Bacteriophages with potential to inactivate Salmonella Typhimurium: Use of single phage suspensions and phage cocktails

Combined effect of SAR-endolysin LysKpV475 with polymyxin B and Salmonella bacteriophage phSE-5

Endolysins are bacteriophage (or phage)-encoded enzymes that catalyse the peptidoglycan breakdown in the bacterial cell wall. The exogenous action of recombinant phage endolysins against Gram-positive organisms has been extensively studied. However, the outer membrane acts as a physical barrier when considering the use of recombinant endolysins to combat Gram-negative bacteria. This study aimed to evaluate the antimicrobial activity of the SAR-endolysin LysKpV475 against Gram-negative bacteria as single or combined therapies, using an outer membrane permeabilizer (polymyxin B) and a phage, free or immobilized in a pullulan matrix. In the first step, the endolysin LysKpV475 in solution, alone and combined with polymyxin B, was tested in vitro and in vivo against ten Gram-negative bacteria, including highly virulent strains and multidrug-resistant isolates. In the second step, the lyophilized LysKpV475 endolysin was combined with the phage phSE-5 and investigated, free or immobilized in a pullulan matrix, against Salmonella enterica subsp. enterica serovar Typhimurium ATCC 13311. The bacteriostatic action of purified LysKpV475 varied between 8.125 μg ml-1 against Pseudomonas aeruginosa ATCC 27853, 16.25 μg ml-1 against S. enterica Typhimurium ATCC 13311, and 32.50 μg ml-1 against Klebsiella pneumoniae ATCC BAA-2146 and Enterobacter cloacae P2224. LysKpV475 showed bactericidal activity only for P. aeruginosa ATCC 27853 (32.50 μg ml-1) and P. aeruginosa P2307 (65.00 μg ml-1) at the tested concentrations. The effect of the LysKpV475 combined with polymyxin B increased against K. pneumoniae ATCC BAA-2146 [fractional inhibitory concentration index (FICI) 0.34; a value lower than 1.0 indicates an additive/combined effect] and S. enterica Typhimurium ATCC 13311 (FICI 0.93). A synergistic effect against S. enterica Typhimurium was also observed when the lyophilized LysKpV475 at ⅔ MIC was combined with the phage phSE-5 (m.o.i. of 100). The lyophilized LysKpV475 immobilized in a pullulan matrix maintained a significant Salmonella reduction of 2 logs after 6 h of treatment. These results demonstrate the potential of SAR-endolysins, alone or in combination with other treatments, in the free form or immobilized in solid matrices, which paves the way for their application in different areas, such as in biocontrol at the food processing stage, biosanitation of food contact surfaces and biopreservation of processed food in active food packing.

Bacteriophages to control Vibrio alginolyticus in live feeds prior to their administration in larviculture

AIMS

This study aimed to evaluate the efficiency of two phages [VB_VaC_TDDLMA (phage TDD) and VB_VaC_SRILMA (phage SRI)] alone and in a cocktail to control Vibrio alginolyticus in brine shrimp before their administration in larviculture.

METHODS AND RESULTS

Phages were isolated from seawater samples and characterized by host spectrum, growth parameters, adsorption rate, genomic analysis, and inactivation efficiency. Both phages belong to the Caudoviricetes class and lack known virulence or antibiotic-resistance genes. They exhibit specificity, infecting only their host, V. alginolyticus CECT 521. Preliminary experiments in a culture medium showed that phage TDD (reduction of 5.8 log CFU ml-1 after 10 h) outperformed phage SRI (reduction of 4.6 log CFU ml-1 after 6 h) and the cocktail TDD/SRI (reduction of 5.2 log CFU ml-1 after 8 h). In artificial marine water experiments with Artemia franciscana, both single phage suspensions and the phage cocktail, effectively inactivated V. alginolyticus in culture water (reduction of 4.3, 2.1, and 1.9 log CFU ml-1 for phages TDD, SRI, and the phage cocktail, respectively, after 12 h) and in A. franciscana (reduction of 51.6%, 87.3%, and 85.3% for phages TDD, SRI, and the phage cocktail, respectively, after 24 h). The two phages and the phage cocktail did not affect A. franciscana natural microbiota or other Vibrio species in the brine shrimp.

CONCLUSIONS

The results suggest that phages can safely and effectively control V. alginolyticus in A. franciscana prior to its administration in larviculture.

Wild-type lytic bacteriophages against Salmonella Heidelberg: Further characterization and effect of prophylactic therapy in broiler chickens

To characterize wild-type bacteriophages and their effect on Salmonella Heidelberg intestinal colonization in broilers, phages combined in a cocktail were continuously delivered via drinking water since the first day after hatching. After challenge with a field strain, broilers were evaluated at regular intervals for S. Heidelberg and bacteriophages in tissues and cecum, and gross and microscopic lesions in organs. Phages were highly virulent against S. Heidelberg by efficiency of plating. One-step growth curves exhibited eclipse period from 20 to 25 min, whereas the lowest latent period and higher burst size found were 45 min and 54 PFU/cell, respectively. Bacteriophage whole genomic sequencing analyses revealed a lack of genes related to lysogeny, antimicrobial resistance, and virulence factors. Relevant gross or microscopic lesions were absent in tissues analyzed from treated broilers. Although numerically stable bacteriophage concentrations were detected in the cecal contents of treated broilers, no significant difference was found for the S. Heidelberg cecal load in comparison to the untreated group and for the prevalence of positive tissues throughout the evaluated period. The phages produced turbid plaques against some S. Heidelberg re-isolated from treated broilers, suggesting the evolving of a resistant subpopulation. Overall, the results provide new evidence of the safety and in vitro replication of such phages in S. Heidelberg. Nevertheless, continuous administration of the phage suspension most likely induced the development of bacteriophage-resistant mutants, which might have affected the in vivo effect. Therefore, a putative administration protocol should be based on other strategies, such as short-term therapy at pre-harvest age.

Partial Characterization of Three Bacteriophages Isolated from Aquaculture Hatchery Water and Their Potential in the Biocontrol of Vibrio spp

Bacteriophages are currently considered one of the most promising alternatives to antibiotics under the 'One Health' approach due to their ability to effectively combat bacterial infections. This study aimed to characterize Vibrio species in hatchery water samples collected from an aquaculture farm and investigate the biocontrol potential of their bacteriophages. Vibrio spp. (n = 32) isolates confirmed by LNA probe-based qPCR were used as hosts. Three Vibrio phages were isolated. IKEM_vK exhibited a broad host range, infecting V. harveyi (n = 8), V. alginolyticus (n = 2), V. azureus (n = 1), and V. ordalii (n = 1). IKEM_v5 showed lytic activity against V. anguillarum (n = 4) and V. ordalii (n = 1), while IKEM_v14 was specific to V. scophtalmi (n = 4). The morphological appearance of phages and their lytic effects on the host were visualized using scanning electron microscopy (SEM). All three phages remained relatively stable within the pH range of 6-11 and up to 60 °C. The lytic activities and biofilm inhibition capabilities of these phages against planktonic Vibrio cells support their potential applications in controlling vibriosis in aquaculture systems.

