Effect of Management of Grassland on Prey Availability and Physiological Condition of Nestling of Red-Backed Shrike Lanius collurio

The study aimed to determine the influence of grassland management on the potential food base of the red-backed shrike Lanius collurio and the condition of chicks in the population inhabiting semi-natural grasslands in the Narew floodplain. The grassland area was divided into three groups: extensively used meadows, intensively used meadows fertilised with mineral fertilisers, and intensively used meadows fertilised with liquid manure, and selected environmental factors that may influence food availability were determined. Using Barber traps, 1825 samples containing 53,739 arthropods were collected, and the diversity, abundance, and proportion of large arthropods in the samples were analysed depending on the grassland use type. In the bird population, the condition of the chicks was characterised by the BCI (Body Condition Index) and haematological parameters (glucose level, haemoglobin level, haematocrit, and H:L ratio). The diversity of arthropods was highest in extensively used meadows. Still, the mean abundance and proportion of arthropods over 1 cm in length differed significantly for Orthoptera, Hymenoptera, Arachne, and Carabidae between grassland use types, with the highest proportion of large arthropods and the highest abundance recorded in manure-fertilised meadows. The highest Body Condition Indexes and blood glucose levels of nestlings indicating good nestling nutrition were recorded in nests of birds associated with extensive land use. The H:L ratio as an indicator of the physiological condition of nestlings was high on manure-fertilised and extensively managed meadows, indicating stress factors associated with these environments. This suggests that consideration should be given to the effects of chemicals, such as pesticides or drug residues, that may come from slurry poured onto fields on the fitness of red-backed shrike chicks.

Exclusion of older adults from randomized controlled trials in rheumatoid arthritis

OBJECTIVES

To assess eligibility criteria that either explicitly or implicitly exclude older patients from randomized controlled trials (RCTs) in RA.

METHODS

Our analysis included RCTs of pharmacological interventions registered with ClinicalTrials.gov and started between 2013 and 2022. Co-primary outcomes were proportions of trials with an upper age limit and the eligibility criteria indirectly increasing risk of the exclusion of older adults.

RESULTS

A total of 143/290 (49%) trials had an upper age limit of 85 years or less. Multivariable analysis showed that the odds of an upper age limit were significantly lower in trials performed in the USA [adjusted odds ratio (aOR), 0.34; CI, 0.12-0.99; P = 0.04] and intercontinental trials (aOR, 0.4; CI, 0.18-0.87; P = 0.02). In total, 154/290 (53%) trials had at least one eligibility criterion implicitly excluding older adults. These included specific comorbidities (n = 114; 39%), compliance concerns (n = 67; 23%), and broad and vague exclusion criteria (n = 57; 20%); however, we found no significant associations between these criteria and trial characteristics. Overall, 217 (75%) trials either explicitly or implicitly excluded older patients; we also noted a trend towards increasing proportion of these trials over time. Only one trial (0.3%) enrolled solely patients aged 65 and older.

CONCLUSION

Older adults are commonly excluded from RCTs in RA based on both age limits and other eligibility criteria. This seriously limits the evidence base for the treatment of older patients in clinical practice. Given the growing prevalence of RA in older adults, relevant RCTs should be more inclusive to them.

Exclusion of older patients from randomized clinical trials in Parkinson's disease

Prevalence of Parkinson's disease (PD) increases with age. The purpose of this study was to evaluate the eligibility criteria in randomized clinical trials (RCTs) in PD, especially those limiting the enrollment of older adults. We examined RCTs of pharmacological and non-pharmacological anti-parkinsonian interventions registered with ClinicalTrials.gov and started from 2013 through 2022. Primary outcome was proportion of RCTs with an upper age limit of 85 years of age or less. Secondary outcome was proportion of RCTs with other exclusion criteria. Associations between trial characteristics and the presence of the age limits were determined using logistic regression. Our study included 420 RCTs. Two hundred thirty-nine (57%) of these had an upper age limit of 85 years of age or less. Proportion of these trials significantly increased over time. The odds of the presence of an upper age limit were significantly associated with the investigational site location, phase, and timeframe for the primary endpoint assessment. Three hundred fifty-six (85%) trials had other eligibility criteria limiting the enrollment of older patients; these often (n = 285; 68%) included cognitive impairment. Overall, 386 (92%) RCTs either explicitly excluded older adults or had criteria indirectly limiting their enrollment. Underrepresentation of older patients in clinical trials in PD considerably reduces the generalizability of their results. Some eligibility criteria should be modified to enable the investigators to assess the benefits and harms of new therapeutic interventions in older adults. This problem is important in view of rapidly growing number of older patients with PD.

Stability study in selected conditions and biofilm-reducing activity of phages active against drug-resistant Acinetobacter baumannii

Acinetobacter baumannii is currently a serious threat to human health, especially to people with immunodeficiency as well as patients with prolonged hospital stays and those undergoing invasive medical procedures. The ever-increasing percentage of strains characterized by multidrug resistance to widely used antibiotics and their ability to form biofilms make it difficult to fight infections with traditional antibiotic therapy. In view of the above, phage therapy seems to be extremely attractive. Therefore, phages with good storage stability are recommended for therapeutic purposes. In this work, we present the results of studies on the stability of 12 phages specific for A. baumannii under different conditions (including temperature, different pH values, commercially available disinfectants, essential oils, and surfactants) and in the urine of patients with urinary tract infections (UTIs). Based on our long-term stability studies, the most optimal storage method for the A. baumannii phage turned out to be - 70 °C. In contrast, 60 °C caused a significant decrease in phage activity after 1 h of incubation. The tested phages were the most stable at a pH from 7.0 to 9.0, with the most inactivating pH being strongly acidic. Interestingly, ethanol-based disinfectants caused a significant decrease in phage titers even after 30 s of incubation. Moreover, copper and silver nanoparticle solutions also caused a decrease in phage titers (which was statistically significant, except for the Acba_3 phage incubated in silver solution), but to a much lesser extent than disinfectants. However, bacteriophages incubated for 24 h in essential oils (cinnamon and eucalyptus) can be considered stable.

