Survival of a Shiga toxin-encoding bacteriophage in a compost model

Benefits and Challenges of Applying Bacteriophage Biocontrol in the Consumer Water Cycle

Bacteria (including disinfection- and antibiotic-resistant bacteria) are abundant in the consumer water cycle, where they may cause disease, and lead to biofouling and infrastructure damage in distributions systems, subsequently resulting in significant economic losses. Bacteriophages and their associated enzymes may then offer a biological control solution for application within the water sector. Lytic bacteriophages are of particular interest as biocontrol agents as their narrow host range can be exploited for the targeted removal of specific bacteria in a designated environment. Bacteriophages can also be used to improve processes such as wastewater treatment, while bacteriophage-derived enzymes can be applied to combat biofouling based on their effectiveness against preformed biofilms. However, the host range, environmental stability, bacteriophage resistance and biosafety risks are some of the factors that need to be considered prior to the large-scale application of these bacterial viruses. Characteristics of bacteriophages that highlight their potential as biocontrol agents are thus outlined in this review, as well as the potential application of bacteriophage biocontrol throughout the consumer water cycle. Additionally, the limitations of bacteriophage biocontrol and corresponding mitigation strategies are outlined, including the use of engineered bacteriophages for improved host ranges, environmental stability and the antimicrobial re-sensitisation of bacteria. Finally, the potential public and environmental risks associated with large-scale bacteriophage biocontrol application are considered, and alternative applications of bacteriophages to enhance the functioning of the consumer water cycle, including their use as water quality or treatment indicators and microbial source tracking markers, are discussed.

Genetically engineered bacteriophages as novel nanomaterials: applications beyond antimicrobial agents

Bacteriophages, also known as phages, are viruses that replicate in bacteria and archaea. Phages were initially discovered as antimicrobial agents, and they have been used as therapeutic agents for bacterial infection in a process known as "phage therapy." Recently, phages have been investigated as functional nanomaterials in a variety of areas, as they can function not only as therapeutic agents but also as biosensors and tissue regenerative materials. Phages are nontoxic to humans, and they possess self-assembled nanostructures and functional properties. Additionally, phages can be easily genetically modified to display specific peptides or to screen for functional peptides via phage display. Here, we demonstrated the application of phage nanomaterials in the context of tissue engineering, sensing, and probing.

Persistence of a Stx-Encoding Bacteriophage in Minced Meat Investigated by Application of an Improved DNA Extraction Method and Digital Droplet PCR

Shiga toxin-producing Escherichia coli (STEC) are important food-borne pathogens with Shiga toxins as the main virulence factor. Shiga toxins are encoded on Shiga toxin-encoding bacteriophages (Stx phages). Stx phages may exist as free bacteriophages in the environment or in foods or as prophages integrated into the host genome. From a food safety perspective, it is important to have knowledge on the survival and persistence of Stx phages in food products since these may integrate into the bacterial hosts through transduction if conditions are right. Here, we present the results from a study investigating the survival of a Stx phage in minced meat from beef stored at a suboptimal temperature (8°C) for food storage along with modifications and optimizations of the methods applied. Minced meat from beef was inoculated with known levels of a labeled Stx phage prior to storage. Phage filtrates were used for plaque assays and DNA extraction, followed by real-time PCR and digital droplet PCR (ddPCR). The results from the pilot study suggested that the initial DNA extraction protocol was not optimal, and several modifications were tested before a final protocol was defined. The final DNA extraction protocol comprised ultra-centrifugation of the entire phage filtrate for concentrating phages and two times phenol–chloroform extraction. The protocol was used for two spiking experiments. The DNA extraction protocol resulted in flexibility in the amount of DNA available for use in PCR analyses, ultimately increasing the sensitivity of the method used for quantification of phages in a sample. All three quantification methods employed (i.e., plaque assays, real-time PCR, and ddPCR) showed similar trends in the development of the phages during storage, where ddPCR has the benefit of giving absolute quantification of DNA copies in a simple experimental setup. The results indicate that the Stx phages persist and remain infective for at least 20 days under the storage conditions used in the present study. Stx phages in foods might represent a potential risk for humans. Although it can be speculated that transduction may take place at 8°C with subsequent forming of STEC, it can be expected to be a rare event. However, such an event may possibly take place under more optimal conditions, such as an increase in storage temperature of foods or in the gastrointestinal tract of humans.

