Development of an in vitro homeostasis model between airway epithelial cells, bacteria and bacteriophages: a time-lapsed observation of cell viability and inflammatory response

Bacteriophages represent the most extensive group of viruses within the human virome and have a significant impact on general health and well-being by regulating bacterial population dynamics. Staphylococcus aureus, found in the anterior nostrils, throat and skin, is an opportunistic pathobiont that can cause a wide range of diseases, from chronic inflammation to severe and acute infections. In this study, we developed a human cell-based homeostasis model between a clinically isolated strain of S. aureus 141 and active phages for this strain (PYO^Sa141) isolated from the commercial Pyophage cocktail (PYO). The cocktail is produced by Eliava BioPreparations Ltd. (Tbilisi, Georgia) and is used as an add-on therapy for bacterial infections, mainly in Georgia. The triptych interaction model was evaluated by time-dependent analysis of cell death and inflammatory response of the nasal and bronchial epithelial cells. Inflammatory mediators (IL-8, CCL5/RANTES, IL-6 and IL-1β) in the culture supernatants were measured by enzyme-linked immunosorbent assay and cell viability was determined by crystal violet staining. By measuring trans-epithelial electrical resistance, we assessed the epithelial integrity of nasal cells that had differentiated under air-liquid interface conditions. PYO^Sa141 was found to have a prophylactic effect on airway epithelial cells exposed to S. aureus 141 by effectively down-regulating bacterial-induced inflammation, cell death and epithelial barrier disruption in a time-dependent manner. Overall, the proposed model represents an advance in the way multi-component biological systems can be simulated in vitro.

Novel lytic bacteriophage vB_GEC_EfS_9 against Enterococcus faecium

Enterococcus spp. is a common commensal microorganism, however, some strains can cause opportunistic infections in humans. Treatment of Enterococcus faecium-related endocarditis, urinary and genital tract infections, meningitis, septicemia, and even neonatal sepsis is often complicated by antibiotic resistance. The spread of multi-resistant bacterial strains has renewed interest in phage therapy, which has many advantages: Its advantages include a much lower frequency of resistance development compared to antibiotics and strict specificity, which allows affecting of only their target microbes without disturbing necessary microbiome. We isolated and characterized a virulent bacteriophage which is active against Enterococcus faecium clinical strains. The phage, which was designated as vB_GEC_EfS_9 was studied in terms of its growth pattern and adsorption rate, as well as its host range. The whole genome of the phage was sequenced and analyzed. Obtained results indicate that phage vB_GEC_EfS_9 is a virulent phage which has a very good potential for therapeutic use against strains of E. faecium.

Phage Therapy Experience at the Eliava Phage Therapy Center: Three Cases of Bacterial Persistence

In this retrospective descriptive study we focus on cases of three patients who underwent phage therapy procedures at Eliava Phage Therapy Center (EPTC) in Tbilisi, Georgia. Patients with chronic infectious diseases related to Pseudomonas aeruginosa (two patients, lower respiratory tract infection (LRTI)) and Klebsiella pneumoniae (one patient, urinary tract infection (UTI)) are among those very few EPTC patients whose pathogens persisted through phage therapy. By looking at bacterial strains and personalized phages used against them we tried to point towards possible adaptation strategies that are employed by these pathogens. Genome restriction-based Pulsed Field Gel Electrophoresis (PFGE) profiling of strains isolated before and after phage therapy hints towards two strategies of adaptation. In one patient case (Pseudomonas aeruginosa related lung infection) bacterial strains before and after phage therapy were indistinguishable according to their PFGE profiles, but differed in their phage susceptibility properties. On the other hand, in two other patient cases (Pseudomonas aeruginosa related LRTI and Klebsiella pneumoniae related UTI) bacterial adaptation strategy seemed to have resulted in diversification of infecting strains of the same species. With this work we want to attract more attention to phage resistance in general as well as to its role in phage therapy.

