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Öğe Antimicrobial susceptibility profile of ceftolozane/tazobactam, ceftazidime/avibactam and cefiderocol against carbapenem-resistant Pseudomonas aeruginosa clinical isolates from Türkiye(Springer, 2024) Buyukyanbolu, Ecem; Genc, Leyla; Cyr, Elizabeth A.; Karakus, Mehmet; Comert, Fusun; Otlu, Baris; Aktas, ElifPurpose Carbapenem resistant Pseudomonas aeruginosa (CR-PA) is escalating worldwide and leaves clinicians few therapeutic options in recent years, beta-lactam/beta-lactamase inhibitor combinations (ceftolozane-tazobactam, ceftazidime-avibactam) and a new siderophore cephalosporin (cefiderocol) have been approved for the treatment of P. aeruginosa infection and have shown potent activity against isolates defined as carbapenem resistant. The aim of this study was to determine the phenotypic profile of these agents against CR-PA in the emerging setting of carbapenemases. Methods CR-PA clinical isolates were collected from three teaching hospitals in different geographical regions between January 2017-December 2021. All isolates were subjected to phenotypic carbapenemase testing using modified carbapenem inactivation method. MICs were determined by reference broth microdilution and evaluated according to EUCAST standards, while genotypic profiling was determined using PCR methods. Results 244 CR-PA sourced most frequently from the respiratory tract (32.2%), blood (20.4%) and urine (17.5%) were evaluated. Of all isolates, 32 (13.1%) were phenotypically and 38 (15.6%) were genotypically defined as carbapenemase-positive. The most common carbapenemase was GES (63.1%), followed by VIM (15.8%). The MIC50/90(S%) of ceftazidime/avibactam, ceftolozane/tazobactam and cefiderocol in all CR-PA isolates were 4 and 32 (80%), 1 and > 64 (69%) and 0.25 and 1 mg/L (96%), respectively. Cefiderocol was also the most active agent in carbapenemase-positive isolates (90%). Conslusion While ceftolozane/tazobactam and ceftazidime/avibactam remained highly active against CR-PA devoid of carbapenemases, cefiderocol provided potent in vitro activity irrespective of carbapenemase production. When considering the potential clinical utility of newer agents against CR-PA, regional variations in carbapenemase prevalence must be considered.Öğe Evaluation of emm gene types, toxin gene profiles and clonal relatedness of group A streptococci(Assoc Basic Medical Sci Federation Bosnia & Herzegovina Sarajevo, 2013) Mengeloglu, Firat Zafer; Aktas, Elif; Otlu, Baris; Comert, Fusun; Kulah, Canan; Tas, Ebru; Sumbuloglu, VildanThe aim of this study is to evaluate antibiotic susceptibilities, emm gene types, toxin gene profiles and clonal relatedness of group A streptococci (GAS) isolates obtained from patients and carriers. A total of 79 clinical isolates from patients and 60 isolates from carriers were included in the study. Emm typing, toxin gene detection for speA, speB, speC, speG and smeZ genes and pulsed-field gel electrophoresis (PFGE) was performed. Twenty-one distinct emm types were detected; the most common types were emm12, emm89, emm1, emm77, emm4 and emm3. The. detection rates of both emm types and the toxin genes didn't differ significantly between patients and carriers. The presence of speA and smeZ was significantly higher in emm1 and speG was significantly lower in emm4 when compared to the other emm types. The rate of clustering obtained with PFGE wasn't significantly different in patients and carriers. As a result, twelve of the 21 emm types detected in this study were covered by the 26-valent vaccine, constituting 77.7% of the emm typeable isolates; however the emm4 type which is one of the most common types in the present study is not among this coverage. (C) 2013 Association of Basic Medical Sciences of FB&H. All rights reservedÖğe Evaluation of the Carbapenem Inactivation Method for Detection of Carbapenemase-Producing Gram-Negative Bacteria in Comparison with the RAPIDEC CARBA NP(Mary Ann Liebert, Inc, 2017) Aktas, Elif; Malkocoglu, Gulsah; Otlu, Baris; Cicek, Aysegul Copur; Kulah, Canan; Comert, Fusun; Sandalli, CemalTimely