Bacteriophages as an alternative for biological control of biofilm-forming Salmonella enterica

Salmonellosis is one of the most common foodborne diseases worldwide. Surface adherence and biofilm formation are among the main strategies evolved by Salmonella to survive under harsh conditions and are risk factors for its spread through the food chain. Owing to the increase in antimicrobial resistance, there is a growing need to develop other methods to control foodborne pathogens, and bacteriophages have been suggested as a potential alternative for this purpose. The aim of this study was to evaluate bacteriophages as a biological control of Salmonella enterica serotypes to inhibit and remove bacterial biofilms. A total of 12 S. enterica isolates were selected for this study, all of which were biofilm producers. Seven bacteriophages were tested, individually and in a cocktail, for their host range and efficiency of plating (EOP). The phage cocktail was evaluated for its antibiofilm effect against the Salmonella biofilms. Phages UPF_BP1, UPF_BP2, UPF_BP3, UPF_BP6, and 10:2 possessed a broad lytic spectrum and could infect all S. enterica strains. Phages 10:2, UPF_BP6, and UPF_BP3 had high EOP in 10, 9, and 9 out of the 12 S. enterica strains, respectively. The cocktail was able to infect all S. enterica strains and had a high EOP in 10 out of 12 S. enterica isolates, presenting a broader host range than any of the tested single phages. A wide variation of inhibition among strains was observed, ranging from 14.72% to 88.53%. Multidrug-resistant and strong biofilm producer strains showed high biofilm inhibition levels by phage cocktail. Our findings demonstrate the ability of the cocktail to prevent biofilm formation and remove formed biofilms of Salmonella. These results indicate that the phage cocktail is a promising candidate to be used as an alternative for the control of Salmonella biofilms through surface conditioning.

Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica

The ability of virulent bacteriophages to lyse bacteria influences bacterial evolution, fitness, and population structure. Knowledge of both host susceptibility and resistance factors is crucial for the successful application of bacteriophages as biological control agents in clinical therapy, food processing, and agriculture. In this study, we isolated 12 bacteriophages termed SPLA phage which infect the foodborne pathogen Salmonella enterica. To determine phage host range, a diverse collection of Enterobacteriaceae and Salmonella enterica was used and genes involved in infection by six SPLA phages were identified using Salmonella Typhimurium strain ST4/74. Candidate host receptors included lipopolysaccharide (LPS), cellulose, and BtuB. Lipopolysaccharide was identified as a susceptibility factor for phage SPLA1a and mutations in LPS biosynthesis genes spontaneously emerged during culture with S. Typhimurium. Conversely, LPS was a resistance factor for phage SPLA5b which suggested that emergence of LPS mutations in culture with SPLA1a represented collateral sensitivity to SPLA5b. We show that bacteria-phage co-culture with SPLA1a and SPLA5b was more successful in limiting the emergence of phage resistance compared to single phage co-culture. Identification of host susceptibility and resistance genes and understanding infection dynamics are critical steps in the rationale design of phage cocktails against specific bacterial pathogens.IMPORTANCEAs antibiotic resistance continues to emerge in bacterial pathogens, bacterial viruses (phage) represent a potential alternative or adjunct to antibiotics. One challenge for their implementation is the predisposition of bacteria to rapidly acquire resistance to phages. We describe a functional genomics approach to identify mechanisms of susceptibility and resistance for newly isolated phages that infect and lyse Salmonella enterica and use this information to identify phage combinations that exploit collateral sensitivity, thus increasing efficacy. Collateral sensitivity is a phenomenon where resistance to one class of antibiotics increases sensitivity to a second class of antibiotics. We report a functional genomics approach to rationally design a phage combination with a collateral sensitivity dynamic which resulted in increased efficacy. Considering such evolutionary trade-offs has the potential to manipulate the outcome of phage therapy in favor of resolving infection without selecting for escape mutants and is applicable to other virus-host interactions.

Potential of an Isolated Bacteriophage to Inactivate Klebsiella pneumoniae: Preliminary Studies to Control Urinary Tract Infections

Urinary tract infections (UTIs) caused by resistant Klebsiella pneumoniae can lead to severe clinical complications and even death. An alternative treatment option for infected patients is using bacteriophages. In the present study, we isolated phage VB_KPM_KP1LMA (KP1LMA) from sewage water using a K. pneumoniae strain as a host. Whole-genome analysis indicated that the genome was a double-stranded linear 176,096-bp long DNA molecule with 41.8% GC content and did not contain virulence or antibiotic resistance genes. The inactivation potential of phage KP1LMA was assessed in broth at an MOI of 1 and 10, and a maximum inactivation of 4.9 and 5.4 log CFU/mL, respectively, was observed after 9 h. The efficacy at an MOI of 10 was also assessed in urine to evaluate the phage's performance in an acidic environment. A maximum inactivation of 3.8 log CFU/mL was observed after 9 h. The results suggest that phage KP1LMA could potentially control a UTI caused by this strain of K. pneumoniae, indicating that the same procedure can be used to control UTIs caused by other strains if new specific phages are isolated. Although phage KP1LMA has a narrow host range, in the future, efforts can be made to expand its spectrum of activity and also to combine this phage with others, potentially enabling its use against other K. pneumoniae strains involved in UTIs.

Newly isolated phages preying on Pseudomonas syringae pv. garcae: In vitro and ex vivo inactivation studies in coffee plant leafs

Coffee canker, or bacterial halo blight (BHB) of coffee, is a disease caused by the phytopathogenic bacterium Pseudomonas syringae pv. garcae (Psg), having been found for the first time in 1955, in the Garça region (State of São Paulo), and which has stood out in the Brazilian coffee plantations in recent years, leading to severe economic losses that seriously affect coffee trade. The treatments available are still scarce, involving frequent spraying of coffee plantations with either copper derivatives or the antibiotic kasugamycin. However, these compounds should be avoided due to environmental toxicity and the development of bacterial resistances. Herein we report the isolation and physical/biological characterisation of two novel lytic phages and their efficacy in the control of Psg. Phages ph002F and ph004F were isolated from coffee plant leaves in Brazil (Sorocaba/SP and Itu/SP cities), using Psg IBSBF-158 as the host. According to the transmission electron microscopy analyses, both phages belong to the class Caudoviricetes and present myovirus-like morphotypes. Phages ph002F and ph004F showed eclipse times of 5 min and 20 min, respectively, and a burst size of 123 PFU/host cell and 12 PFU/host cell, respectively, allowing to conclude they replicate well in Psg IBSBF-158 with latency periods of 50 min. Phage ph002F (reduction of 4.59 log CFU/mL, compared to uninfected culture) was more effective in inactivating Psg than phage ph004F (reduction of 3.85 log CFU/mL) after 10 h of incubation at a MOI of 10. As a cocktail, the two phages were highly effective in reducing the bacterial load (reduction of 5.26 log CFU/mL at a MOI of 0.1 or reduction of 5.03 log CFU/mL at a MOI of 10, relative to untreated culture), after 12 h of treatment. This study provides evidence that the isolated phages are promising candidates against the causative agent of BHB in coffee plants.

Use of Bacteriophages to Target Intracellular Pathogens

Bacteriophages (phages) have shown great potential as natural antimicrobials against extracellular pathogens (eg, Escherichia coli or Klebsiella pneumoniae), but little is known about how they interact with intracellular targets (eg, Shigella spp., Salmonella spp., Mycobacterium spp.) in the mammalian host. Recent research has demonstrated that phages can enter human cells. However, for the design of successful clinical applications, further investigation is required to define their subcellular behavior and to understand the complex biological processes that underlie the interaction with their bacterial targets. In this review, we summarize the molecular evidence of phage internalization in eucaryotic cells, with specific focus on proof of phage activity against their bacterial targets within the eucaryotic host, and the current proposed strategies to overcome poor penetrance issues that may impact therapeutic use against the most clinically relevant intracellular pathogens.

Impact of mutagenesis and lateral gene transfer processes in bacterial susceptibility to phage in food biocontrol and phage therapy

Introduction

The emergence of resistance and interference mechanisms to phage infection can hinder the success of bacteriophage-based applications, but the significance of these mechanisms in phage therapy has not been determined. This work studies the emergence of Salmonella isolates with reduced susceptibility to a cocktail of three phages under three scenarios: i) Salmonella cultures (LAB), ii) biocontrol of cooked ham slices as a model of food safety (FOOD), and iii) oral phage therapy in broilers (PT).

