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

Characterization of a T4-like Bacteriophage vB_EcoM-Sa45lw as a Potential Biocontrol Agent for Shiga Toxin-Producing Escherichia coli O45 Contaminated on Mung Bean Seeds

Application of lytic bacteriophages is a promising and alternative intervention technology to relieve antibiotic resistance pressure and control bacterial pathogens in the food industry. Despite the increase of produce-associated outbreaks caused by non-O157 Shiga toxin-producing E. coli (STEC) serogroups, the information of phage application on sprouts to mitigate these pathogens is lacking. Therefore, the objective of this study was to characterize a T4-like Escherichia phage vB_EcoM-Sa45lw (or Sa45lw) for the biocontrol potential of STEC O45 on mung bean seeds. Phage Sa45lw belongs to the Tequatrovirus genus under the Myoviridae family and displays a close evolutionary relationship with a STEC O157-infecting phage AR1. Sa45lw contains a long-tail fiber gene (gp37), sharing high genetic similarity with the counterpart of Escherichia phage KIT03, and a unique tail lysozyme (gp5) to distinguish its host range (STEC O157, O45, ATCC 13706, and Salmonella Montevideo and Thompson) from phage KIT03 (O157 and Salmonella enterica). No stx, antibiotic resistance, and lysogenic genes were found in the Sa45lw genome. The phage has a latent period of 27 min with an estimated burst size of 80 PFU/CFU and is stable at a wide range of pH (pH 3 to pH 10.5) and temperatures (-80°C to 50°C). Phage Sa45lw is particularly effective in reducing E. coli O45:H16 both in vitro (MOI = 10) by 5 log and upon application (MOI = 1,000) on the contaminated mung bean seeds for 15 min by 2 log at 25°C. These findings highlight the potential of phage application against non-O157 STEC on sprout seeds. IMPORTANCE Seeds contaminated with foodborne pathogens, such as Shiga toxin-producing E. coli, are the primary sources of contamination in produce and have contributed to numerous foodborne outbreaks. Antibiotic resistance has been a long-lasting issue that poses a threat to human health and the food industry. Therefore, developing novel antimicrobial interventions, such as bacteriophage application, is pivotal to combat these pathogens. This study characterized a lytic bacteriophage Sa45lw as an alternative antimicrobial agent to control pathogenic E. coli on the contaminated mung bean seeds. The phage exhibited antimicrobial effects against both pathogenic E. coli and Salmonella without containing virulent or lysogenic genes that could compromise the safety of phage application. In addition, after 15 min of phage treatment, Sa45lw mitigated E. coli O45:H16 on the contaminated mung bean seeds by a 2-log reduction at room temperature, demonstrating the biocontrol potential of non-O157 Shiga toxin-producing E. coli on sprout seeds.

Low-Temperature Virus vB_EcoM_VR26 Shows Potential in Biocontrol of STEC O26:H11

Shiga toxin-producing Escherichia coli (STEC) O26:H11 is an emerging foodborne pathogen of growing concern. Since current strategies to control microbial contamination in foodstuffs do not guarantee the elimination of O26:H11, novel approaches are needed. Bacteriophages present an alternative to traditional biocontrol methods used in the food industry. Here, a previously isolated bacteriophage vB_EcoM_VR26 (VR26), adapted to grow at common refrigeration temperatures (4 and 8 °C), has been evaluated for its potential as a biocontrol agent against O26:H11. After 2 h of treatment in broth, VR26 reduced O26:H11 numbers (p < 0.01) by > 2 log10 at 22 °C, and ~3 log10 at 4 °C. No bacterial regrowth was observed after 24 h of treatment at both temperatures. When VR26 was introduced to O26:H11-inoculated lettuce, ~2.0 log10 CFU/piece reduction was observed at 4, 8, and 22 °C. No survivors were detected after 4 and 6 h at 8 and 4 °C, respectively. Although at 22 °C, bacterial regrowth was observed after 6 h of treatment, O26:H11 counts on non-treated samples were >2 log10 CFU/piece higher than on phage-treated ones (p < 0.02). This, and the ability of VR26 to survive over a pH range of 3-11, indicates that VR26 could be used to control STEC O26:H11 in the food industry.