Effect of nature protection and management of grassland on biodiversity - Case from big flooded river valley (NE Poland)

Agriculturally used meadows are habitats whose biodiversity depends on anthropogenic disturbances such as fertilization or mowing. Intensified agricultural practices (too frequent mowing, use of mineral fertilizers and insecticides) lead to declines in the abundance and species diversity of the biota inhabiting them. The intensification of agricultural production in north-eastern Poland relates primarily to the increase in cattle numbers and the intensification of grassland management, but many areas were included in Natura 2000 network. Our study was aimed at indicating the impact of diverse use of meadows on the species richness and diversity of invertebrates, amphibians, and birds in the grasslands of Narew river valley, Special Bird Protection Area, where the intensification of grassland use was noted in the last decades, and part of the meadows was included in the agri-environmental program. The agri-environmental program is a very good tool for the protection of grassland biotic diversity. The highest taxonomic richness and diversity of the studied animal groups were found in meadows included in these programs with extensive use, while the lowest was in the over- and intensively used meadows fertilized with mineral fertilizers and liquid manure. Only the meadows in the agri-environment program were inhabited by the fire-bellied toad and the tree frog - amphibians from Annex IV of the Habitats Directive. The number of breeding bird species globally threatened (IUCN Red List), listed in Annex I of the EU Birds Directive, and with negative population trend in Europe (SPEC1-3) was highest in meadows included in EU conservation programs. The main factors reducing biotic diversity in the grassland of flooded river valley were the high number of grassland mowing per season, intensive fertilization, especially with liquid manure, the great distance of meadows to the river, low soil humidity, and low share of shrubs and trees in the meadows border zone.

Therapeutic Phages as Modulators of the Immune Response: Practical Implications

While the medical community awaits formal proof of the efficacy of phage therapy, as is required by evidence-based medicine, existing data suggest that phages could also be applied based on their non-antibacterial action, especially phage-mediated immunomodulation. Promising avenues have been revealed by findings indicating that phages may mediate diverse actions in the immune system, while the list of phages able to dampen the aberrant immunity associated with a variety of disorders continuously grows. Here we summarize what is known in this field and possible options for the future. While available data are still scarce and preliminary, it appears that "phage repurposing" is worthy of more research, which could reveal new perspectives on applying phage therapy in contemporary medicine.

Pharmacokinetic and Pharmacodynamic Obstacles for Phage Therapy From the Perspective of Clinical Practice

Bacteriophages present unique features that enable targeted killing of bacteria, including strains resistant to many antibiotics. However, phage pharmacokinetics and pharmacodynamics constitute much more complex and challenging aspects for researchers than those attributable to antibiotics. This is because phages are not just chemical substances, but also biological nanostructures built of different proteins and genetic material that replicate within their bacterial hosts and may induce immune responses acting as simple antigens. Here, we present a few examples of how primary general assumptions on phage pharmacokinetics and pharmacodynamics are verified by current preclinical and clinical observations, leading to conclusions that may not be obvious at first but are of significant value for the final success of phage therapy in humans.

Eligibility criteria in clinical trials in breast cancer: a cohort study

BACKGROUND

Breast cancer (BC) is the most common cancer type in women. The purpose of this study was to assess the eligibility criteria in recent clinical trials in BC, especially those that can limit the enrollment of older patients as well as those with comorbidities and poor performance status.

METHODS

Data on clinical trials in BC were extracted from ClinicalTrials.gov. Co-primary outcomes were proportions of trials with different types of the eligibility criteria. Associations between trial characteristics and the presence of certain types of these criteria (binary variable) were determined with univariate and multivariate logistic regression.

RESULTS

Our analysis included 522 trials of systemic anticancer treatments started between 2020 and 2022. Upper age limits, strict exclusion criteria pertaining to comorbidities, and those referring to inadequate performance status of the patient were used in 204 (39%), 404 (77%), and 360 (69%) trials, respectively. Overall, 493 trials (94%) had at least one of these criteria. The odds of the presence of each type of the exclusion criteria were significantly associated with investigational site location and trial phase. We also showed that the odds of the upper age limits and the exclusion criteria involving the performance status were significantly higher in the cohort of recent trials compared with cohort of 309 trials started between 2010 and 2012 (39% vs 19% and 69% vs 46%, respectively; p < 0.001 for univariate and multivariate analysis in both comparisons). The proportion of trials with strict exclusion criteria was comparable between the two cohorts (p > 0.05). Only three of recent trials (1%) enrolled solely patients aged 65 or 70 and older.

CONCLUSIONS

Many recent clinical trials in BC exclude large groups of patients, especially older adults, individuals with different comorbidities, and those with poor performance status. Careful modification of some of the eligibility criteria in these trials should be considered to allow investigators to assess the benefits and harms of investigational treatments in participants with characteristics typically encountered in clinical practice.

Phage Interactions with the Nervous System in Health and Disease

The central nervous system manages all of our activities (e.g., direct thinking and decision-making processes). It receives information from the environment and responds to environmental stimuli. Bacterial viruses (bacteriophages, phages) are the most numerous structures occurring in the biosphere and are also found in the human organism. Therefore, understanding how phages may influence this system is of great importance and is the purpose of this review. We have focused on the effect of natural bacteriophages in the central nervous system, linking them to those present in the gut microbiota, creating the gut-brain axis network, as well as their interdependence. Importantly, based on the current knowledge in the field of phage application (e.g., intranasal) in the treatment of bacterial diseases associated with the brain and nervous system, bacteriophages may have significant therapeutic potential. Moreover, it was indicated that bacteriophages may influence cognitive processing. In addition, phages (via phage display technology) appear promising as a targeted therapeutic tool in the treatment of, among other things, brain cancers. The information collected and reviewed in this work indicates that phages and their impact on the nervous system is a fascinating and, so far, underexplored field. Therefore, the aim of this review is not only to summarize currently available information on the association of phages with the nervous system, but also to stimulate future studies that could pave the way for novel therapeutic approaches potentially useful in treating bacterial and non-bacterial neural diseases.

