planet, their genomic and functional characterization may be of paramount importance for the discovery of novel genes with potential applications.

Bacteriophage amplification - A comparison of selected methods

The bactericidal properties of bacteriophages have been used almost since the moment of the discovery of bacterial viruses. In the light of the rapidly growing number of antibiotic-resistant bacteria, phage therapy is considered one of the most promising alternatives to classical treatment. Phage amplification is one of the most common procedures of working with phages, and high-titer preparations are beneficial at the experimental stage of studies as well as in practice. The objective of this study was to compare five commonly applied methods of phage amplification: (i) pooled plaques method, (ii) the plate wash method, (iii) the agar culture method, (iv) the two-stage culture method, and (v) in liquid culture. All methods were tested for fifteen different phages. The results described herein indicate that there is no optimal, universal method for phage amplification, and the most effective method has to be established individually for each phage.

Characterization and whole-genome sequencing of broad-host-range Salmonella-specific bacteriophages for bio-control

Salmonella Enteritidis (S. Enteritidis), which could cause human disease and death by consuming the contaminated food, is an important zoonotic pathogen. With the rapid increase of antibiotic resistance all over the world, bacteriophage-based bio-control has gradually attracted public attention widely. In order to find a suitable phage treating S. Enteritidis infection, four phages infecting S. Enteritidis were isolated from poultry fecal samples. Host range showed that four phages had a broad-host-range to Salmonella isolates. The morphological analysis illustrated that all of those phages were classified as the Myoviridae family. The one-step growth curve indicated that bacteriophage BPSELC-1 has a short latent period of about 10 min and a large burst size of 500 pfu/cell in comparison to the other three phages. Then phage BPSELC-1 was sequenced and conducted in vitro experiment. The genome of phage BPSELC-1 is 86,996 bp in size and has 140 putative genes containing structure proteins-encoding genes, tRNA genes and DNA replication or nucleotide metabolism genes. Importantly, no known virulence-associated, antibiotic and lysogeny-related genes were identified in the genome of BPSELC-1. In vitro experiment of phage treatment pointed out that the number of viable S. Enteritidis ATCC 13076 was reduced by 5.9×log₁₀ at MOI of 10² after 4 h. To the best of our knowledge, the phage BPSELC-1 exhibited higher efficiency in S. Enteritidis treatment compared to previous studies. Moreover, it is promising to be used as a broad-spectrum candidate against Salmonella infections in commercial owing to its broad-host-range.

A broad-spectrum phage controls multidrug-resistant Salmonella in liquid eggs

Salmonella is a foodborne pathogen constantly threating public health. The widespread use of antibiotics and globalization of the food industry result in rapid growth of drug-resistance. Eggs contaminated by multidrug-resistant (MDR) Salmonella are one of the riskiest factors of salmonellosis, which are frequently associated with outbreaks worldwide. Thus, there are increasing needs for the development of new technologies in controlling MDR pathogens and for the confirmation of their practical efficiency in target food matrices. In this study, 43 Salmonella phages were isolated from environmental resources and among them, phage D1-2 was selected since it exhibited the most potent lytic ability and the broadest host spectrum against tested Salmonella strains. Further study demonstrated that D1-2 shows high pH and thermal tolerances and a short latent period, together with a low frequency of emergence of phage resistance. D1-2 effectively inhibited the growth of two MDR Salmonella strains in liquid egg white and egg yolk at both 4 °C and 25 °C. Morphology and phylogeny indicated that D1-2 belongs to the Myoviridae family. Genome analysis of D1-2 revealed a linear dsDNA sequence with no homology to virulence or antibiotic-resistance associated genes, presenting D1-2 is a promising candidate for the biocontrol of MDR Salmonella in highly risky foods.

Bacteriophages as Potential Tools for Detection and Control of Salmonella spp. in Food Systems

The global problem of antibiotic resistance in bacteria is quickly developing in most antibiotics used in hospitals and livestock. Recently, the infections with multi-drug resistant (MDR) bacteria become a major cause of death worldwide. Current antibiotics are not very effective in treating MDR Salmonella infections, which have become a public health threat. Therefore, novel approaches are needed to rapidly detect and effectively control antibiotic-resistant pathogens. Bacteriophages (phages) have seen renewed attention for satisfying those requirements due to their host-specific properties. Therefore, this review aims to discuss the possibility of using phages as a detection tool for recognizing bacterial cell surface receptors and an alternative approach for controlling antibiotic-resistant pathogens in food systems.

