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Antimicrobial resistance in clinical isolates of Clostridioides difficile derived from hospitalised patients in the Czech Republic and Slovakia.
Zíková, Jaroslava ; Krůtová, Marcela (advisor) ; Najmanová, Lucie (referee)
Clostridioides difficile is one of the most common pathogens of healthcare-associated colitis (CDI). However, in recent years there has been an increasing number of reported cases in the community. Causative strain characterization allows us to track the occurrence and spread of certain C. difficile types. To update the current CDI epidemiological situation, between October and November 2021, 342 C. difficile isolates or stool samples from CDI patients for culture were sent from 23 Czech (n=200) and 17 Slovak (n=142) hospitals. All C. difficile isolates were characterized by ribotyping and toxin genes detection. From 342 isolates, 52 different ribotyping profiles were identified. The frequent ribotypes detected were 001, 176, 014, 018 and 020. Genes for toxins A and B were found in all isolates. Genes for binary toxins were detected in 43 (21,5 %) Czech isolates and in 117 (82,4 %) Slovak isolates. Further, selected isolates (n=140, 40,9 %) were subjected to whole-genome sequencing (WGS) and antimicrobial susceptibility testing to 17 antibiotics (E-test). Multilocus sequencing typing determined 30 different sequence types from the 39 included ribotypes. All C. difficile isolates were susceptible to vancomycin, tetracycline, amoxicillin, and meropenem. The most frequently detected antimicrobial...
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Advanced Computational Methods for Increasing the Discriminatory Power of Genotyping Methods
Nykrýnová, Markéta ; Budinská, Eva (referee) ; Hrabák,, Jaroslav (referee) ; Škutková, Helena (advisor)
Tato disertační práce je zaměřena na vytvoření nových výpočetních metod, které zvýší diskriminačních schopnost genotypizačních metod. Hlavní důraz je kladen na odlišení blízce příbuzných bakterií, které pocházejí například z jedné nemocnice či jednoho oddělení. V první části práce jsou popsány současné typizační metody a jsou představeny nové postupy pro identifikaci genetických markerů s vysokou mírou sekvenční variability, pomocí kterých lze lépe rozlišit bakteriální populaci. Navržené metody jsou založeny na výpočtu signálů entropie a analýze nenamapovaných čtení. Druhá část práce se zabývá návrhem nových metod zpracování surových dat z nanopórového sekvenování, které lze použít pro rychlou vysoce citlivou typizaci bakterií bez nutnosti převádět proudové signály na nukleotidové sekvence. Předložená práce přispívá ke zlepšení a zpřesnění rutinně používaných typizačních metod pomocí navržených bioinformatických postupů a představuje unikátní přístup využití doposud experimentální techniky nanopórového sekvenování pro rychlou genotypizaci a analýzu bakterií.
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Current approaches to whole genome sequencing and de novo genome assembly
Halenková, Zuzana ; Reifová, Radka (advisor) ; Röslein, Jan (referee)
The cost of sequencing has fallen almost ten thousand times over the past ten years due to the development of second and third generation sequencers. Sequencing and assembling the whole genome sequence of an organism is thus becoming a more affordable tool which can be utilized in many fields of science. On the way to the complete DNA sequence of an organism, multiple important decisions have to be made. These are crucial for the successful assembly of high- quality whole genome sequence and regard sample preparation, choice of sequencing technique and choice of an appropriate approach to whole genome assembly. This bachelor thesis describes various methods which can be utilized in individual steps of the process and aspects to consider while making the decisions. Keywords: next generation sequencing, third generation sequencing, whole genome sequencing, de novo assembly, genome assembly algorithms
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Genome size estimation in protists
Lukeš, Jiří ; Čertnerová, Dora (advisor) ; Veselská, Tereza (referee)
This bachelor's thesis presents the current knowledge of the size of the genome in protists with a focus on the description and comparison of individual methods that were used to solve this issue. Genome size is a characteristic trait of all living organisms and other physiological features related to genome size are also mentioned. Of the selected methods, the greatest emphasis is placed on the flow cytometry, which is considered reliable and currently provides the most data on the size of protist genomes. In addition to flow cytometry, the contribution of whole genome sequencing to understanding the size of protist genomes is mentioned. Problems with estimating the size of protist genomes results from the heterogeneity of protists as a study group and from the non-uniform procedures within individual methods, which make possible comparisons difficult. Protists are evaluated in the work as an insufficiently studied group, within which the size of the genome varies by approximately 200,000×. The conclusion of the thesis summarizes the current knowledge about the genome size of relatively studied groups of protists. Key Words: Genome size, C-value, Protists, Flow cytometry, whole-genome sequencing, pulsed field gel electrophoresis, Feulgen densitometry, microspectrophotometry
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Leishmania of the subgenus Mundinia: genetical analysis and experimental infections of rodents and vectors.
Bečvář, Tomáš ; Sádlová, Jovana (advisor) ; Modrý, David (referee)
Leishmaniasis is a human and animal disease caused by digenetic parasites of the genus Leishmania, which is now divided into 4 subgenera - L. (Leishmania), L. (Viannia), L. (Sauroleishmania) and L. (Mundinia). Subgenus Mundinia was established in 2016 and consists of 5 species - L. enriettii and L. macropodum are parasites of wild mammals and L. martiniquensis, L. orientalis and unnamed L. sp. from Ghana are infectious to humans. Mundinia are geographically widely dispersed, their distribution covers all continents, except of Antarctica. Despite phlebotomine sand flies (Diptera: Psychodidae) also biting midges (Diptera: Ceratopogonidae) are supposed to be involved in transmission of these species, which is a unique feature for this subgenus. But there is little to no current information on natural reservoir hosts and vector species for any Mundinia species. In this thesis we tested possible vectors and potential model organisms (Guinea-pigs) and reservoir hosts of Mundinia species by experimental infections. We used 3 sand fly species sharing geographical distribution with respective Mundinia species and available in our laboratory for experimental infections. Sand flies from Australia had never been colonised so we used the permissive vector Lu. migonei for testing development of L. macropodum....
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Current approaches to whole genome sequencing and de novo genome assembly
Halenková, Zuzana ; Reifová, Radka (advisor) ; Röslein, Jan (referee)
The cost of sequencing has fallen almost ten thousand times over the past ten years due to the development of second and third generation sequencers. Sequencing and assembling the whole genome sequence of an organism is thus becoming a more affordable tool which can be utilized in many fields of science. On the way to the complete DNA sequence of an organism, multiple important decisions have to be made. These are crucial for the successful assembly of high- quality whole genome sequence and regard sample preparation, choice of sequencing technique and choice of an appropriate approach to whole genome assembly. This bachelor thesis describes various methods which can be utilized in individual steps of the process and aspects to consider while making the decisions. Keywords: next generation sequencing, third generation sequencing, whole genome sequencing, de novo assembly, genome assembly algorithms
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