Biological Properties of 12 Newly Isolated Acinetobacter baumannii-Specific Bacteriophages

Infections with the opportunistic Gram-negative bacterium Acinetobacter baumannii pose a serious threat today, which is aggravated by the growing problem of multi-drug resistance among bacteria, caused by the overuse of antibiotics. Treatment of infections caused by antibiotic-resistant A. baumannii strains with the use of phage therapy is not only a promising alternative, but sometimes the only option. Therefore, phages specific for clinical multi-drug resistant A. baumannii were searched for in environmental, municipal, and hospital wastewater samples collected from different locations in Poland. The conducted research allowed us to determine the biological properties and morphology of the tested phages. As a result of our research, 12 phages specific for A. baumannii, 11 of which turned out to be temperate and only one lytic, were isolated. Their lytic spectra ranged from 11 to 75%. The plaques formed by most phages were small and transparent, while one of them formed relatively large plaques with a clearly marked 'halo' effect. Based on Transmission Electron Microscopy (TEM), most of our phages have been classified as siphoviruses (only one phage was classified as a podovirus). All phages have icosahedral capsid symmetry, and 11 of them have a long tail. Optimal multiplicity of infections (MOIs) and the adsorption rate were also determined. MOI values varied depending on the phage-from 0.001 to 10. Based on similarities to known bacteriophages, our A. baumannii-specific phages have been proposed to belong to the Beijerinckvirinae and Junivirinae subfamilies. This study provides an additional tool in the fight against this important pathogen and may boost the interest in phage therapy as an alternative and supplement to the current antibiotics.

Do Anti-Phage Antibodies Persist after Phage Therapy? A Preliminary Report

Phages are immunogenic and may evoke an immune response following their administration. Consequently, patients undergoing phage therapy (PT) produce phage-neutralizing serum antibodies. The clinical significance of this phenomenon for the success or failure of the therapy is currently unclear. Interestingly, even a strong anti-phage humoral response does not exclude the success of PT. On the other hand, it cannot be ruled out that phage–antibody complexes may be trapped in tissues and organs causing injury and late complications of PT. Therefore, patients should be monitored for the presence of serum antibodies and therapy discontinued if their level is high. Our preliminary data suggest that the kinetics of the disappearance of those antibodies may vary from patient to patient and in some cases may take more than a year.

A Thorough Synthesis of Phage Therapy Unit Activity in Poland-Its History, Milestones and International Recognition

The year 2020 marked 15 years of the Phage Therapy Unit in Poland, the inception of which took place just one year after Poland's accession to the European Union (2004). At first sight, it is hard to find any connection between these two events, but in fact joining the European Union entailed the need to adapt the regulatory provisions concerning experimental treatment in humans to those that were in force in the European Union. These changes were a solid foundation for the first phage therapy center in the European Union to start its activity. As the number of centers conducting phage therapy in Europe and in the world constantly and rapidly grows, we want to grasp the opportunity to take a closer look at the over 15-year operation of our site by analyzing its origins, legal aspects at the local and international levels and the impressive number and diversity of cases that have been investigated and treated during this time. This article is a continuation of our work published in 2020 summarizing a 100-year history of the development of phage research in Poland.

Phage therapy of wound-associated infections

Phages are viruses which can specifically infect bacteria, resulting in their destruction. Bacterial infections are a common complication of wound healing, and experimental evidence from animal models demonstrates promising potential for phage-dependent eradication of wound-associated infections. The studies discussed suggest that phage therapy may be an effective treatment, with important advantages over some current antibacterial treatments. Phage cocktails, as well as co-administration of phages and antibiotics, have been reported to minimise bacterial resistance. Further, phage-antibiotic synergism has been reported in some studies. The ideal dose of phages is still subject to debate, with evidence for both high and low doses to yield therapeutic effects. Novel delivery methods, such as hydrogels, are being explored for their advantages in topical wound healing. There are more and more Good Manufacturing Practice facilities dedicated to manufacturing phage products and phage therapy units across the world, showing the changing perception of phages which is occurring. However, further research is needed to secure the place of phages in modern medicine, with some scientists calling upon the World Health Organisation to help promote phage therapy.

Bacteriophages and antibiotic interactions in clinical practice: what we have learned so far

Bacteriophages (phages) may be used as an alternative to antibiotic therapy for combating infections caused by multidrug-resistant bacteria. In the last decades, there have been studies concerning the use of phages and antibiotics separately or in combination both in animal models as well as in humans. The phenomenon of phage–antibiotic synergy, in which antibiotics may induce the production of phages by bacterial hosts has been observed. The potential mechanisms of phage and antibiotic synergy was presented in this paper. Studies of a biofilm model showed that a combination of phages with antibiotics may increase removal of bacteria and sequential treatment, consisting of phage administration followed by an antibiotic, was most effective in eliminating biofilms. In vivo studies predominantly show the phenomenon of phage and antibiotic synergy. A few studies also describe antagonism or indifference between phages and antibiotics. Recent papers regarding the application of phages and antibiotics in patients with severe bacterial infections show the effectiveness of simultaneous treatment with both antimicrobials on the clinical outcome.

What Are the Potential Benefits of Using Bacteriophages in Periodontal Therapy?

Periodontitis, which may result in tooth loss, constitutes both a serious medical and social problem. This pathology, if not treated, can contribute to the development of, among others, pancreatic cancer, cardiovascular diseases or Alzheimer’s disease. The available treatment methods are expensive but not always fully effective. For this reason, the search for and isolation of bacteriophages specific to bacterial strains causing periodontitis seems to be a great opportunity to target persistent colonization by bacterial pathogens and lower the use of antibiotics consequently limiting further development of antibiotic resistance. Furthermore, antimicrobial resistance (AMR) constitutes a growing challenge in periodontal therapy as resistant pathogens may be isolated from more than 70% of patients with periodontitis. The aim of this review is to present the perspective of phage application in the prevention and/or treatment of periodontitis alongside its complicated multifactorial aetiology and emphasize the challenges connecting composition and application of effective phage preparation.

Bronisława Fejgin (1883-1943): Forgotten Important Contributor to International Microbiology and Phage Therapy

Bronisława Brandla Fejgin was a Polish-born Jewish female physician. Among Fejgin's numerous articles in the field of microbiology, her later work was almost entirely devoted to phage research. Although not equally famous as the phage pioneers from Western Europe, F.W. Twort and F. d'Herelle, Fejgin's contribution to phage research deserves proper recognition. Her studies on phages resulted in the publication of numerous original scientific reports. These articles, published mostly in French, constitute an important source of information and expertise on early attempts towards therapeutic use of phages in humans. The interwar period marks the most intense years in Bronisława Fejgin's research activity, brutally interrupted by her death in the Warsaw Ghetto in 1943. Her microbiology contributions have not been analyzed so far. Thus, the aim of this article is to fill the existing gap in the history of microbiology and phage therapy.

