Ebru EVREN - Academia.edu (original) (raw)

Papers by Ebru EVREN

Research paper thumbnail of Cell counting chamber vs. Sysmex XN-1000 for determining white blood cell count and differentiation for body fluids

Turkish Journal of Biochemistry

Objectives Sterile body fluids (BFs) include key information for the diagnosis and monitoring of ... more Objectives Sterile body fluids (BFs) include key information for the diagnosis and monitoring of a variety of diseases. A cornerstone test is the total white blood cell (WBC) count, which comprises the differential of WBC of body fluid analysis. It is important to test automated hematology analyzers that should be verified using patient samples. The aim of this study is to compare both the performance of the Sysmex XN-1000 system’s body fluid module for cell counting and differentiation to the results of a cell counting chamber. Methods This study was performed on 200 routinely laboratory sent BFs. Cell counts and differentiation were determined with both bright-lined Neubauer Cell Counting Chamber and Sysmex XN-1000 system body fluid mode. Results The correlation coefficients of WBC count by two methods indicated very strong correlation (r≥0.90, p<0.0001) for any specimen except pleural fluid. According to Passing Bablok regression analysis, Sysmex XN-1000 showed acceptable perf...

Research paper thumbnail of İn Vitro Activity of Plazomicin and Underlying Resistance Mechanisms in Enterobacteriaceae İsolated From Blood İsolates From Hospitalized Patients in Turkey

Research paper thumbnail of Repurposing Sitagliptin for COVID-19 in Adults: Clinical Benefits and An Approach for the Mechanism

Flora the Journal of Infectious Diseases and Clinical Microbiology

Research paper thumbnail of Sensitivity Affected by Disease Severity and Serum Sampling Time: a Performance Evaluation of Six SARS-CoV-2 Antibody Immunoassays

Japanese Journal of Infectious Diseases

Comparative validation and clinical performance data are essential for the reliable interpretatio... more Comparative validation and clinical performance data are essential for the reliable interpretation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antibody test results. This study aimed to assess the performance of six SARS-CoV-2 IgG immunoassays in the context of different disease severities. Four automated chemiluminescence immunoassays (Access [Beckman Coulter], Architect [Abbott], Atellica-IM [Siemens], and Elecsys [Roche]) as well as two ELISA assays (SARS-CoV-2 IgG-S1-based and NCP IgG [Euroimmun]) were evaluated using samples from 143 patients as well as 50 pre-pandemic control serum samples. Accuracy and precision tests were performed for validation purposes. Overall sensitivity ranged between 73.38-88.65% and was higher in spike protein-based assays, while the specificity was ≥98% in all immunoassays. The clinical performance of the immunoassays differed depending on disease severity and target antigen. For instance, the IgG response was lower for samples taken <20 days post-symptom onset (87.30%) compared with those taken ≥20 days post-symptom onset (94.80%). Moreover, moderate disease levels led to the highest levels of IgG. Higher levels of antibodies were detected in the clinically moderate disease group. In asymptomatic and mild groups, more antibody positivity was detected with spike protein-based assays. All the assays tested could be used to detect SARS-CoV-2 IgG. However, spikebased assays revealed relatively higher sensitivity rates than nucleoprotein-based assays, particularly in cases of asymptomatic and mild disease.

Research paper thumbnail of Medically important Candida spp. identification: an era beyond traditional methods

Turkish Journal of Medical Sciences

Background/aim: Candida infections are gaining more attention for the last few decades so diagnos... more Background/aim: Candida infections are gaining more attention for the last few decades so diagnostic tools are very important for early diagnosis. Conventional identification of yeasts is time-consuming, molecular methods are more complicated and relatively expensive gold-standard methods. Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) was put into the market due to its speed and high accuracy. The aim of this study was to evaluate the performance of corn meal tween-80 agar (CMTA), CHROMagar Candida medium, and MALDI-TOF MS and to compare the obtained results with DNA sequencing. Materials and methods: The CHROMagar Candida medium, CMTA, and MALDI-TOF MS Biotyper System were used to test 416 isolates. The isolates with discrepant results by at least one of the three methods were subjected to sequence analysis. Results: The identification results of the 351 (%84.4) were compatible with all three methods. When compared to the sequencing results, the most accurate results were obtained by the MALDI-TOF MS, especially for rare Candida species. Conclusion: MALDI-TOF MS is found to be the most accurate identification tool for clinically important Candida strains. CMTA alone should not be used for the final identification of Candida species and the chromogenic medium should always be considered presumptive.