A Quest of Great Importance-Developing a Broad Spectrum Escherichia coli Phage Collection

Shigella ssp. and enterotoxigenic Escherichiacoli are the most common etiological agents of diarrheal diseases in malnourished children under five years of age in developing countries. The ever-growing issue of antibiotic resistance and the potential negative impact of antibiotic use on infant commensal microbiota are significant challenges to current therapeutic approaches. Bacteriophages (or phages) represent an alternative treatment that can be used to treat specific bacterial infections. In the present study, we screened water samples from both environmental and industrial sources for phages capable of infecting E. coli laboratory strains within our collection. Nineteen phages were isolatedand tested for their ability to infect strains within the ECOR collection and E. coli O157:H7 Δstx. Furthermore, since coliphages have been reported to cross-infect certain Shigella spp., we also evaluated the ability of the nineteen phages to infect a representative Shigella sonnei strain from our collection. Based on having distinct (although overlapping in some cases) host ranges, ten phage isolates were selected for genome sequence and morphological characterization. Together, these ten selected phages were shown to infect most of the ECOR library, with 61 of the 72 strains infected by at least one phage from our collection. Genome analysis of the ten phages allowed classification into five previously described genetic subgroups plus one previously underrepresented subgroup.

Two Phages of the Genera Felixounavirus Subjected to 12 Hour Challenge on Salmonella Infantis Showed Distinct Genotypic and Phenotypic Changes

Salmonella Infantis is considered in recent years an emerging Salmonella serovar, as it has been associated with several outbreaks and multidrug resistance phenotypes. Phages appear as a possible alternative strategy to control Salmonella Infantis (SI). The aims of this work were to characterize two phages of the Felixounavirus genus, isolated using the same strain of SI, and to expose them to interact in challenge assays to identify genetic and phenotypic changes generated from these interactions. These two phages have a shared nucleotide identity of 97% and are differentiated by their host range: one phage has a wide host range (lysing 14 serovars), and the other has a narrow host range (lysing 6 serovars). During the 12 h challenge we compared: (1) optical density of SI, (2) proportion of SI survivors from phage-infected cultures, and (3) phage titer. Isolates obtained through the assays were evaluated by efficiency of plating (EOP) and by host-range characterization. Genomic modifications were characterized by evaluation of single nucleotide polymorphisms (SNPs). The optical density (600 nm) of phage-infected SI decreased, as compared to the uninfected control, by an average of 0.7 for SI infected with the wide-host-range (WHR) phage and by 0.3 for SI infected with the narrow-host-range (NHR) phage. WHR phage reached higher phage titer (7 × 1011 PFU/mL), and a lower proportion of SI survivor was obtained from the challenge assay. In SI that interacted with phages, we identified SNPs in two genes (rfaK and rfaB), which are both involved in lipopolysaccharide (LPS) polymerization. Therefore, mutations that could impact potential phage receptors on the host surface were selected by lytic phage exposure. This work demonstrates that the interaction of Salmonella phages (WHR and NHR) with SI for 12 h in vitro leads to emergence of new phenotypic and genotypic traits in both phage and host. This information is crucial for the rational design of phage-based control strategies.

Complete Genome Sequence of Salmonella enterica Serovar Heidelberg Myophage Meda

Salmonella enterica serovar Heidelberg is a multidrug-resistant foodborne pathogen that originated from poultry and cattle. Bacteriophages isolated for this pathogen may be used as biocontrol agents in food products or animals for preventing Salmonella foodborne diseases. Here, we present the complete genome sequence of Salmonella Heidelberg phage Meda.

Discovery of Shiga Toxin-Producing Escherichia coli (STEC)-Specific Bacteriophages From Non-fecal Composts Using Genomic Characterization

