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Öğe A 5-year surveillance of healthcare-associated infections in a university hospital: A retrospective analysis(Sage Publications Inc, 2022) Erdem, İlknur; Yıldırım, İlker; Şafak, Birol; Karaali, Ritvan; Erdal, Berna; Ardıç, Enes; Arar, CavidanObjectives: Nosocomial infections or healthcare-associated infections are a significant public health problem around the world. This study aimed to assess the rate of laboratory-confirmed healthcare-associated infections, frequency of nosocomial pathogens, and the antimicrobial resistance patterns of bacterial isolates in a University Hospital. Methods: A retrospective evaluation of healthcare-associated infections in a University Hospital, between the years 2015 and 2019 in Tekirdag, Turkey. Results: During the 5 years, the incidence densities of healthcare-associated infections in intensive care units and clinics were 10.31 and 1.70/1000 patient-days, respectively. The rates of ventilator-associated pneumonia, central line-associated bloodstream infections, and catheter-associated urinary tract infections in intensive care units were 11.57, 4.02, and 1.99 per 1000 device-days, respectively. The most common healthcare-associated infections according to the primary sites were bloodstream infections (55.3%) and pneumonia (20.4%). 67.5% of the isolated microorganisms as nosocomial agents were Gram-negative bacteria, 24.9% of Gram-positive bacteria, and 7.6% of Candida. The most frequently isolated causative agents were Escherichia coli (16.7%) and Pseudomonas aeruginosa (I 5.7%). The rate of extended-spectrum beta-lactamase production among E. coli isolates was 51.1%. Carbapenem resistance was 29.8% among isolates of P. aeruginosa, 95.1 % among isolates of Acinetobacter baumannii, and 18.2% among isolates of Klebsiella pneumoniae. Colistin resistance was 2.4% among isolates of A. baumannii. Vancomycin resistance was 5.3% among isolates of Enterococci. Conclusion: Our study results demonstrate that healthcare-associated infections are predominantly originated by intensive care units. The microorganisms isolated from intensive care units are highly resistant to many antimicrobial agents. The rising incidence of multidrug-resistant microorganisms indicates that more interventions are urgently needed to reduce healthcare-associated infections in our intensive care units.Öğe A case report of brain abscess caused by carbapenem- resistant Klebsiella pneumoniae(Inst Medicina Tropical Sao Paulo, 2023) Tunçkale, Tamer; Kavak, Çağlar; Şafak, Birol; Gönen, Aysun; Erdem, İlknurThe treatment of infections caused by carbapenem-resistant Klebsiella pneumoniae (CR-Kp) strains is difficult due to the limited antimicrobial options and high mortality. There are many reports on intracranial infections caused by CR-Kp, but only a few on brain abscesses caused by CR-Kp. Here, we present a case of brain abscess caused by CR-Kp successfully treated with combined antibiotics. A 26-year-old male patient was admitted to our hospital due to high fever and headache. His past medical history includes a surgical intervention due to an acute subdural hematoma, performed at an external healthcare center. After the current diagnosis of cerebral abscess, he underwent two surgeries. During the procedure, multiple cerebral abscesses were drained and capsulotomies were performed under ultrasound guidance. The combination of meropenem and vancomycin was started. The contents of the abscesses were sent to the microbiology and pathology laboratory. On the 3rd day of treatment, the medical team was informed that CR-Kp grew in an abscess culture. The patient's treatment was changed to meropenem + colistin + tigecycline. The patient developed electrolyte disturbances during the follow-up and this was considered an adverse effect of colistin. On the 41st day of treatment, colistin was discontinued, fosfomycin was added, and meropenem and tigecycline were maintained. Treatment was discontinued on the 68th day, when the patient was discharged. The general condition of the patient, who has been followed up for two years, is satisfactory. The treatment of CR-Kp infections should be individualized, and the pharmacokinetics and pharmacodynamics of antibiotics should be considered in each case.