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Browsing by Subject "faagiterapia"

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  • Hietikko, Alli (2019)
    Antibiotic-resistant bacteria are an increasing threat to global health, caused by the excessive use of antibiotics and the lack of new antimicrobial agents being introduced to the market. New approaches to prevent and cure bacterial infections are needed to halt the growing crisis. One of the most promising alternatives is phage therapy which utilizes bacteriophages to target and kill pathogens with specificity. Pseudomonas aeruginosa is a common opportunistic pathogen that is intrinsically resistant to antibiotics, making it one of the most heavily studied targets of phage therapy. In this study, I characterized four P. aeruginosa phages, fHo-Pae01, PA1P1, PA8P1 and PA11P1, and evaluate their potency in therapeutic applications. Bioinformatic analysis of the genomes revealed the phages to be genetically highly similar and belonging to the Pbunavirus genus of the Myoviridae family. No genes encoding harmful toxins, antibiotic-resistance, or lysogeny were predicted. On the other hand, many of the predicted genes had unknown functions. The host ranges of the phages were assessed using 47 clinical P. aeruginosa strains and predicted host receptor binding tail proteins were compared. Some correlation between the host ranges and mutations in the tail proteins were observed but this alone was not sufficient to explain the differences in the host ranges. The recently isolated vB_PaeM_fHoPae01 (fHo-Pae01) phage was further characterized by a one-step growth curve and imaged with a promising atomic force microscopy method that had not been used before in the Skurnik group. Though the imaging results failed to provide any further knowledge of the phage, the 70-minute-long latent period of infection could be determined from the growth curve. Anion- exchange chromatography was found inefficient in purifying the fHo-Pae01 phage, so alternative methods such as endotoxin columns should be used when purifying these phages for patient use. In conclusion, all four phages appeared to be safe for therapeutic use based on current knowledge, and PA1P1 and PA11P1 were the most promising candidates due to their broad host ranges.
  • Pankka, Salla (2023)
    The objective of this thesis was to isolate and characterize new bacteriophages (phages) against clinical Klebsiella pneumoniae strains for phage therapy. K. pneumoniae is causing an emerging threat to global health due to its broad antibiotic resistance profile and hypervirulent strains. New treatment options are urgently needed to defeat the crisis. Phage therapy could provide one option to treat multiresistant K. pneumoniae infections. In this thesis, five new phages were isolated and characterized from Finnish wastewater and Georgian river water against two clinical K. pneumoniae strains. The three phages from Georgian river water, fMtkKpn01, fMtkKpn03, and fMtkKpn04, resembled Drulisviruses based on phylogenetic analysis. The two phages from Finnish wastewater, fJoKpn03 and fJoKpn05 were phylogenetically distinct. fJoKpn03 couldn’t be classified. fJoKpn05 resembled Weberviruses. Based on sequence analysis, none of the phage genomes included any harmful genes that would prevent their use in phage therapy. All phages demonstrated a 6-hour total inhibition to host bacterial growth. Their host range was determined to be narrow, only infecting their respective host strains from the 80 bacterial strains tested. All the phages tolerated high pH well. fJoKpn03 was the only one tolerating very low pH. All phages showed a synergistic effect on the inhibition of bacterial growth when applied together with piperacillin. In conclusion, all five phages proved potential for phage therapy. They demonstrated inhibitory action against K. pneumoniae strains with capsule types against which there previously were no phages in our collection. Due to their narrow host range, they could be suited for personalized phage therapy or used in combination therapy with antibiotics to increase efficacy and duration of action. fJoKpn03 could provide an opportunity for oral administration due to its broad pH stability profile.
  • Mustonen, Markus (2024)
    The increase of antibiotic resistance is one of the major healthcare threats globally. One potential way to battle against antibiotic resistant bacterial infections is to treat them with the natural opponents of bacteria, bacteriophages, known as phage therapy. The aim of this thesis was to identify new bacteriophages against clinically notable bacterial species such as Escherichia coli, Burkholderia cepacia, Enterococcus faecalis and Enterococcus faecium. Bacteriophages were screened from various origins such as hospital sewage samples, soil samples and manure samples, collected in between 2019 and 2022. The isolated bacteriophages were then initially characterized to evaluate their potential use in phage therapy. In this thesis, two phages (fHo-Eco16, fHo-Eco17) against clinical E. coli isolate and one phage (fHo-Efa06) against clinical E. faecalis isolate were found from the recently collected Finnish hospital sewage sample pool. Both E. coli phages were classified as Felixounaviruses belonging to family of Ounavirinae and class of Caudoviricetes. Enterococcus phage fHo-Efa06 was characterized as Saphexavirus belonging to class of Caudoviricetes. Preliminary genome annotation did not reveal any characteristics of lysogenic lifecycle, or antibiotic resistance or bacterial toxin genes, which would prevent the use of phages in phage therapy. Both E. coli phages (fHo-Eco16, fHo-Eco17) showed narrow host range infecting only the primary host bacterial isolate but none of 29 other tested clinical E. coli isolates. Phage fHo-Efa06 showed relatively broad host range properties infecting nine tested E. faecalis isolates out of 20 tested E. faecalis isolates but no infection capabilities against six tested clinical E. faecium isolates. In conclusion, freshly collected hospital sewage seemed to be optimal environment to find bacteriophages against clinical bacterial isolates. Furthermore, phages fHo-Eco16, fHo-Eco17 and fHo-Efa06 did not display any strictly unsuitable properties which could prevent their use in phage therapy. In turn, to obtain the definitive certainty on the usability of the phages in therapeutic use, in-depth host range screening together with detailed functional and structural annotation for the phage genomes of fHo-Efa06, fHo-Eco16 and fHo-Eco17 should be completed.