Composting is a complex biodegradable process that converts organic materials into nutrients to facilitate crop yields, and, if well managed, can render bactericidal effects. Majority of research focused on detection of enteric pathogens, such as Shiga toxin-producing Escherichia coli (STEC) in fecal composts. Recently, attention has been emphasized on bacteriophages, such as STEC-specific bacteriophages, associated with STEC from the fecal-contaminated environment because they are able to sustain adverse environmental condition during composting process. However, little is known regarding the isolation of STEC-specific bacteriophages in non-fecal composts. Thus, the objectives were to isolate and genomically characterize STEC-specific bacteriophages, and to evaluate its association with STEC in non-fecal composts. For bacteriophage isolation, the samples were enriched with non-pathogenic E. coli (3 strains) and STEC (14 strains), respectively. After purification, host range, plaque size, and phage morphology were examined. Furthermore, bacteriophage genomes were subjected to whole-genome sequencing using Illumina MiSeq and genomic analyses. Isolation of top six non-O157 and O157 STEC utilizing culture methods combined with PCR-based confirmation was also conducted. The results showed that various STEC-specific bacteriophages, including vB_EcoM-Ro111lw, vB_EcoM-Ro121lw, vB_EcoS-Ro145lw, and vB_EcoM-Ro157lw, with different but complementary host ranges were isolated. Genomic analysis showed the genome sizes varied from 42kb to 149kb, and most bacteriophages were unclassified at the genus level, except vB_EcoM-Ro111lw as FelixO1-like viruses. Prokka predicted less than 25% of the ORFs coded for known functions, including those essential for DNA replication, bacteriophage structure, and host cell lysis. Moreover, none of the bacteriophages harbored lysogenic genes or virulence genes, such as stx or eae. Additionally, the presence of these lytic bacteriophages was likely attributed to zero isolation of STEC and could also contribute to additional antimicrobial effects in composts, if the composting process was insufficient. Current findings indicate that various STEC-specific bacteriophages were found in the non-fecal composts. In addition, the genomic characterization provides in-depth information to complement the deficiency of biological features regarding lytic cycle of the new bacteriophages. Most importantly, these bacteriophages have great potential to control various serogroups of STEC.

Complete Genome Sequences of Two Salmonella Viruses, VSe11 and VSe102 (Family Myoviridae, Subfamily Ounavirinae), with a Very High Degree of Similarity

Two lytic double-stranded DNA bacteriophages, VSe11 and VSe102, infecting broad-spectrum Salmonella enterica were isolated from the sewage of two different poultry farms. The phage genomes comprise 86,360 bp and 86,365 bp, respectively, with a G+C content of 39.0%, and both contain 129 putative coding sequences.

Pf16 and phiPMW: Expanding the realm of Pseudomonas putida bacteriophages

We present the analysis of two novel Pseudomonas putida phages, pf16 and phiPMW. Pf16 represents a peripherally related T4-like phage, and is the first of its kind infecting a Pseudomonad, with evidence suggesting cyanophage origins. Extensive divergence has resulted in pf16 occupying a newly defined clade designated as the pf16-related phages, lying at the interface of the Schizo T-Evens and Exo T-Evens. Recombination with an ancestor of the P. putida phage AF is likely responsible for the tropism of this phage. phiPMW represents a completely novel Pseudomonas phage with a genome containing substantial genetic novelty through its many hypothetical proteins. Evidence suggests that this phage has been extensively shaped through gene transfer events and vertical evolution. Phylogenetics shows that this phage has an evolutionary history involving FelixO1-related viruses but is in itself highly distinct from this group.

Complete Genome Sequence of Citrobacter freundii Myophage Mijalis

Citrobacter freundii is responsible for various opportunistic nosocomial infections. Phage therapies against C. freundii may prove useful in human medicine for treatment of infections caused by the ubiquitous bacteria. Here, we announce the complete genome sequence of the C. freundii Felix O1-like myophage Mijalis and present its features.

Modified Bacteriophage S16 Long Tail Fiber Proteins for Rapid and Specific Immobilization and Detection of Salmonella Cells

