Genomske analize izbranih sevov bakterije Escherichia coli

Mubi, Gal (author), Starčič Erjavec, Marjanca (mentor), Accetto, Tomaž (comentor)

Sekvenciranje celotnega genoma (WGS) omogoča natančno analizo genetskih značilnosti bakterij. V tej nalogi smo s pomočjo WGS analizirali genome 13 kliničnih uropatogenih sevov bakterije Escherichia coli (UPEC), ki so jih izolirali iz urina bolnikov z okužbo urinarnega trakta (UTI). Na podlagi pridobljenih genomskih zaporedij smo bioinformacijsko proučili njihovo filogenetsko ozadje, prisotnost genov, povezanih z virulenco (VAG), genov za odpornost proti antibiotikom (ARG) in genov za sintezo biofilmov ter ocenili vlogo mobilnih genetskih elementov pri horizontalnem prenosu genov (HGT). Večino kliničnih sevov smo uvrstili v filogenetsko skupino B2, ki je povezana z visoko patogenostjo. Pri sevih iz skupine A smo zaznali šibkejši virulentni potencial, vendar obsežen profil odpornosti. Pri 69 % sevov smo zaznali večkratno odpornost proti protimikrobnih učinkovinam (MDR), pri čemer sta seva DL07 in DL17 izstopala zaradi prisotnosti plazmidno kodiranih in redkih ARG, ki imajo zapise za odpornost proti makrolidom in amfenikolom. Na podlagi analize genov za sintezo biofilmov smo pri veliki večini sevov uspeli identificirati kromosomsko kodirane gene za sintezo celuloze, kurli fimbrij in kolanske kisline, z izjemo odsotnosti genov za sintezo kolanske kisline pri sevih DL09, DL14 in DL90. Rezultati potrjujejo visoko raven genetske pestrosti med vsemi 13 kliničnimi sevi in nakazujejo na kompleksne mehanizme evolucijskih prilagoditev, ki vključujejo tako horizontalni prenos genov, kot tudi raznolikost v možnosti tvorbe biofilma, njihovem virulentnem potencialu in odpornosti proti antibiotikom.

• Language: Slovenian
• Keywords: uropatogena E. coli, virulenca, odpornost proti antibiotikom, biofilm, horizontalni genski prenos, bioinformatika
• Work type: Master's thesis/paper
• Typology: 2.09 - Master's Thesis
• Organization: BF - Biotechnical Faculty
• Publisher: [G. Mubi]
• Year: 2025
• PID: 20.500.12556/RUL-167949
• UDC: 579.25:575.111
• COBISS.SI-ID: 229828611
• Publication date in RUL: 21.03.2025

Secondary language

• Language: English
• Title: Genomic analyses of selected Escherichia coli

Abstract

Whole-genome sequencing (WGS) enables precise analysis of the genetic characteristics of bacteria. In this study, we used WGS to analyze 13 clinical uropathogenic Escherichia coli (UPEC) strains, isolated from urine samples of patients with urinary tract infections (UTIs). Bioinformatic methods were used to investigate the phylogenetic background, the presence of virulence-associated genes (VAG), antibiotic resistance genes (ARG), and biofilm synthesis genes, as well as to assess the role of mobile genetic elements in horizontal gene transfer (HGT). The majority of the UPEC strains studied were asigned to phylogenetic group B2, which is known for its high pathogenic potential. The strains from phylogenetic group A exhibited a weaker virulence profile but a broader resistance spectrum. Multidrug resistance (MDR) was detected in 69% of strains, with DL07 and DL17 standing out due to the presence of plasmid-encoded and rare ARGs conferring resistance to macrolides and amphenicols. Analysis of biofilm synthesis genes revealed that most strains carried chromosomally encoded genes for cellulose, curli fimbriae, and colanic acid, with exception of strains DL09, DL14, and DL90, which lacked colanic acid biosynthesis genes. The results obtained confirm a high degree of genetic diversity among all 13 UPEC strains studied and point to complex evolutionary adaptation mechanisms, including horizontal gene transfer, variations in biofilm formation potential, virulence, and antibiotic resistance profiles.

• Keywords: uropatogenic E. coli, virulence, antibiotic resistance, biofilm, horizontal gene transfer