Methods

S. Typhimurium ATCC 14028 RifR variants with reduced phage susceptibility were isolated from the three scenarios and conventional and molecular microbiology techniques were applied to study them.

Results and discussion

In LAB, 92% of Salmonella isolates lost susceptibility to all three phages 24 h after phage infection. This percentage was lower in FOOD, with 4.3% of isolates not susceptible to at least two of the three phages after seven days at 4°C following phage treatment. In PT, 9.7% and 3.3 % of isolates from untreated and treated broilers, respectively, displayed some mechanism of interference with the life cycle of some of the phages. In LAB and FOOD scenarios, resistant variants carrying mutations in rfc and rfaJ genes involved in lipopolysaccharide synthesis (phage receptor) were identified. However, in PT, the significant decrease of EOP, ECOI, and burst size observed in isolates was prompted by lateral gene transfer of large IncI1 plasmids, which may encode phage defense mechanisms. These data indicate that the acquisition of specific conjugative plasmids has a stronger impact than mutagenesis on the emergence of reduced phage-susceptibility bacteria in certain environments. In spite of this, neither mechanism seems to significantly impair the success of Salmonella biocontrol and oral phage therapy.

Bacteriophage cocktail application for Campylobacter mitigation - from in vitro to in vivo

BACKGROUND

Effective strategies are urgently needed to control Campylobacteriosis, one of the most important foodborne gastrointestinal diseases worldwide. Administering bacteriophages (phages) is under evaluation as a possible intervention strategy in primary poultry production to reduce the public health risk of human infection. A major challenge is the translation of results from small-scale animal studies to large broiler flocks. In this study, the in vitro lytic activity of 18 Campylobacter-specific group II phages and 19 group III phages were examined singly, and in different combinations from the same group and from both groups using a planktonic killing assay. Based on these results, a combination of phage NCTC 12,673 (group III) and vB_CcM-LmqsCPL1/1 (group II) was selected for in vivo application in a seeder bird model to study its effectiveness under conditions as close as possible to field conditions. One hundred eighty Ross 308 broiler chickens were divided into a control and a treatment group. Ten days post hatch, seeder birds were orally inoculated with the C. jejuni target strain. Phages were administered via drinking water at a total concentration of 107 PFU/mL four, three, and two days before necropsy.

RESULTS

Combining group II and group III phages resulted in significantly higher in vitro growth inhibition against the C. jejuni target strain BfR-CA-14,430 than single application or combinations of phages from the same group. The results of the animal trial showed that the application of the two phages significantly reduced Campylobacter counts in cloacal swabs. At necropsy, Campylobacter counts in colonic content of the treatment group were significantly reduced by 2 log10 units compared to the control group.

CONCLUSIONS

We demonstrated that combining phages of groups II and III results in significantly increased lytic activities. The in vitro results were successfully translated into practical application in a study design close to field conditions, providing new data to apply phages in conventional broiler flocks in the future. Phage application reduced the fecal Campylobacter excretion and Campylobacter concentrations in the colon of broilers.

WGS analysis of two Staphylococcus aureus bacteriophages from sewage in China provides insights into the genetic feature of highly efficient lytic phages

The study of bacteriophages is experiencing a resurgence with the increasing development of antimicrobial resistance in Staphylococcus aureus. Nonetheless, the genetic features of highly efficient lytic S. aureus phage remain to be explored. In this study, two lytic S. aureus phages, SapYZU11 and SapYZU15, were isolated from sewage samples from Yangzhou, China. The phage morphology, one-step growth, host spectrum and lytic activity of these phages were examined, and their whole-genome sequences were analysed and compared with 280 published genomes of staphylococcal phages. The structural organisation and genetic contents of SapYZU11 and SapYZU15 were investigated. The Podoviridae phage SapYZU11 and Herelleviridae phage SapYZU15 effectively lysed all of the 53 S. aureus strains isolated from various sources. However, SapYZU15 exhibited a shorter latent period, larger burst size and stronger bactericidal ability with an anti-bacterial rate of approximately 99.9999% for 24 h. Phylogenetic analysis revealed that Herelleviridae phages formed the most ancestral clades and the S. aureus Podoviridae phages were clustered in the staphylococcal Siphoviridae phage clade. Moreover, phages in different morphology families contain distinct types of genes associated with host cell lysis, DNA packaging and lysogeny. Notably, SapYZU15 harboured 13 DNA metabolism-related genes, 5 lysin genes, 1 holin gene and 1 DNA packaging gene. The data suggest that S. aureus Podoviridae and Siphoviridae phages originated from staphylococcal Herelleviridae phages, and the module exchange of S. aureus phages occurred in the same morphology family. Moreover, the extraordinary lytic capacity of SapYZU15 was likely due to the presence of specific genes associated with DNA replication, DNA packaging and the lytic cycle.

An Edible Biopolymeric Microcapsular Wrapping Integrating Lytic Bacteriophage Particles for Salmonella enterica: Potential for Integration into Poultry Feed

This research work aimed at developing an edible biopolymeric microcapsular wrapping (EBMW) integrating lytic bacteriophage particles for Salmonella enterica, with potential application in poultry feed for biocontrol of that pathogen. This pathogen is known as one of the main microorganisms responsible for contamination in the food industry and in foodstuff. The current techniques for decontamination and pathogen control in the food industry can be very expensive, not very selective, and even outdated, such as the use of broad-spectrum antibiotics that end up selecting resistant bacteria. Hence, there is a need for new technologies for pathogen biocontrol. In this context, bacteriophage-based biocontrol appears as a potential alternative. As a cocktail, both phages were able to significantly reduce the bacterial load after 12 h of treatment, at either multiplicity of infection (MOI) 1 and 10, by 84.3% and 87.6%, respectively. Entrapment of the phage virions within the EBMW matrix did not exert any deleterious effect upon their lytic activity. The results obtained showed high promise for integration in poultry feed aiming at controlling Salmonella enterica, since the edible biopolymeric microcapsular wrapping integrating lytic bacteriophage particles developed was successful in maintaining lytic phage viability while fully stabilizing the phage particles.

Phages for treatment of Salmonella spp infection

Salmonella, is one of the bacterial genera having more than 2500 serogroups is one of the most prominent food borne pathogen that is capable of causing disease out breaks among humans and animals. Recent reports clearly shows that this pathogen is evolved and it developed drug resistant towards most of the commercially available antibiotics. In order to overcome this emerging resistance, Bacteriophage therapy is one of the alternative solutions. It is more pathogen specific, high potency, and thereby highly safe for consumption. This chapter discuss about Rapid screening and Detection Methods Associated with Bacteriophage for Salmonella, commercially available phage products and regulatory status, Salmonella endolysins and future prospects of phage therapy.

Surface conditioning with bacteriophages reduces biofilm formation of Salmonella Heidelberg

Salmonella remains one of the most common foodborne pathogens worldwide, and its resistance to antimicrobials has increased considerably over the years. In this context, was evaluated the action of three bacteriophages isolated or combined in inhibiting the adhesion and removal of Salmonella Heidelberg biofilm on a polystyrene surface. The bacteriophages UPF_BP1, UPF_BP2, UPF_BP3 and a pool of them were used for biocontrol of Salmonella Heidelberg biofilms on polystyrene surface in the action times of 3, 6 and 9 h. Individual and combined phages exhibited reductions in Salmonella Heidelberg adhesion of up to 83.4% and up to 64.0% in removal of preformed biofilm. The use of synergistic combinations between the phages is the most indicated option due to its potential to reduce biofilms. The use of the bacteriophage pool in surface conditioning is an alternative in the control of Salmonella Heidelberg biofilms.