Bacteriophage-based assays and biosensors rival traditional antibody-based immunoassays for detection of low-level Salmonella contaminations. In this study, we harnessed the binding specificity of the long tail fiber (LTF) from bacteriophage S16 as an affinity molecule for the immobilization, enrichment, and detection of Salmonella We demonstrate that paramagnetic beads (MBs) coated with recombinant gp37-gp38 LTF complexes (LTF-MBs) are highly effective tools for rapid affinity magnetic separation and enrichment of Salmonella Within 45 min, the LTF-MBs consistently captured over 95% of Salmonella enterica serovar Typhimurium cells from suspensions containing from 10 to 105 CFU · ml-1, and they yielded equivalent recovery rates (93% ± 5%, n = 10) for other Salmonella strains tested. LTF-MBs also captured Salmonella cells from various food sample preenrichments, allowing the detection of initial contaminations of 1 to 10 CFU per 25 g or ml. While plating of bead-captured cells allowed ultrasensitive but time-consuming detection, the integration of LTF-based enrichment into a sandwich assay with horseradish peroxidase-conjugated LTF (HRP-LTF) as a detection probe produced a rapid and easy-to-use Salmonella detection assay. The novel enzyme-linked LTF assay (ELLTA) uses HRP-LTF to label bead-captured Salmonella cells for subsequent identification by HRP-catalyzed conversion of chromogenic 3,3',5,5'-tetramethylbenzidine substrate. The color development was proportional for Salmonella concentrations between 102 and 107 CFU · ml-1 as determined by spectrophotometric quantification. The ELLTA assay took 2 h to complete and detected as few as 102 CFU · ml-1S Typhimurium cells. It positively identified 21 different Salmonella strains, with no cross-reactivity for other bacteria. In conclusion, the phage-based ELLTA represents a rapid, sensitive, and specific diagnostic assay that appears to be superior to other currently available tests.IMPORTANCE The incidence of foodborne diseases has increased over the years, resulting in major global public health issues. Conventional methods for pathogen detection can be laborious and expensive, and they require lengthy preenrichment steps. Rapid enrichment-based diagnostic assays, such as immunomagnetic separation, can reduce detection times while also remaining sensitive and specific. A critical component in these tests is implementing affinity molecules that retain the ability to specifically capture target pathogens over a wide range of in situ applications. The protein complex that forms the distal tip of the bacteriophage S16 long tail fiber is shown here to represent a highly sensitive affinity molecule for the specific enrichment and detection of Salmonella Phage-encoded long tail fibers have huge potential for development as novel affinity molecules for robust and specific diagnostics of a vast spectrum of bacteria.

Complete Genome Sequence of Escherichia coli Phage vB_EcoM_Alf5

Here, we announce the complete genome sequence of the Escherichia coli myophage vB_EcoM_Alf5 belonging to the genus Felixo1virus, whose members have not been comprehensively studied at the molecular level. Phage vB_EcoM_Alf5 infects E. coli K-12-derived laboratory strains and therefore is well suited for functional studies.

Novel "Superspreader" Bacteriophages Promote Horizontal Gene Transfer by Transformation

Bacteriophages infect an estimated 10²³ to 10²⁵ bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub "superspreaders," releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation. Two novel Escherichia coli phage superspreaders, SUSP1 and SUSP2, liberated four evolutionarily distinct plasmids with equal efficiency, including two close relatives of prominent antibiotic resistance vectors in natural environments. SUSP2 also mediated the extensive lateral transfer of antibiotic resistance in unbiased communities of soil bacteria from Maryland and Wyoming. Furthermore, the addition of SUSP2 to cocultures of kanamycin-resistant E. coli and kanamycin-sensitive Bacillus sp. bacteria resulted in roughly 1,000-fold more kanamycin-resistant Bacillus sp. bacteria than arose in phage-free controls. Unlike many other lytic phages, neither SUSP1 nor SUSP2 encodes homologs to known hydrolytic endonucleases, suggesting a simple potential mechanism underlying the superspreading phenotype. Consistent with this model, the deletion of endonuclease IV and the nucleoid-disrupting protein ndd from coliphage T4, a phage known to extensively degrade chromosomal DNA, significantly increased its ability to promote plasmid transformation. Taken together, our results suggest that phage superspreaders may play key roles in microbial evolution and ecology but should be avoided in phage therapy and other medical applications.

IMPORTANCE

Bacteriophages (phages), viruses that infect bacteria, are the planet's most numerous biological entities and kill vast numbers of bacteria in natural environments. Many of these bacteria carry plasmids, extrachromosomal DNA elements that frequently encode antibiotic resistance. However, it is largely unknown whether plasmids are destroyed during phage infection or released intact upon phage lysis, whereupon their encoded resistance could be acquired and manifested by other bacteria (transformation). Because phages are being developed to combat antibiotic-resistant bacteria and because transformation is a principal form of horizontal gene transfer, this question has important implications for biomedicine and microbial evolution alike. Here we report the isolation and characterization of two novel Escherichia coli phages, dubbed "superspreaders," that promote extensive plasmid transformation and efficiently disperse antibiotic resistance genes. Our work suggests that phage superspreaders are not suitable for use in medicine but may help drive bacterial evolution in natural environments.