detection of carbapenemases by both phenotypic and genotypic methods is essential for developing strategies to control the spread of infections by carbapenem-resistant isolates and related morbidity and mortality. The aim of this study was to compare the performance of a commercial kit, the RAPIDEC (R) CARBA NP, and an in-house technique, the carbapenem inactivation method (CIM), against a panel of 136 carbapenemase and noncarbapenemase-producing Enterobacteriaceae, Acinetobacter baumannii, and Pseudomonas aeruginosa isolates. RAPIDEC CARBA NP displayed 99% sensitivity and 100% specificity, whereas the sensitivity and specificity were 78% and 100% for the CIM test, respectively. A slight modification of the CIM test, a prolonged incubation time of 4 hours instead of two, increased the sensitivity of the test to 90% by diminishing false negativity particularly for A. baumannii. In conclusion, both tests possess a high performance and are practical for the detection of carbapenemases. Although RAPIDEC CARBA NP is a more rapid and reliable method, the CIM test may represent a useful tool for microbiology laboratories due to its simplicity and availability at any laboratory with low cost.Öğe Femoral Hemodialysis Catheter-Related Bacteremia Due to Globicatella sanguinis: Challenges in Species Identification(Ankara Microbiology Soc, 2017) Aktas, Elif; Gursoy, Nafia Canan; Sakaci, Tamer; Koc, Yener; Hamidi, Aziz Ahmad; Bulut, Emin; Erdemir, DuyguIn this case, catheter-related bacteremia due to Globicatella sanguinis in a 43 years old female patient undergoing hemodialysis with the diagnosis of diabetic nephropathy was presented and the methods in the laboratory diagnosis of the rare opportunistic pathogen, Globicatella cins, were nvestigated. A set of peripheral blood cultures and simultaneous catheter culture was obtained from the patient in third of May 2016. Biochemical tests, Phoenix (Becton Dickinson, USA) and MicroScan (Beckman Coulter, USA) automated systems and matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF MS) based Microflex MS (Bruker, Daltonics, Germany) and VITEK MS (database v2.0) (bioMerieux, France) systems were used for the identification of the cultured bacteria. Partial 16S rDNA sequencing was done by using specific p8FPL 5'-AGT TTG ATC ATG GCT CAG-3' and p806R 5'-GGA CTA CCA GGG TAT CTA AT-3' primers. Minimal inhibitory concentrations (MICs) for vancomycin, erythromycin, imipenem, cefotaxime and benzypenicillin were determined by agar gradient method. The blood and catheter cultures yielded the same type of bacterial colonies. Alfa-hemolytic, catalase negative colonies observed on blood agar plates after an over night incubation yielded gram-positive cocci on Gram staining. In Sisli Hamidiye Etfal Hospital, the isolate was identifed as G. sulfidifaciens (score value > 2) by Bruker MS system and as G. sanguinis by Phoenix automated system. In Inonu University, the isolate could not be identified by Microscan automated system while VITEK MS named the isolate as 99.9% G. sanguinis and 98.3% G. sulfidifaciens. The 16S rDNA sequencing identifed the isolate as 100% G. sanguinis (GenBank accessionno. KJ680157.1). The MIC values were 0.38 mu g/ml, 1.5 mu g/ml, 0.38 mu g/ ml, > 32 mu g/ml and 64 mu g/ml for vancomycin, eryrthromycin, imipenem, cefotaxime and benzylpenicillin, respectively. The patient was diagnosed as catheter-related bacteremia and vancomycin (1 x 1 g IV/72 h) was used for up to 10 days. No fever and bacterial growth in cultures were present in her control visits. As G. sanguinis is not among the commonly encountered pathogens and due to difficulties in laboratory diagnosis, it may be missedor mis-identified in clinical laboratories. BD Phoenix and Bruker MS data bases lack G. sulfidifaciens and G. sanguinis, respectively, while the Globicatella genus is not present in MicroScan database. The increased number of medical implementations and the increasing number of immunosuppressed patient populations in recenty ears will lead to the emergence of rare bacteria. Increasing the diagnostic power of clinical microbiology laboratories by conventional and molecular methods and renewal of the databases of commercial identification systems by expanding the pathogen spectrum are significantly important for the prevention and control of infections caused by these agents.