Characterization of antibiotic resistance and virulance genes in clinical Klebsiella pneumoniae isolates producing NDM-1 carbapenemase

Klebsiella pneumoniae is one of the most important pathogens in healthcare-related infections. Carbapenems are often used to treat infections caused by K. pneumoniae, which produce Extended spectrum β-lactamases (ESBL). However, the prevalence of carbapenem-resistant K. pneumoniae (KDKp), which is associated with high mortality rates, has been increasing in recent years. This situation has become an important public health problem worldwide. Recently, several hypervirulent and carbapenemase-producing isolates which further complicates the situation have been reported. More comprehensive genomic and phenotypic data are needed to better understand the mechanisms of resistance and virulence, and therefore to develop effective treatment strategies for infections caused by multidrug-resistant K. pneumoniae. In this study, 108 KDKp isolates isolated from various clinical samples and defined by Vitek-2 automated system were obtained from the stocks of Kırşehir Ahi Evran University Training and Research Hospital, Microbiology Laboratory. Of the 108 carbapenem-resistant isolates, 53 were found to have the blaNDM-1 resistance gene, and these isolates were included in the study. ESBL (blaTEM, blaSHV, blaCTX-M1, blaCTX-M2, blaOXA-1, blaPER-1, blaGES and blaVEB), carbapenemase (blaVIM, blaIMP, blaNDM-1, blaKPC and blaOXA-48), plasmid-mediated fluoroquinolone resistance genes (qnrA, qnrB, qnrS, aac(6')-ıb-cr) and Class-1 integron content of KDKp isolates were determined by PCR using specific primers. Hypermucoviscous properties of KDKp isolates were determined by string test and virulence gene content (rmpA, magA, wcaG, uge, wabG, ycfM, fimH, mrkD, kpn, allS, ureA, entB, fepA, iroD, iroN, ybtA, fyuA, iutA, kfuBC and cnf-1) was determined by multiplex and simplex PCR. The presence of pLVPK-derivative loci (iutA, rmpA, iroN) was used to determine hypervirulent isolates. K-antigen typing of KDKp isolates was determined using wzi gene sequences. While the genetic relatedness between the isolates was determined by rep-PCR, their epidemiological clonal similarities were determined by MLST analysis. As a result of this thesis study, it was determined that all of the KDKp isolates carried the blaCTX-M1 and aac-6'-Ib-cr genes. This is followed by blaTEM with 92.45%, qnrS with 90.56%, blaSHV and blaOXA-1 with 88.67%, blaOXA-48 with 71.69%, blaCTX-M2 with 20%, qnrB with 9.43% and blaVEB with 4%. In the study, qnrA, blaPER-1, blaGES, blaVIM, blaIMP, and blaKPC genes could not be detected in any isolate. When the class-1 integron contents were examined, 77.35% of the isolates were classified as In27 (dfrA12–orfF–aadA2). 63.37% of the KDKp isolates were evaluated as hypervirulants because they contained all pLVPK-derivative loci (iut A, rmpA, iro N). As a result of the string test, it was found that 9.43% of the isolates had hypermucoviscous phenotype. At the same time, the most common K-antigen type in KDKp isolates was wzi64 with a rate of 84.90%. As a result of MLST analysis, the most common ST type among KDKp isolates is ST2096, which was determined in 38 of the 53 isolates (71.69%). This is a detailed study in which carbapenem resistance, virulence factors, K-antigen type, and epidemiological clonal similarities of K. pneumoniae isolates are investigated. This thesis study is important both to prevent the spread of carbapenem-resistant infections and to plan to develop effective treatments.