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    Characterization of uropathogenic Escherichia coli strains obtained from urology outpatient clinic of Ege Medical Faculty in İzmir
    (2012) Giray B.; Uçar F.B.; Aydemir S.S.
    Aim: To identify the papG gene and its allelic variation in uropathogenic Escherichia coli (UPEC) strains isolated from patients with acute pyelonephritis and cystitis. Materials and methods: Seventy-five E. coli strains isolated from patients admitted to the University of Ege Medical Faculty urology outpatient clinic were isolated and identified phenotypically. All of these strains were examined for the papG gene and allelic distribution of this gene with the multiplex polymerase chain reaction technique. Results: papG genes were found in 24 of 75 E. coli strains. Of these 24 strains, 7 (29%) had papG class II only, 8 (33%) had class III only, and 9 (38%) had both class II and III. Phylogenetically, it was found that 31 belonged to group B2, 19 to group D, 20 to group A, and 5 to group Bl. Serotyping was performed and the positivity was found to be 39%. When the antibiotic resistance profiles of the 75 strains were evaluated, 41 (55%) of them were found to be resistant to ampicillin, 35 (47%) to ciprofloxacin, and 35 (47%) to trimethoprim/sulfamethoxazole. In addition, 23 strains (31%) produced extended-spectrum beta-lactamase. Conclusion: In this study, the rate of papG-positive strains was found to be low. However, there is no consensus on the molecular definition of UPEC. Although the presence of the papG gene indicates that the strains are UPEC, absence of the papG gene does not suggest that the strains are not UPEC. © TÜBİTAK.
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    Comparison of phenotypic methods and polymerase chain reaction for the detection of carbapenemase production in clinical Klebsiella pneumoniae isolates [Klinik Klebsiella pneumoniae Izolatlarinda Karbapenemaz Üretiminin Saptanmasinda Polimeraz Zincir Reaksiyonu ve Fenotipik Yöntemlerin Karşilaştirilmasi]
    (Ankara Microbiology Society, 2017) Tekintaş Y.; Çilli F.; Eraç B.; Yaşar M.; Aydemir S.S.; Limoncu M.H.
    Being a member of the Enterobacteriaceae family, Klebsiella pneumoniae is an opportunistic pathogen that inhabits normal human microbiota and causes predominantly hospital-acquired infections. The emergence of K.pneumoniae isolates which are resistant particularly to the carbapenem group of antibiotics has led to an increase in hospitalization period, mortality and morbidity. Although different rates of resistance are observed between countries, regions and even healthcare facilities, there has been a rapid increase in the prevalence of carbapenem-resistant strains in the last 10 years. Fast and correct identification of carbapenem-resistant strains is important for the successful treatment of infections caused by these resistant bacteria. The objective of this study was to investigate the presence and the types of carbapenemases in carbapenem-resistant K.pneumoniae strains using "MASTDISCS™ ID carbapenemase detection disc set", a commercial product that can be used for this purpose, and "Carbapenem Inactivation Method (CIM)", a relatively new method, and compare the results of these methods by polymerase chain reaction (PCR). For this purpose, we used 54 K.pneumoniae strains isolated in 2015-2016, that were resistant to any of the ertapenem, meropenem or imipenem antibiotics. The identification of the strains was performed using VITEK MS and their antibiotic susceptibility tests were carried out using the VITEK 2 Compact® automated system. For the strains that were found resistant to carbapenems in the automated system, the minimum inhibitor concentration (MIC) values were determined by the gradient testing method according to the recommendations of "The European Committee on Antimicrobial Susceptibility Testing (EUCAST)". The blaOXA-48 blaIMP, blaNDM, blaVIM, and bloSIM genes were investigated with PCR among these isolates. Phenotypic enzyme typing was performed in the carbapenem-resistant strains using the "MASTDISCS™ ID carbapenemase detection disc set" and "Carbapenem Inactivation Method (CIM)". REP-PCR was used to reveal clonal relationship of the isolates. The 54 K.pneumoniae isolates were found as resistant to carbapenem and the MIC50 and MIC90 values of imipenem, meropenem and ertapenem were 32 µg/ml. Only 33 of the strains had blaOXA-48 and two of them had only blaNDM, the remaining 19 strains had both of these two genes. The blaIMP' blaVIM and blaSIM genes were not encountered in any of the isolates. When the isolates were assessed by the REP-PCR method, six main clones were detected. The "MASTDISCS™ ID carbapenemase detection disc set" was able to detect all the carbapenemase producing strains and it remained incapable of distinguishing OXA-48 in the strains which had both OXA-48 and metallo beta lactamase (MBL) enzymes. The CIM method showed a low rate of positivity (46.15%) in the strains containing blaOXA-48, but was found much more successful in the strains containing blaNDM with a detection rate of 85.71%. In this study, it was concluded that the Mastdiscs-ID method could be successfully used to detect the presence of blaOXA-48 which has a high prevalence in our country.