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- Yüksek Lisans TeziAçık Erişim2026Trabzon Fatih Devlet hastanesinde izole edilen klebsiella pneumoniae genomunun biyoinformatik analizi
Şeyma Nur Tosun
Son yıllarda antimikrobiyal direnç küresel ölçekte hızlı bir şekilde artmakta ve bir ülkeden diğerine yayılmaktadır. Son 80 yılda antibiyotiklerin yaygın ve yanlış kullanımı antimikrobiyal direncin oluşmasına neden olmuştur. Klebsiella pneumoniae (K. pneumoniae) ciddi enfeksiyonlara neden olan bir patojendir. K. pneumoniae kaynaklı en sık rastlanan enfeksiyon üriner sistem enfeksiyonlarıdır. K. pneumoniae yayılımı temel sağlık problemi haline gelmiştir. K. pneumoniae'nın sebep olduğu enfeksiyonlarda çoklu antibiyotik direnci nedeniyle tedavi seçeneklerinin kısıtlı olması enfeksiyonun yayılmasına ve ölüme yol açar. Bu yüzden K. pneumoniae izolatlarının genomik analizleri, direnç mekanizmalarının aydınlatılması ve etkili kontrol stratejilerinin geliştirilmesi açısından kritik bir öneme sahiptir. Bu tezde Trabzon Fatih Devlet Hastanesinden temin edilen K. pneumoniae K102 suşu kullanıldı. Suşun tüm genom dizilemesi (WGS) gerçekleştirildi ve antimikrobiyal dirençlilikle ilişkili kromozomal ve genetik elementler araştırıldı. K102 suşunun antibiogramı, EUCAST Fenotipik 2017 programı kullanılarak elde edildi. K. pneumoniae K102 suşunda; ampisilin, seftriakson, sefepim, ertapenem, meropenem, siprofloksasin, kolistin, trimetoprin, sefuroksim aksetil, piperasilin/tazobaktam, sefazolin, sefuroksim, sefoksitin ve seftazidime karşı dirençli; amikasin ve gentamisine duyarlı; tigesikline ise orta duyarlı bulundu. Ayrıca suşta metiltransferaz, kapsül, faj, pili, flagella, fimbria, beta-laktamaz ve virülans faktörleri genleri tespit edildi. Bu araştırmada suşun tüm genom analizi MLST analizi, PlasmidFinder 2.1, ISFinder, BRIG, PHAST, ResFinder 3.2 ve VFDB programları kullanılarak gerçekleştirildi.
- MakaleAçık Erişim2020Investigation of Fosfomycin and Chloramphenicol Susceptibility of Carbapenemase-Producing Klebsiella pneumoniae Strains
Borsa, Baris Ata; Güngördü-Dalar, Zeynep; Karakullukçu, Asiye; Özalp, Veli Cengiz; Aygün, Gokhan
Objective: Antimicrobial resistance is one of the most mportant health problems of recent years. Multidrug-resistant Klebsiella pneumoniae strains have been causing serious problems in many countries including Turkey in recent years. Aim of this study was to detect molecular mechanisms behind the carbapenem resistance in carbapenem-resistant K. pneurnoniae strains isolated from rectal swab samples and investigate the susceptibility of two potentially alternative drugs, fosfornycin, and chloramphenicol. Methods: 46 K. pneumoniae strains isolated from rectal screening cultures of intensive care unit patients by using MacConkey agar containing 2 mg/L meropenem were included in this study. Carbapenem resistance of strains were confirmed by minimum inhibitor concentrations of meropenem obtained with gradient strip test. Presence of the bla(KPC,) bla(NDM) and bla(OXA), bla(IMP) and bla(VIM) genes were investigated by the real-time polymerase chain reaction. Broth microdilution method was used to investigate chloramphenicol susceptibility, and gradient strip test was used to investigate fosfomycin susceptibility of the strains. Results: At least one carbapenemase gene was detected in all K. pneumoniae strains. While all strains were found positive for the presence of OXA-48 type carbapenemase gene, 12 (26%) out of 46 were positive for both OXA-48 and NDM-1 carbapenemase genes, and only one (2%) strain was positive for OXA-48, NDM-1, and IMP-1 carbapenemase genes. Only 3 (6%) out of 46 strains were found susceptible to fosfomycin while 23 (50%) of them were susceptible to chloramphenicol. Additionally, we observed that the resistance rates to fosfomycin and chloamphenicol tended to be higher among carbapenemase producers. Conclusions: It is estimated that fosfomycin is not going to be a good option for the treatment of infections caused by carbapenemresistant K. pneumoniae strains in Turkey since only 6% of them were susceptible. Although the chloramphenicol susceptibility rate (50%) was higher than fosfomycin, further clinical studies are required to provide a better knowledge about the usage of this antibiotic in systemic infections. Moreover, multiple carbapenemase producers tended to be more resistant to fosfomycin and also chloramphenicol.
- MakaleAçık Erişim2018Next-generation sequencing of plasmid carrying blaOXA-48 in Klebsiella pneumoniae from Turkey
Düzgün, Azer Özad; Saral, Ayşegül
A carbapenem-resistant Klebsiella pneumoniae strain was isolated in Turkey in 2012 and blaNDM-1 and blaOXA-48 genes were observed in this strain. The aim of this study was to investigate transferability of plasmid bearing blaOXA-48 in K. pneumoniae and to use whole-genome sequencing in order to understand the genetic context of plasmid. K. pneumoniae strain was used as donor in conjugation experiments. Antibiotic susceptibility profile of selected transconjugant was determined. Plasmid was isolated from transconjugant colony and was named as pKPT. Complete sequencing of the pKPT was conducted using a next-generation sequencing. Annotation of the contigs was performed using the Geneious R9, followed by finding open reading frames (ORFs) with selected web-based tools. BLAST analysis was performed at the NCBI BLAST server to determine genes showing more than 90% similarity with these ORFs. Results of antibiotic susceptibility test showed that transconjugant colony was resistant to ampicillin/ sulbactam, piperacillin, and piperacillin/tazobactam. The pKPT plasmid had a length of 45,217 bp and an average G + C content of 49%. Blast analysis revealed that pKPT was included in the IncL/M incompatibility group. The pKPT was found to contain blaOXA-48 within Tn1999.2 transposon without any other antibiotic resistance gene.