Pojavnost odpornosti proti kolistinu in molekularna opredelitev proti kolistinu odpornih po Gramu negativnih bacilov v osrednjeslovenski regiji

Germ, Julija (author), Pirš, Mateja (mentor)

Ozadje: Kolistin učinkuje proti številnim po Gramu negativnim bacilom (GNB). Desetletja se v humani medicini skorajda ni uporabljal, uporabljali pa so ga v veterini. Zaradi naraščanja odpornosti GNB proti antibiotikom, kar je porajajoči se javnozdravstveni problem, postaja znova zanimiv za zdravljenje, podatki o pojavnosti proti kolistinu odpornih izolatov (ColR) pa so omejeni. Namen doktorske naloge je bil razjasniti razsežnost problema ColR, ugotoviti delež s ColR-GNB koloniziranih bolnikov na enotah intenzivnega zdravljenja (IE), oceniti uporabnost metod za hitro določanje ColR-izolatov ter s sekvenciranjem celotnega genoma na modelu Escherichia coli pridobiti poglobljene informacije o izolatih ColR v osrednjeslovenskem prostoru. Metode: S selektivnim gojiščem smo na ColR presejalno testirali izolate GNB. Pri 1176 prospektivno zbranih izolatih GNB smo določili minimalno inhibitorno koncentracijo za kolistin. Nadzorne kužnine bolnikov na IE smo analizirali z dvema protokoloma. Rezultate treh metod za hitro določanje ColR smo primerjali z rezultati mikrodilucije. Sekvencirali smo celotni genom 21 izolatov ColR E. coli. Rezultati: Deleži ColR med izolati E. coli, Klebsiella pneumoniae, Enterobacter spp., Citrobacter spp., Pseudomonas aeruginosa in Acinetobacter baumannii so bili 3,4 %, 6,3 %, 24,7 %, 5,1 %, 11,7 % in 23,7 %. Uvedli smo dvostopenjsko epidemiološko spremljanje ColR s specifičnostjo 99,5 % in občutljivostjo 87,5 %. S ColR je bilo koloniziranih 9,4 % bolnikov. Za najustreznejši test za hitro določanje ColR sta se izkazala Rapid Polymyxin NP (Enterobacterales) in Rapid ResaPolymyxin NP (A. baumannii). Pri enem ColR-izolatu E. coli smo našli gen mcr-1, pri ostalih ColR-izolatih smo našli le kromosomske mutacije genov povezanih z odpornostjo proti kolistinu. Zaključki: Ugotovili smo višji delež ColR izolatov od pričakovanega. Za ugotavljanje kolonizacije s ColR je optimalen protokol s predinkubacijo. Nekaj metod za hitro določanje ColR-izolatov je obetavnih, rezultat je potrebno potrditi z mikrodilucijo. Odpornost posredovana z genom mcr-1 pri E. coli je redka, prevladujejo kromosomske mutacije, izolati se pojavljajo sporadično.

• Language: Slovenian
• Keywords: odpornost proti kolistinu, epidemiološko spremljanje, testi za hitro določanje proti kolistinu odpornih izolatov, geni mcr, sekvenciranje celotnega genoma
• Work type: Doctoral dissertation
• Organization: MF - Faculty of Medicine
• Year: 2023
• PID: 20.500.12556/RUL-147399
• Publication date in RUL: 05.07.2023

Secondary language

• Language: English
• Title: Occurence of colistin resistance and molecular characterisation of colistin resistant gram-negative bacilli in Central Slovenian region

Abstract

Background: The antibiotic colistin is effective against many Gram-negative bacilli (GNB). For decades, it was almost no longer used in human medicine, but it was used in veterinary medicine. Due to the increasing resistance of GNB to antibiotics, it is again interesting for the treatment of patients, though data of colistin-resistant isolates (ColR) are scarce. The purpose of the thesis was to assess the extent of the ColR problem, to determine the proportion of ColR GNB colonisied patients in intensive care units (ICU), to evaluate the usefulness of methods for the rapid determination of ColR isolates, and to obtain in-depth information about ColR isolates in the central Slovenian region. Methods: The minimal inhibitory concentration for colistin for 1176 prospectively collected GNB isolates was determined. Control samples from ICU patients were processed using two protocols. The results of three methods for rapid determination of ColR were compared with the results of the reference method. The whole genome of 21 colR Escherichia coli isolates was sequenced and analyzed. Results: Colistin resistance rates were 3.4%, 6.3%, 24.7%, 5.1%, 11.7% and 23.7% among E. coli, Klebsiella pneumoniae, Enterobacter spp., Citrobacter spp., Pseudomonas aeruginosa and Acinetobacter baumannii isolates, respectively. A two-step epidemiologocial screening with specificity of 99.5% and sensitivity of 87.5% was introduced. 9.4% of ICU patientes were colonised with ColR isolates. Rapid Polymyxin NP (Enterobacterales) and Rapid ResaPolymyxin NP (A. baumannii) proved to be the most suitable tests for the rapid determination of ColR. A single mcr-1 gene was found in an E. coli isolate, in other isolates chromosomal adaptation were found. Conclusions: ColR rates among GNB isolates were higher than expected. Based on our findings, protocol with pre-enrichment step is mandatory to identify ColR carriers. Two methods for rapid detection of ColR isolates were promising, but the final result must be confirmed with the reference method. Sequencing of ColR E. coli isolates revealed sporadic cases of ColR isolates with complex resistance mechanisms.

• Keywords: colistin resistance, epidemiological screening, tests for rapid detection of colistin resistant gram—negative bacilli, mcr-genes, whole genome sequencing