There and back again: a dendrimer's tale

The development of molecular nanostructures with well-defined particle size and shape is of eminent interest in biomedicine. Among many studied nanostructures, dendrimers represent the group of those most thoroughly characterized ones. Due to their unique structure and properties, dendrimers are very attractive for medical and pharmaceutical applications. Owing to the controllable cavities inside the dendrimer, guest molecules may be encapsulated, and highly reactive terminal groups are susceptible to further modifications, e.g., to facilitate target delivery. To understand the potential of these nanoparticles and to predict and avoid any adverse cellular reactions, it is necessary to know the mechanisms responsible for an efficient dendrimer uptake and the destination of their intracellular journey. In this article, we summarize the results of studies describing the dendrimer uptake, traffic, and efflux mechanisms depending on features of specific nanoparticles and cell types. We also present mechanisms of dendrimers responsible for toxicity and alteration in signal transduction pathways at the cellular level.

A New Pipeline for Designing Phage Cocktails Based on Phage-Bacteria Infection Networks

In recent years, the spread of antibiotic-resistant bacteria and efforts to preserve food microbiota have induced renewed interest in phage therapy. Phage cocktails, instead of a single phage, are commonly used as antibacterial agents since the hosts are unlikely to become resistant to several phages simultaneously. While the spectrum of activity might increase with cocktail complexity, excessive phages could produce side effects, such as the horizontal transfer of genes that augment the fitness of host strains, dysbiosis or high manufacturing costs. Therefore, cocktail formulation represents a compromise between achieving substantial reduction in the bacterial loads and restricting its complexity. Despite the abovementioned points, the observed bacterial load reduction does not increase significantly with the size of phage cocktails, indicating the requirement for a systematic approach to their design. In this work, the information provided by host range matrices was analyzed after building phage-bacteria infection networks (PBINs). To this end, we conducted a meta-analysis of 35 host range matrices, including recently published studies and new datasets comprising Escherichia coli strains isolated during ripening of artisanal raw milk cheese and virulent coliphages from ewes' feces. The nestedness temperature, which reflects the host range hierarchy of the phages, was determined from bipartite host range matrices using heuristic (Nestedness Temperature Calculator) and genetic (BinMatNest) algorithms. The latter optimizes matrix packing, leading to lower temperatures, i.e., it simplifies the identification of the phages with the broadest host range. The structure of infection networks suggests that generalist phages (and not specialist phages) tend to succeed in infecting less susceptible bacteria. A new metric (Φ), which considers some properties of the host range matrices (fill, temperature, and number of bacteria), is proposed as an estimator of phage cocktail size. To identify the best candidates, agglomerative hierarchical clustering using Ward's method was implemented. Finally, a cocktail was formulated for the biocontrol of cheese-isolated E. coli, reducing bacterial counts by five orders of magnitude.

Characterisation of Vibrio Species from Surface and Drinking Water Sources and Assessment of Biocontrol Potentials of Their Bacteriophages

The aim of this study was to characterise Vibrio species of water samples collected from taps, boreholes, and dams in the North West province, South Africa, and assess biocontrol potentials of their bacteriophages. Fifty-seven putative Vibrio isolates were obtained on thiosulfate-citrate-bile-salt-sucrose agar and identified using biochemical tests and species-specific PCRs. Isolates were further characterised based on the presence of virulence factors, susceptibility to eleven antibiotics, and biofilm formation potentials. Twenty-two (38.60%) isolates were confirmed as Vibrio species, comprising V. harveyi (45.5%, n = 10), V. parahaemolyticus (22.7%, n = 5), V. cholerae (13.6%, n = 3), V. mimicus (9.1%, n = 2), and V. vulnificus (9.1%, n = 2). Three of the six virulent genes screened were positively amplified; four V. parahaemolyticus possessed the tdh (18.18%) and trh (18.18%) genes, while the zot gene was harboured by 3 V. cholerae (13.64%) and one V. mimicus (4.55%) isolate. Isolates revealed high levels of resistance to cephalothin (95.45%), ampicillin (77.27%), and streptomycin (40.91%), while lower resistances (4.55%–27.27%) were recorded for other antimicrobials. Sixteen (72.7%) isolates displayed multiple antibiotic-resistant properties. Cluster analysis of antibiotic resistance revealed a closer relationship between Vibrio isolates from different sampling sites. The Vibrio species displayed biofilm formation potentials at 37°C (63.6, n = 14), 35°C (50%, n = 11), and 25°C (36.4%, n = 8). Two phages isolated in this study (vB_VpM_SA3V and vB_VcM_SA3V) were classified as belonging to the family Myoviridae based on electron microscopy. These were able to lyse multidrug-resistant V. parahaemolyticus and V. cholerae strains. These findings not only indicate the presence of antibiotic-resistant virulent Vibrio species from dam, borehole, and tap water samples that could pose a health risk to humans who either come in contact with or consume water but also present these lytic phages as alternative agents that can be exploited for biological control of these pathogenic strains.