Research paper thumbnail of Comparison of a novel antigen detection test with reverse transcription polymerase chain reaction assay for laboratory diagnosis of SARS-CoV-2 infection

Infection

Molecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time ... more Molecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction (RT-PCR) in respiratory specimens is considered the gold standard method. This method is highly sensitive and specific but it has some limitations such as being expensive and requiring special laboratory equipment and skilled personnel. RapidFor™ Antigen Rapid Test Kit is a commercially available Ag-RDT which is produced in Turkey and designed to detect the nucleocapsid antigen of SARS-CoV-2 in nasopharyngeal swab samples. The aim of this study was to evaluate the performance of this novel SARS-CoV-2 antigen detection considering the RT-PCR method as the gold standard. Four hundred forty-four nasopharyngeal swab samples which were collected from the patients who met clinical criteria of COVID-19 from ten centers in Turkey between September 2020 and February 2021 were included in the study. All the nasopharyngeal swab samples were tested for SARS-CoV-2 RNA using commercial RT-PCR kits (Bioeksen and A1 Lifesciences, İstanbul, Turkey) according to the manufacturer's instructions. Viral loads were assessed according to the cycle threshold (Ct) values. RapidFor™ SARS-CoV-2 antigen test (Vitrosens Biotechnology, Istanbul, Turkey) was used to investigate the presence of SARS-CoV-2 antigen in all samples following the manufacturer's instructions. Out of 444 nasopharyngeal swab samples tested, 346 (77.9%) were positive and 98 (22.1%) were negative for SARS-CoV-2 RNA by RTPCR. Overall sensitivity of the RapidFor™. Antigen Rapid Test Kit was 80.3% whereas specificity was found to be 87.8%. Positivity rate of rapid antigen test in samples with Ct values over 25 and below 30 was 82.7%, while it increased to 95.7% in samples 20 ≤ Ct < 25 and reached 100% in samples with Ct values below 20. RapidFor™ SARS-CoV-2 Ag test might be a good choice in the screening of symptomatic and asymptomatic patients and their contacts for taking isolation measures early, with advantages over RT-PCR as being rapid, easy and being applicable in every laboratory and even at point of care.

Research paper thumbnail of Retrospective Evaluation of Risk Factors for Invasive Candida Infections in a Medical Intensive Care Unit

Infectious Diseases and Clinical Microbiology, 2022

Objective: We aimed to detect the risk factors for invasive candida infections by evaluating the ... more Objective: We aimed to detect the risk factors for invasive candida infections by evaluating the fungal strains cultivated from samples taken in a medical intensive care unit (ICU). Materials and Methods: We investigated fungal growths between January 1, 2016, and December 1, 2018, retrospectively. All reported fungal growths and demographic characteristics, clinical features, treatments and outcomes of the patients with fungal growths were recorded. Results: Fungal growths were reported from 384 different samples obtained from 179 ICU patients. The most common strain was determined to be C. albicans (47.9%). The incidence of non-albicans Candida strains was increased over the years (2016-44%, 2017-52.5%, 2018-49%), most significantly C. glabrata (7.7% to 14.6%). The most common strain was C. parapsilosis (57.9%) in patients with candidemia, and infection was more severe among them. Fluconazole resistance was rare. When patients with and without fungal growth were compared, a significant difference was found between groups in terms of age, acute physiology and chronic health evaluation II (APACHE II) score, length of ICU and hospital stay, ICU and hospital mortality (p<0.001, p=0.011, p<0.001, p=0.031, p=0.016). Candida score was significantly higher in candidemic patients (3.0 vs 0.0 p<0.001). Conclusion: Among fungal growths in samples from critically ill patients, the incidence of non-albicans Candida strains was gradually increasing. Older age, higher APACHE II score, and longer hospital and ICU stay were associated with fungal growths.