The Site-Specific Recombination System of the Escherichia coli Bacteriophage Φ24B

Stx bacteriophages are members of the lambdoid group of phages and are responsible for Shiga toxin (Stx) production and the dissemination of Shiga toxin genes (stx) across shigatoxigenic Escherichia coli (STEC). These toxigenic bacteriophage hosts can cause life-threatening illnesses, and Stx is the virulence determinant responsible for the severe nature of infection with enterohemorrhagic E. coli, a subset of pathogenic STEC. Stx phages are temperate, and in the present study, the identification of what is actually required for Stx phage Φ24_B and bacterial DNA recombination was tested using both in vitro and in situ recombination assays. It is well established that phage λ, which underpins most of what we understand about lambdoid phage biology, requires its own encoded phage attachment site (attP) of 250 bp, a host-encoded attachment site (attB) of 21 bp, and a host-encoded DNA binding protein known as integration host factor (IHF). The assays applied in this study enabled the manipulation of the phage attachment site (attP) and the bacterial attachment site (attB) sequences and the inclusion or exclusion of a host-encoded accessory element known as integration host factor. We were able to demonstrate that the minimal attP sequence required by Φ24_B phage is between 350 and 427 bp. Unlike phage λ, the minimal necessary flanking sequences for the attB site do not appear to be equal in size, with a total length between 62 and 93 bp. Furthermore, we identified that the Φ24_B integrase does not require IHF to drive the integration and the recombination process. Understanding how this unusual Stx phage integrase works may enable exploitation of its promiscuous nature in the context of genetic engineering.

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.

Composting To Inactivate Foodborne Pathogens for Crop Soil Application: A Review

Compost is organic material that has been degraded into a nutrient-stabilized humus-like substance through intense microbial activity, which can provide essential plant nutrients (nitrogen, phosphorus) to aid in the growth of fruits and vegetables. Compost can be generated from animal waste feedstocks; these can contain human pathogens, which can be inactivated through the heat and microbial competition promoted during the composting process. Outbreaks of infections caused by bacterial pathogens such as Escherichia coli O157:H7, Salmonella, and Listeria monocytogenes on fruit and vegetable commodities consumed raw emphasize the importance of minimizing the risk of pathogenic contamination on produce commodities. This review article investigates factors that affect the reduction and survival of bacterial foodborne pathogens during the composting process. Interactions with indigenous microorganisms, carbon:nitrogen ratios, and temperature changes influence pathogen survival, growth, and persistence in finished compost. Understanding the mechanisms of pathogen survival during the composting process and mechanisms that reduce pathogen populations can minimize the risk of pathogen contamination in the cultivation of fruits and vegetables.

Shigatoxin encoding Bacteriophage ϕ24B modulates bacterial metabolism to raise antimicrobial tolerance

How temperate bacteriophages play a role in microbial infection and disease progression is not fully understood. They do this in part by carrying genes that promote positive evolutionary selection for the lysogen. Using Biolog phenotype microarrays and comparative metabolite profiling we demonstrate the impact of the well-characterised Shiga toxin-prophage ϕ24_B on its Escherichia coli host MC1061. As a lysogen, the prophage alters the bacterial physiology by increasing the rates of respiration and cell proliferation. This is the first reported study detailing phage-mediated control of the E. coli biotin and fatty acid synthesis that is rate limiting to cell growth. Through ϕ24_B conversion the lysogen also gains increased antimicrobial tolerance to chloroxylenol and 8-hydroxyquinoline. Distinct metabolite profiles discriminate between MC1061 and the ϕ24_B lysogen in standard culture, and when treated with 2 antimicrobials. This is also the first reported use of metabolite profiling to characterise the physiological impact of lysogeny under antimicrobial pressure. We propose that temperate phages do not need to carry antimicrobial resistance genes to play a significant role in tolerance to antimicrobials.

Evaluation of calcium cyanamide addition during co-composting of manure and maize straw in a forced-aeration static-pile system

BACKGROUND

Composting is one of the most environmentally friendly treatments to inactivate pathogenic organisms or reduce them to acceptable levels. However, even under thermal conditions, some pathogenic organisms such as E. coli could exist for a long time in composting. Such great persistence may increase the possibility of outbreaks of these organisms and further increase the environmental load. Calcium cyanamide (CaCN₂) has recently been recognized to have the fungicidal effect on the pathogens of the soilborne diseases. So, the present study determined the effect of CaCN₂ addition on composting progress as an antimicrobial agent and an amendment during forced-aeration static-pile composting of cow manure, which was mainly aimed to inhibit the pathogens that had not been inactivated by heat during composting.