Human β-Defensin 2 and Its Postulated Role in Modulation of the Immune Response

Studies described so far suggest that human β-defensin 2 is an important protein of innate immune response which provides protection for the human organism against invading pathogens of bacterial, viral, fungal, as well as parasitical origin. Its pivotal role in enhancing immunity was proved in infants. It may also be considered a marker of inflammation. Its therapeutic administration has been suggested for maintenance of the balance of systemic homeostasis based on the appropriate composition of the microbiota. It has been suggested that it may be an important therapeutic tool for modulating the response of the immune system in many inflammatory diseases, offering new treatment modalities. For this reason, its properties and role in the human body discussed in this review should be studied in more detail.

ClinicalTrials.gov as a Source of Information About Expanded Access Programs: Cohort Study

BACKGROUND

ClinicalTrials.gov (CT.gov) is the most comprehensive internet-based register of different types of clinical studies. Expanded access is the use of unapproved drugs, biologics, or medical devices outside of clinical trials. One of the key problems in expanded access is the availability to both health care providers and patients of information about unapproved treatments.

OBJECTIVE

We aimed to evaluate CT.gov as a potential source of information about expanded access programs.

METHODS

We assessed the completeness of information in the records of 228 expanded access programs registered with CT.gov from February 2017 through May 2020. Moreover, we examined what percentage of published expanded access studies has been registered with CT.gov. Logistic regression (univariate and multivariate) and mediation analyses were used to identify the predictors of the absence of some information and a study's nonregistration.

RESULTS

We found that some important data were missing from the records of many programs. Information that was missing most often included a detailed study description, facility information, central contact person, and eligibility criteria (55.3%, 54.0%, 41.7%, and 17.5% of the programs, respectively). Multivariate analysis showed that information about central contact person was more likely to be missing from records of studies registered in 2017 (adjusted OR 21.93; 95% CI 4.42-172.29; P<.001). This finding was confirmed by mediation analysis (P=.02). Furthermore, 14% of the programs were registered retrospectively. We also showed that only 33 of 77 (42.9%) expanded access studies performed in the United States and published from 2014 through 2019 were registered with CT.gov. However, multivariate logistic regression analysis showed no significant association between any of the variables related to the studies and the odds of study nonregistration (P>.01).

CONCLUSIONS

Currently, CT.gov is a quite fragmentary source of data on expanded access programs. This problem is important because CT.gov is the only publicly available primary source of information about specific programs. We suggest the actions that should be taken by different stakeholders to fully exploit this register as a source of information about expanded access.

Conflicts of interest in oncology expanded access studies

Expanded access is a treatment use of investigational drugs, biologicals or medical devices outside of clinical trials. The purpose of our study was to assess self-reported conflicts of interest (COIs) in oncology expanded access studies. One hundred fifty-eight oncology expanded access studies published from 2013 through 2020 were included. The pharmaceutical industry funded either completely or in part 94 studies (59.49%). The authors disclosed mostly financial COIs, while the number of the reported nonfinancial conflicts was relatively small (3528 and 57 COIs, respectively). The number of articles in which at least one author had a financial COI was 118 (74.68%). The most common financial COI types included advisory board membership/consulting (1471 COIs; 41.7%), followed by honoraria (570 COIs; 16.16%) and research funding (441 COIs; 12.5%). Logistic regression was performed to identify predictors of disclosing financial COIs and positive study's conclusions. On univariate analysis, financial COIs were more likely to occur in studies with at least one center located in the United States (odds ratio [OR], 5.62; 95% confidence interval [CI], 1.57-35.98; P = .02). We also found that positive conclusions about the studied treatments were less likely in studies without industry funding (OR, 0.26; CI, 0.08-0.77; P = .01). Most of the research on COIs in oncology performed to date focused on other types of studies, especially clinical trials. To our knowledge, our study is the first to evaluate COIs in oncology expanded access studies.

Therapeutic Perspectives and Mechanistic Insights of Phage Therapy in Allotransplantation

Bacterio(phages) are bacteria-infecting viruses that employ host translation machinery to replicate, and upon cell lysis, release new particles into the environment. As a result, phages are prey-specific, thus making targeted phage therapy (PT) possible. Indeed, pre- and posttransplant bacterial infections pose a substantial risk to allograft recipients in their clinical course. Moreover, with the increasing threat of antibiotic resistance, the interest in PT as a potential solution to the crisis of multidrug-resistant bacterial pathogens has rapidly grown. Although little is known about the specific characteristics of the phage-directed immune responses, recent studies indicate phages exert anti-inflammatory and immunomodulatory functions, which could be beneficial in allotransplantation (allo-Tx). PT targeting multidrug-resistant Klebsiella pneumoniae, Mycobacterium abscessus, and Pseudomonas aeruginosa have been successfully applied in renal, lung, and liver allo-Tx patients. In parallel, the gastrointestinal microbiota appears to influence allo-Tx immunity by modulating the endoplasmic reticulum stress and autophagy signaling pathways through hepatic EP4/CHOP/LC3B platforms. This review highlights the current relevant immunobiology, clinical developments, and management of PT, and lays the foundation for future potential standard care use of PT in allo-Tx to mitigate early allograft dysfunction and improve outcomes. In conclusion, with novel immunobiology and metabolomics insights, harnessing the potential of PT to modulate microbiota composition/diversity may offer safe and effective refined therapeutic means to reduce risks of infections and immunosuppression in allo-Tx recipients.

