Bioinformatic analysis of klebsiella pneumoniae genome isolated in Trabzon Fatİh state hospital

In recent years, antimicrobial resistance has been rapidly increasing on a global scale and is spreading from one country to another. The widespread and incorrect use of antibiotics in the last 80 years has led to the formation of antimicrobial resistance. Klebsiella pneumoniae (K. pneumoniae) is a pathogen that causes serious infections. The most common infection caused by K. pneumoniae is urinary tract infections. The spread of K. pneumoniae has become a major health problem. The limited treatment options due to multiple antibiotic resistance in infections caused by K. pneumoniae lead to the spread of the infection and death. Therefore, genomic analyses of K. pneumoniae isolates are of critical importance for elucidating resistance mechanisms and developing effective control strategies. In this thesis, K. pneumoniae K102 strain obtained from Trabzon Fatih State Hospital used. Whole genome sequencing (WGS) of the strain was performed to investigate chromosomal and genetic elements associated with antimicrobial resistance. The antibiogram of the K102 strain was determined using the EUCAST Phenotypic 2017 criteria. The K. pneumoniae K102 strain was found to be resistant to ampicillin, ceftriaxone, cefepime, ertapenem, meropenem, ciprofloxacin, colistin, trimethoprim, cefuroxime axetil, piperacillin/tazobactam, cefazolin, cefuroxime, cefoxitin, and ceftazidime; susceptible to amikacin and gentamicin; and intermediately susceptible to tigecycline. Furthermore, genes encoding methyltransferases, capsules, phages, pili, flagella, fimbriae, beta-lactamases, and virulence factors were identified within the strain. Whole genome analysis was conducted using MLST analysis, PlasmidFinder 2.1, ISFinder, BRIG, PHAST, ResFinder 3.2, and VFDB tools.