METHODS

The mixtures of dairy cow manure and maize straw with addition of 2 % CaCN₂ or no addition were composted for 63 days. The physical, chemical and biological changes in compost mixtures were examined during composting. The data were statistically analyzed using ANOVA procedure from SAS software (version 9.0).

RESULTS

The results showed that the addition of CaCN₂ significantly increased the maximum temperature and lengthened the duration of the thermophilic phase, and increased the percent T-N but decreased C/N ratio. For microbiological test, the addition of CaCN₂ shortened the time to inactivate E. coli, and increased the total average population of thermophilic bacteria but did not significantly influence that of mesophilic bacteria.

CONCLUSION

The results indicated that the addition of CaCN₂, at least at the additive content of 2 % could benefit the thermophilic phase and the composting could quickly reach the sanitary standard during the composting of manure with maize straw in a forced-aeration static-pile system. This finding will contribute to solve the feces disposal problems.

The Survival of a Temperate vtx Bacteriophage and an Anti-Verocytotoxigenic Escherichia coli O157 Lytic Phage in Water and Soil Samples

Verocytotoxigenic (vtx) Escherichia coli (VTEC) are zoonotic foodborne pathogens with the vtx operon encoded by lambdoid bacteriophage (phage). Despite much research on the host bacteria, similar data on the persistence of verocytotoxin converting phage and the ecological niches where transduction occurs are lacking and novel VTEC of important public health significance, have and continue to emerge. This study investigated the survival of a temperate vtx bacteriophage (24_B ::kanamycin^R ) in water (raw farm, pasteurized farm, laboratory tap and autoclaved purified water) and soil (sandy loam and loam soil). It also examined the persistence of an anti-VTEC lytic phage (e11/2) in the same matrices as this may be one option for controlling the emergence of novel VTEC, especially in farm ecological niches where other control options, such as chemical, heat or high pressure treatments, are not feasible. Samples inoculated with 24_B ::kanamycin^R and e11/2 bacteriophage (8 log₁₀ pfu/ml or pfu/g) separately were incubated at 4°C and 14°C, representative Irish Winter and Summer temperatures, respectively, and tested every 2 days for 40 days. The transduction of 24_B ::kanamycin^R was also continuously assessed. Both phages survived with reductions observed, regardless of matrix or storage temperature. Moreover, 24_B ::kanamycin^R was able to transduce its host E. coli strain. It was therefore concluded that aquatic and soil environments on farms may serve as a vtx phage reservoir and transduction point but anti-VTEC phage is a possible biocontrol option.

UV-Sensitivity of Shiga Toxin-Converting Bacteriophage Virions Φ24B, 933W, P22, P27 and P32

Shiga toxin-converting bacteriophages (Stx phages) are present as prophages in Shiga toxin-producing Escherichia coli (STEC) strains. Theses phages can be transmitted to previously non-pathogenic E. coli cells making them potential producers of Shiga toxins, as they bear genes for these toxins in their genomes. Therefore, sensitivity of Stx phage virions to various conditions is important in both natural processes of spreading of these viruses and potential prophylactic control of appearance of novel pathogenic E. coli strains. In this report we provide evidence that virions of Stx phages are significantly more sensitive to UV irradiation than bacteriophage λ. Following UV irradiation of Stx virions at the dose of 50 J/m², their infectivity dropped by 1–3 log₁₀, depending on the kind of phage. Under these conditions, a considerable release of phage DNA from virions was observed, and electron microscopy analyses indicated a large proportion of partially damaged virions. Infection of E. coli cells with UV-irradiated Stx phages resulted in significantly decreased levels of expression of N and cro genes, crucial for lytic development. We conclude that inactivation of Stx virions caused by relatively low dose of UV light is due to damage of capsids that prevents effective infection of the host cells.

Implications of free Shiga toxin-converting bacteriophages occurring outside bacteria for the evolution and the detection of Shiga toxin-producing Escherichia coli

In this review we highlight recent work that has increased our understanding of the distribution of Shiga toxin-converting phages that can be detected as free phage particles, independently of Shiga toxin-producing bacteria (STEC). Stx phages are a quite diverse group of temperate phages that can be found in their prophage state inserted within the STEC chromosome, but can also be found as phages released from the cell after activation of their lytic cycle. They have been detected in extraintestinal environments such as water polluted with feces from humans or animals, food samples or even in stool samples of healthy individuals. The high persistence of phages to several inactivation conditions makes them suitable candidates for the successful mobilization of stx genes, possibly resulting in the genes reaching a new bacterial genomic background by means of transduction, where ultimately they may be expressed, leading to Stx production. Besides the obvious fact that Stx phages circulating between bacteria can be, and probably are, involved in the emergence of new STEC strains, we review here other possible ways in which free Stx phages could interfere with the detection of STEC in a given sample by current laboratory methods and how to avoid such interference.