BIOLOGICAL CHARACTERIZATION OF BACTERIOPHAGES AGAINST STREPTOCOCCUS AGALACTIAE

Streptococcus agalactiae, also known as group B streptococci, was first isolated from cow's milk with mastitis, and it was first identified in 1930 by Rebecca Lancefield. GBS or streptococcus agalacticae is a gram-positive cocci, beta-hemolytic, facultative anaerobic, which is a harmless inhabitant of the normal human microflora. About 30% of the population is an asymptomatic carrier of this microbe. However, it was considered the leading cause of neonatal invasions upon its discovery. GBS is encapsulated in a polysaccharide capsule, which is a major virulence factor, and 10 serotypes of group B streptococci are known for their immunological activity. According to the existing studies, vaginal colonization is most often caused by type Ia, III, and V in other countries of the world. Today number of invasive GBS diseases continues to increase and it remains a significant pathogen among both infants and adults. The use of broad-spectrum antibiotics has certainly played a major role in the fight against infections, although the number of antibiotic-resistant strains has increased and thus modern medicine starts new insights into alternative antibacterials. Bacteriophages are often suggested as an alternative therapeutic agent against bacterial infections. In the present study, our aim was to isolate and study bacteriophages active against group B streptococci. Between March 2019 and March 2020, 257 anovaginal swabs were collected at "Nia Oniashvili Clinic" Tbilisi, Georgia, and Clinic "Curatio"by using standard bacterial identification procedures, in particular group B streptococcus identification guideline provided by CDC we identified 87 Streptococcus agalactiae strains. We used both standard and modified methods to isolate bacteriophages and study their life cycle, which were developed by the team. In this study, two bacteriophages active against Streptococcus agalactiae were identified: vB_GBS_1 (Syphoviridae) and vB_GBS_2 (Syphoviridae). The biological characteristics, morphology, adsorption, and host range were studied.

Intravesical bacteriophages for treating urinary tract infections in patients undergoing transurethral resection of the prostate: a randomised, placebo-controlled, double-blind clinical trial

BACKGROUND

Urinary tract infections (UTIs) are among the most prevalent microbial diseases and their financial burden on society is substantial. In the context of increasing antibiotic resistance, finding alternative treatments for UTIs is a top priority. We aimed to determine whether intravesical bacteriophage therapy with a commercial bacteriophage cocktail is effective in treating UTI.

METHODS

We did a randomised, placebo-controlled, clinical trial, at the Alexander Tsulukidze National Centre of Urology, Tbilisi, Georgia. Men older than 18 years of age, who were scheduled for transurethral resection of the prostate (TURP), with complicated UTI or recurrent uncomplicated UTI but no signs of systemic infection, were allocated by block randomisation in a 1:1:1 ratio to receive intravesical Pyo bacteriophage (Pyophage; 20 mL) or intravesical placebo solution (20 mL) in a double-blind manner twice daily for 7 days, or systemically applied antibiotics (according to sensitivities) as an open-label standard-of-care comparator. Urine culture was taken via urinary catheter at the end of treatment (ie, day 7) or at withdrawal from the trial. The primary outcome was microbiological treatment response after 7 days of treatment, measured by urine culture; secondary outcomes included clinical and safety parameters during the treatment period. Analyses were done in a modified intention-to-treat population of patients having received at least one dose of the allocated treatment regimen. This trial is registered with ClinicalTrials.gov, NCT03140085.

FINDINGS

Between June 2, 2017, and Dec 14, 2018, 474 patients were screened for eligibility and 113 (24%) patients were randomly assigned to treatment (37 to Pyophage, 38 to placebo, and 38 to antibiotic treatment). 97 patients (28 Pyophage, 32 placebo, 37 antibiotics) received at least one dose of their allocated treatment and were included in the primary analysis. Treatment success rates did not differ between groups. Normalisation of urine culture was achieved in five (18%) of 28 patients in the Pyophage group compared with nine (28%) of 32 patients in the placebo group (odds ratio [OR] 1·60 [95% CI 0·45-5·71]; p=0·47) and 13 (35%) of 37 patients in the antibiotic group (2·66 [0·79-8·82]; p=0·11). Adverse events occurred in six (21%) of 28 patients in the Pyophage group compared with 13 (41%) of 32 patients in the placebo group (OR 0·36 [95% CI 0·11-1·17]; p=0·089) and 11 (30%) of 37 patients in the antibiotic group (0·66 [0·21-2·07]; p=0·47).

