Praćenje dinamike promjene urinarne mikrobiote djelovanjem antibiotika sekvencioniranjem 16S rRNA gena

master's thesis

• Title (english): Urinary microbiota dynamics during antibiotic therapy determined by 16S rRNA gene sequencing
• Author: Tea Širac
• Mentor: Jurica Žučko (mentor)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Biochemical Engineering); (Section for Bioinformatics); Zagreb
• Defense date and country: 2016-09-22, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

Urinarne infekcije predstavljaju jednu od najčešćih infekcija uzrokovanu bakterijama. Većina ih je uzrokovana bakterijom Escherichia coli i češće su prisutne kod žena prvenstveno zbog anatomskih razlika. Napredak tehnologije sekvencioniranja omogućio nam je direktno sekvencioniranje okolišnih uzoraka čime se omogućilo sekvencioniranje bakterija koje se ne mogu kultivirati u laboratoriju. Svrha ovog rada bila je praćenje promjene urinarnog mikrobioma uslijed djelovanja antibiotika Cefalina kod pacijentice s urinarnom infekcijom. Praćenje se provodilo sekvencioniranjem 16S rRNA gena, točnije V3 i V4 varijabilnih regija pomoću posebno dizajniranih početnica. Pokazano je da uzorak prije terapije ima najmanju bioraznolikost pri čemu uzročnik infekcije, nepoznata bakterija iz porodice Enterobacteriaeceae, prevladava sa zastupljenošću većom od 95%. Korištenjem antibiotika dolazi do naglog zamjenjivanja uropatogenih bakterija sa bakterijskim rodovima uobičajenim u urinarnom mikrobiomu, najviše Lactobacillus vrstama. Ta bakterijska vrsta ima zaštitnu ulogu, te pomaže u održavanju normalne mikrobiote.

Abstract (english)

Urinary tract infections (UTI) are among the most common bacterial infections. Most UTIs are caused by uropathogenic Escherichia coli and they are more often present in women primarily due to anatomical reasons. Progress in sequencing technology allowed us to sequence environmental samples which enable sequencing of the non-culturable bacteria. The purpose of this study was to monitor changes in urinary microbiome in patient with UTI who receives antibiotic therapy. Monitoring was carried out by sequencing 16S rRNA gene, specifically V3 and V4 variable region using specially designed primes. It is shown that the pre-treatment sample has the lowest biodiversity. In that sample prevails an unknown Enterobacteiaceae bacteria, which is the cause of infection, with over 95%. The use of antibiotics leads to the rapid replace of urophatogenic bacteria with bacterial genera common in urinary microbiome – Lactobacillus. They have a protective role and help maintain normal microbiota.

• Keywords: urinarni mikrobiom; 16S rRNA sekvencioniranje; urinarna infekcija; QIIME program; bioraznolikost
• Keywords (english): urinary microbiome; 16S rRNA sequencing; urinary infection; QIIME pipeline; biodiversity
• Language: croatian
• URN:NBN: urn:nbn:hr:159:366769
• Study programme: Title: Molecular Biotechnology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka molekularne biotehnologije (magistar/magistra inženjer/inženjerka molekularne biotehnologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Repository: Repository of the Faculty of Food Technology and Biotechnology
• Created on: 2017-04-24 12:41:49