Development and application of a method for the purification of free shigatoxigenic bacteriophage from environmental samples

Shiga toxin producing Escherichia coli (STEC) strains are foodborne pathogens whose ability to produce Shiga toxin (Stx) is due to the integration of Stx-encoding lambdoid bacteriophage (Stx phage). Circulating, infective Stx phages are very difficult to isolate, purify and propagate such that there is no information on their genetic composition and properties. Here we describe a novel approach that exploits the phage's ability to infect their host and form a lysogen, thus enabling purification of Stx phages by a series of sequential lysogen isolation and induction steps. A total of 15 Stx phages were rigorously purified from water samples in this way, classified by TEM and genotyped using a PCR-based multi-loci characterisation system. Each phage possessed only one variant of each target gene type, thus confirming its purity, with 9 of the 15 phages possessing a short tail-spike gene and identified by TEM as Podoviridae. The remaining 6 phages possessed long tails, four of which appeared to be contractile in nature (Myoviridae) and two of which were morphologically very similar to bacteriophage lambda (Siphoviridae).

Comparative genomics of Shiga toxin encoding bacteriophages

Background

Stx bacteriophages are responsible for driving the dissemination of Stx toxin genes (stx) across their bacterial host range. Lysogens carrying Stx phages can cause severe, life-threatening disease and Stx toxin is an integral virulence factor. The Stx-bacteriophage vB_EcoP-24_B, commonly referred to as Ф24_B, is capable of multiply infecting a single bacterial host cell at a high frequency, with secondary infection increasing the rate at which subsequent bacteriophage infections can occur. This is biologically unusual, therefore determining the genomic content and context of Ф24_B compared to other lambdoid Stx phages is important to understanding the factors controlling this phenomenon and determining whether they occur in other Stx phages.

Results

The genome of the Stx2 encoding phage, Ф24_B was sequenced and annotated. The genomic organisation and general features are similar to other sequenced Stx bacteriophages induced from Enterohaemorrhagic Escherichia coli (EHEC), however Ф24_B possesses significant regions of heterogeneity, with implications for phage biology and behaviour. The Ф24_B genome was compared to other sequenced Stx phages and the archetypal lambdoid phage, lambda, using the Circos genome comparison tool and a PCR-based multi-loci comparison system.

Conclusions

The data support the hypothesis that Stx phages are mosaic, and recombination events between the host, phages and their remnants within the same infected bacterial cell will continue to drive the evolution of Stx phage variants and the subsequent dissemination of shigatoxigenic potential.

High stability of Stx2 phage in food and under food-processing conditions

Bacteriophages (phages) carrying Shiga toxin genes constitute a major virulence attribute in enterohemorrhagic Escherichia coli (EHEC). Several EHEC outbreaks have been linked to food. The survival of such strains in different foods has received much attention, while the fate of the mobile Shiga toxin-converting phages (Stx phages) has been less studied. We have investigated the stability of an Stx phage in several food products and examined how storage, food processing, and disinfection influence the infectivity of phage particles. The study involved a recombinant Stx phage (Δstx::cat) of an E. coli O103:H25 strain from a Norwegian outbreak in 2006. Temperature, matrix, and time were factors of major importance for the stability of phage particles. Phages stored at cooling temperatures (4°C) showed a dramatic reduction in stability compared to those stored at room temperature. The importance of the matrix was evident at higher temperatures (60°C). Phages in ground beef were below the detection level when heated to 60°C for more than 10 min, while phages in broth exposed to the same heating conditions showed a 5-log-higher stability. The phages tolerated desiccation poorly but were infective for a substantial period of time in solutions. Under moist conditions, they also had a high ability to tolerate exposure to several disinfectants. In a dry-fermented sausage model, phages were shown to infect E. coli in situ. The results show that Stx phage particles can maintain their infectivity in foods and under food-processing conditions.