INTERPRETATION

Intravesical bacteriophage therapy was non-inferior to standard-of-care antibiotic treatment, but was not superior to placebo bladder irrigation, in terms of efficacy or safety in treating UTIs in patients undergoing TURP. Moreover, the bacteriophage safety profile seems to be favourable. Although bacteriophages are not yet a recognised or approved treatment option for UTIs, this trial provides new insight to optimise the design of further large-scale clinical studies to define the role of bacteriophages in UTI treatment.

FUNDING

Swiss Continence Foundation, the Swiss National Science Foundation, and the Swiss Agency for Development and Cooperation.

TRANSLATIONS

For the Georgian and German translations of the abstract see Supplementary Materials section.

IDENTIFICATION AND ANTIBIOTIC SUSCEPTIBILITY PATTERNS OF STREPTOCOCCUS AGALACTIAE

GBS-Group B streptococcus or Streptococcus agalactiae is a Gram-positive coccus found in 20% of healthy women as part of normal gastrointestinal and genital tract flora. It is associated with pathogenicity in immunocompromised, elderly and pregnant adults as well as infants and neonates. GBS are encapsulated organisms and sub divided into ten antigenically distinct capsular serotypes. GBS case treatment mainly performed with Penicillin G but Erythromicyn, Vancomycin and Clindamycin are recommended for penicillin-allergic individuals. In this study between March 2019 and September 2019 an anovaginal swabs were collected from 80 women at 35-37 weeks of gestation and 39 were identified as str. agalactiae. 24 str. agalactiae strains provided by clinic "Curation" were isolated from urine, vagina and rectum. Culturing, identification of GBS were carried out according to standard microbiological methods. Antimicrobial susceptibility profiles were determined by disk diffusion method. Our results revealed that in total from 104 samples 29% were Str. agalactiae. All GBS strains were all sensitive to Penicillin, Ampicilin and Vancomycin. 25% were resistant to Erythromycin and 13% to Clindamycin. Our study has shown that the prevalence of Streptococcus agalactiae in Georgia quite high and especially with Erythromycin-resistant strains, which makes treatment of penicillin allergic patients problematic. In this case only hope is vancomycin. Fortunately, vancomycin-resistant strains have not been identified; however the problem is still relevant. Obtained data could be used as a base for further epidemiological studies and also managing targeted new approaches of treatment and prevention of GBS.

Adapted Bacteriophages for Treating Urinary Tract Infections

Urinary tract infections (UTIs) are among the most widespread microbial diseases and their economic impact on the society is substantial. The continuing increase of antibiotic resistance worldwide is worrying. As a consequence, well-tolerated, highly effective therapeutic alternatives are without delay needed. Although it has been demonstrated that bacteriophage therapy may be effective and safe for treating UTIs, the number of studied patients is low and there is a lack of randomized controlled trials (RCTs). The present study has been designed as a two-phase prospective investigation: (1) bacteriophage adaptation, (2) treatment with the commercially available but adapted Pyo bacteriophage. The aim was to evaluate feasibility, tolerability, safety, and clinical/microbiological outcomes in a case series as a pilot for a double-blind RCT. In the first phase, patients planned for transurethral resection of the prostate were screened (n = 130) for UTIs and enrolled (n = 118) in the study when the titer of predefined uropathogens (Staphylococcus aureus, E. coli, Streptococcus spp., Pseudomonas aeruginosa, Proteus mirabilis) in the urine culture was ≥104 colony forming units/mL. In vitro analysis showed a sensitivity for uropathogenic bacteria to Pyo bacteriophage of 41% (48/118) and adaptation cycles of Pyo bacteriophage enhanced its sensitivity to 75% (88/118). In the second phase, nine patients were treated with adapted Pyo bacteriophage and bacteria titer decreased (between 1 and 5 log) in six of the nine patients (67%). No bacteriophage-associated adverse events have been detected. The findings of our prospective two-phase study suggest that adapted bacteriophage therapy might be effective and safe for treating UTIs. Thus, well-designed RCTs are highly warranted to further define the role of this potentially revolutionizing treatment option.