Bacteriophages specific to Shiga toxin-producing Escherichia coli exist in goat feces and associated environments on an organic produce farm in Northern California, USA

Shiga toxin-producing Escherichia coli (STECs) contamination of produce, as a result of contact with ruminant fecal material, has been associated with serious foodborne illness. Bacteriophages (phages) that infect STECs have primarily been reported to be of cattle origin. However, they likely exist in other environments or in animals that share habitats with cattle, such as goats. To explore the presence and diversity of phages specific to STEC O157 and the top six non-O157 STECs in goat-associated environments, environmental samples consisting of feces (goat and cattle) and soil samples were collected monthly for six months from an organic produce farm. A variety of phages belonging to the Myoviridae, Siphoviridae, and Podoviridae families were isolated from all goat fecal and half of the soil samples. The most commonly isolated phages belonged to Myoviridae and were lytic against STEC O103. The isolated phages had different host ranges, but collectively, showed lytic activity against O157 and the top six non-O157 STEC strains excluding O121. Two non-O157 STECs (O174: H21 and O-antigen-negative: H18) were isolated from soil and cattle feces, respectively. Although prior studies have reported that goats shed STEC into the environment, the findings of the current study suggest that goat feces may also contain lytic STEC-specific phages. The phages of goat origin have the capacity to infect STECs implicated in causing foodborne outbreaks, making them potential candidates for biocontrol pending additional characterization steps. Further work is needed to determine if the addition of goats to the farm environment could potentially reduce the presence of STECs.

Isolation and characterization of a novel Escherichia coli O157:H7-specific phage as a biocontrol agent

PURPOSE

Escherichia coli O157:H7 is one of the major foodborne pathogens of global public concern. Bacteriophages (phages) have emerged as a promising alternative to antibiotics for controlling pathogenic bacteria. Here, a lytic E. coli O157:H7-specific phage (KFS-EC) was isolated, identified, and characterized to evaluate its potential as a biocontrol agent for E. coli O157:H7.

METHODS

KFS-EC was isolated from slaughterhouse in Korea. Morphological analysis, genomic analysis and several physiological tests were performed to identify and characterize the KFS-EC.

RESULTS

A specificity test indicated KFS-EC was strictly specific to E. coli O157:H7 strains among 60 bacterial strains tested. Morphological and phylogenetic analyses confirmed that KFS-EC belongs to the Rb49virus genus, Tevenvirinae subfamily, and the Myoviridae family of phages. KFS-EC genome consists of 164,725 bp and a total of 270 coding sequence features, of which 114 open reading frames (ORFs) were identified as phage functional genes. KFS-EC does not contain genes encoding lysogenic property and pathogenicity, which ensure its safe application. KFS-EC was relatively stable (~1 log decrease) under stressed conditions such as temperatures (20 °C-50 °C), pHs (3-11), organic solvents (ethanol and chloroform), and biocides (0.1% citric acid, 1% citric acid, and 0.1% peracetic acid). KFS-EC was able to inhibit E. coli O157:H7 efficiently at a multiplicity of infection (MOI) of 0.01 for 8 h with greater inhibitory effect and durability and was stable at 4 °C and 22 °C over a 12-week storage period.

CONCLUSIONS

Our results suggest that KFS-EC could be used as a biocontrol agent to E. coli O157:H7.