Selection and characterization of bacteriophages specific to Salmonella Choleraesuis in swine

Background and Aim

Salmonella Choleraesuis is the most common serotype that causes salmonellosis in swine. Recently, the use of bacteriophages as a potential biocontrol strategy has increased. Therefore, this study aimed to isolate and characterize bacteriophages specific to S. Choleraesuis associated with swine infection and to evaluate the efficacy of individual phages and a phage cocktail against S. Choleraesuis strains in simulated intestinal fluid (SIF).

Materials and Methods

Three strains of S. Choleraesuis isolated from pig intestines served as host strains for phage isolation. The other 10 Salmonella serovars were also used for the phage host range test. The antibiotic susceptibility of the bacterial strains was investigated. Water samples from natural sources and drain liquid from slaughterhouses were collected for phage isolation. The isolated phages were characterized by determining the efficiency of plating against all Salmonella strains and the stability at a temperature range (4°C-65°C) and at low pH (2.5-4.0) in simulated gastric fluids (SGFs). Furthermore, morphology and genomic restriction analyses were performed for phage classification phages. Finally, S. Choleraesuis reduction in the SIF by the selected individual phages and a phage cocktail was investigated.

Results

The antibiotic susceptibility results revealed that most Salmonella strains were sensitive to all tested drugs. Salmonella Choleraesuis KPS615 was multidrug-resistant, showing resistance to three antibiotics. Nine phages were isolated. Most of them could infect four Salmonella strains. Phages vB_SCh-RP5i3B and vB_SCh-RP61i4 showed high efficiency in infecting S. Choleraesuis and Salmonella Rissen. The phages were stable for 1 h at 4°C-45°C. However, their viability decreased when the temperature increased to 65°C. In addition, most phages remained viable at a low pH (pH 2.5-4.0) for 2 h in SGF. The efficiency of phage treatment against S. Choleraesuis in SIF showed that individual phages and a phage cocktail with three phages effectively reduced S. Choleraesuis in SIF. However, the phage cocktails were more effective than the individual phages.

Conclusion

These results suggest that the newly isolated phages could be promising biocontrol agents against S. Choleraesuis infection in pigs and could be orally administered. However, further in vivo studies should be conducted.

Isolation and Molecular Characterization of Two Novel Lytic Bacteriophages for the Biocontrol of Escherichia coli in Uterine Infections: In Vitro and Ex Vivo Preliminary Studies in Veterinary Medicine

E. coli is one of the etiological agents responsible for pyometra in female dogs, with conventional treatment involving ovariohysterectomy. Here, we report the isolation and full characterization of two novel lytic phages, viz. vB_EcoM_Uniso11 (ph0011) and vB_EcoM_Uniso21 (ph0021). Both phages belong to the order Caudovirales and present myovirus-like morphotypes, with phage ph0011 being classified as Myoviridae genus Asteriusvirus and phage ph0021 being classified as Myoviridae genus Tequatrovirus, based on their complete genome sequences. The 348,288 bp phage ph0011 and 165,222 bp phage ph0021 genomes do not encode toxins, integrases or antimicrobial resistance genes neither depolymerases related sequences. Both phages were shown to be effective against at least twelve E. coli clinical isolates in in vitro antibacterial activity assays. Based on their features, both phages have potential for controlling pyometra infections caused by E. coli. Phage ph0011 (reduction of 4.24 log CFU/mL) was more effective than phage ph0021 (reduction of 1.90 log CFU/mL) after 12 h of incubation at MOI 1000. As a cocktail, the two phages were highly effective in reducing the bacterial load (reduction of 5.57 log CFU/mL) at MOI 100, after 12 h of treatment. Both phages were structurally and functionally stabilized in vaginal egg formulations.

Complete genome sequencing of a Tequintavirus bacteriophage with a broad host range against Salmonella Abortus equi isolates from donkeys

Salmonella enterica subspecies enterica serovar abortus equi (S. Abortus equi) is the most common cause of abortion in mares. It has recently been found to cause abortion in donkeys more frequently in China. A novel virulent bacteriophage vB_SabS_Sds2 (hereafter designated as Sds2) was isolated from the feces of donkeys using a S. Abortus equi strain as a host. Phage Sds2 had an isometric polyhedral head and an uncontracted long tail, belonging to the Tequintavirus, Markadamsvirinae, Demerecviridae, Caudovirales. The genome of phage Sds2 was 114,770 bp, with a GC content of 40.26%. The genome contained 160 open reading frames (ORFs), and no ORFs were associated with pathogenicity, drug resistance, or lysogenization by sequence analysis. Both genome annotation and phylogenetic analysis indicated that phage Sds2 was highly similar to T5-like bacteriophages. Phage Sds2 could lyse 100% (30/30) of S. Abortus equi strains, 25.3% (24/95) of other serotypes of Salmonella strains, and 27.6% (8/29) of Escherichia coli strains using the double-layer agar plate method. The in vitro test showed that phage Sds2 had high bactericidal activity against S. Abortus equi at a wide range of MOIs. The in vivo test indicated that phage Sds2 had an inhibitory effect on abortion in mice challenged with S. Abortus equi. In general, phage Sds2 is a novel lytic phage with a wide host range and has the potential to prevent abortion caused by S. Abortus equi.

A phage cocktail combined with the enteric probiotic Lactobacillus reuteri ameliorated mouse colitis caused by S. typhimurium

Salmonella enterica serovar Typhimurium (S. typhimurium) is one of the most important foodborne pathogens that causes colitis in humans. In this study, we compared the effects of a therapeutic treatment using a phage cocktail (Pc) in combination or not with Lactobacillus reuteri (L. reuteri) in an S. typhimurium-induced colitis murine model. An oral administration of 4 × 10⁸ CFU per mouse of S. typhimurium resulted in intestinal barrier disruption and severe inflammatory symptoms. S. typhimurium in the colon of the mice treated with the Pc and L. reuteri (PcLR) combination were completely removed compared to those in the single Pc or single L. reuteri treatment groups. Furthermore, compared with the infected group, the intestinal barrier and colonic pathological damage were significantly improved in the PcLR-treated group. Additionally, the short-chain fatty acid (SCFA) levels in the feces of the mice in the PcLR treatment group were significantly increased compared to those in the feces of the mice in the infected group. In addition, the combination of Pc with acetate and reuterin released by L. reuteri (PcReAc) can also achieve the same effect as PcLR treatment. Thus, these results indicated that the acetate and reuterin released by L. reuteri play an important role in the treatment. The extraordinary therapeutic effects of PcLR and PcReAc depend on the specific bactericidal activity of Pc and the broad-spectrum bactericidal activity and immunomodulation of L. reuteri (or acetate and reuterin) in the host. This study provides a new concept for the treatment of inflammatory diseases caused by intestinal pathogens.

Formulation of phage cocktails and evaluation of their interaction with antibiotics in inhibiting carbapenemase-producing Klebsiella pneumoniae in vitro in Kenya

Background: The development of alternative control measures, such as phage therapy or adjunctive therapy, is urgently needed to manage the dissemination of carbapenemase-producing Klebsiella pneumoniae.Objective: This study aimed to evaluate the therapeutic potential of formulated phage cocktails and their interaction with select antibiotics in inhibiting the growth of carbapenemase-producing K. pneumoniae clinical isolate in vitro in Kenya.Methods: The study was conducted from February 2021 to October 2021 at the Institute of Primate Research, Nairobi, Kenya. Phage cocktails were formulated based on the morphology and biological properties of precipitated Klebsiella phages. The efficacy of individual bacteriophages and phage cocktails as well as their combination with antibiotics were determined for their inhibitory activity on carbapenemase-producing K. pneumoniae (KP20).Results: The precipitated bacteriophages were members of Myoviridae, Siphoviridae and Podoviridae. Regarding the evaluation of the phage cocktails, the absorbances at 600 nm of the bacterial culture treated with the two-phage cocktail (2φ MA) ranged from 0.173 to 0.246 at 16 h and 20 h whereas it peaked from 2.116 to 2.190 for the positive control. Moreover, the results of the adjunctive therapy showed that the optical density at 600 nm of the bacterial culture treated with 2φ MA was 0.186 at 24 h post-incubation time while it was 0.099 with the bacterial culture treated with imipenem in combination with 2φ MA.Conclusion: This study demonstrated that the two-phage cocktail in combination with imipenem was able to synergistically delay the increase in carbapenemase-producing K. pneumoniae growth in vitro.