NEW TEMPERATE ENTEROCOCCUS PHAGE VB_GEC_EFS_2 WITH POTENTIAL OF LYSOGENIC CONVERSION

Bacteriophages represent the widest group of viruses, from which only virulent phages are used as antibacterial agent. But the picture in the case of temperate phage is absolutely different; many lysogenic phages express gene products that have subtle effects on the phenotype of the host cell. This process is called lysogenic conversion. In present study we characterized new temperate Enterococcus faecium phage vB_GEC_EFS_2, which was isolated from river Mtkvari. The phage is a member of Siphoviridae family. Whole genome of phage vB_GEC-EfS_2 was sequenced and analyzed. Total length of the genome of phage vB_GEC_EFS_2 is 38 508bp, The assembly contains 65 ORFs, among them - 3 lysis genes , genes coded 13 structural proteins, 1 DNA replication-associated gene, 1 gene coded integration, 3 - lysis-lysogenic cycle regulation, 43 hypothetical proteins. One holin gene contained "Haemolysin XhIA" domain which is surface associated haemolisyn. We isolated and purified holin gene and determine its haemolitic activity alongside with vB_GEC_EfS_2 phage lysate. We clarified the XhIA domain function and role in protein's haemolytic nature and described another kind of lysogenic conversion.

Bacteriophages for treating urinary tract infections in patients undergoing transurethral resection of the prostate: a randomized, placebo-controlled, double-blind clinical trial

Background

Urinary tract infections (UTI) are among the most prevalent microbial diseases and their financial burden on society is substantial. The continuing increase of antibiotic resistance worldwide is alarming. Thus, well-tolerated, highly effective therapeutic alternatives are urgently needed. Although there is evidence indicating that bacteriophage therapy may be effective and safe for treating UTIs, the number of investigated patients is low and there is a lack of randomized controlled trials.

Methods and design

This study is the first randomized, placebo-controlled, double-blind trial investigating bacteriophages in UTI treatment. Patients planned for transurethral resection of the prostate are screened for UTIs and enrolled if in urine culture eligible microorganisms ≥10⁴ colony forming units/mL are found. Patients are randomized in a double-blind fashion to the 3 study treatment arms in a 1:1:1 ratio to receive either: a) bacteriophage (i.e. commercially available Pyo bacteriophage) solution, b) placebo solution, or c) antibiotic treatment according to the antibiotic sensitivity pattern. All treatments are intended for 7 days. No antibiotic prophylaxes will be given to the double-blinded treatment arms a) and b). As common practice, the Pyo bacteriophage cocktail is subjected to periodic adaptation cycles during the study. Urinalysis, urine culture, bladder and pain diary, and IPSS questionnaire will be completed prior to and at the end of treatment (i.e. after 7 days) or at withdrawal/drop out from the study. Patients with persistent UTIs will undergo antibiotic treatment according to antibiotic sensitivity pattern.

Discussion

Based on the high lytic activity and the potential of resistance optimization by direct adaptation of bacteriophages, and considering the continuing increase of antibiotic resistance worldwide, bacteriophage therapy is a very promising treatment option for UTIs. Thus, our randomized controlled trial investigating bacteriophages for treating UTIs will provide essential insights into this potentially revolutionizing treatment option.

Trial registration

This study has been registered at clinicaltrials.gov (www.clinicaltrials.gov/ct2/show/NCT03140085). April 27, 2017.

Immobilization of bacteriophage in wound-dressing nanostructure

Opportunistic bacteria that cause life-threatening infections are still a central problem associated with a healthcare setting. Bacteriophage capsid immobilization on nanostructured polymers maximizes its tail exposure and looks promising in applications toward skin-infections as alternative to antibiotics standardly used. The main goal of this work was to investigate the covalent immobilization of vB_Pae_Kakheti25 bacteriophage capsid on polycaprolactone (PCL) nanofibers (non-woven textile), as a potential effective antimicrobial, laundry resistant and non-toxic dressing for biomedical use. Surface analyses showed that the immobilization of vB_Pae_Kakheti25 bacteriophage capsid on PCL nanofibres oriented bacteriophage tails to interact with bacteria. Furthermore, antimicrobial assays showed a very effective 6 log bacterial reduction, which was equivalent to 99.9999%, after immediate and 2 hours of contact, even following 25 washing cycles (due to covalent bond). The activity of PCL-vB_Pae_Kakheti25 against P. aeruginosa was immediate and its reduction was complete.