Isolation and Characterization of Phages Active against Paenibacillus larvae Causing American Foulbrood in Honeybees in Poland

The aim of this study was the isolation and characterization, including the phage effect on honeybees in laboratory conditions, of phages active against Paenibacillus larvae, the causative agent of American Foulbrood-a highly infective and easily spreading disease occurring in honeybee larva, and subsequently the development of a preparation to prevent and treat this dangerous disease. From the tested material (over 2500 samples) 35 Paenibacillus spp. strains were obtained and used to search for phages. Five phages specific to Paenibacillus were isolated and characterized (ultrastructure, morphology, biological properties, storage stability, and genome sequence). The characteristics were performed to obtain knowledge of their lytic potential and compose the final phage cocktail with high antibacterial potential and intended use of future field application. Preliminary safety studies have also been carried out on healthy bees, which suggest that the phage preparation administered is harmless.

Anti-biofilm activity of bacteriophages and lysins in chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is an otolaryngological disease with a recalcitrant nature, predominantly due to antibiotic resistant bacteria and the biofilm formation. The intracellular residency of Staphylococcus aureus bacteria was observed in CRS. The overall prevalence of CRS is estimated between 5-15% in the human population, and biofilms were formed in sinuses in 40-80% of cases. The bacterial species S. aureus and Pseudomonas aeruginosa are known to form difficult to treat biofilms in CRS. Bacteriophages (phages) or lysins can be alternatives to antibiotics in the biofilm treatment. The application of a P. aeruginosa phage cocktail ex vivo decreased biofilm biomass of bacterial isolates from the sinuses of CRS patients by a median of 70%. Further, animal studies performed on a sheep sinusitis model demonstrated significant reduction in S. aureus and P. aeruginosa biofilm biomass by phage cocktails while maintaining safe prolonged topical application (up to 20 days). Staphylococcal lysin P128 used at a concentration of ≥12.5 µg/ml in vitro against the biofilm of methicillin sensitive S. aureus (MSSA) and methicillin resistant S. aureus (MRSA) isolates from the sinuses of CRS patients demonstrated a significant reduction of the biofilm (up to 95.5%). Staphylococcal lysin CHAP(k) applied in vivo in mice nasal infection caused a significant 2 log reduction of S. aureus suggesting its potential use against bacteria in nasal mucosa. Furthermore, a beneficial effect of phage therapy in the treatment of chronic sinusitis in humans was observed. Here, we summarize the recent, quite scarce data regarding phage application in chronic rhinosinusitis and look further into this phenomenon. Keywords: bacteriophages; biofilm; chronic rhinosinusitis; lysins; phage therapy.

Immune Response to Therapeutic Staphylococcal Bacteriophages in Mammals: Kinetics of Induction, Immunogenic Structural Proteins, Natural and Induced Antibodies

Bacteriophages are able to affect the human immune system. Phage-specific antibodies are considered as major factors shaping phage pharmacokinetics and bioavailability. So far, general knowledge of phage antigenicity nevertheless remains extremely limited. Here we present comparative studies of immunogenicity in two therapeutic bacteriophages, A3R and 676Z, active against Staphylococcus aureus, routinely applied in patients at the Phage Therapy Unit, Poland. Comparison of the overall ability of whole phages to induce specific antibodies in a murine model revealed typical kinetics of IgM and IgG induction by these two phages. In further studies we identified the location of four phage proteins in the virions, with the focus on the external capsid head (Mcp) or tail sheath (TmpH) or an unidentified precise location (ORF059 and ORF096), and we confirmed their role as structural proteins of these viruses. Next, we compared the immune response elicited by these proteins after phage administration in mice. Similar to that in T4 phage, Mcp was the major element of the capsid that induced specific antibodies. Studies of protein-specific sera revealed that antibodies specific to ORF096 were able to neutralize antibacterial activity of the phages. In humans (population level), none of the studied proteins plays a particular role in the induction of specific antibodies; thus none potentially affects in a particular way the effectiveness of A3R and 676Z. Also in patients subjected to phage therapy, we did not observe increased specific immune responses to the investigated proteins.

Ethics codes and medical decision making

OBJECTIVE

The objective of this study is to analyze guidance about medical decision making contained in ethics codes. The primary question we address is which of the main decision-making models - informed decision making (IDM), shared decision making (SDM), or paternalism - is promoted by these codes.

METHODS

We manually searched codes of medical ethics for guidance on medical decision making. Our analysis focused on the major international code, the World Medical Association International Code of Medical Ethics (ICME), and national codes of the US, Canada, Australia, New Zealand, the UK, Ireland, Germany, France and Norway.

RESULTS

The ICME does not promote any specific model of medical decision making. 10 of the 11 analyzed national codes contain guidance about IDM, while only four refer to SDM. Some codes contain articles which are imprecise with regard to the question of medical decision making.

CONCLUSIONS

All of the analyzed national codes should be updated or amended. In particular, given the great importance of SDM in medicine, codes which do not contain relevant guidance should be updated.

PRACTICE IMPLICATIONS

Relevant amendments introduced to ethics codes could contribute to promoting of adequate standards of medical decision making (especially those regarding SDM) among doctors.

Temperate Bacteriophages-The Powerful Indirect Modulators of Eukaryotic Cells and Immune Functions

Bacteriophages are natural biological entities that limit the growth and amplification of bacteria. They are important stimulators of evolutionary variability in bacteria, and currently are considered a weapon against antibiotic resistance of bacteria. Nevertheless, apart from their antibacterial activity, phages may act as modulators of mammalian immune responses. In this paper, we focus on temperate phages able to execute the lysogenic development, which may shape animal or human immune response by influencing various processes, including phagocytosis of bacterial invaders and immune modulation of mammalian host cells.

Public availability of results of ClinicalTrials.gov-registered expanded access studies

AIMS

Expanded access is the use of investigational treatments outside of clinical trials. Results of expanded access studies provide insights into how investigational treatments work in real-world settings. The objective of this study was to evaluate public availability of results of expanded access studies.

METHODS

Eligible expanded access studies were identified in ClinicalTrials.gov (CT.gov). Publications matching records of individual studies were searched for in Medline and Embase. In addition, we assessed whether results of the included studies were publicly available from other sources including CT.gov, sponsor web sites and conference proceedings.

RESULTS

After median time of 49.5 (interquartile range, 36.7-64.7) months from study completion, the results of 69 out of the 152 included studies (45.39%) were publicly available, either as a journal publication (53 studies; 34.87%) or from other source (16 studies; 10.52%). The percentage of studies whose results were available as a journal publication after 12, 24, 36 and 48 months from study completion was 13.2, 21.1, 33.1 and 35.7%, respectively. The percentage of studies whose results were publicly available from any source (including journal publications) at 12, 24, 36 and 48 months were 19.1, 29.6, 43.2 and 47.5%, respectively.

