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CNV detection in bacterial genomes
Lacinová, Michaela ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
This master thesis deals with analysis of structural variation of genome and with methods of its sequencing across all generations. Subsequently it contains a description of copy number variation and methods of its detection. The experimental part focuses on algorithm proposal for CNV detection according analysis and testing of uneven coverage in genome, variable representation of GC content and distance of sequence reads. Finally, the algorithm for detecting copy number variation is tested on genomic data of bacteria Klebsiella pneumoniae.
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Genotyping of Klebsiella pneumoniae isolates
Nykrýnová, Markéta ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This master thesis deals with typing of Klebsiella pneumoniae isolates. The first part of the thesis introduces molecular typing methods. Then bacterial genomes and Klebsiella pneumoniae are characterized. Following part describes data validation, assembly of genomes and proposed algorithm for finding genes with high variability. In last part obtained results are presented and validated on other genomes of Klebsiella pneumoniae.
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Antibiotic resistance profile determination in hybrid assembled bacterial genomes
Dzurčaninová, Natália ; Škutková, Helena (referee) ; Nykrýnová, Markéta (advisor)
Antibiotická rezistencia je vážny problém vo väčšine spôsobený zmenami v bakteriálnom genóme. Získavanie a uchovávanie spoľahlivých bakteriálnych genomických dát je preto nevyhnutné pre štúdium mechanizmov a prenosu antibiotickej rezistencie. Táto práca popisuje bakteriálny genóm, antibiotickú rezistenciu a nástroje pre jej identifikáciu spolu s procesmi nevyhnutnými pre zisk genómov, sekvenáciu a skladanie. Sústreďuje sa na hybridné skladanie genómov spravidla vysoko rezistentných baktérií Klebsiella pneumoniae a ich nasledujúcich analýz. Cieľom týchto analýz je skonštruovať profily antibiotických rezistencií a určiť fylogenetickú príbuznosť genómov.
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Antibiotic resistance profile determination in hybrid assembled bacterial genomes
Dzurčaninová, Natália ; Škutková, Helena (referee) ; Nykrýnová, Markéta (advisor)
Antibiotická rezistencia je vážny problém vo väčšine spôsobený zmenami v bakteriálnom genóme. Získavanie a uchovávanie spoľahlivých bakteriálnych genomických dát je preto nevyhnutné pre štúdium mechanizmov a prenosu antibiotickej rezistencie. Táto práca popisuje bakteriálny genóm, antibiotickú rezistenciu a nástroje pre jej identifikáciu spolu s procesmi nevyhnutnými pre zisk genómov, sekvenáciu a skladanie. Sústreďuje sa na hybridné skladanie genómov spravidla vysoko rezistentných baktérií Klebsiella pneumoniae a ich nasledujúcich analýz. Cieľom týchto analýz je skonštruovať profily antibiotických rezistencií a určiť fylogenetickú príbuznosť genómov.
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Diagnostics and therapy of polyresistant bacteria in the Hospital Havlíčkův Brod
KOSTKOVÁ, Monika
Antibiotic resistance is a problem not only in our country but also in the world. The incidence of polyresistant bacterial species, which cause serious and difficult-to-treat infections, is increasing. This issue has implications for both patients' health and healthcare costs. The practical part of my bachelor thesis was performed in the Laboratory of clinical mikrobiology (ONHB). Samples were taken from ONHB, from the Psychiatric Hospital and from general practitioners from around Havlíčkův Brod. In my work, I visited strains of Klebsiella pneumoniae and Pseudomonas aeruginosa, which are often the cause of nosocomial infections. The first step was the correct isolation and diagnosis of bacteria and examination of the susceptibility of bacteria to antibiotics, where I used the disk diffusion method, the minimum inhibitory concentration and methods for the detection of broad-spectrum -lactamases. The aim of this work was to determine the representation of the number of these bacteria in the community and in the hospital environment, where I assumed that the incidence of resistant bacteria in the hospital environment is higher. I also dealt with the development of resistance of these bacteria to given antibiotics in the period 2017-2022. In conclusion, I drew attention to the correct principles of antibiotics and thus to the prevention of antibiotic resistance, as well as the possibilities of prevention and treatment of nosocomial infections.
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CNV detection in bacterial genomes
Lacinová, Michaela ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
This master thesis deals with analysis of structural variation of genome and with methods of its sequencing across all generations. Subsequently it contains a description of copy number variation and methods of its detection. The experimental part focuses on algorithm proposal for CNV detection according analysis and testing of uneven coverage in genome, variable representation of GC content and distance of sequence reads. Finally, the algorithm for detecting copy number variation is tested on genomic data of bacteria Klebsiella pneumoniae.