Isolation and Molecular Characterization of a Novel Lytic Bacteriophage That Inactivates MDR Klebsiella pneumoniae Strains

The worldwide increase in serious infections caused by multidrug-resistant (MDR) K. pneumoniae emphasizes the urgent need of new therapeutic strategies for the control of this pathogen. There is growing interest in the use of bacteriophages (or phages) to treat K. pneumoniae infections, and newly isolated phages are needed. Here, we report the isolation and physical/biological/molecular characterization of a novel lytic phage and its efficacy in the control of MDR K. pneumoniae. The phage vB_KpnS_Uniso31, referred to hereafter as phage Kpn31, was isolated from hospital wastewater using K. pneumoniae CCCD-K001 as the host. Phage Kpn31 presents a siphovirus-like morphotype and was classified as Demerecviridae; Sugarlandvirus based on its complete genome sequence. The 113,444 bp Kpn31 genome does not encode known toxins or antimicrobial resistance genes, nor does it encode depolymerases related sequences. Phage Kpn31 showed an eclipse time of 15 min and a burst size of 9.12 PFU/host cell, allowing us to conclude it replicates well in K. pneumoniae CCCD-K001 with a latency period of 30 min. Phage Kpn31 was shown to be effective against at least six MDR K. pneumoniae clinical isolates in in vitro antibacterial activity assays. Based on its features, phage Kpn31 has potential for controlling infections caused by MDR K. pneumoniae.

Isolation of Three Coliphages and the Evaluation of Their Phage Cocktail for Biocontrol of Shiga Toxin-Producing Escherichia coli O157 in Milk

Shiga toxin-producing Escherichia coli (STEC) O157 is a well-known foodborne pathogen and a leading cause of many intestinal diseases. In this study, we explore the use of a phage cocktail to help control STEC O157 in broth and milk. We isolated three virulent phages from sanitary sewages using a STEC O157 as the indicator bacterium. Phenotypical characterizations revealed that these three phages belong to the Myoviridae family and were stable at different temperatures and pH. They displayed a short latent period between 10 and 20 min, and a burst size (32-65 per infected cell). No virulence factors and drug resistance genes were found in their genomes. Bacterial lysis assays showed that a phage cocktail comprising these three phages was more effective (at least 4.32 log reduction) against STEC O157 at 25 °C with multiplicity of infection (MOI) = 1000 in broth medium. At 4 °C, a 3.8 log reduction in the number of viable STEC O157 after 168-h treatment with phage cocktail at MOI = 1000 was observed in milk, compared to phage-free bacterial control group. Characterizations of phages suggest they could be developed into novel therapeutic agents to control STEC O157 in milk production.

Phenotypic characterization and genome analysis of a novel Salmonella Typhimurium phage having unique tail fiber genes

Salmonella enterica serovar Typhimurium is a foodborne pathogen causing occasional outbreaks of enteric infections in humans. Salmonella has one of the largest pools of temperate phages in its genome that possess evolutionary significance for pathogen. In this study, we characterized a novel temperate phage Salmonella phage BIS20 (BIS20) with unique tail fiber genes. It belongs to the subfamily Peduovirinae genus Eganvirus and infects Salmonella Typhimurium strain (SE-BS17; Acc. NO MZ503545) of poultry origin. Phage BIS20 was viable only at biological pH and temperature ranges (pH7 and 37 °C). Despite being temperate BIS20 significantly slowed down the growth of host strain for 24 h as compared to control (P < 0.009). Phage BIS20 features 29,477-base pair (bp) linear DNA genome with 53% GC content and encodes for 37 putative ORFs. These ORFs have mosaic arrangement as indicated by its ORF similarity to various phages and prophages in NCBI. Genome analysis indicates its similarity to Salmonella enterica serovar Senftenberg prophage (SEStP) sequence (Nucleotide similarity 87.7%) and Escherichia virus 186 (~ 82.4% nucleotide similarity). Capsid genes were conserved however those associated with tail fiber formation and assembly were unique to all members of genus Eganvirus. We found strong evidence of recombination hotspot in tail fiber gene. Our study identifies BIS20 as a new species of genus Eganvirus temperate phages as its maximum nucleotide similarity is 82.4% with any phage in NCBI. Our findings may contribute to understanding of origin of new temperate phages.

Isolation, characterization and application of bacteriophage PSDA-2 against Salmonella Typhimurium in chilled mutton

Salmonella is a common foodborne pathogen, especially in meat and meat products. Lytic phages are promising alternatives to conventional methods for Salmonella biocontrol in food and food processing. In this study, a virulent bacteriophage (PSDA-2) against Salmonella enterica serovar Typhimurium was isolated from the sewage and it was found that PSDA-2 belongs to Cornellvirus genus of Siphoviridae family by morphological and phylogenetic analysis. Based on the one-step growth curve, PSDA-2 has a short latent period (10 min) and a high burst size (120 PFU/cell). The stability test in vitro reveals that PSDA-2 is stable at 30–70°C and pH 3–10. Bioinformatics analysis show that PSDA-2 genome consists of 40,062 bp with a GC content of 50.21% and encodes 63 open reading frames (ORFs); no tRNA genes, lysogenic genes, drug resistance genes and virulence genes were identified in the genome. Moreover, the capacity for PSDA-2 to control Salmonella Typhimurium in chilled mutton was investigated. The results show that incubation of PSDA-2 at 4°C reduced recoverable Salmonella by 1.7 log CFU/mL and 2.1 log CFU/mL at multiplicity of infection (MOI) of 100 and 10,000 respectively, as relative to the phage-excluded control. The features of phage PSDA-2 suggest that it has the potential to be an agent to control Salmonella.

Characterization and in vitro testing of newly isolated lytic bacteriophages for the biocontrol of Pseudomonas aeruginosa

Aim: Two lytic phages were isolated using P. aeruginosa DSM19880 as host and fully characterized. Materials & methods: Phages were characterized physicochemically, biologically and genomically. Results & conclusion: Host range analysis revealed that the phages also infect some multidrug-resistant (MDR) P. aeruginosa clinical isolates. Increasing MOI from 1 to 1000 significantly increased phage efficiency and retarded bacteria regrowth, but phage ph0034 (reduction of 7.5 log CFU/ml) was more effective than phage ph0031 (reduction of 5.1 log CFU/ml) after 24 h. Both phages belong to Myoviridae family. Genome sequencing of phages ph0031 and ph0034 showed that they do not carry toxin, virulence, antibiotic resistance and integrase genes. The results obtained are highly relevant in the actual context of bacterial resistance to antibiotics.