Characterization and Testing the Efficiency of Acinetobacter baumannii Phage vB-GEC_Ab-M-G7 as an Antibacterial Agent

Acinetobacter baumannii is a gram-negative, non-motile bacterium that, due to its multidrug resistance, has become a major nosocomial pathogen. The increasing number of multidrug resistant (MDR) strains has renewed interest in phage therapy. The aim of our study was to assess the effectiveness of phage administration in Acinetobacter baumannii wound infections in an animal model to demonstrate phage therapy as non-toxic, safe and alternative antibacterial remedy. Using classical methods for the study of bacteriophage properties, we characterized phage vB-GEC_Ab-M-G7 as a dsDNA myovirus with a 90 kb genome size. Important characteristics of vB-GEC_Ab-M-G7include a short latent period and large burst size, wide host range, resistance to chloroform and thermal and pH stability. In a rat wound model, phage application effectively decreased the number of bacteria isolated from the wounds of successfully treated animals. This study highlights the effectiveness of the phage therapy and provides further insight into treating infections caused by MDR strains using phage administration.

Bacteriophage Delivery by Nebulization and Efficacy Against Phenotypically Diverse Pseudomonas aeruginosa from Cystic Fibrosis Patients

BACKGROUND

The rise in antibiotic-resistant Pseudomonas aeruginosa and the considerable difficulty in eradicating it from patients has re-motivated the study of bacteriophages as a therapeutic option. For this to be effective, host range and viability following nebulization need to be assessed. Host-range has not previously been assessed for the Liverpool Epidemic Strain (LES) isolates that are the most common cystic fibrosis-related clone of P. aeruginosa in the UK. Nebulization studies have not previously been linked to clinically relevant phages.

METHODS

84 phenotypically variable isolates of the LES were tested for susceptibility to seven bacteriophages known to have activity against P. aeruginosa. Five of the phages were from the Eliava Institute (IBMV) and 2 were isolated in this study. The viability of the two bacteriophages with the largest host ranges was characterized further to determine their ability to be nebulized and delivered to the lower airways. Phages were nebulized into a cascade impactor and the phage concentration was measured.

RESULTS

The bacteriophages tested killed between 66%-98% of the 84 Liverpool Epidemic Strain isolates. Two isolates were multi phage resistant, but were sensitive to most first line anti-Pseudomonal antibiotics. The amount of viable bacteriophages contained in particles that are likely to reach the lower airways (<4.7 μm) was 1% for the Omron and 12% AeroEclipse nebulizer.

CONCLUSIONS

Individual P. aeruginosa bacteriophages can lyse up to 98% of 84 phenotypically diverse LES strains. High titers of phages can be effectively nebulized.

Quality and safety requirements for sustainable phage therapy products

The worldwide antibiotic crisis has led to a renewed interest in phage therapy. Since time immemorial phages control bacterial populations on Earth. Potent lytic phages against bacterial pathogens can be isolated from the environment or selected from a collection in a matter of days. In addition, phages have the capacity to rapidly overcome bacterial resistances, which will inevitably emerge. To maximally exploit these advantage phages have over conventional drugs such as antibiotics, it is important that sustainable phage products are not submitted to the conventional long medicinal product development and licensing pathway. There is a need for an adapted framework, including realistic production and quality and safety requirements, that allowsa timely supplying of phage therapy products for ‘personalized therapy’ or for public health or medical emergencies. This paper enumerates all phage therapy product related quality and safety risks known to the authors, as well as the tests that can be performed to minimize these risks, only to the extent needed to protect the patients and to allow and advance responsible phage therapy and research.

