Characterization and Genomic Analysis of Escherichia coli O157:H7 Bacteriophage FEC14, a New Member of Genus Kuttervirus

Genomic and Proteomic Analysis of Six Vi01-like Phages Reveals Wide Host Range and Multiple Tail Spike Proteins

Enterobacteriaceae is a large family of Gram-negative bacteria composed of many pathogens, including Salmonella and Shigella. Here, we characterize six bacteriophages that infect Enterobacteriaceae, which were isolated from wastewater plants in the Wasatch front (Utah, United States). These phages are highly similar to the Kuttervirus vB_SenM_Vi01 (Vi01), which was isolated using wastewater from Kiel, Germany. The phages vary little in genome size and are between 157 kb and 164 kb, which is consistent with the sizes of other phages in the Vi01-like phage family. These six phages were characterized through genomic and proteomic comparison, mass spectrometry, and both laboratory and clinical host range studies. While their proteomes are largely unstudied, mass spectrometry analysis confirmed the production of five hypothetical proteins, several of which unveiled a potential operon that suggests a ferritin-mediated entry system on the Vi01-like phage family tail. However, no dependence on this pathway was observed for the single host tested herein. While unable to infect every genus of Enterobacteriaceae tested, these phages are extraordinarily broad ranged, with several demonstrating the ability to infect Salmonella enterica and Citrobacter freundii strains with generally high efficiency, as well as several clinical Salmonella enterica isolates, most likely due to their multiple tail fibers.

Engineering of Salmonella Phages into Novel Antimicrobial Tailocins

Due to the extensive use of antibiotics, the increase of infections caused by antibiotic-resistant bacteria is now a global health concern. Phages have proven useful for treating bacterial infections and represent a promising alternative or complement to antibiotic treatment. Yet, other alternatives exist, such as bacteria-produced non-replicative protein complexes that can kill their targeted bacteria by puncturing their membrane (Tailocins). To expand the repertoire of Tailocins available, we suggest a new approach that transforms phages into Tailocins. Here, we genetically engineered the virulent Ackermannviridae phage S117, as well as temperate phages Fels-1, -2 and Gifsy-1 and -2, targeting the food pathogen Salmonella, by deleting the portal vertex or major capsid gene using CRISPR-Cas9. We report the production of Tailocin particles from engineered virulent and temperate phages able to kill their native host. Our work represents a steppingstone that taps into the huge diversity of phages and transforms them into versatile puncturing new antimicrobials.

SW16-7, a Novel Ackermannviridae Bacteriophage with Highly Effective Lytic Activity Targets Salmonella enterica Serovar Weltevreden

Salmonella enterica serovar Weltevreden is a foodborne pathogen commonly transmitted through fresh vegetables and seafood. In this study, a lytic phage, SW16-7, was isolated from medical sewage, demonstrating high infectivity against S. Weltevreden, S. London, S. Meleagridis, and S. Give of Group O:3. In vitro inhibition assays revealed its effective antibacterial effect for up to 12 h. Moreover, analysis using the Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) showed that SW16-7's genome does not contain any virulence factors or antibiotic resistance genes, indicating its potential as a promising biocontrol agent against S. Weltevreden. Additionally, a TSP gene cluster was identified in SW16-7's genome, with TSP1 and TSP2 showing a high similarity to lysogenic phages ε15 and ε34, respectively, in the C-terminal region. The whole-genome phylogenetic analysis classified SW16-7 within the Ackermannviridae family and indicated a close relationship with Agtrevirus, which is consistent with the ANI results.

Combine thermal processing with polyvalent phage LPEK22 to prevent the Escherichia coli and Salmonella enterica contamination in food

Thermal processing is the most frequently used method to destruct bacteria in food processing. However, insufficient thermal processing may lead to the outbreak of foodborne illness. This study combined thermal processing with thermostable phage to prevent food contamination. The thermostable phages were screened which can retain activity at 70 °C for 1 h. Among them, the polyvalent phage LPEK22 was obtained to lyse Escherichia coli and Salmonella enterica, especially several multi-drug resistant bacteria. In milk (liquid food matrix), LPEK22 significantly reduced the E. coli by 5.00 ± 0.18 log₁₀ CFU/mL and S. enterica by 4.20 ± 0.23 log₁₀ CFU/mL after thermal processing at 63 °C for 30 min. For beef sausage (solid food matrix), LPEK22 significantly reduced the E. coli by 2.34 ± 0.17 log₁₀ CFU/cm² and S. enterica by 1.54 ± 0.13 log₁₀ CFU/cm² after thermal processing at 66 °C for 90 s. Genome analysis revealed that LPEK22 was a novel phage with a unique tail spike protein belonging to the family of Ackermannviridae. LPEK22 did not contain lysogenic, drug-resistant, and virulent genes that may compromise the safety of food application. These results determined that LPEK22, a novel polyvalent Ackermannviridae phage, could combine with thermal processing to prevent drug-resistant E. coli and S. enterica both in vitro and in foods.