Comparision of biological and genomic characteristics of five virulent bacteriophages against Enterobacter hormaechei

Enterobacter hormaechei is a zoonotic bacteria that may cause respiratory diseases in animals and neonatal sepsis in humans. Bacteriophages are increasingly considered as potential biocontrol agents to control pathogens in the food industry. In this study, five E. hormaechei virulent phages, named as Ehp-YZU08, Ehp-YZU10, Ehp-YZU9-1, Ehp-YZU9-2 and Ehp-YZU9-3, were isolated from sewage in China and analyzed for their biological and whole-genome characteristics, and a comparative genomic analysis was performed to study the functional genes and phylogenetic evolution of phages. The results showed that four of the phage strains belong to the Podoviridae family and one belongs to the Myoviridae family. The burst sizes were 70-283 PFU/cell after a latent period of 5-40 min. Phages were able to survive in a pH range of 5-10 and resist temperatures up to 60 °C for 60 min. The sequencing results showed that the full length of the genomes of the five phages ranged from 39,502 to 173,418 bp. Each phage contained multiple genes related to phage replication, and genes related to bacterial virulence or drug resistance were not found. The five phages belonged to three different groups by a construction of a phylogenetic tree, and the significant genetic evolutionary distance from each E. hormaechei phage was observed. The inhibition assay showed that all five phages could completely inhibit the growth of E. hormaechei at 37 °C within 8 h, suggesting that the phages in this study have great potential for the development of biocontrol agents against E. hormaechei in the food industry.

Uses of Bacteriophages as Bacterial Control Tools and Environmental Safety Indicators

Bacteriophages are bacterial-specific viruses and the most abundant biological form on Earth. Each bacterial species possesses one or multiple bacteriophages and the specificity of infection makes them a promising alternative for bacterial control and environmental safety, as a biotechnological tool against pathogenic bacteria, including those resistant to antibiotics. This application can be either directly into foods and food-related environments as biocontrol agents of biofilm formation. In addition, bacteriophages are used for microbial source-tracking and as fecal indicators. The present review will focus on the uses of bacteriophages like bacterial control tools, environmental safety indicators as well as on their contribution to bacterial control in human, animal, and environmental health.

A Validation System for Selection of Bacteriophages against Shiga Toxin-Producing Escherichia coli Contamination

Shiga toxin-producing Escherichia coli (STEC) can cause severe infections in humans, leading to serious diseases and dangerous complications, such as hemolytic-uremic syndrome. Although cattle are a major reservoir of STEC, the most commonly occurring source of human infections are food products (e.g., vegetables) contaminated with cow feces (often due to the use of natural fertilizers in agriculture). Since the use of antibiotics against STEC is controversial, other methods for protection of food against contaminations by these bacteria are required. Here, we propose a validation system for selection of bacteriophages against STEC contamination. As a model system, we have employed a STEC-specific bacteriophage vB_Eco4M-7 and the E. coli O157:H7 strain no. 86-24, bearing Shiga toxin-converting prophage ST2-8624 (Δstx2::cat gfp). When these bacteria were administered on the surface of sliced cucumber (as a model vegetable), significant decrease in number viable E. coli cells was observed after 6 h of incubation. No toxicity of vB_Eco4M-7 against mammalian cells (using the Balb/3T3 cell line as a model) was detected. A rapid decrease of optical density of STEC culture was demonstrated following addition of a vB_Eco4M-7 lysate. However, longer incubation of susceptible bacteria with this bacteriophage resulted in the appearance of phage-resistant cells which predominated in the culture after 24 h incubation. Interestingly, efficiency of selection of bacteria resistant to vB_Eco4M-7 was higher at higher multiplicity of infection (MOI); the highest efficiency was evident at MOI 10, while the lowest occurred at MOI 0.001. A similar phenomenon of selection of the phage-resistant bacteria was also observed in the experiment with the STEC-contaminated cucumber after 24 h incubation with phage lysate. On the other hand, bacteriophage vB_Eco4M-7 could efficiently develop in host bacterial cells, giving plaques at similar efficiency of plating at 37, 25 and 12 °C, indicating that it can destroy STEC cells at the range of temperatures commonly used for vegetable short-term storage. These results indicate that bacteriophage vB_Eco4M-7 may be considered for its use in food protection against STEC contamination; however, caution should be taken due to the phenomenon of the appearance of phage-resistant bacteria.

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

Applications of bacteriophages against intracellular bacteria

Infectious diseases pose a significant threat to both human and animal populations. Intracellular bacteria are a group of pathogens that invade and survive within the interior of eukaryotic cells, which in turn protect them from antibacterial drugs and the host immune system. Limited penetration of antibacterials into host cells results in insufficient bacterial clearance and treatment failure. Bacteriophages have, over the decades, been proved to play an important role in combating bacterial infections (phage therapy), making them an important alternative to classical antibiotic strategies today. Phages have been found to be effective at killing various species of extracellular bacteria, but little is still known about how phages control intracellular infections. With advances in phage genomics and mechanisms of delivery and cell uptake, the development of phage-based antibacterial strategies to address the treatment of intracellular bacteria has general potential. In this review, we present the current state of knowledge regarding the application of bacteriophages against intracellular bacteria. We cover phage deployment against the most common intracellular pathogens with special attention to therapeutic and preventive strategies.

Application of the Resazurin Cell Viability Assay to Monitor Escherichia coli and Salmonella Typhimurium Inactivation Mediated by Phages

Bacterial inactivation using bacteriophages (or phages) has emerged as an effective solution for bacterial infections, but the screening methods used to evaluate the effectiveness of the phages to inactivate bacteria are not fast, reliable or precise enough. The efficiency of bacterial inactivation by phages has been evaluated by monitoring bacterial concentration either by counting colony-forming units (CFU), a laborious and time-consuming method, or by monitoring the optical density (OD), a less sensitive method. In this study, the resazurin cell viability assay was used to monitor the viability of bacteria from different genera during the inactivation by different phages, and the results were compared with the standard methods used to assess bacterial inactivation. The results showed that the resazurin colorimetric cell viability assay produces similar results to the standard method of colony-counting and giving, and also more sensitive results than the OD method. The resazurin assay can be used to quickly obtain the results of the cell viability effect profile using two different bacterial strains and several different phages at the same time, which is extremely valuable in screening studies. Moreover, this methodology is established as an effective, accurate and rapid method when compared to the ones widely used to monitor bacterial inactivation mediated by phages.

Bacteriophages with Potential to Inactivate Aeromonas hydrophila in Cockles: In Vitro and In Vivo Preliminary Studies

The recurrent emergence of infection outbreaks associated with shellfish consumption is of extreme importance for public health. The present study investigated the potential application of phages AH-1, AH-4, and AH-5 to inactivate Aeromonas hydrophila, a causative agent of infections in humans associated with bivalve shellfish consumption. The inactivation of A. hydrophila was assessed in vitro, using a liquid culture medium, and in vivo, using artificially contaminated cockles with A. hydrophila ATCC 7966. In the in vitro experiments, all phages were effective against A. hydrophila, but phage AH-1 (with a maximum reduction of 7.7 log colonies forming units CFU/mL) was more effective than phages AH-4 and AH-5 (with reductions of 4.9 and 4.5 log CFU/mL, respectively). The cocktails AH-1/AH-4, AH-1/AH-5, AH-4/AH-5, and AH-1/AH-4/AH-5 were slightly more effective than the single phage suspensions. The phages presented a low emergence rate of phage-resistant mutants. When artificially contaminated cockles were treated in static seawater with phage AH-1, around 44% of the added A. hydrophila (1.0 log CFU/g) was inactivated. The results of this study suggest that phage therapy can be an effective alternative to control human pathogenic bacteria during depuration.