Reservoir of bacterial exotoxin genes in the environment

Many bacteria produce secreted virulence factors called exotoxins. Exotoxins are often encoded by mobile genetic elements, including bacteriophage (phage). Phage can transfer genetic information to the bacteria they infect. When a phage transfers virulence genes to an avirulent bacterium, the bacterium can acquire the ability to cause disease. It is important to understand the role played by the phage that carry these genes in the evolution of pathogens. This is the first report of an environmental reservoir of a bacterial exotoxin gene in an atypical host. Screening bacterial isolates from the environment via PCR identified an isolate with a DNA sequence >95% identical to the Staphylococcus aureus enterotoxin A gene (sea). 16S DNA sequence comparisons and growth studies identified the environmental isolate as a psychrophilic Pseudomonas spp. The results indicate that the sea gene is present in an alternative bacterial host, providing the first evidence for an environmental pool of exotoxin genes in bacteria.

Real-time quantification of mcrA, pmoA for methanogen, methanotroph estimations during composting

Composting is the controlled biological decomposition of organic matter by microorganisms during predominantly aerobic conditions. It is being increasingly adopted due to its benefits in nutrient recycling, soil reclamation, and urban land use. However, it poses an environmental concern related to its contribution to greenhouse gas production. During composting, activities of methanogenic and methanotrophic communities influence the net methane (CH4) release into the atmosphere. Using quantitative polymerase chain reaction (qPCR), this study was aimed at assessing the changes in the methyl-coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) copy numbers for estimation of methanogenic and methanotrophic communities, respectively. Open-windrow composting of beef cattle (Bos Taurus L.) manure with temperatures reaching > 55 degrees C was effective indegrading commensal Escherichia coli within the first week. Quantification of community DNA revealed significant differences in mcrA and pmoA copy numbers between top and middle sections. Consistent mcrA copy numbers (7.07 to 8.69 log copy number g(-1)) were detected throughout the 15-wk composting period. However, pmoA copy number varied significantly over time, with higher values during Week 0 and 1 (6.31 and 5.41 log copy number g(-1), respectively) and the lowest at Week 11 (1.6 log copy number g(-1)). Net surface CH4 emissions over the 15-wk period were correlated with higher mcrA copy number. Higher net ratio of mrA: pmoA copy numbers was observed when surface CH4 flux was high. Our results indicate that mcrA and pmoA copy numbers vary during composting and that methanogen and methanotroph populations need to be examined in conjunction with net CH4 emissions from open-windrow composting of cattle feedlot manure.

Development and validation of a qPCR-based method for quantifying Shiga toxin-encoding and other lambdoid bacteriophages

To address whether seasonal variability exists among Shiga toxin-encoding bacteriophage (Stx phage) numbers on a cattle farm, conventional plaque assay was performed on water samples collected over a 17 month period. Distinct seasonal variation in bacteriophage numbers was evident, peaking between June and August. Removal of cattle from the pasture precipitated a reduction in bacteriophage numbers, and during the winter months, no bacteriophage infecting Escherichia coli were detected, a surprising occurrence considering that 10(31) tailed-bacteriophages are estimated to populate the globe. To address this discrepancy a culture-independent method based on quantitative PCR was developed. Primers targeting the Q gene and stx genes were designed that accurately and discriminately quantified artificial mixed lambdoid bacteriophage populations. Application of these primer sets to water samples possessing no detectable phages by plaque assay, demonstrated that the number of lambdoid bacteriophage ranged from 4.7 x 10(4) to 6.5 x 10(6) ml(-1), with one in 10(3) free lambdoid bacteriophages carrying a Shiga toxin operon (stx). Specific molecular biological tools and discriminatory gene targets have enabled virus populations in the natural environment to be enumerated and similar strategies could replace existing propagation-dependent techniques, which grossly underestimate the abundance of viral entities.

Selected antimicrobial resistance during composting of manure from cattle administered sub-therapeutic antimicrobials