Öğe Burkholderia cepacia complex bacteremia outbreaks among non-cystic fibrosis patients in the pediatric unit of a university hospital(Turkish J Pediatrics, 2021) Tüfekci, Sinan; Şafak, Birol; Nalbantoğlu, Burçin; Samancı, Nedim; Kiraz, NuriBackground. Burkholderia cepacia complex (Bcc) comprises multi-drug resistant, Gram-negative, motile, and aerobic bacteria. Bcc causes severe nosocomial infections particularly in patients with intravascular catheters and in those with cystic fibrosis. We studied a Bcc outbreak in non-cystic fibrosis patients. Methods. We analyzed data from six patients hospitalized at our center. Blood cultures identified as infectious were incubated onto 5% blood sheep agar, chocolate agar, and eosin methylene blue (EMB) agar. We examined possible sites that could be sources of infection at the clinic. We confirmed isolations with pulsed-field gel electrophoresis (PFGE) tests. Results. The first patient was hospitalized due to left renal agenesis, urinary tract infection, and renal failure. Bcc was isolated in blood cultures obtained due to high fever on the third day of hospitalization. We stopped new patient hospitalizations after detecting Bcc in blood cultures of other five patients. We did not detect further positive specimens obtained from other clinic and the patient rooms. PFGE patterns were similar in all clinical isolates of Bcc indicating that the outbreak had originated from the source. Conclusions. Bcc infection should be considered in cases of nosocomial outbreaks of multi-drug resistant organisms that require hospitalization at intensive care units. Control measures should be taken for prevention of nosocomial infections and required investigations should be done to detect the source of infection.Öğe Curcumin-meropenem synergy in carbapenem resistant klebsiella pneumoniae curcumin-meropenem synergy(Tehran University of Medical Sciences, 2021) Gülen, Dumrul; Şafak, Birol; Erdal, Berna; Günaydın, BurakBackground and Objectives: The frequency of multiple resistant bacterial infections, including carbapenems, is increasing worldwide. As the decrease in treatment options causes difficulties in treatment, interest in new antimicrobials is increasing. One of the promising natural ingredients is curcumin. It is known to be effective in bacteria such as Pseudomonas aerugi-nosa, Escherichia coli, Burkholderia pseudomallei through efflux pump inhibition, toxin inhibition and enzymes. However, because its bioavailability is poor, it seffectiveness occurs in combination with antibiotics. In the study, the interaction of meropenem and curcumin in carbapenemase producing strains of Klebsiella pneumoniae was tested. Materials and Methods: Thirty-nine Klebsiella pneumoniae isolates, resistant to meropenem, were used in this study. From those 15 MBL, 6 KPC, 17 OXA-48 and 1 AmpC resistance pattern were detected by combination disk method. Meropenem and Curcumin MIC values were determined by liquid microdilution. Checkerboard liquid microdilution was used to determine the synergy between meropenem and curcumin. Results: Synergistic effects were observed in 4 isolates producing MBL, 3 isolates producing KPC, 4 isolates producing OXA-48, and 1 isolates producing AmpC (totally 12 isolates) according to the calculated FICI. No antagonistic effects were observed in any isolates. Conclusion: Curcumin was thought to be an alternative antimicrobial in combination therapies that would positively con-tribute to the treatment of bacterial infection. The effectiveness of this combination should be confirmed by other in vitro and clinical studies. © 2021 The Authors. Published by Tehran University of Medical Sciences.