  • Horsma-Heikkinen, Jenni (2020)
    The antibiotic resistance of pathogenic bacteria is becoming a major problem in treating bacterial infections and development of new antibiotics is very challenging. In traditional phage therapy the bacteriophages, viruses that infect bacteria, are being used as an optional treatment to eliminate infectious agents. Methicillin resistant Staphylococcus aureus (MRSA) is resistant to several currently used antibiotics and is one of the most common antibiotic resistant bacteria causing infections. Therefore, it is a potential target for the phage therapy. Some of the Staphylococcus aureus strains produce several different enzymes and toxins which can be harmful to patients. Products developed for phage therapy purposes need be free from the material originated from host bacteria. In this study, three different methods were tested for the purification of bacteriophages infecting S. aureus. The main goal was to produce phage lysates with purity and phage concentration suitable for therapeutic purposes using a fast and aseptic procedure upgradable for large volumes. The tested methods were ultrafiltration with filter tubes from two different manufacturers (Sartorius Vivaspin 6 ja Merck Millipore Amicon Ultra 4), polyethylene glycol (PEG) precipitation and ion exchange chromatography. Three different bacteriophage strains were used. One was isolated from a commercial Russian phage therapy product (vB_SauM_fRuSau02) and the other two from feces of pigs (vB_SauS_fPf-Sau02 and vB_SauS_fPfSau03). Host bacteria strains for the first bacteriophage were S. aureus strains TB4 and 13KP originally isolated from human infections. Two host strains for the latter two phages were MRSA strains isolated from healthy pigs. Purification of the phage lysates was evaluated by measurement of enterotoxins produced by S. aureus bacteria, measurement of free double stranded DNA (dsDNA), and by cytotoxicity test in cell cultures. All evaluation methods were commercially available tests. To determine how much of the bacteriophages were lost in the process, the phage concentrations of the lysates were determined before and after the purification and recovery rates were calculated for the viruses. After two separate ultrafiltrations, the recovery rates of the bacteriophages were mainly good, but there was a lot of variation in the results. The lowest recovery rate calculated was 5%, the highest 57%, and the mean of all the rates 24%. In this study the ion exchange chromatography was combined with ultrafiltration which was used in pre-cleaning of the lysates and changing the phages in a buffer suitable for the chromatography. The recovery rates from the ion exchange chromatography varied between 14-26% but the results may be affected by the ultrafiltration steps performed before and after, since a lot of variation was seen in ultrafiltration processes. PEG precipitation was performed for one phage lysate only in order to compare the laboriousness of the method and the rates of the recovery to the other methods used. The rate of recovery from the PEG precipitation was 9,5% which was fairly low. The purity of this lysate was not evaluated since the method was estimated to be too laborious compared to the other methods. Ultrafiltration turned out to be an efficient method in the removal of small protein molecules, such as enterotoxins from bacteriophage lysates. With two sequential ultrafiltrations 96-99% of the enterotoxins in the lysates were removed. The removal of the free dsDNA was also successful but there was variation between the phage lysates. Approximately 67-93% of the free dsDNA was removed but it is possible that some of the measured DNA originated from lysed bacteriophages as their genome also consists of dsDNA. Ion exchange chromatography produced extremely well purified phage products. The fractions had no enterotoxins left or the amount was below the detection limit of the test (<0,5-1 ng/g). Ion exchange chromatography was able to remove 96-99% of the free dsDNA of the lysates. It is possible that some of the DNA left in the lysates originated from the bacteriophages lysed during the process or in storage after that. When comparing how simple and fast the methods were, the ultrafiltration turned out to be superior. It can be used in fast production of bacteriophage products for the treatment of S. aureus infections. The purification achieved with the ultrafiltration should be adequate for a topical use of the product. When higher purity products are required, e.g. for administrating the product intravenously, ion exchange chromatography might be a safer option.