Genomics of Three New Bacteriophages Useful in the Biocontrol of Salmonella

Non-typhoid Salmonella is the principal pathogen related to food-borne diseases throughout the world. Widespread antibiotic resistance has adversely affected human health and has encouraged the search for alternative antimicrobial agents. The advances in bacteriophage therapy highlight their use in controlling a broad spectrum of food-borne pathogens. One requirement for the use of bacteriophages as antibacterials is the characterization of their genomes. In this work, complete genome sequencing and molecular analyses were carried out for three new virulent Salmonella-specific bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) able to infect a broad range of Salmonella strains. Sequence analysis of the genomes of UAB_Phi20, UAB_Phi78, and UAB_Phi87 bacteriophages did not evidence the presence of known virulence-associated and antibiotic resistance genes, and potential immunoreactive food allergens. The UAB_Phi20 genome comprised 41,809 base pairs with 80 open reading frames (ORFs); 24 of them with assigned function. Genome sequence showed a high homology of UAB_Phi20 with Salmonella bacteriophage P22 and other P22likeviruses genus of the Podoviridae family, including ST64T and ST104. The DNA of UAB_Phi78 contained 44,110 bp including direct terminal repeats (DTR) of 179 bp and 58 putative ORFs were predicted and 20 were assigned function. This bacteriophage was assigned to the SP6likeviruses genus of the Podoviridae family based on its high similarity not only with SP6 but also with the K1-5, K1E, and K1F bacteriophages, all of which infect Escherichia coli. The UAB_Phi87 genome sequence consisted of 87,669 bp with terminal direct repeats of 608 bp; although 148 ORFs were identified, putative functions could be assigned to only 29 of them. Sequence comparisons revealed the mosaic structure of UAB_Phi87 and its high similarity with bacteriophages Felix O1 and wV8 of E. coli with respect to genetic content and functional organization. Phylogenetic analysis of large terminase subunits confirms their packaging strategies and grouping to the different phage genus type. All these studies are necessary for the development and the use of an efficient cocktail with commercial applications in bacteriophage therapy against Salmonella.

Incomplete LPS Core-Specific Felix01-Like Virus vB_EcoM_VpaE1

Bacteriophages represent a valuable source for studying the mechanisms underlying virus-host interactions. A better understanding of the host-specificity of viruses at the molecular level can promote various phage applications, including bacterial diagnostics, antimicrobial therapeutics, and improve methods in molecular biology. In this study, we describe the isolation and characterization of a novel coliphage, vB_EcoM_VpaE1, which has different host specificity than its relatives. Morphology studies, coupled with the results of genomic and proteomic analyses, indicate that vB_EcoM_VpaE1 belongs to the newly proposed genus Felix01likevirus in the family Myoviridae. The genus Felix01likevirus comprises a group of highly similar phages that infect O-antigen-expressing Salmonella and Escherichia coli (E. coli) strains. Phage vB_EcoM_VpaE1 differs from the rest of Felix01-like viruses, since it infects O-antigen-deficient E. coli strains with an incomplete core lipopolysaccharide (LPS). We show that vB_EcoM_VpaE1 can infect mutants of E. coli that contain various truncations in their LPS, and can even recognize LPS that is truncated down to the inner-core oligosaccharide, showing potential for the control of rough E. coli strains, which usually emerge as resistant mutants upon infection by O-Ag-specific phages. Furthermore, VpaE1 can replicate in a wide temperature range from 9 to 49 °C, suggesting that this virus is well adapted to harsh environmental conditions. Since the structural proteins of such phages tend to be rather robust, the receptor-recognizing proteins of VpaE1 are an attractive tool for application in glycan analysis, bacterial diagnostics and antimicrobial therapeutics.

Complete Genome Sequence of Citrobacter freundii Myophage Mordin

Citrobacter freundii is a Gram-negative opportunistic pathogen that is associated with urinary tract infections. Bacteriophages infecting C. freundii can be used as an effective treatment to fight these infections. Here, we announce the complete genome sequence of the C. freundii Felix O1-like myophage Mordin and describe its features.

Complete Genome Sequence of Citrobacter freundii Myophage Michonne

Citrobacter freundii is a Gram-negative opportunistic pathogen that causes dangerous infections such as neonatal meningitis. C. freundii also harbors antibiotic resistance, making phages infecting this host valuable tools. Here, we announce the complete genome of the C. freundii FelixO1-like myophage Michonne and describe its notable features.