Öğe Determination and Genotype Distribution of Rotavirus Gastroenteritis in Pediatric Patients Admitted to a Tertiary Care Hospital(Ankara Microbiology Soc, 2022) Caneriği, Fatime Habibe; Şafak, BirolAcute infectious gastroenteritis is a prevalent disease worldwide, and most of the cases are caused by viral pathogens. Many different viruses, including Rotavirus (RV), Norovirus, Adenovirus, and Astro-viruses, are responsible for most acute viral gastroenteritis cases. According to the Centers for Disease Control and Prevention (CDC), viral gastroenteritis infections cause more than 200 000 child mortalities each year worldwide. One of the best strategies to reduce the global burden of RV gastroenteritis is the development and administration of effective vaccines. However, since there are differences in the coverage of the vaccines, the choice of appropriate vaccine for localized genotypes based on regions is important. The aim of this study was to detect the RV infections in our region and to perform genotyping using real time polymerase chain reaction (Rt-PCR) and high resolution melting (HRM) analysis. A total of 341 stool samples collected from pediatric patients were tested. Lateral flow immunochromatographic assay principle based assay was used for antigen detection. RT-PCR and HRM were applied for genotype analysis. Similar to the data from our country and Eastern Mediterranean region, RV positivity in stool samples was 23.1%. The majority of the patients (51%) were aged 0-2 years and the vast majority of the patients, with a rate of 77%, were between the ages of 0-5. Most of the cases were detected in the winter months, especially in February. The distribution of 40 samples, whose G genotype could be detected, was as follows: G2, 21 (52.5%); G1, 11 (27.5%); G9, 5 (12.5%); G3, 2 (5%); G4, 1 (2.5%). The distribution of 53 samples, whose P genotype could be detected, was as follows: P4, 44 (83.0%); P9, 8 (15.1%); P10, 1 (1.9%). Among those whose genotype could be detected, the most prevalent genotypes were G2 with 52.5% and P4 with 83%. When the distribution of 25 samples was evaluated, in which RV G and P genotypes were detected simultaneously, G1 P [4] 11 (44%), G2P[9] 5 (20%), G9P[4] 5 (20%), G2P[4] 2 (8%), G3P[10] 1 (4%), and G4P[4] 1 (4%) genotypes were determined, respectively. The most commonly observed genotype was G1 P[4]. In the HRM analysis, it was observed that the melting curve peaks were at different temperatures in nine of the G2 genotype samples and 16 of the P4 and P9 genotype samples. Thus, genotyping with HRM analysis could not be fully finalized, especially for G2 and P. Of the Rota Teq (R) and Rotarix (TM) vaccines administered on demand in our country, Rota Teq (R) is considered the vaccine that has the widest coverage for the genotypes observed in our country and region. ROTASIIL (R) vaccine, which covers all the genotypes in our region (G1, G2, G3, G4, G9) is not available in our country. The emergence of the strains with the potential to increase the current burden of RV disease should be continuously monitored, as different results are obtained by region and year, even within the same country. Thus, the emergence of vaccine-resistant strains can be followed up, especially in countries with higher viral diversity.