Geni za dejavnike virulence in odpornost proti protimikrobnim učinkovinam pri sevih vrste Escherichia coli izoliranih iz kraških vodonosnikov

Kotnik, Kaja (author), Ambrožič Avguštin, Jerneja (mentor), Mulec, Janez (co-mentor)

V raziskavi smo analizirali 100 izolatov Escherichia coli, ki so bili izolirani iz kraških vodonosnikov, ki jih je vzorčili na Inštitutu za raziskovanje krasa ZRC SAZU. Zaradi poroznih tal se kontaminacije v krasu širijo hitreje. E. coli je komenzalna bakterija, ki naseljuje prebavni sistem toplokrvnih živali, in je eden glavnih indikatorjev za fekalno onesnaženje vode. Problematičnost E. coli se pojavi, ko iz komenzalne bakterije nastane patogena, ki povzroča različne okužbe. Vse bolj so razširjeni patogeni sevi, ki so tudi odporni proti protimikrobnim učinkovinam, kar otežuje zdravljenje. Cilj magistrske naloge je bil, da genotipiziramo izolate iz kraških vodonosnikov in ugotovimo njihovo patogenost in rezistentnost proti izbranim protimikrobnim učinkovinam. Preverili smo klonalnost izoliranih sevov z metodo ERIC-PCR ter uporabili molekularne metode za določevanje filogenetskih skupin. Ob tem smo preverili prisotnost 39 genov za dejavnike virulence, določili ali vzorci fenotipsko hemolizirajo ter testirali odpornost proti sedmim izbranim protimikrobnim učinkovinam. Ugotovili smo, da največ izolatov spada v filogenetsko skupino B1 (36 %) in A (32 %). Ugotovili smo prisotnost večih primerkov, ki so imeli večji nabor genov za dejavnike virulence. Najbolj virulenten izolat je spadal v skupino B2, imel je prisotnih 22 od 39 testiranih genov za DV. Samo 12 vzorcev je bilo odpornih na vsaj eno izbrano protimikrobno učinkovino. Med njimi smo izbrali tri, pri katerih smo preverili ali se odpornost lahko širi s konjugacijo. Pri dveh izolatih se je plazmid z genom za odpornost uspešno prenesel v recipientski sev.

• Language: Slovenian
• Keywords: Escherichia coli, vodonosniki, kras, filogenetske skupine, geni povezani z dejavniki virulence, konjugativni plazmidi
• Work type: Master's thesis/paper
• Organization: BF - Biotechnical Faculty
• Year: 2020
• PID: 20.500.12556/RUL-120288
• COBISS.SI-ID: 30965251
• Publication date in RUL: 18.09.2020

Secondary language

• Language: English
• Title: Virulence factor-associated genes and antimicrobial resistance genes in Escherichia coli strains isolated from karst aquifers

Abstract

In the study we analyzed 100 Escherichia coli isolates from karst aquifers sampled by the Karst Research Institute ZRC SAZU. Porous ground is responsible for a rapid spread of the contamination into karst ecosystems. E. coli is a commensal bacteria that inhabits the digestive tract of warm-blooded animals and is one of the main indicators of fecal water pollution. The problem of E. coli occurs when it turns into a pathogen as a commensal and as such can cause various infections. Pathogenic strains that are also resistant to antimicrobial agents (which makes treatments more difficult) are becoming increasingly widespread. The aim of the master's thesis was to genotype isolates from karst aquifers and determine how pathogenic and resistant they are. Using the ERIC -PCR-method we checked the clonality of the isolates, used molecular methods to determine phylogenetic groups, checked the presence of 39 genes related to virulence factors, determined whether the strains express phenotypic haemolysis, and tested the resistance against selected seven antimicrobial agents. We found that most samples belonged to the phylogenetic groups B1 (36%) and A (32%). We found that several strains had a larger set of virulence-related genes. Our most virulent isolate belonged to the group B2. It had 22 of the 39 tested genes. Only 12 samples were resistant to at least one of the selected antimicrobial agents. We selected three of them and tested whether the resistance could be transmitted by conjugation. For two isolates we confirmed that the plasmid with the resistance gene was successfully transferred to the recipient strain.

• Keywords: Escherichia coli, aquifers, karst, phylogenetic groups, genes associated with virulence factors, conjugative plasmids