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Monitoring and detection of Escherichia coli and Klebsiella pneumoniae strains with Extended Spectrum Beta-Lactamase (ESBL) production in Hospital Prachatice, a. s. in 2014-2018.
TVRDKOVÁ, Pavla
The ever increasing resistance of bacteria is a grave issue world-wide. Some bacteria are resistant naturally but for other resistance is acquired. As a result, we can encounter bacterium that would formerly be quite easily killed by administering antibiotics but, in the course of time, as a result of, for example, communication between various bacteria species and strains in the form of various mutations and, frequently, after the administration of incorrect antibiotic and the effects of selective antibiotic pressure, the same bacterium becomes resistant to antibiotics. One of the types of such acquired resistance is the production of broad-spectrum beta-lactamases ESBL. The objective of this thesis is to establish the representation and development of ESBL production in Escherichia coli strains and Klebsiella pneumoniae strains as these make the most frequent producers of these broad-spectrum beta-lactamases, in certain hospital departments and in various types of clinical materials over the period of 5 years. In addition, the thesis focuses on the development of antibiotic resistance, accordingly, over the 5 year period. Data gathering and utilization of methods took place at the Medical Microbiology Department of the Prachatice Hospital (Nemocnice Prachatice, a.s.). To identify microbes to a more precise level, the commercial set ENTEROtest 24 N and INDOL test were used. The disk diffusion method and method for determining the minimum inhibitory concentration were used to determine sensitivity to antimicrobial agents. The commercial set MASTDISC AmpC and ESBL (D68C) were used to detect ESBL. The outcomes indicated that the number of Escherichia coli strains producing ESBL and Klebsiella pneumoniae strains producing ESBL grew almost each year (with the exception of 2016). The outcomes also indicated that the greatest number of ESBL producers were found with Klebsiella pneumoniae strains. Furthermore, the ESBL producers were grouped depending on hospital departments in which most frequent occurrences were found; the most frequent ESBL occurrence of both producers was found in the department of internal medicine. Additionally, the ESBL producers were grouped based on capture in various types of clinical materials; the greatest quantities of both microbes were found in urine. Based on these findings, the development of antibiotic resistance for both microbes over the period of 5 years was analyzed on samples of urine. When monitoring antibiotic resistance development, no considerable growths in bacterial strains resistant to individual anti-microbial agents was found over the 5 year period. Only for 3rd generation cephalosporins, there was a certain growth in resistance detected almost every year for both microbes. Namely, Escherichia coli isolates showed a growth from 6 % to 9 % and Klebsiella pneumoniae isolates showed a growth from 29 % to 33 % in the percentual quantity of strains resistant to these antibiotics.
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Genotyping Of Klebsiella Pneumoniae Isolates
Nykrýnová, Markéta
Typing methods capable of distinguishing bacterial strain are essential for epidemiologist because they help to prevent and control infections. Unfortunately, many typing methods are timeconsuming, expensive and reproducibility of their results is questionable. Therefore, we propose a new genotyping method, which is capable of identifying genes with high rate of variability to distinguish different bacterial strains.
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Genotyping of Klebsiella pneumoniae isolates
Nykrýnová, Markéta ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This master thesis deals with typing of Klebsiella pneumoniae isolates. The first part of the thesis introduces molecular typing methods. Then bacterial genomes and Klebsiella pneumoniae are characterized. Following part describes data validation, assembly of genomes and proposed algorithm for finding genes with high variability. In last part obtained results are presented and validated on other genomes of Klebsiella pneumoniae.
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Development of antibiotic resistance in the region Písek in 2000-2010
MAREŠOVÁ, Lucie
This bachleor´ s dissertation is aimed to the developement of antibiotical resistance by choosed kinds of bacteria, particulary Pseudomonas aeruginosa, Escherichia coli and Klebsiella pneumoniae in the region of Písek and also in the whole Czech Republic during the period 2000-2010. There is described matter of the antibiotical resistance, antimicrobial agents and also information about the EARS-Net system in the beginning of this work. The practical part contains the evaluation of resistance spread in the region of Pisek according to the data of clinical microbiology of Nemocnice Pisek, the spread of resistance in the Czech Republic according to the EARS-Net and also the consumption of individual groups of antibiotics according to the State Institute for Drug Control. Antibiotical resistance is spreading constantly, for example because of inappropriate usage of the antibiotics or insufficient information about pathogens that cause infectious diseases the most frequently.
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