CONCLUSION

Results of a considerable proportion of expanded access studies are not publicly available. In view of the growing importance of real-world data, sponsors and principal investigators of those studies should always consider making their findings public.

Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future

The current problems with increasing bacterial resistance to antibacterial therapies, resulting in a growing frequency of incurable bacterial infections, necessitates the acceleration of studies on antibacterials of a new generation that could offer an alternative to antibiotics or support their action. Bacteriophages (phages) can kill antibiotic-sensitive as well as antibiotic-resistant bacteria, and thus are a major subject of such studies. Their efficacy in curing bacterial infections has been demonstrated in in vivo experiments and in the clinic. Unlike antibiotics, phages have a narrow range of specificity, which makes them safe for commensal microbiota. However, targeting even only the most clinically relevant strains of pathogenic bacteria requires large collections of well characterized phages, whose specificity would cover all such strains. The environment is a rich source of diverse phages, but due to their complex relationships with bacteria and safety concerns, only some naturally occurring phages can be considered for therapeutic applications. Still, their number and diversity make a detailed characterization of all potentially promising phages virtually impossible. Moreover, no single phage combines all the features required of an ideal therapeutic agent. Additionally, the rapid acquisition of phage resistance by bacteria may make phages already approved for therapy ineffective and turn the search for environmental phages of better efficacy and new specificity into an endless race. An alternative strategy for acquiring phages with desired properties in a short time with minimal cost regarding their acquisition, characterization, and approval for therapy could be based on targeted genome modifications of phage isolates with known properties. The first example demonstrating the potential of this strategy in curing bacterial diseases resistant to traditional therapy is the recent successful treatment of a progressing disseminated Mycobacterium abscessus infection in a teenage patient with the use of an engineered phage. In this review, we briefly present current methods of phage genetic engineering, highlighting their advantages and disadvantages, and provide examples of genetically engineered phages with a modified host range, improved safety or antibacterial activity, and proven therapeutic efficacy. We also summarize novel uses of engineered phages not only for killing pathogenic bacteria, but also for in situ modification of human microbiota to attenuate symptoms of certain bacterial diseases and metabolic, immune, or mental disorders.

The Role of Antibiotic Resistant A. baumannii in the Pathogenesis of Urinary Tract Infection and the Potential of Its Treatment with the Use of Bacteriophage Therapy

Acinetobacter baumannii are bacteria that belong to the critical priority group due to their carbapenems and third generation cephalosporins resistance, which are last-chance antibiotics. The growing multi-drug resistance and the ability of these bacteria to form biofilms makes it difficult to treat infections caused by this species, which often affects people with immunodeficiency or intensive care unit patients. In addition, most of the infections are associated with catheterization of patients. These bacteria are causative agents, inter alia, of urinary tract infections (UTI) which can cause serious medical and social problems, because of treatment difficulties as well as the possibility of recurrence and thus severely decrease patients' quality of life. Therefore, a promising alternative to standard antibiotic therapy can be bacteriophage therapy, which will generate lower costs and will be safer for the treated patients and has real potential to be much more effective. The aim of the review is to outline the important role of drug-resistant A. baumannii in the pathogenesis of UTI and highlight the potential for fighting these infections with bacteriophage therapy. Further studies on the use of bacteriophages in the treatment of UTIs in animal models may lead to the use of bacteriophage therapy in human urinary tract infections caused by A. baumannii in the future.

Animal Models in the Evaluation of the Effectiveness of Phage Therapy for Infections Caused by Gram-Negative Bacteria from the ESKAPE Group and the Reliability of Its Use in Humans

The authors emphasize how extremely important it is to highlight the role played by animal models in an attempt to determine possible phage interactions with the organism into which it was introduced as well as to determine the safety and effectiveness of phage therapy in vivo taking into account the individual conditions of a given organism and its physiology. Animal models in which phages are used make it possible, among other things, to evaluate the effective therapeutic dose and to choose the possible route of phage administration depending on the type of infection developed. These results cannot be applied in detail to the human body, but the knowledge gained from animal experiments is invaluable and very helpful. We would like to highlight how useful animal models may be for the possible effectiveness evaluation of phage therapy in the case of infections caused by gram-negative bacteria from the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species) group of pathogens. In this review, we focus specifically on the data from the last few years.

The Rationale for Using Bacteriophage to Treat and Prevent Periprosthetic Joint Infections

Prosthetic joint infection (PJI) is a devastating complication after a joint replacement. PJI and its treatment have a high monetary cost, morbidity, and mortality. The lack of success treating PJI with conventional antibiotics alone is related to the presence of bacterial biofilm on medical implants. Consequently, surgical removal of the implant and prolonged intravenous antibiotics to eradicate the infection are necessary prior to re-implanting a new prosthetic joint. Growing clinical data shows that bacterial predators, called bacteriophages (phages), could be an alternative treatment strategy or prophylactic approach for PJI. Phages could further be exploited to degrade biofilms, making bacteria more susceptible to antibiotics and enabling potential combinatorial therapies. Emerging research suggests that phages may also directly interact with the innate immune response. Phage therapy may play an important, and currently understudied, role in the clearance of PJI, and has the potential to treat thousands of patients who would either have to undergo revision surgery to attempt to clear an infections, take antibiotics for a prolonged period to try and suppress the re-emerging infection, or potentially risk losing a limb.

The Presence of Bacteriophages in the Human Body: Good, Bad or Neutral?

The presence of bacteriophages (phages) in the human body may impact bacterial microbiota and modulate immunity. The role of phages in human microbiome studies and diseases is poorly understood. However, the correlation between a greater abundance of phages in the gut in ulcerative colitis and diabetes has been suggested. Furthermore, most phages found at different sites in the human body are temperate, so their therapeutic effects and their potential beneficial effects remain unclear. Hence, far, no correlation has been observed between the presence of widespread crAssphage in the human population and human health and diseases. Here, we emphasize the beneficial effects of phage transfer in fecal microbiota transplantation (FMT) in Clostridioides difficile infection. The safety of phage use in gastrointestinal disorders has been demonstrated in clinical studies. The significance of phages in the FMT as well as in gastrointestinal disorders remains to be established. An explanation of the multifaceted role of endogenous phages for the development of phage therapy is required.