Öğe A First Insight into Escherichia coli ST131 High-Risk Clone Among Extended-Spectrum Beta-Lactamase-Producing Urine Isolates in Istanbul with the Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry and Real-Time PCR(Mary Ann Liebert, Inc, 2017) Aktas, Elif; Otlu, Baris; Erdemir, Duygu; Ekici, Hatice; Bulut, EminObjectives: We aim to investigate, as a first insight, the presence and rates of high-risk Escherichia coli ST131 clone in Istanbul and evaluate antimicrobial resistance and CTX-M-15 production of ST131 and non-ST131 isolates. The use of MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry) to detect E. coli ST131 clone is also evaluated. Materials and Methods: A total of 203 extended-spectrum beta-lactamase (ESBL)-producing urinary isolates from a training hospital in Istanbul were investigated. Detection of E. coli ST131 was done by MALDI-TOF MS and real-time PCR melting curve analysis. The presence of CTX-M and CTX-M-15 beta-lactamases was investigated by PCR and sequence analysis. Results: Of the 203 isolates, 81 (39.9%) and 75 (36.9%) isolates were identified as ST131 clone by PCR and MALDI-TOF MS, respectively. Resistance to ciprofloxacin was significantly higher among ST131 isolates. A total of 169 (83.5%) isolates produced CTX-M beta-lactamase, of which 72 (43%) were CTX-M-15. The production of CTX-M and CTX-M-15 were significantly higher among ST131 isolates. Conclusions: We have demonstrated, for the first time, high rates of ST131 clone among ESBL-producing E. coli isolates in Istanbul, a region with high rates of resistance to third-generation cephalosporins and fluoroquinolones. Further investigation of this high-risk clone and its contribution to high antimicrobial resistance in Turkey is essential. MALDI-TOF MS is a useful tool for detection of high-risk clones and associated resistance patterns, simultaneous to bacterial identification.Öğe High Genetic Diversity among Stenotrophomonas maltophilia Isolates from Single Hospital: Nosocomial Outbreaks or Genotypic Profile Changes during Subcultures(Unıv saıns malaysıa, sch medıcal scıences, health campus, 16150 kubang kerıan, kelantan, 00000, malaysıa, 2018) Guvenir, Meryem; Otlu, Baris; Tunc, Emine; Aktas, Elif; Suer, KayaBackground: Stenotrophomonas maltophilia is a non-fermentative gram-negative bacillus which is widely recognised as an important nosocomial pathogen causing pneumonia, blood-stream, wound and urinary tract infections, particularly in immunosuppressed patients. The aim of this study was to evaluate a nosocomial outbreak of by S. maltophilia in an intensive care unit of a tertiary hospital and evaluate unexpected multiclonality. Methods: A total of 11 isolates from respiratory cultures in intensive care unit of a 24 bed tertiary hospital obtained over a one months period and one isolate obtained from the nebuliser during environmental screening were investigated. The bacteria were identified by Phoenix 100 system. The clonal relatedness was evaluated by PFGE and semi-automated repetitive sequence-based PCR. Genotyping tests were repeated for 10 serial subcultures. Results: PFGE and DiversiLab yielded 10 genotypic profiles for 12 isolates. Four to eight different genotypes were observed from 10 subcultures of the same isolate. Conclusion: We conclude that, high genetic diversity and supposed multiclonal appearance of the outbreak isolates may be due to changing profiles during subcultures most probably depending on hypermutation.