Is Shiga Toxin-Producing Escherichia coli O45 No Longer a Food Safety Threat? The Danger is Still Out There

Many Shiga toxin-producing Escherichia coli (STEC) strains, including the serogroups of O157 and most of the top six non-O157 serotypes, are frequently associated with foodborne outbreaks. Therefore, they have been extensively studied using next-generation sequencing technology. However, related information regarding STEC O45 strains is scarce. In this study, three environmental E. coli O45:H16 strains (RM11911, RM13745, and RM13752) and one clinical E. coli O45:H2 strain (SJ7) were sequenced and used to characterize virulence factors using two reference E. coli O45:H2 strains of clinical origin. Subsequently, whole-genome-based phylogenetic analysis was conducted for the six STEC O45 strains and nine other reference STEC genomes, in order to evaluate their evolutionary relationship. The results show that one locus of enterocyte effacement pathogenicity island was found in all three STEC O45:H2 strains, but not in the STEC O45:H16 strains. Additionally, E. coli O45:H2 strains were evolutionarily close to E. coli O103:H2 strains, sharing high homology in terms of virulence factors, such as Stx prophages, but were distinct from E. coli O45:H16 strains. The findings show that E. coli O45:H2 may be as virulent as E. coli O103:H2, which is frequently associated with severe illness and can provide genomic evidence to facilitate STEC surveillance.

Characterization of Non-O157 STEC Infecting Bacteriophages Isolated from Cattle Faeces in North-West South Africa

Non-O157 Shiga toxin-producing Escherichia coli (STEC) E. coli are emerging pathotypes that are frequently associated with diseases in humans around the world. The consequences of these serogroups for public health is a concern given the lack of effective prevention and treatment measures. In this study, ten bacteriophages (phages; SA20RB, SA79RD, SA126VB, SA30RD, SA32RD, SA35RD, SA21RB, SA80RD, SA12KD and SA91KD) isolated from cattle faeces collected in the North-West of South Africa were characterized. Activity of these phages against non-O157 STEC isolates served as hosts for these phages. All of the phages except SA80RD displayed lytic against non-O157 E. coli isolates. Of 22 non-O157 E. coli isolates, 14 were sensitive to 9 of the 10 phages tested. Phage SA35RD was able to lyse 13 isolates representing a diverse group of non-O157 E. coli serotypes including a novel O-antigen Shiga toxigenic (wzx-Onovel5:H19) strain. However, non-O157 E. coli serotypes O76:H34, O99:H9, O129:H23 and O136:H30 were insensitive to all phages. Based on transmission electron microscopy, the non-O157 STEC phages were placed into Myoviridae (n = 5) and Siphoviridae (n = 5). Genome of the phage ranged from 44 to 184.3 kb. All but three phages (SA91KD, SA80RD and SA126VB) were insensitive to EcoRI-HF and HindIII nucleases. This is the first study illustrating that cattle from North-West South Africa harbour phages with lytic potentials that could potentially be exploited for biocontrol against a diverse group of non-O157 STEC isolated from the same region.

Characterization of a Lytic Bacteriophage as an Antimicrobial Agent for Biocontrol of Shiga Toxin-Producing Escherichia coli O145 Strains

Shiga toxin-producing Escherichia coli (STEC) O145 is one of the most prevalent non-O157 serogroups associated with foodborne outbreaks. Lytic phages are a potential alternative to antibiotics in combatting bacterial pathogens. In this study, we characterized a Siphoviridae phage lytic against STEC O145 strains as a novel antimicrobial agent. Escherichia phage vB_EcoS-Ro145clw (Ro145clw) was isolated and purified prior to physiological and genomic characterization. Then, in vitro antimicrobial activity against an outbreak strain, E. coli O145:H28, was evaluated. Ro145clw is a double-stranded DNA phage with a genome 42,031 bp in length. Of the 67 genes identified in the genome, 21 were annotated with functional proteins, none of which were stx genes. Ro145clw had a latent period of 21 min and a burst size of 192 phages per infected cell. The phage could sustain a wide range of pH (pH 3 to pH 10) and temperatures (-80 °C to -73 °C). Ro145clw was able to reduce E. coli O145:H28 in lysogeny broth by approximately 5 log at 37 °C in four hours. These findings indicate that the Ro145clw phage is a promising antimicrobial agent that can be used to control E. coli O145 in adverse pH and temperature conditions.

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.

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 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.