Öğe Investigation of antiphospholipid antibody syndrome markers in the etiology of recurrent miscarriage(2021) Görgülü, Vildan; Aktepe, Orhan Cem; Şafak, BirolThis study aimed to determine the markers of antiphospholipid antibody syndrome (APS), which has an important place in the etiology of recurrent miscarriage, and toprovide guidance for the treatment of the related disorders. This prospective observational study was performed on 120 female patients admitted to the Obstetrics andGynecology outpatient clinics due to recurrent pregnancy loss. Blood samples were analyzed using the Enzyme-Linked Immunosorbent Assay (ELISA) technique to findout the levels of APS-associated anticardiolipin (ACA), anti-beta2-glycoprotein I (a?2GPI), anti-annexin V (aANXV), anti-prothrombin (aPT), and antiphosphatidylserine(aPS) antibodies. A statistically significant difference was found between increased age groups and the number of miscarriages (p=0.03, p<0.05). There were no significantdifferences between the age groups by the time of miscarriage (p=0.35, p<0.05). ACA positivity (75%, n = 90) and anti-annexin V positivity (50.8%, n = 61) werehigher than the positive results found in other tests(p=0.01, p<0.05). Antiphospholipid antibodies (APAs) showed significantly different positivity levels by the age groups(p=0.01, p<0.05). The positivity levels of APAs were significantly different by the number of miscarriages (p=0.01, p<0.05). Other antibody levels were not statisticallysignificantly different. The frequency of positive APA levels increases with advancing age and a high number of miscarriages in association with the etiology of recurrentmiscarriage. Among the subgroups of these antibodies, ACA and anti-annexin V can serve as highly appropriate diagnostic markers in recurrent miscarriage.Öğe Kolistin Antimikrobiyal Duyarlılık Testinin Vıtek 2 ve Sıvı Mikrodilüsyon Yöntemleriyle Karşılaştırmalı Olarak Değerlendirilmesi(2020) Şafak, Birol; Tombak, Özge; Topkaya, Aynur ErenAmaç: Kolistin için hassas duyarlılık test yöntemlerine ihtiyaç vardır. Çalışmamızda VITEK 2 (bioMérieux, Marcy-L’Etoile, Fransa) otomatize sistem ile sıvı mikrodilüsyon yöntemini karşılaştırarak, VITEK 2 yönteminin kolistin duyarlılığını saptamadaki etkinliğini belirlemeyi amaçladık.Materyal ve Metot: Çeşitli Gram negatif bakterilerin kolistin duyarlılığı için laboratuvarımızda kullandığımız VITEK 2 otomatize sistem ve sıvı mikrodilüsyon yöntemini geriye dönük olarak karşılaştırıldı. Suşların tanımlanması konvansiyonel mikrobiyolojik yöntemler ve VITEK 2 otomatize bakteri tanımlama sistemi kullanılarak yapıldı. Bulgular: Çoğunluğu yoğun bakım ünitelerinden (n=56) izole edilen suşlar olmak üzere 104 Gram negatif mikroorganizmanın kolistin duyarlılık sonuçları karşılaştırıldı. Sıvı mikrodilüsyon yöntemi referans alındığında VITEK 2 ile 7 çok büyük hata (% 6.7), 4 büyük hata (% 3.8) tespit edildi. VITEK 2 için duyarlılık %92.9, özgüllük %20, pozitif prediktif değer %95.8, negatif prediktif değer % 12.5 olarak bulundu. Sonuç: Çalışmamızda VITEK 2, % 6.7’lik çok büyük hata oranı ve <% 90genel uyum oranıyla yöntem kabulu için gerekli kriterleri sağlayamadı. Kolistin duyarlılığını saptamada VITEK 2’nin kullanılabilirliği ile ilgili çok sayıda çalışmada farklı sonuçlar olsa da çalışmamızda yöntem kabulü için gerekli kriterleri sağlayamamıştır.Öğe Should Hepatitis C Virus Antibody Be Used for Screening Purposes?(Galenos Yayincilik, 2018) Şafak, Birol; Tombak, Özge; Eren Topkaya, AynurObjectives: In this study, hepatitis C virus (HCV) RNA results were retrospectively investigated in patients with reactive HCV antibodies. Materials and Methods: HCV antibody test was performed ELISA method. Enzyme linked fluorescence assay was used as a different method. The quantitative HCV RNA test was carried out by AmpliPrep/COBAS TaqMan HCV test. Results: HCV antibody reactivity was detected in 358 of 28081 samples, 255 samples collected from 358 anti-HCV positive-patients and were tested for HCV RNA were included in the study. The detected HCV RNA positivity rate was 5.8% in patients who had low titer reactive HCV antibody and 76.3% in patients, who had high titer reactive HCV antibody. Nine of 23980 samples, which were screened for preoperative preparation, had reactive HCV RNA. One hundred thirty seven of 4101 samples, which were obtained for diagnostic purposes in the gastroenterology and infectious diseases clinics, were HCV RNA positive. Conclusion: Positive results should be confirmed with HCV RNA testing; if possible, testing for HCV antibodies with other methods, before HCV RNA testing, will decrease the number of tests using molecular methods; and screening for HCV antibodies is not cost-effective especially in populations with a low prevalence of HCV antibody positivity.