Comparative analysis of the biological and physical properties of Enterococcus faecalis bacteriophage vB_EfaS_GEC-EfS_3 and Streptococcus mitis bacteriophage vB_SmM_GEC-SmitisM_2

Enterococcus faecalis and Streptococcus mitis are common commensal inhabitants of the human gastrointestinal and genitourinary tracts. However, both species can be opportunistic pathogens and cause disease in nosocomial settings. These infections can be difficult to treat because of the frequency of antibiotic resistance among these strains. Bacteriophages are often suggested as an alternative therapeutic agent against these infections. In this study, E. faecalis and S. mitis strains were isolated from female patients with urinary tract infections. Bacteriophages active against these strains were isolated from sewage water from the Mtkvari River. Two phages, designated vB_EfaS_GEC-EfS_3 (Syphoviridae) and vB_SmM_GEC-SmitisM_2 (Myoviridae), were specific for E. faecalis and S. mitis, respectively. Each phage's growth patterns and adsorption rates were quantified. Sensitivity to ultraviolet light and temperature was determined, as was host range and serology. The S. mitis bacteriophage was found to be more resistant to ultraviolet light and exposure to high temperatures than the E. faecalis bacteriophage, despite having a much greater rate of replication. While each phage was able to infect a broad range of strains of the same species as the host species from which they were isolated, they were unable to infect other host species tested.

Characterization of lytic Pseudomonas aeruginosa bacteriophages via biological properties and genomic sequences

Pseudomonas aeruginosa is an important cause of infections, especially in patients with immunodeficiency or diabetes. Antibiotics are effective in preventing morbidity and mortality from Pseudomonas infection, but because of spreading multidrug-resistant bacterial strains, bacteriophages are being explored as an alternative therapy. Two newly purified broad host range Pseudomonas phages, named vB_Pae-Kakheti25 and vB_Pae-TbilisiM32, were characterized as candidates for use in phage therapy. Morphology, host range, growth properties, thermal stability, serology, genomic sequence, and virion composition are reported. When phages are used as bactericides, they are used in mixtures to overcome the development of resistance in the targeted bacterial population. These two phages are representative of diverse siphoviral and podoviral phage families, respectively, and hence have unrelated mechanisms of infection and no cross-antigenicity. Composing bactericidal phage mixtures with members of different phage families may decrease the incidence of developing resistance through a common mechanism.

Molecular detection of OXA carbapenemase genes in multidrug-resistant Acinetobacter baumannii isolates from Iraq and Georgia

The aim of this study was to determine the susceptibility to imipenem (IPM) of Acinetobacter baumannii isolates from different countries and to characterise the carbapenemase-encoding genes in IPM-resistant isolates. A total of 12 A. baumannii strains collected in Belgium (n=2), Iraq (n=8) and Georgia (n=2) were included in the study. Identification of the isolates was confirmed using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Antibiotic susceptibility testing was performed by the disk diffusion method, and Etest was used to determine the IPM minimum inhibitory concentrations (MICs) of resistant isolates. The presence of carbapenemase-encoding genes was investigated by polymerase chain reaction (PCR). All A. baumannii isolates were eventually identified by MALDI-TOF MS with high score values. Amongst the 12 strains, 6 were found to be resistant to IPM (MICs ≥16 μg/mL), comprising clinical isolates from wound infections of soldiers who were injured either during the Iraq war in 2007 (5 isolates) or during the Georgian-Russian war in 2008 (1 isolate from Georgia). All isolates contained ISAba1 and bla(OXA-51-like), but isolates from Iraq contained the bla(OXA-23) gene located on a plasmid whereas the isolate from Georgia contained the bla(OXA-24) gene located on the chromosome. None of the IPM-resistant isolates contained the bla(OXA-58)- or bla(NDM-1)-encoding genes. In conclusion, these results re-emphasise the worldwide dissemination of OXA carbapenemase genes in multidrug-resistant clinical isolates of A. baumannii and, to the best of our knowledge, report the first IPM-resistant A. baumannii strain isolated from a patient during the Georgian-Russian war with the bla(OXA-24) gene located on the chromosome.