Phage Therapy: Towards a Successful Clinical Trial

While phage therapy carried out as compassionate use (experimental therapy) has recently flourished, providing numerous case reports of supposedly healed patients, clinical trials aiming to formally prove their value in accord with current regulatory requirements have failed. In light of the current issue of increasing antibiotic resistance, the need for a final say regarding the place of phage therapy in modern medicine is evident. We analyze the possible factors that may favor success or lead to the failure of phage therapy: quality of phage preparations, their titer and dosage, as well as external factors that could also contribute to the outcome of phage therapy. Hopefully, better control of these factors may eventually bring about long-awaited positive results.

Ethics framework for treatment use of investigational drugs

BACKGROUND

Expanded access is the use of investigational drugs (IDs) outside of clinical trials. Generally it is performed in patients with serious and life-threatening diseases who cannot be treated satisfactorily with authorized drugs. Legal regulations of expanded access to IDs have been introduced among others in the USA, the European Union (EU), Canada and Australia. In addition, in the USA an alternative to expanded access is treatment under the Right-to-Try law. However, the treatment use of IDs is inherently associated with a number of ethically relevant problems.

MAIN TEXT

The objective of this article is to present a coherent framework made up of eight requirements which have to be met for any treatment use of an ID to be ethical. These include a justified need for the use of an ID, no threat to clinical development of the ID, adequate scientific evidence to support the treatment, patient's benefit as the primary goal of the use of an ID, informed decision of a patient, fair access of patients to IDs, independent review, as well as the dissemination of treatment results.

CONCLUSIONS

While this framework is essentially consistent with the legal regulations of expanded access of the USA, the EU, Canada and Australia, it is substantially wider in scope because it addresses some important issues that are not covered by the regulations. Overall, the framework that we developed minimizes the risks and threats, and maximizes potential benefits to each of the four key stakeholders involved in the treatment use of IDs including patients, doctors, drug manufacturers, and society at large.

Phage Prevalence in the Human Urinary Tract-Current Knowledge and Therapeutic Implications

Recent metagenomic analyses imply an immense abundance of phages in the human body. Samples collected from different sites (lungs, skin, oral cavity, intestines, ascitic fluid, and urine) reveal a generally greater number of phage particles than that of eukaryotic viruses. The presence of phages in those tissues and fluids reflects the paths they must overcome in the human body, but may also relate to the health statuses of individuals. Besides shaping bacterial metabolism and community structure, the role of phages circulating in body fluids has not been fully understood yet. The lack of relevant reports is especially visible with regard to the human urobiome. Certainly, phage presence and the role they have to fulfill in the human urinary tract raises questions on potential therapeutic connotations. Urinary tract infections (UTIs) are among the most common bacterial infections in humans and their treatment poses a difficult therapeutic dilemma. Despite effective antibiotic therapy, these infections tend to recur. In this review, we summarized the recent data on phage presence in the human urinary tract and its possible implications for health and disease.

Anti-phage serum antibody responses and the outcome of phage therapy

We examined the appearance of serum anti-phage antibodies in 25 patients with chronic sinusitis treated with phage therapy (PT). Approximately 30% of patients with weak antibody responses responded positively to PT, which was similar to the results of treatment achieved in a group of patients with high antibody production. In addition, there was no correlation between antibody level and the outcome of PT. These data, derived from a homogenous group of patients, confirm our earlier findings suggesting that the prognostic significance of serum anti-phage antibodies for the outcome of PT should be determined by relevant clinical trials.

Sepsis, Phages, and COVID-19

Phage therapy has emerged as a potential novel treatment of sepsis for which no decisive progress has been achieved thus far. Obviously, phages can help eradicate local bacterial infection and bacteremia that may occur in a syndrome. For example, phages may be helpful in correcting excessive inflammatory responses and aberrant immunity that occur in sepsis. Data from animal studies strongly suggest that phages may indeed be an efficient means of therapy for experimentally induced sepsis. In recent years, a number of reports have appeared describing the successful treatment of patients with sepsis. Moreover, novel data on the anti-viral potential of phages may be interpreted as suggesting that phages could be used as an adjunct therapy in severe COVID-19. Thus, clinical trials assessing the value of phage therapy in sepsis, including viral sepsis, are urgently needed.

The effects of T4 and A5/80 phages on the expression of immunologically important genes in differentiated Caco-2 cells*

Introduction: Bacteriophages are an abundant component of the mucosal microbiota in humans and some animal species. Intestinal epithelial cells (IECs) are the key element responsible for the induction and regulation of immune responses in the gut mucosa. The objective of this study was to evaluate the effects of T4 and A5/80 bacteriophages on the expression of immunologically important genes in Caco-2, a model cell line for IECs. Materials & Method: Bacteriophages were added to cultures of differentiated Caco-2 cells for 12 hours, while control cultures were treated with phosphate-buffered saline (PBS). Expression of genes in Caco-2 cells was determined using custom-made RT2 Profiler PCR Arrays, which allow for the evaluation of gene expression with the sensitivity and specificity of real-time PCR. We evaluated the expression of 21 genes which are important for the immune functions of IECs, including IL1B, IL6, IL7, IL10, IL15, IL18, IL25, IL33, TGFB1, TNF, CXCL8, CCL2, TSLP, FCER2, PIGR, DEFB4A, CAMP, REG3G, TNFSF13, TNFSF13B, and MUC2. Results: Both examined phages significantly influenced the expression of a number of genes compared with control cultures. In particular, T4 significantly increased the expression of the CCL2 and DEFB4A genes, while A5/80 induced the expression of the PIGR gene. Discussion: Together with the findings from previous studies, our results suggest that by modulating the expression of some genes, bacteriophages may affect immune responses in the gut mucosa.