Öğe The gut microbiome in epilepsy(Academic Press, 2020) Şafak, Birol; Altunan, Bengü; Topçu, Birol; Topkaya, Aynur ErenThe close relationship between epilepsy and autoimmune diseases and the fact that the cause of epilepsy is idiopathic in 60% of cases suggest that intestinal microbiota may play a role in the etiology of epilepsy. In this study, we analyzed and compared the intestinal microbiota composition of patients with idiopathic focal epilepsy (n = 30) and healthy volunteer group (n = 10) by 16s ribosomal DNA sequencing. Proteobacteria phylum was found to be higher in patients with epilepsy (25.4%) than in healthy volunteers group (1.5%). The genera of Campylobacter, Delftia, Haemophilus, Lautropia, Neisseria among Proteobacteria phylum were found to be statistically significantly higher in patients with epilepsy than in healthy volunteers (p < 0.05). Fusobacteria phylum was detected in 10.6% of the patients with epilepsy but not in the healthy volunteer group. The genus of the Fusobacteria phylum was found as Leptotrichia and Fusobacterium. In our study, taxonomic drift and significant differences in the intestinal microbiota of patients with epilepsy according to healthy volunteer group showed that autoimmune mechanisms and inflammation may have a role in the etiology of epilepsy. Our data should be supported by other studies as to the role of the intestinal microbiome in the prevention and treatment of epilepsy. © 2019 Elsevier LtdÖğe Türkiye'de Bir Devlet Hastanesinde 2010-2016 Yılları Arasında Pseudomonas Aerugınosa Antimikrobiyal Duyarlılık Sonuçları(2018) Şafak, Birol; Kılınç, Osman; Tunç, Nedim; Topçu, BirolPseudomonas aeruginosa, nozokomiyal pnömoni, dolaşım sistemi infeksiyonları, üriner infeksiyon ve deri infeksiyonları gibi sağlık hizmetleri gerektiren infeksiyon etkenlerinin önemli bir bölümünü oluşturur. Bu çalışma, yıllara göre P.aeruginosa'nın antimikrobiyal duyarlılığının değişimini belirleyerek antimikrobiyal kullanım politikasının oluşturulmasına yardımcı olmayı amaçlamıştır.Hastanemizde 2010-2016 yılları arasında izole edilen P.aeruginosa suşlarının antimikrobiyal duyarlılıkları, örnek türleri ve hastaların demografik verileri retrospektif olarak incelenmiştir. Verileri aktarmak ve analiz etmek için Windows istatistik paket programı PASW Statistics 18 kullanılmıştır. Değişkenler arasındaki ilişkiler ki-kare testi ile analiz edilmiştir.Yatarak tedavi olan, 0-92 yaş aralığında bulunan 350 (% 35.9) kadın ve 625 (% 64.1) erkek hastadan 975 P.aeruginosa suşu izole edilmiştir. Örneklerin çoğunluğunun (529, % 54.3) yoğun bakım ünitesinde yatan hastalara ait olduğu tespit edilmiştir. P.aeruginosa, en sık solunum sistem örneklerinde izole edilmiştir. Ayakta tedavi gören, yaşları 0-95 arasında değişen 127 (% 33.1) kadın ve 257 (% 66.9) erkek hastada üreme saptanmıştır. Kliniklere göre dağılımına bakıldığında en sık pediatri polikliniğinden gelen örneklerde izole edilmiştir. Ayaktan tedavi gören hastaların en sık idrar örneğinde izole edilmiştir. En etkili antibiyotiklerin ayaktan hastalarda amikasin, piperazin-tazobaktam, imipenem ve meropenem, yatarak tedavi gören hastalarda aminoglikozid ve karbapenem olduğu tespit edilmiştir. Yıllara göre yatan hastalarda seftazidim, piperasilin-tazobaktam, gentamisin ve amikasin duyarlılığında artış, ayaktan hastalarda piperasilin-tazobaktam ve siprofloksasin duyarlılığında ise azalma görülmüştür.Klinik sonuçların optimizasyonu için etkili antimikrobiyal tedavinin hızlı başlatılmasının gerekli olduğu göz önüne alındığında, her hastane duyarlılık oranlarını izlemelidir. Böylece ampirik antimikrobik seçimi ve uygun tedavinin belirlenmesi için bir kılavuz oluşturulmalıdır