Research paper thumbnail of The role of galactomannan test results in the diagnosis of pediatric invasive aspergillosis

Infectious Diseases, 2021

Abstract Background Invasive aspergillosis (IA) is an important cause of morbidity and mortality ... more Abstract Background Invasive aspergillosis (IA) is an important cause of morbidity and mortality in immunosuppressed children. Early detection of the infection can improve prognosis in this patient population. Objectives To investigate the utility of Aspergillus galactomannan antigen assay (GM-EIA) as a diagnostic tool for IA in at-risk paediatric patients. Patients/Methods For the study, 659 GM-EIA results from 59 patients diagnosed with IA and 3368 GM-EIA results from 351 subjects without evidence for IA (controls) were reviewed retrospectively. Three cut-off values (i.e. ≥0.5, ≥1, ≥1.5) were specified to determine GM-EIA positivity. Results The median age was 6.3 years for boys and 14.5 years for girls. There was a significant difference between the girls and boys in terms of age (p < 0.01). For proven/probable/possible IA patients, sensitivity of 67.8% and specificity of 59.8% were detected when the ≥0.5 cut-off value was used for GM-EIA-positivity. The specificity increased to 80% at the cut-off of ≥1 and to 88% at the cut-off of ≥1.5. False positivity rates were 9.14, 3, and 1.45% at the ≥0.5, ≥1 and ≥1.5 cut-offs respectively. In the proven/probable IA group, sensitivity and negative predictive values were 86.9 and 97.2% at the ≥0.5 cut-off, 85.7 and 97.9%, at the ≥1 cut-off and 84.2 and 98.1% at ≥1.5 cut-off respectively. The positive likelihood ratio was 7.57 and the odds ratio was 42.67 at ≥1.5 cut-off. Conclusion The GM-EIA may be used for both screening and diagnostic purposes in paediatric patients using a cut-off value of ≥1.5 for GM-EIA positivity.

Research paper thumbnail of COVID-19 ve Bakteriyel Ko-İnfeksiyon: Fusobacterium Bakteriyemisi

Flora the Journal of Infectious Diseases and Clinical Microbiology, 2021

Coronavirus Disease 2019 (COVID-19) is a viral infection first seen in Wuhan, China, in December ... more Coronavirus Disease 2019 (COVID-19) is a viral infection first seen in Wuhan, China, in December 2019 and then affected the whole world by causing a pandemic. The disease may be asymptomatic, and symptoms such as fever, cough, shortness of breath, weakness, headache, and sore throat can be seen. Various bacterial infections may accompany the process in some COVID-19 patients. In this case, accompanying Fusobacterium nucleatum bacteremia in a patient diagnosed with COVID-19 was examined.

Research paper thumbnail of Lökosit ve Trombositten Zengin Fibrinin Escherichia Coli ve Enterococcus Faecalis'e Karşı Antibakteriyel Etkileri

Acta Medica Alanya, 2021

Bu çalışmanın amacı, lökosit ve trombositten zengin fibrinin (TZF) Escherichia coli'ye (E. Coli) ... more Bu çalışmanın amacı, lökosit ve trombositten zengin fibrinin (TZF) Escherichia coli'ye (E. Coli) ve Enterococcus faecalis'e (E. Faecalis) karşı in vitro antibakteriyel etkilerini araştırmaktır. Gereç ve yöntemler: Çalışma 21 hasta (10 kadın, 11 erkek, yaş aralığı 21-32 yaş) üzerinde yürütülmüştür. Katılımcılardan elde edilen kan örnekleri kullanılarak TZF hazırlanmıştır. TZF'nin E. coli ve E. faecalis ATCC standart suşlarına antibakteriyel aktivitesi Kirby Bauer disk difüzyon yöntemi kullanılarak test edilmiştir. Bulgular: Beklenen sonuçlar kontrol diski ile elde edilmesine rağmen, TZF'nin değerlendirilen bakterilere karşı inhibisyon zonu göstermediği tespit edilmiştir Sonuç: TZF, E.coli'ye ve E. faecalis'e karşı inhibisyon bölgesi göstermemiştir.