Phages in Therapy and Prophylaxis of American Foulbrood - Recent Implications From Practical Applications

American foulbrood is one of the most serious and yet unsolved problems of beekeeping around the world, because it causes a disease leading to the weakening of the vitality of honey bee populations and huge economic losses both in agriculture and horticulture. The etiological agent of this dangerous disease is an extremely pathogenic spore-forming bacterium, Paenibacillus larvae, which makes treatment very difficult. What is more, the use of antibiotics in the European Union is forbidden due to restrictions related to the prevention of the presence of antibiotic residues in honey, as well as the global problem of spreading antibiotic resistance in case of bacterial strains. The only available solution is burning of entire bee colonies, which results in large economic losses. Therefore, bacteriophages and their lytic enzymes can be a real effective alternative in the treatment and prevention of this Apis mellifera disease. In this review, we summarize phage characteristics that make them a potentially useful tool in the fight against American foulbrood. In addition, we gathered data regarding phage application that have been described so far, and attempted to show practical implications and possible limitations of their usage.

Treatment of recurrent urinary tract infections in a 60-year-old kidney transplant recipient. The use of phage therapy

We would like to demonstrate the difficulty of treatment in a patient after kidney transplantation (KTX) who developed chronic urinary tract infection (UTI) with a multi-drug resistant ESBL-producing Klebsiella pneumoniae. The patient underwent several treatment interventions including supportive therapy with bacteriophages. This article presents a case of a 60-year-old patient after KTX repeatedly admitted to the hospital with recurrent UTIs caused by ESBL-producing Klebsiella pneumoniae showing variable susceptibility to carbapenems and full susceptibility to colistin only. KTX was performed due to renal insufficiency caused by polycystic kidney disease. The patient experienced 12 severe episodes of UTI due to K pneumoniae within 15 months since transplantation. In an attempt to curb the ongoing infections, phage therapy (PT) was applied on the experimental basis, coordinated by the Phage Therapy Unit of the Hirszfeld Institute in Wroclaw, Poland. Eventually, the patient fully recovered following nephrectomy of his own left kidney where cysts were the suspected reservoir of bacteria. The patient completed 29 days of PT. PT caused no reported side effects in the described case of the KTX recipient, although its role in controlling chronic UTI caused by K pneumoniae is unclear. More studies are needed in the population of kidney transplant recipients.

Phage Therapy in Poland - a Centennial Journey to the First Ethically Approved Treatment Facility in Europe

Although phage discovery is an unquestionable merit of the English bacteriologist Frederick W. Twort and the Canadian-French microbiologist Félix d'Hérelle, who both discovered phages over 100 years ago, the Polish history of phage studies also dates back to those years. In contrast to the Western world, developing phage treatment in Poland has never been abandoned despite the country's tense history marked by the Second World War (WWII) and the communism era. Today, Poland takes a prominent and remarkable place in the phage research area. Furthermore, established in 2005, the Phage Therapy Unit at the Hirszfeld Institute of Immunology and Experimental Therapy in Wrocław, the first such center within European borders, has quickly become a model for other centers in the world facing the issue of widespread antibiotic resistance. This article constitutes an attempt to fill the gap in the scientific literature by providing a comprehensive summary of the long tradition of phage research in Poland.

Microbiota in organ transplantation: An immunological and therapeutic conundrum?

The gastrointestinal (GI) tract microbiota is an environmental factor that regulates host immunity in allo-transplantation (allo-Tx). It is required for the development of resistance against pathogens and the stabilization of mucosa-associated lymphoid tissue. The gut-microbiota axis may also precipitate allograft rejection by producing metabolites that activate host cell-mediated and humoral immunity. Here, we discuss new insights into microbial immunomodulation, highlighting ongoing attempts to affect commensal colonization in an attempt to ameliorate allograft rejection cascade. Recent progress on the use of antibiotics to modulate GI microbiota diversity and innate-adaptive immune interface are discussed. Our focus on the microbiota's influence of endoplasmic reticulum (ER) stress and autophagy signaling through hepatic EP4/CHOP/LC3B platforms reveals a novel molecular pathway and potential biomarkers determining the progression of allo-Tx damage. Understanding and harnessing the potential of microbiome/bacteriophage therapies may offer safe and effective means for personalized treatment to reduce risks of infections and immunosuppression in allo-Tx.

Legal regulations, ethical guidelines and recent policies to increase transparency of clinical trials

Timely and accurate dissemination of outcomes is essential to accomplish main benefits of scientific research including clinical trials. Clinical trial results can be disseminated in two main ways: by publication in a peer-reviewed journal and by posting on a publicly available clinical trial register. The credibility of the literature on clinical trials is significantly diminished because a high percentage of trials is not published. While current legal regulations both in the European Union (EU) and the USA impose a duty to submit summary results of clinical trials to a respective register (EU Clinical Trial Register and ClinicalTrials.gov, respectively), the compliance with this requirement has been generally inadequate. Trial outcomes can be also made accessible by data sharing. However, in spite of the wide promotion of this idea, the access of investigators to participant-level datasets remains limited. The main objective of this review is to discuss current legal regulations, international standards, ethical guidelines and recent policies pertaining to dissemination of clinical trial results.

Induction of Phage-Specific Antibodies by Two Therapeutic Staphylococcal Bacteriophages Administered per os

In therapeutic phage applications oral administration is a common and well-accepted delivery route. Phages applied per os may elicit a specific humoral response, which may in turn affect phage activity. We present specific anti-phage antibody induction in mice receiving therapeutic staphylococcal bacteriophage A3R or 676Z in drinking water. The schedule comprised: (1) primary exposure to phages for 100 days, followed by (2) diet without phage for 120 days, and (3) secondary exposure to the same phage for 44 days. Both phages induced specific antibodies in blood (IgM, IgG, IgA), even though poor to ineffective translocation of the phages to blood was observed. IgM reached a maximum on day 22, IgG increased from day 22 until the end of the experiment. Specific IgA in the blood and in the gut were induced simultaneously within about 2 months; the IgA level gradually decreased when phage was removed from the diet. Importantly, phage-specific IgA was the limiting factor for phage activity in the gastrointestinal tract. Multicopy proteins (major capsid protein and tail morphogenetic protein H) contributed significantly to phage immunogenicity (IgG), while the baseplate protein gpORF096 did not induce a significant response. Microbiome composition assessment by next-generation sequencing (NGS) revealed that no important changes correlated with phage treatment.