Öğe High Genetic Diversity among Stenotrophomonas maltophilia Isolates from Single Hospital: Nosocomial Outbreaks or Genotypic Profile Changes during Subcultures(Univ Sains Malaysia, Sch Medical Sciences, 2018) Guvenir, Meryem; Otlu, Baris; Tunc, Emine; Aktas, Elif; Suer, KayaBackground: Stenotrophomonas maltophilia is a non-fermentative gram-negative bacillus which is widely recognised as an important nosocomial pathogen causing pneumonia, blood-stream, wound and urinary tract infections, particularly in immunosuppressed patients. The aim of this study was to evaluate a nosocomial outbreak of by S. maltophilia in an intensive care unit of a tertiary hospital and evaluate unexpected multiclonality. Methods: A total of 11 isolates from respiratory cultures in intensive care unit of a 24 bed tertiary hospital obtained over a one months period and one isolate obtained from the nebuliser during environmental screening were investigated. The bacteria were identified by Phoenix 100 system. The clonal relatedness was evaluated by PFGE and semi-automated repetitive sequence-based PCR. Genotyping tests were repeated for 10 serial subcultures. Results: PFGE and DiversiLab yielded 10 genotypic profiles for 12 isolates. Four to eight different genotypes were observed from 10 subcultures of the same isolate. Conclusion: We conclude that, high genetic diversity and supposed multiclonal appearance of the outbreak isolates may be due to changing profiles during subcultures most probably depending on hypermutation.Öğe INVESTIGATION OF AN OUTBREAK OF SALMONELLA TYPHI IN BATTALGAZI DISTRICT, MALATYA-TURKEY(Soc Brasileira Microbiologia, 2009) Iseri, Latife; Bayraktar, Mehmet Refik; Aktas, Elif; Durmaz, RizaSalmonella Typhi infections are important public health problems for the developing countries. In this study we investigated the molecular epidemiology of a suspected well-water borne S. Typhi outbreak occurred in a district of Malatya-Turkey. This outbreak affected 10 patients in two days. Arbitrary primed polymerase chain reaction (AP-PCR) based typing showed two clones, one had seven, and the other had three strains, supporting outbreak speculation. By adding chlorine to wells by local municipal authority, the outbreak ended within a very short time (about ten days).Öğe Investigation of High-Risk ST131 Clone in ESBL-Producing Escherichia coli Isolates Isolated from Urine and Non-urinary Clinical Specimens with MALDI-TOF MS and Real Time PCR(Ankara Microbiology Soc, 2018) Cizmeci, Zeynep; Otlu, Baris; Aktas, Elif; Ordekci, Seyhan; Acikgoz, Ozlem; Gulec, NurayIn recent years, the ST131 clone was identified as a high risk pandemic clone among Escherichia coli isolates by multilocus sequence typing (MLST) studies and has been associated with extended spectrum beta-lactamase (ESBL) production (often with CTX-M-15) and antibiotic resistance especially against fluoroquinolones. The aim of this study was to determine the rate of high risk ST131 clone in ESBL producing E.coli isolates in our region, to investigate the sensitivity of MALDI-TOF MS in the detection of ST1 31 clone, and to compare the frequency of antimicrobial resistance among ST131 and non-ST1 31 isolates. A total of 251 urinary and 50 non-urinary E.coli isolates identified in our hospital central laboratory between February 2016-February 2017 were included in the study. Real-time PCR and MALDI-TOF MS methods were used for the detection of E.coli ST131 clone. For the statistical evaluation of the rate of antibiotic resistance among isolates of ST131 and non-ST131 clones, chi-square test was used. p value under 0.05 was considered as significant. Of the 301 isolates, 110 (36.6%) and 92 (30.6%) isolates were identified as ST131 clone by real-time PCR and MALDI-TOF MS, respectively. According to real-time PCR results, 91 (36.3%) of 251 urinary isolates and 19 (38%) of 50 non-urinary isolates were found as ST1 31 clone; there was no statistically significant difference between the groups. Ciprofloxacin resistance was found to be significantly higher in ST131 isolates than the non-ST131 isolates (78.2%, n= 86 vs. 53.4%, n= 102). No statistically significant difference was determined for the other antibiotics tested. For the detection of E.coli ST131 clone; sensitivity of MALDI-TOF MS was 84%, specificity was 100% while positive predictive value was 100% and negative predictive value was 92%. In conclusion, further investigation of the high risk E.coli ST1 31 clone in our country, in which ESBL ratios and antibiotic resistance rates, especially in fluoroquinolones, are high, is important for the development of new strategies to control antibiotic resistance. MALDI-TOF MS method is particularly useful for easy and fast detection of the high risk E.coli ST131 clone.