Composting is being increasingly employed for the recycling of nutrients in manure from the livestock industry. However, composting manure from animals fed antimicrobials has not been well characterized. In this study, compost windrows were prepared using manure collected from cattle (Bos Taurus L.) fed tylosin (TY), chlortetracycline-sulphamethazine (TS), and control cattle (no antimicrobials). The objectives of the 18-wk trial were to quantitatively assess the survival of total E. coli, E. coli resistant to ampicillin (Amp(r)) and tetracycline (Tet(r)), and select tetracycline (tet) and erythromycin resistance methylase (erm) genes. We found that while compost windrows did not reach the recommended temperature of 55 degrees C for 15 d, composting reduced high initial levels of total, Amp(r), and Tet(r) E. coli as early as Week 2. A significant antimicrobial effect on total (P = 0.04) and Amp(r) (P = 0.03) E. coli was observed. Significant antimicrobial x time interactions were observed from Week 0 to Week 3 (Total E. coli: P = 0.04; Amp(r): P = 0.02; Tet(r): P = <0.001). Low absolute abundance of tet and erm genes (<10(6) copies g(-1)) was found and the resistance genes displayed different dynamics; tet(A,C) and erm(A) increased marginally at Week 11 relative to Week 0 and 5 and the remaining genes (tet(G), RPP tet, erm(B), erm(C), erm(F), erm(T), and erm(X)) decreased for most time points and treatments. These results indicate that even though composting reduces antimicrobial resistant E. coli, tet and erm genes could still be detected. Our experiments reiterate advantages of polymerase chain reaction (PCR)-based quantitative assays over cultivation-based methods for the rapid identification of composting effectiveness in eliminating resistance genes before land application.

Stx-phages: drivers and mediators of the evolution of STEC and STEC-like pathogens

Bacteriophages, also known as phages, are viruses that infect bacteria. Until recently they have been ignored by most of the scientific community, but their impact upon our world is enormous. They are the most abundant lifeform on the globe and drive the diversity and abundance of bacteria around us, including, in many instances, the pathogenic profiles of many of mankind's most feared bacterial pathogens. This article focuses on how a group of bacteriophages, Stx-phages, which carry the genes encoding Shiga toxin, have driven and are driving the emergence of Shiga toxin-producing pathogens such as the infamous Escherichia coli O157:H7. Since the emergence of this foodborne pathogen as a cause of significant human disease in 1982, more than 500 different serogroups of E. coli have been reported to produce Shiga toxin, as well as a few other organisms. These events and many more are all controlled by the biology of Stx-phages.

Multilocus characterization scheme for shiga toxin-encoding bacteriophages

Shiga toxin-producing Escherichia coli (STEC) strains are food-borne pathogens whose ability to produce Shiga toxin (Stx) is due to integration of Stx-encoding lambdoid bacteriophages. These Stx phages are both genetically and morphologically heterogeneous, and here we report the design and validation of a PCR-based multilocus typing scheme. PCR primer sets were designed for database variants of a range of key lambdoid bacteriophage genes and applied to control phages and 70 stx(+) phage preparations induced from a collection of STEC isolates. The genetic diversity residing within these populations could be described, and observations were made on the heterogeneity of individual gene targets, including the unexpected predominance of short-tailed phages with a highly conserved tail spike protein gene. Purified Stx phages can be profiled using this scheme, and the lambdoid phage-borne genes in induced STEC preparations can be identified as well as those residing in the noninducible prophage complement. The ultimate goal is to enable robust and realistically applicable epidemiological studies of Stx phages and their traits. The impact of Stx phage on STEC epidemiology is currently unknown.

Short-tailed stx phages exploit the conserved YaeT protein to disseminate Shiga toxin genes among enterobacteria

Infection of Escherichia coli by Shiga toxin-encoding bacteriophages (Stx phages) was the pivotal event in the evolution of the deadly Shiga toxin-encoding E. coli (STEC), of which serotype O157:H7 is the most notorious. The number of different bacterial species and strains reported to produce Shiga toxin is now more than 500, since the first reported STEC infection outbreak in 1982. Clearly, Stx phages are spreading rapidly, but the underlying mechanism for this dissemination has not been explained. Here we show that an essential and highly conserved gene product, YaeT, which has an essential role in the insertion of proteins in the gram-negative bacterial outer membrane, is the surface molecule recognized by the majority (ca. 70%) of Stx phages via conserved tail spike proteins associated with a short-tailed morphology. The yaeT gene was initially identified through complementation, and its role was confirmed in phage binding assays with and without anti-YaeT antiserum. Heterologous cloning of E. coli yaeT to enable Stx phage adsorption to Erwinia carotovora and the phage adsorption patterns of bacterial species possessing natural yaeT variants further supported this conclusion. The use of an essential and highly conserved protein by the majority of Stx phages is a strategy that has enabled and promoted the rapid spread of shigatoxigenic potential throughout multiple E. coli serogroups and related bacterial species. Infection of commensal bacteria in the mammalian gut has been shown to amplify Shiga toxin production in vivo, and the data from this study provide a platform for the development of a therapeutic strategy to limit this YaeT-mediated infection of the commensal flora.