Bio-Control of Salmonella Enteritidis in Foods Using Bacteriophages

Two lytic phages, vB_SenM-PA13076 (PA13076) and vB_SenM-PC2184 (PC2184), were isolated from chicken sewage and characterized with host strains Salmonella Enteritidis (SE) ATCC13076 and CVCC2184, respectively. Transmission electron microscopy revealed that they belonged to the family Myoviridae. The lytic abilities of these two phages in liquid culture showed 104 multiplicity of infection (MOI) was the best in inhibiting bacteria, with PC2184 exhibiting more activity than PA13076. The two phages exhibited broad host range within the genus Salmonella. Phage PA13076 and PC2184 had a lytic effect on 222 (71.4%) and 298 (95.8%) of the 311 epidemic Salmonella isolates, respectively. We tested the effectiveness of phage PA13076 and PC2184 as well as a cocktail combination of both in three different foods (chicken breast, pasteurized whole milk and Chinese cabbage) contaminated with SE. Samples were spiked with 1 × 10(4) CFU individual SE or a mixture of strains (ATCC13076 and CVCC2184), then treated with 1 × 10(8) PFU individual phage or a two phage cocktail, and incubated at 4 °C or 25 °C for 5 h. In general, the inhibitory effect of phage and phage cocktail was better at 4 °C than that at 25 °C, whereas the opposite result was observed in Chinese cabbage, and phage cocktail was better than either single phage. A significant reduction in bacterial numbers (1.5-4 log CFU/sample, p < 0.05) was observed in all tested foods. The two phages on the three food samples were relatively stable, especially at 4 ºC, with the phages exhibiting the greatest stability in milk. Our research shows that our phages have potential effectiveness as a bio-control agent of Salmonella in foods.

Complete Genome Sequence of Escherichia coli O145:NM Bacteriophage vB_EcoM_AYO145A, a New Member of O1-Like Phages

Previously, bacteriophage vB_EcoM_AYO145A, which lyses Shiga toxin-producing Escherichia coli O145:NM, was classified as an O1-like virus of the Myoviridae family. Here, we report the complete genome sequence of this phage and a comparative genomic analysis with other known O1-like phages.

Feces of feedlot cattle contain a diversity of bacteriophages that lyse non-O157 Shiga toxin-producing Escherichia coli

This study aimed to isolate and characterize bacteriophages that lyse non-O157 Shiga toxin-producing Escherichia coli (STEC) from cattle feces. Of 37 non-O157 STEC-infecting phages isolated, those targeting O26 (AXO26A, AYO26A, AYO26B), O103 (AXO103A, AYO103A), O111 (AXO111A, AYO111A), O121 (AXO121A, AXO121B), and O145 (AYO145A, AYO145B) were further characterized. Transmission electron microscopy showed that the 11 isolates belonged to 3 families and 6 genera: the families Myoviridae (types rV5, T4, ViI, O1), Siphoviridae (type T5), and Podoviridae (type T7). Genome size of the phages as determined by pulsed-field gel electrophoresis ranged from 38 to 177 kb. Excluding phages AXO26A, AYO103A, AYO145A, and AYO145B, all other phages were capable of lysing more than 1 clinically important strain from serogroups of O26, O91, O103, O111, O113, O121, and O128, but none exhibited infectivity across all serogroups. Moreover, phages AYO26A, AXO121A, and AXO121B were also able to lyse 4 common phage types of STEC O157:H7. Our findings show that a diversity of non-O157 STEC-infecting phages are harbored in bovine feces. Phages AYO26A, AYO26B, AXO103A, AXO111A, AYO111A, AXO121A, and AXO121B exhibited a broad host range against a number of serogroups of STEC and have potential for the biocontrol of STEC in the environment.

Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Myophage Mushroom

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a leading cause of foodborne illness worldwide. Over the past two decades, strains resistant to antibiotics have begun to emerge, highlighting the need for alternative treatment strategies such as bacteriophage therapy. Here, we present the complete genome of Mushroom, an S. Typhimurium myophage.

Complete Genome Sequence of Citrobacter freundii Myophage Moogle

Citrobacter freundii is an opportunistic pathogen that has been linked to nosocomial infections, such as brain abscesses and pneumonia. Further study on phages infecting C. freundii may provide therapeutics for these infections. Here, we announce the complete genome sequence of the FelixO1-like myophage Moogle and describe its features.