Research paper thumbnail of Ceftazidime – Avibactam susceptibility among carbapenem-resistant Enterobacterales in a pilot study in Turkey

Acta Microbiologica et Immunologica Hungarica, 2021

This study aimed to detect carbapenemase genes and to determine the in vitro susceptibility of Ce... more This study aimed to detect carbapenemase genes and to determine the in vitro susceptibility of Ceftazidime-Avibactam (CZA) in Enterobacterales isolates. Carbapenemase genes were detected by polymerase chain reaction. CZA sensitivity of isolates was evaluated with broth microdilution (BMD) and disk diffusion methods. A total of 318 carbapenem-resistant Enterobacterales isolates were included. Most of the isolates (n = 290, 91.2%) were identified as Klebsiella pneumoniae. The most common carbapenemase type was OXA-48 (n = 82, 27.6%). CZA susceptibility was evaluated in 84 isolates with OXA-48 and KPC carbapenemase activity. Both BMD and disk diffusion methods revealed that 95.2% of the isolates were sensitive to CZA; whereas, 4 (4.76%) isolates were resistant to CZA. Among colistin resistant isolates, 96.5% (n = 80) of them were susceptible to CZA. Our study demonstrated high in vitro efficacy of CZA in Enterobacterales isolates producing OXA-48 carbapenemase. High susceptibility rate...

Research paper thumbnail of Antibody response to two doses of inactivated SARS‐CoV‐2 vaccine (CoronaVac) in kidney transplant recipients

Transplant Infectious Disease, 2021

Background: Coronavirus Disease-19 (COVID-19) has high mortality in kidney transplant recipients ... more Background: Coronavirus Disease-19 (COVID-19) has high mortality in kidney transplant recipients (KTR), and vaccination against severe acute respiratory syndromecoronavirus-2 (SARS-CoV-2) is vital for this population. Although the humoral response to messenger RNA vaccines was shown to be impaired in KTR, there is a lack of data regarding the antibody response to inactivated vaccines. We investigated the antibody response to two consequent doses of the inactivated SARS-CoV-2 vaccine (CoronaVac; Sinovac Biotech, China). Methods: A total of 118 patients from two centers were included. The levels of anti-SARS-CoV-2 immunoglobulin-G antibodies against the nucleocapsid and spike antigens were determined with enzyme immunoassay (DIA.PRO; Milano, Italy) before the vaccine and one month after the second dose of the vaccine. Thirty-three patients were excluded due to antibody positivity in the serum samples obtained before vaccination. Results: Eighty-five patients, 47 of whom were female, with a mean age of 46 ± 12, were included in the statistical analysis. The maintenance immunosuppressive therapy comprised tacrolimus (88.2%), mycophenolate (63.6%), and low-dose steroids (95.3%) in the majority of the patients. After a median of 31 days following the second dose of the vaccine, only 16 (18.8%) patients developed an antibody response. The median (IQR) antibody level was 52.5 IU/ml (21.5-96). Age (48 vs. 38, p = .005) and serum creatinine levels (1.14 vs. 0.91, p = .04) were higher in non-responders and were also found to be independently associated with the antibody response (odds ratio (OR): 0.93, p = 0.012 and 0.15, p = 0.045, respectively) in multivariate analysis. Conclusion: In this study, we found the antibody response to the inactivated vaccine to be considerably low (18.8%) in KTR. Increased age and impaired renal function were associated with worse antibody response. Based on the knowledge that mRNA vaccines yield better humoral responses, this special population might be considered for additional doses of mRNA vaccination.

Research paper thumbnail of Response to SARS-CoV-2 associated GuillainBarre syndrome after awaking on the ICU: Consider differentials

Research paper thumbnail of An unusual course of SARS-CoV-2 infection: Challenging diagnosis of Guillain-Barré Syndrome

Tuberk Toraks, 2021

An unusual course of SARS-CoV-2 infection: Challenging diagnosis of Guillain-Barré Syndrome COVID... more An unusual course of SARS-CoV-2 infection: Challenging diagnosis of Guillain-Barré Syndrome COVID-19, caused by severe acute respiratory syndrome coronavirus-2, typically presents with respiratory symptoms and fever, but still a variety of clinical presentations have been reported. In this study, it was aimed to report a case of COVID-19 with an atypical presentation and an atypical course. As well, the recovery phase was complicated with GBS and consequently cytomegalovirus infection. It should be kept in mind that patients with COVID-19 severe disease need to be followed for neurological and other complications which may arise during the course of critical illness.