CAM-21, a novel lytic phage with high specificity towards Escherichia coli O157:H7 in food products

Escherichia coli O157:H7 is a foodborne pathogen that has become a serious global concern for food safety. Despite the application of different traditional biocontrol methods in the food industry, food borne disease outbreaks linked to this organism remain. Due to their high specificity, lytic bacteriophages are promising antimicrobial agents that could be utilized to control pathogens in foods. In this study, a novel Escherichia phage, CAM-21, was isolated from a dairy farm environment. CAM-21 showed targeted host specificity towards various serotypes of Shiga toxin-producing E. coli, including O157:H7, O26, O103, and O145. Morphological analyses revealed that CAM-21 has a polyhedron capsid and a contractile tail with a diameter of about 92.83 nm, and length of about 129.75 nm, respectively. CAM-21 showed a strong inhibitory effect on the growth of E. coli O157:H7, even at a multiplicity of infection (MOI) of as low as 0.001. Phage adsorption and one-step growth analysis indicated that the target pathogen was rapidly lysed by CAM-21 that exhibited a short latent time (20 min). Electron microscopic and genomic DNA analyses suggested that CAM-21 is a lytic phage, classified as a new species in the Tequatrovirus genus of the Myoviridae Family. Based on whole genome sequencing, CAM-21 has a double-stranded DNA with 166,962 bp, 265 open reading frames and 11 tRNA. The genome of CAM-21 did not encode toxins, virulence factors, antibiotic resistance, lysogeny or allergens. Phylogenetic and genomic comparative analyses suggested that CAM-21 is a T4-like phage species. The growth of E. coli O157:H7 was effectively controlled in milk, ground beef and baby spinach at MOIs of 1000 and 10,000. CAM-21 significantly (P ≤ 0.05) reduced the bacterial counts of the treated foods, ranging from 1.4-2.0 log CFU/mL in milk to 1.3-1.4 log CFU/g in ground beef and baby spinach. These findings suggest that the lytic phage, CAM-21, is a potential candidate for controlling E. coli O157:H7 contamination in foods.

Characterization of polyvalent Escherichia phage Sa157lw for the biocontrol potential of Salmonella Typhimurium and Escherichia coli O157:H7 on contaminated mung bean seeds

Seeds are one of the primary sources of contamination with foodborne pathogens, such as pathogenic Escherichia coli, and various Salmonella serovars, for produce, particularly sprouts. Due to the susceptibility of sprout growth to chemical-based antimicrobials and the rising issue of antimicrobial resistance, developing innovative antimicrobial interventions is an urgent need. Therefore, the objective of this study was to characterize Escherichia phage Sa157lw (or Sa157lw) for the biocontrol potential of Salmonella Typhimurium and E. coli O157:H7 on contaminated mung bean seeds. Phage Sa157lw was subjected to whole-genome sequencing and biological characterization, including morphology, one-step growth curve, and stress stability tests. Later, antimicrobial activity was determined in vitro and upon application on the mung bean seeds artificially contaminated with E. coli O157:H7 or Salmonella Typhimurium. Sa157lw possessed a contractile tail and belonged to the Kuttervirus genus under the Ackermannviridae family, sharing a close evolutionary relationship with E. coli phage ECML-4 and Kuttervirus ViI; however, tail spike genes (ORF_102 and ORF_104) were the primary region of difference. Comparative genomics showed that Sa157lw encoded a cluster of tail spike genes—including ORF_101, ORF_102, and ORF_104—sharing high amino acid similarity with the counterfeits of various Salmonella phages. Additionally, Sa157lw harbored a unique tail fiber (ORF_103), possibly related to the receptors binding of O157 strains. The genomic evidence accounted for the polyvalent effects of Sa157lw against E. coli O157:H7 and various Salmonella serovars (Typhimurium, Enteritidis, Agona, Saintpaul, and Heidelberg). Furthermore, the phage did not contain any virulence, antibiotic-resistant, or lysogenic genes. Sa157lw had a 30-min latent period on both E. coli O157:H7 and Salmonella Typhimurium, with an estimated burst size of 130 and 220 PFU/CFU, respectively, and was stable at a wide range of temperatures (4–60°C) and pH (pH4 to pH10). The phage application demonstrated a strong anti-E. coli O157:H7 and anti-Salmonella Typhimurium effects in 1.1 and 1.8 log reduction on the contaminated mung bean seeds after overnight storage at 22°C. These findings provide valuable insights into the polyvalent Sa157lw as a potential biocontrol agent of Salmonella Typhimurium and E. coli O157:H7 on sprout seeds.