Öğe Molecular characterization of carbapenem-resistant Enterobacteriaceae yields increasing rates of NDM-1 carbapenemases and colistin resistance in an OXA-48-endemic area(Taylor & Francis Ltd, 2017) Cizmeci, Zeynep; Aktas, Elif; Otlu, Baris; Acikgoz, Ozlem; Ordekci, SeyhanWe aimed to characterize carbapenem-resistant isolates in a tertiary hospital in Istanbul, Turkey, high-prevelance area for OXA-48 producers. About 76 Enterobacteriaceae clinical isolates were included. Carbapenemase production was detected by Carbapenem Inactivation Method and carbapenemase genes were investigated by PCR. The clonal relationships were evaluated by AP-PCR. Nineteen Klebsiella pneumoniae isolates were colistin resistant. About 75 isolates yielded carbapenemase by CIM. 52 OXA-48, 17 NDM-1 and 2 VIM-5 carbapenemase genes were detected. Co-production of 'OXA-48 and NDM-1' and 'OXA-48 and VIM-5' were demonstrated in two Klebsiella pneumoniae isolates. The total clustering rate was 20.2%. About 69 Klebsiella pneumoniae yielded 60 profiles and 12 isolates formed five clusters. We have demonstrated the presence of OXA-48 carbapenemases in the majority of isolates in a large collection of carbapenemase-producing isolates from a single hospital. The relatively high rates of NDM-1-producing isolates and colistin resistance is noteworthy.Öğe The Optimization of a Rapid Pulsed-Field Gel Electrophoresis Protocol for the Typing of Acinetobacter baumannii, Escherichia coli and Klebsiella spp.(Natl Inst Infectious Diseases, 2009) Durmaz, Riza; Otlu, Baris; Koksal, Fatih; Hosoglu, Salih; Ozturk, Recep; Ersoy, Yasemin; Aktas, ElifPulsed-field gel electrophoresis (PFGE) is the most common genotyping method used for the typing of a number of bacterial species. Generally, investigators use their own custom-developed protocol, but a standardized PFGE protocol would allow the comparison of typing results between laboratories and the tracing of strains around the country. In the present study, we optimized a PFGE protocol for subtyping of Acinetobacter baumannii, Escherichia coli and Klebsiella spp., which are commonly isolated from nosocomial infections in many hospitals. Reproducibility of our PFGE procedure was studied three times at 2- to 3-week intervals. Epidemiological concordance of the optimized PFGE procedure was tested on seven isolates of A. baumannii from a previous outbreak and seven A. baumannii isolates randomly selected among the clinical isolates. The optimized PFGE procedure was evaluated on a total of 174 clinical isolates including 62 A. baumannii, 50 E. coli and 62 Klebsiella spp. The inter-laboratory reproducibility of the optimized protocol was tested at four laboratories. The optimized procedure is completed in 28 h after culturing. It is likely to be cost-effective, due to the reduction in the time, reagent volume and enzyme concentration needed. The procedure showed high concordance with epidemiological data. There were no non-typeable isolates among the tested bacteria. It is reproducible and versatile. This protocol can be used to identify outbreaks and monitor the spreading rate of nosocomial infections caused by the tested bacterial isolates. Furthermore, due to its high intra- and inter-laboratory reproducibility, the protocol has the potential to be useful for comparing PFGE fingerprinting profiles of the isolates from different settings.