Application of a novel phage vB_SalS-LPSTLL for the biological control of Salmonella in foods

Salmonella is one of the most common foodborne pathogens around the world. Phages are envisioned as a new strategy to control foodborne pathogenic bacteria and food safety. A Salmonella specific lytic phage vB_SalS-LPSTLL (LPSTLL) was selected for food applications on the basis of lytic range, lytic efficiency, functional stability and characteristics. Phage LPSTLL was able to lyse 11 Salmonella serotypes, which represents the broadest range reported Salmonella phages, and was able to suppress the growth of Salmonella enterica in liquid culture over nine hours. LPSTLL exhibited rapid reproductive activity with a short latent period and a large burst size in one-step growth experiment. LPSTLL remained active over a pH range of 3.0 to 12.0, and at incubation temperatures up to 60 °C for 60 min, indicating wide applicability for food processing and storage. Significant reductions of viable Salmonella were observed in diverse foods (milk, apple juice, chicken and lettuce) with reductions up to 2.8 log CFU/mL recorded for milk. Sensory evaluation indicated that treatment with phage LPSTLL did not alter the visual or tactile quality of food matrices. Genome analysis of LPSTLL indicated the absence of any virulence or antimicrobial resistance genes. Genomic comparisons suggest phage LPSTLL constitutes a novel member of a new genus, the LPSTLLvirus with the potential for Salmonella biocontrol in the food industry.

How Broad Is Enough: The Host Range of Bacteriophages and Its Impact on the Agri-Food Sector

Novel bacteriophages (phages) possessing a broad host range are consistently and routinely reported, yet there is presently no consensus on the definition of “broad host range.” As phages are increasingly being used in the development of methods for the detection and biocontrol of human pathogens, it is important to address the limitations associated with the host range. For instance, unanticipated host range breadth may result in the detection of nonpathogenic targets, thereby increasing the false-positive rate. Moreover, a broad host range is generally favored in biocontrol applications despite the risk of undesirable ancillary effects against nontarget species. Here, we discuss the research progress, applications, and implications of broad host range phages with a focus on tailed broad host range phages infecting human pathogens of concern in the Agri-Food sector.

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.

Phage cocktail powder for Pseudomonas aeruginosa respiratory infections

Phage cocktail broadens the host range compared with a single phage and minimizes the development of phage-resistant bacteria thereby promoting the long-term usefulness of inhaled phage therapy. In this study, we produced a phage cocktail powder by spray drying three Pseudomonas phages PEV2 (podovirus), PEV1 and PEV20 (both myovirus) with lactose (80 wt%) and leucine (20 wt%) as excipients. Our results showed that the phages remained viable in the spray dried powder, with little to mild titer reduction (ranging from 0.11 to 1.3 logs) against each of their specific bacterial strains. The powder contained spherical particles with a small volume median diameter of 1.9 µm (span 1.5), a moisture content of 3.5 ± 0.2 wt%., and was largely amorphous with some crystalline peaks, which were assigned to the excipient leucine, as shown in the X-ray diffraction pattern. When the powder was dispersed using the low- and high-resistance Osmohalers, the fine particle fraction (FPF, wt. % of particles < 5 µm in the aerosols relative to the loaded dose) values were 45.37 ± 0.27% and 62.69 ± 2.1% at the flow rate of 100 and 60 L/min, respectively. In conclusion, the PEV phage cocktail powder produced was stable, inhalable and efficacious in vitro against various MDR P. aeruginosa strains that cause pulmonary infections. This formulation will broaden the bactericidal spectrum and reduce the emergence of resistance in bacteria compared with single-phage formulations reported previously.

Phage Biocontrol of Campylobacter: A One Health Approach

Human infections by Campylobacter species are among the most reported bacterial gastrointestinal diseases in the European Union and worldwide with severe outcomes in rare cases. Considering the transmission routes and farm animal reservoirs of these zoonotic pathogens, a comprehensive One Health approach will be necessary to reduce human infection rates. Bacteriophages are viruses that specifically infect certain bacterial genera, species, strains or isolates. Multiple studies have demonstrated the general capacity of phage treatments to reduce Campylobacter loads in the chicken intestine. However, phage treatments are not yet approved for extensive use in the agro-food industry in Europe. Technical inconvenience is mainly related to the efficacy of phages, depending on the optimal choice of phages and their combination, as well as application route, concentration and timing. Additionally, regulatory uncertainties have been a major concern for investment in commercial phage-based products. This review addresses the question as to how phages can be put into practice and can help to solve the issue of human campylobacteriosis in a sustainable One Health approach. By compiling the reported findings from the literature in a standardized manner, we enabled inter-experimental comparisons to increase our understanding of phage infection in Campylobacter spp. and practical on-farm studies. Further, we address some of the hurdles that still must be overcome before this new methodology can be adapted on an industrial scale. We envisage that phage treatment can become an integrated and standardized part of a multi-hurdle anti-bacterial strategy in food production. The last part of this chapter deals with some of the issues raised by legal authorities, bringing together current knowledge on Campylobacter-specific phages and the biosafety requirements for approval of phage treatment in the food industry.

Kiwifruit bacterial canker: an integrative view focused on biocontrol strategies

Phage-based biocontrol strategies can be an effective alternative to control Psa-induced bacterial canker of kiwifruit. The global production of kiwifruit has been seriously affected by Pseudomonas syringae pv. actinidiae (Psa) over the last decade. Psa damages both Actinidia chinensis var. deliciosa (green kiwifruit) but specially the susceptible Actinidia chinensis var. chinensis (gold kiwifruit), resulting in severe economic losses. Treatments for Psa infections currently available are scarce, involving frequent spraying of the kiwifruit plant orchards with copper products. However, copper products should be avoided since they are highly toxic and lead to the development of bacterial resistance to this metal. Antibiotics are also used in some countries, but bacterial resistance to antibiotics is a serious worldwide problem. Therefore, it is essential to develop new approaches for sustainable agriculture production, avoiding the emergence of resistant Psa bacterial strains. Attempts to develop and establish highly accurate approaches to combat and prevent the occurrence of bacterial canker in kiwifruit plants are currently under study, using specific viruses of bacteria (bacteriophages, or phages) to eliminate the Psa. This review discusses the characteristics of Psa-induced kiwifruit canker, Psa transmission pathways, prevention and control, phage-based biocontrol strategies as a new approach to control Psa in kiwifruit orchards and its advantages over other therapies, together with potential ways to bypass phage inactivation by abiotic factors.

An Optimized Bacteriophage Cocktail Can Effectively Control Salmonella in vitro and in Galleria mellonella

Salmonella spp. is a leading cause of gastrointestinal enteritis in humans where it is largely contracted via contaminated poultry and pork. Phages can be used to control Salmonella infection in the animals, which could break the cycle of infection before the products are accessible for consumption. Here, the potential of 21 myoviruses and a siphovirus to eliminate Salmonella in vitro and in vivo was examined with the aim of developing a biocontrol strategy to curtail the infection in poultry and swine. Together, the phages targeted the twenty-three poultry and ten swine prevalent Salmonella serotype isolates tested. Although individual phages significantly reduced bacterial growth of representative isolates within 6 h post-infection, bacterial regrowth occurred 1 h later, indicating proliferation of resistant strains. To curtail bacteriophage resistance, a novel three-phage cocktail was developed in vitro, and further investigated in an optimized Galleria mellonella larva Salmonella infection model colonized with representative swine, chicken and laboratory strains. For all the strains examined, G. mellonella larvae given phages 2 h prior to bacterial exposure (prophylactic regimen) survived and Salmonella was undetectable 24 h post-phage treatment and throughout the experimental time (72 h). Administering phages with bacteria (co-infection), or 2 h post-bacterial exposure (remedial regimen) also improved survival (73-100% and 15-88%, respectively), but was less effective than prophylaxis application. These pre-livestock data support the future application of this cocktail for further development to effectively treat Salmonella infection in poultry and pigs. Future work will focus on cocktail formulation to ensure stability and incorporation into feeds and used to treat the infection in target animals.

