Primerjava genotipov bakterije Escherichia coli z betalaktamazami z razširjenim spektrom delovanja iz človeških in okoljskih vzorcev : raziskovalni podatki, obravnavani v doktorskem delu

Marič, Leon (author), Janežič, Sandra (author), Rupnik, Maja (author)

Bakterija Escherichia coli z encimi β-laktamaze z razširjenim spektrom delovanja (ESBL) je ena izmed glavnih prioritet pri spremljanju proti antibiotikom odpornih bakterij. Njena prisotnost je dobro raziskana v človeškem in živalskem rezervoarju, medtem ko je v okoljskem rezervoarju manj. Namen naše raziskave je bil primerjati genotipe ESBL-producentnih E. coli iz človeških in okoljskih virov v Sloveniji ter oceniti njihovo genetsko sorodnost. Med junijem 2023 in majem 2024 smo zbrali 561 človeških in 564 okoljskih izolatov iz treh slovenskih regij. Okoljske vzorce smo pridobili iz vode in sedimenta različnih vodnih virov, vključno z rekami, pritoki, jezeri, gramoznicami ter vtoki čistilnih naprav. S sekvenciranjem celotnih genomov smo izvedli multilokusno sekvenčno tipizacijo (MLST) in tipizacijo na osnovi jedrnega genoma (cgMLST), določili gene ESBL ter analizirali prisotnost plazmidov. Skupno smo identificirali 196 sekvenčnih tipov. Okoljski izolati so izkazovali večjo genetsko raznolikost kot človeški, pri katerih je zelo prevladoval sekvenčni tip ST131 (45 %). Med obema rezervoarjema smo našli 48 skupnih sekvenčnih tipov, kar predstavlja 77 % vseh izolatov. Določili smo tudi več klonalnih skupin, ki so vključevale izolate iz obeh rezervoarjev. Med ESBL geni je v obeh rezervoarjih prevladoval gen blaCTX-M-15. Večjo raznolikost plazmidov smo zaznali pri okoljskih izolatih. Hkrati smo identificirali ESBL-kodirajoče plazmide z enakimi replikonskimi tipi tako v človeškem kot okoljskem rezervoarju. Rezultati kažejo na pomembno genetsko povezanost med človeškim in okoljskim rezervoarjem ter poudarjajo pomen vključevanja okoljskega nadzora v strategije spremljanja bakterij, odpornih proti antibiotikom.

• Language: Slovenian
• Keywords: E. coli, odpornost proti antibiotikom, Eno zdravje, okolje, epidemiologija
• Typology: 2.20 - Complete scientific database of research data
• Geographic coverage: Slovenija: Prekmurje, Podravje in Gorenjska
• Time coverage: Od junija 2023 do maja 2024
• Organization: BF - Biotechnical Faculty
• Year: 2026
• PID: 20.500.12556/RUL-181375
• Data col. methods: Observation:Laboratory; Experiment; Experiment: Laboratory; Experiment: Field/Intervention
• Publication date in RUL: 06.04.2026

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: English
• Title: Comparison of genotypes of extended-spectrum betalactamases producing Escherichia coli from human and environmental samples : research data underlying the doctoral dissertation

Abstract

Extended-spectrum β-lactamases (ESBL)-producing Escherichia coli represents one of the main priorities in the surveillance of antibiotic-resistant bacteria. Its presence is well studied in human and animal reservoirs, whereas it is less explored in environmental reservoirs. The aim of our study was to compare the genotypes of ESBL-producing E. coli from human and environmental sources in Slovenia and to assess their genetic relatedness. Between June 2023 and May 2024, we collected 561 human and 564 environmental isolates from three regions of Slovenia. Environmental samples were obtained from water and sediment of various aquatic sources, including rivers, tributaries, lakes, gravel pits, and inflows to wastewater treatment plants. Whole-genome sequencing was used to perform multilocus sequence typing (MLST) and core genome MLST (cgMLST), to identify ESBL genes, and to analyze plasmid content. In total, 196 sequence types were identified. Environmental isolates showed greater genetic diversity than human isolates, in which sequence type ST131 strongly predominated (45%). A total of 48 sequence types were shared between the two reservoirs, representing 77% of all isolates. Several clonal groups were also identified, comprising isolates from both reservoirs. Among ESBL genes, blaCTX-M-15 predominated in both reservoirs. Greater plasmid diversity was observed in environmental isolates. At the same time, ESBL-encoding plasmids with identical replicon types were identified in both human and environmental reservoirs. The results indicate a significant genetic linkage between human and environmental reservoirs and highlight the importance of including environmental surveillance in strategies for monitoring antibiotic-resistant bacteria.

• Keywords: E. coli, AMR, One health, environment, epidemiology

Projects

• Funder: EU - Evropska unija
• Funding programme: EU4Health
• Project number: 101112671
• Name: Konsolidacija in integracija sekvenciranja celotnega genoma v rutinski monitoring v Sloveniji
• Acronym: SLOSEQ

• Funder: ARIS - Slovenian Research and Innovation Agency
• Project number: P3-0387
• Name: Mikrobiote pri ljudeh - vloga v zdravju in pri boleznih