Öğe Species distribution, antifungal susceptibility and clonal relatedness of Candida isolates from patients in neonatal and pediatric intensive care units at a medical center in Turkey(Edizioni Int Srl, 2008) Kuzucu, Cigdem; Durmaz, Riza; Otlu, Baris; Aktas, Elif; Gulcan, Hande; Cizmeci, ZaynepThe aim of this study was to assess species distribution, antifungal susceptibility and clonal relationships among Candida strains isolated from a group of pediatric/neonatal intensive care (PICU/NICU) patients that had a very high mortality rate (76%). The cases of 21 patients (19 with candidemia, 2 with Candida meningitides) treated over a 1-year period in a Turkish hospital PICU and NICU were retrospectively analyzed. Twenty-eight Candida isolates were detected from blood (20), cerebrospinal fluid (CSF) (2) and other specimens (6). Candida species were identified using the API ID 32C System. Susceptibility testing was done (all 28 isolates) for amphotericin B, fluconazole and itraconazole using the broth microdilution method. Arbitrarily primed polymerase chain reaction (AP-PCR) was used for molecular typing of the 3 most common ones; C. albicans (15), C. parapsilosis (6), and C. pelliculosa (4). Electrophoretic karyotyping (EK) was done to check clonal identity obtained by AP-PCR. Of the 20 blood isolates, 8 (40%) were C. albicans, 12 (60%) were non-albicans Candida, and one of the 2 CSF isolates was C. albicans. The overall species distribution was as follows: 15 C. albicans isolates, 6 C. parapsilosis isolates, 4 C. pelliculosa isolates, 2 C. famata isolates and I C. tropicalis isolate. Amphotericin B had the best antifungal activity with a MIC90 of 0.125 mu g/ml, and the rates of susceptibility to fluconazole and itraconazole were 93% and 82%, respectively AP-PCR revealed 11 genotypes (4 were identical pairs, 7 were distinct) among the 15 C albicans isolates, 2 genotypes (5 were classified in the same type) among the 6 C. parapsilosis isolates, and 4 separate genotypes for the 4 C. pelliculosa isolates. Karyotyping results correlated well with the AP-PCR findings. As indicated in the previous research, our results confirmed that non-albicans Candida species have become more frequently causative agents for invasive fungal infections in the ICU. Transmission of C. albicans and C pelliculosa was relatively low, but transmission of C. parapsilosis was high, suggesting that more effective control and very strict treatment protocols are needed for patients having high mortality and invasive fungal infection in ICU.Öğe VIM-1, VIM-2, and GES-5 Carbapenemases Among Pseudomonas aeruginosa Isolates at a Tertiary Hospital in Istanbul, Turkey(Mary Ann Liebert, Inc, 2017) Malkocoglu, Guelsah; Aktas, Elif; Bayraktar, Banu; Otlu, Baris; Bulut, Mehmet EminWorldwide increase in carbapenem resistance and transferable carbapenemases are significant challenges in treatment of Pseudomonas aeruginosa infections. In this study, investigation of carbapenemase production in carbapenem-resistant P. aeruginosa isolates recovered from clinical specimens in a tertiary hospital was aimed. A total of 84 carbapenem-resistant P. aeruginosa isolates were examined. Carbapenem inactivation method (CIM) was used for phenotypic detection of carbapenemase production. The existence of bla(KPC), bla(NDM), bla(IMP), bla(VIM), bla(OXA-48), and bla(GES) genes was investigated by polymerase chain reaction (PCR). Subtypes of the detected genes were identified by sequence analysis. Arbitrarily primed PCR (AP-PCR) was performed to evaluate the clonal relationship among the isolates. The presence of high-risk clones in carbapenemase producers was investigated by Matrix-assisted laser desorption/ionizationtime of flight mass spectrometry (MALDI-TOF MS). Three isolates (3.5%) were identified as carbapenemase producers by CIM tests, while PCR tests demonstrated three isolates carrying carbapenemase genes as well. bla(VIM) gene was found in two isolates and bla(GES) gene was found in one isolate. Sequence analysis demonstrated that the carbapenemases were VIM-1, VIM-2, and GES-5. AP-PCR yielded high clonal diversity among the isolates. According to MALDI-TOF MS analysis, none of the carbapenemase-producing strains belonged to the high-risk clones. In conclusion, the presence of VIM-1, VIM-2, and GES-5 type carbapenemases in P. aeruginosa isolates was demonstrated for the first time in our hospital, GES-5 being reported for the second time in Turkey. Our results will lead strategies for controlling the spread of carbapenemases and contribute to epidemiological data from Turkey.