Biocontrol Approaches against Escherichia coli O157:H7 in Foods

Shiga-toxin-producing Escherichia coli O157:H7 is a well-known water- and food-borne zoonotic pathogen that can cause gastroenteritis in humans. It threatens the health of millions of people each year; several outbreaks of E. coli O157:H7 infections have been linked to the consumption of contaminated plant foods (e.g., lettuce, spinach, tomato, and fresh fruits) and beef-based products. To control E. coli O157:H7 in foods, several physical (e.g., irradiation, pasteurization, pulsed electric field, and high-pressure processing) and chemical (e.g., using peroxyacetic acid; chlorine dioxide; sodium hypochlorite; and organic acids, such as acetic, lactic, and citric) methods have been widely used. Although the methods are quite effective, they are not applicable to all foods and carry intrinsic disadvantages (alteration of sensory properties, toxicity, etc.). Therefore, the development of safe and effective alternative methods has gained increased attention recently. Biocontrol agents, including bacteriophages, probiotics, antagonistic bacteria, plant-derived natural compounds, bacteriocins, endolysins, and enzymes, are rapidly emerging as effective, selective, relatively safe for human consumption, and environmentally friendly alternatives. This paper summarizes advances in the application of biocontrol agents for E. coli O157:H7 control in foods.

Subtypes of tail spike proteins predicts the host range of Ackermannviridae phages

Phages belonging to the Ackermannviridae family encode up to four tail spike proteins (TSPs), each recognizing a specific receptor of their bacterial hosts. Here, we determined the TSPs diversity of 99 Ackermannviridae phages by performing a comprehensive in silico analysis. Based on sequence diversity, we assigned all TSPs into distinctive subtypes of TSP1, TSP2, TSP3 and TSP4, and found each TSP subtype to be specifically associated with the genera (Kuttervirus, Agtrevirus, Limestonevirus, Taipeivirus) of the Ackermannviridae family. Further analysis showed that the N-terminal XD1 and XD2 domains in TSP2 and TSP4, hinging the four TSPs together, are preserved. In contrast, the C-terminal receptor binding modules were only conserved within TSP subtypes, except for some Kuttervirus TSP1s and TSP3s that were similar to specific TSP4s. A conserved motif in TSP1, TSP3 and TSP4 of Kuttervirus phages may allow recombination between receptor binding modules, thus altering host recognition. The receptors for numerous uncharacterized phages expressing TSPs in the same subtypes were predicted using previous host range data. To validate our predictions, we experimentally determined the host recognition of three of the four TSPs expressed by kuttervirus S117. We confirmed that S117 TSP1 and TSP2 bind to their predicted host receptors, and identified the receptor for TSP3, which is shared by 51 other Kuttervirus phages. Kuttervirus phages were thus shown encode a vast genetic diversity of potentially exchangeable TSPs influencing host recognition. Overall, our study demonstrates that comprehensive in silico and host range analysis of TSPs can predict host recognition of Ackermannviridae phages.

Microencapsulated phages show prolonged stability in gastrointestinal environments and high therapeutic efficiency to treat Escherichia coli O157:H7 infection

Escherichia coli (E. coli) O157:H7 bacterial infection causes severe disease in mammals and results in substantial economic losses worldwide. Due to the development of antibiotic resistance, bacteriophage (phage) therapy has become an alternative to control O157:H7 infection. However, the therapeutic effects of phages are frequently disappointing because of their low resistance to the gastrointestinal environment. In this study, to improve the stability of phages in the gastrointestinal tract, E. coli O157:H7 phages were microencapsulated and their in vitro stability and in vivo therapeutic efficiency were investigated. The results showed that compared to free phages, the resistance of microencapsulated phages to simulated gastric fluid and bile salts significantly increased. The microencapsulated phages were efficiently released into simulated intestinal fluid, leading to a better therapeutic effect in rats infected with E. coli O157:H7 compared to the effects of the free phages. In addition, the microencapsulated phages were more stable during storage than the free phages, showing how phage microencapsulation can play an essential role in phage therapy.