Newly isolated lytic bacteriophages for Staphylococcus intermedius, structurally and functionally stabilized in a hydroxyethylcellulose gel containing choline geranate: Potential for transdermal permeation in veterinary phage therapy

In the present research work, we propose a new antimicrobial treatment for pyoderma via cutaneous permeation of bacteriophage particles conveyed in a hydroxyethylcellulose (HEC) gel integrating ionic liquid as a permeation enhancer. Ionic liquids are highly viscous fluids constituted exclusively by ions, that are usually hydrolytically stable and promote solubilization of amphipathic molecules such as proteins, hence serving as green solvents and promoting the transdermal permeation of biomolecules. In the research effort entertained herein, the synthesis and use of choline geranate for integrating a HEC gel aiming at the structural and functional stabilization of a cocktail of isolated lytic bacteriophage particles was sought, aiming at transdermal permeation in the antimicrobial treatment of animal pyoderma. The results obtained showed a high ability of the ionic liquid in enhancing transdermal permeation of the bacteriophage particles, with concomitant high potential of the HEC gel formulation in the antimicrobial treatment of animal skin infections.

Phage therapy as a potential approach in the biocontrol of pathogenic bacteria associated with shellfish consumption

Infectious human diseases acquired from bivalve shellfish consumption constitute a public health threat. These health threats are largely related to the filter-feeding phenomenon, by which bivalve organisms retain and concentrate pathogenic bacteria from their surrounding waters. Even after depuration, bivalve shellfish are still involved in outbreaks caused by pathogenic bacteria, which increases the demand for new and efficient strategies to control transmission of shellfish infection. Bacteriophage (or phage) therapy represents a promising, tailor-made approach to control human pathogens in bivalves, but its success depends on a deep understanding of several factors that include the bacterial communities present in the harvesting waters, the appropriate selection of phage particles, the multiplicity of infection that produces the best bacterial inactivation, chemical and physical factors, the emergence of phage-resistant bacterial mutants and the life cycle of bivalves. This review discusses the need to advance phage therapy research for bivalve decontamination, highlighting their efficiency as an antimicrobial strategy and identifying critical aspects to successfully apply this therapy to control human pathogens associated with bivalve consumption.

Exploring the feasibility of Salmonella Typhimurium-specific phage as a novel bio-receptor

The purpose of this study was aimed to isolate a Salmonella Typhimurium-specific phage (KFS-ST) from washing water in a poultry processing facility and to investigate the feasibility of the KFS-ST as a novel bio-receptor for the magnetoelastic (ME) biosensor method. KFS-ST against S. Typhimurium was isolated, propagated, and purified using a CsCl-gradient ultracentrifugation. Morphological characteristics of KFS-ST were analyzed using transmission electron microscopy (TEM). Its specificity and efficiency of plating analysis were conducted against 39 foodborne pathogens. The temperature and pH stabilities of KFS-ST were investigated by the exposure of the phage to various temperatures (−70°C–70°C) and pHs (1–12) for 1 h. A one-step growth curve analysis was performed to determine the eclipse time, latent time and burst size of phage. The storage stability of KFS-ST was studied by exposing KFS-ST to various storage temperatures (−70°C, −20°C, 4°C, and 22°C) for 12 weeks. KFS-ST was isolated and purified with a high concentration of (11.47 ± 0.25) Log PFU/mL. It had an icosahedral head (56.91 ± 2.90 nm) and a non-contractile tail (225.49 ± 2.67 nm), which was classified into the family of Siphoviridae in the order of Caudovirales. KFS-ST exhibited an excellent specificity against only S. Typhimurium and S. Enteritidis, which are considered two of the most problematic Salmonella strains in the meat and poultry. However, KFS-ST did not exhibit any specificity against six other Salmonella and 27 non-Salmonella strains. KFS-ST was stable at temperature of 4°C to 50°C and at pH of 4 to 12. The eclipse time, latent time, and burst size of KFS-ST were determined to be 10 min, 25 min and 26 PFU/ infected cell, respectively. KFS-ST was relatively stable during the 12-week storage period at all tested temperatures. Therefore, this study demonstrated the feasibility of KFS-ST as a novel bio-receptor for the detection of S. Typhimurium and S. Enteritidis in meat and poultry products using the ME biosensor method.

Efficacy of novel phages for control of multi-drug resistant Escherichia coli O177 on artificially contaminated beef and their potential to disrupt biofilm formation

Contaminated beef is a prominent source of foodborne pathogens such as Escherichia coli O177. Susceptibility of nine multi-drug resistant E. coli O177 strains against eight individual phages and six phage cocktails was assessed using polystyrene microplate titer plate. Further, 180 beef samples were independently inoculated with E. coli O177 cells in triplicates and treated with eight individual phages and six phage cocktails to determine their efficacy in inhibiting bacteria growth at 4 °C over a 7-day incubation period. Results revealed that all E. coli O177 strains were susceptible to the phages. A significant log reduction in viable E. coli O177 cell counts was observed on beef samples upon phage treatment over the 7-day incubation period. Two individual phages and three phage cocktails reduced E. coli cell counts to levels below the detection limit (1.0 log₁₀ CFU/g). Log reduction of viable E. coli cell counts ranged from 2.10 to 7.81 CFU/g for individual phages and from 2.86 to 7.81 CFU/g for cocktails. Individual phages and phage cocktails inhibited E. coli O177 biofilm formation with phage cocktails showing high efficacy. Furthermore, phage cocktails showed greater efficacy in destroying pre-formed biofilm than individual phages. Based on these findings, we concluded that phage cocktails developed in this study could be used to reduce E. coli O177 contamination and extend the shelf-life of stored raw beef.

Application of MS bacteriophages on contaminated trimmings reduces Escherichia coli O157 and non-O157 in ground beef

According to the United States Food and Drug Administration (FDA) agency, bacteriophage solutions targeting the serotype O157:H7 are Generally Recognized as Safe (GRAS) to control STEC during beef processing. However, outbreaks involving the "Big Six" STEC increased the industry concern about those serotypes. The objective of this study was to test the efficacy of MS bacteriophages to reduce the "Big Six" non-O157 STEC in beef. The lysing efficacy of phages isolated for each specific serotype varied from 96.2% to 99.9% in vitro. When applied to contaminated trim, reductions ranging from 0.7 to 1.3 Log of all STEC were observed in ground beef. Bacteriophages may provide an additional barrier against the "Big Six" STEC in ground beef. Results of this research provide support documentation to the FDA to extend GRAS status for bacteriophages as processing aids against all adulterant STEC.

Isolation and application of bacteriophages alone or in combination with nisin against planktonic and biofilm cells of Staphylococcus aureus

Staphylococcus aureus is a notorious foodborne pathogen since it has ability to produce variety of toxins including heat-stable enterotoxin, form biofilm, and acquire resistance to antibiotics. Biocontrol of foodborne pathogens by lytic bacteriophages garners increasing interest from both researchers and food industry. In the present study, 29 phages against S. aureus were successfully isolated from chicken, pork, and fish. Characterization of the isolates revealed that phage SA46-CTH2 belonging to Podoviridae family had a number of features suitable for food industry applications such as wide host range, short latent period, large burst size, high stress tolerance, and a genome free of virulence genes. Furthermore, phage SA46-CTH2 alone or in combination with nisin exhibited great efficacy in reducing planktonic and biofilm cells of S. aureus at various conditions tested. The combination of phage SA46-CTH2 and nisin was also found to be able to inhibit the regrowth of S. aureus at both 37 and 24 °C.Key points• A total of 29 S. aureus phages were successfully isolated from fish, pork, and chicken products. • Phage SA46-CTH2 was characterized by host range, morphology, and genome sequencing. • SA46-CTH2 significantly reduced both planktonic and biofilm cells of S. aureus. • Combination of SA46-CTH2 and nisin inhibited the regrowth of S. aureus.