Research paper thumbnail of Traumatic Wound Infection Caused By Bacillus Cereus

Journal of Ankara University Faculty of Medicine, 2020

Bacillus cereus, doğada yaygın olarak bulunan, aerobik, sporlu, Gram-pozitif çomaktır (1). Virüla... more Bacillus cereus, doğada yaygın olarak bulunan, aerobik, sporlu, Gram-pozitif çomaktır (1). Virülansı genellikle düşüktür ve klinik örneklerden izole edildiğinde genellikle "kontaminant" olarak yorumlanır (2). Ancak, salgıladığı toksinlerle veya doku invazyonu yaparak besin zehirlenmesi yanı sıra, post-travmatik kutanöz ve subkütanöz enfeksiyonlar, nekrotizan fasiit, selülit, miyonekroz, akut ve kronik osteomiyelit gibi lokal ve sistemik enfeksiyonlara da neden olmaktadır (1,3). Bu yazıda B. cereus'un sebep olduğu post-travmatik bir yara enfeksiyonu olgusu sunularak konuyla ilgili literatür özetlenecektir. Olgu Sunumu 35 yaşında, Diabetes Mellitus'u olan erkek hasta, ateşli silah yaralanması sonrası sol ayak bileğinde tibia ve fibula kırığı nedeniyle acil servise getirildi. Muayenesinde; genel durumu orta, bilinci açık olan hastanın vital bulguları; nabız: 129/dak, solunum: 18/dak, kan basıncı: 83/65 mmHg olarak tespit edildi. Sol ayak bileğinde, geniş doku hasarı ve kemiğin ekspoze olduğu parçalı kırık mevcuttu. Yara distalinde nabızlar zayıf palpe edilmekteydi ve kapiller dolum mevcuttu. Yara yeri 3000 cc serum fizyolojikle (SF) yıkandıktan sonra kısa bacak atele alınarak hastaya kristalize insülin ve intravenöz hidrasyon başlandı. Ayak/ayak bileği grafisinde sol distal Bacillus cereus is an aerobic, endospore-forming Gram-positive rod found widely in nature, including soil, dust and mud, rotting organic matter, fresh and salt water, vegetables and fomites. When isolated from clinical specimens it is often interpreted as a "contaminant". However, it may present as an etiological agent in both gastrointestinal and extraintestinal infections. In this case report, we have presented a post-traumatic wound infection due to B. cereus in a 35 year-old, diabetic patient who have applied to hospital with gunshot injury and operated due to tibia and fibula fractures. B. cereus should not always be considered as a contaminant when cultured in the laboratory and should be kept in mind as a pathogen especially post-operative and post-traumatic wound infections.

Research paper thumbnail of Characterization of Klebsiella pneumoniae Coproducing KPC and NDM-1 Carbapenemases from Turkey

Microbial Drug Resistance, 2019

Aims: The emergence of multidrug-resistant and carbapenem-resistant Klebsiella pneumoniae has bec... more Aims: The emergence of multidrug-resistant and carbapenem-resistant Klebsiella pneumoniae has became a major public health threat. In this study, we describe the characteristics of isolates coproducing KPC and NDM-1 carbapenemases from patients hospitalized at an emergency unit in Ankara, Turkey, between January and August 2018. The isolates were characterized by antibiogram susceptibility, carbapenemase and extended-spectrum beta-lactamase production, plasmid-mediated colistin (COL) resistance, and high-level aminoglycoside resistance. Pulsed field gel electrophoresis (PFGE), sequencing, wzi typing, multilocus sequence typing, and plasmid analysis were used to investigate the epidemiological relationship between the isolates. Results: All isolates were found to be resistant to amoxicillin-clavulanic acid, piperacillin-tazobactam, cefotaxime, cefoxitin, cefuroxime, ceftazidime, cefepime, imipenem, meropenem, ertapenem, amikacin, gentamicin, ciprofloxacin, levofloxacin, and trimethoprim-sulfamethoxazole. The minimum inhibitory concentration values for imipenem, meropenem, and ertapenem were >32 μg/mL, and >256 μg/mL for amikacin and gentamicin, and two isolates were found to be susceptible to both tigecycline and COL. All strains were positive for SHV, CTX-M, and rmtC, and negative for mcr-1 genes. A/C and FIIAS plasmids were found in all isolates. All isolates had the same PFGE pattern: wzi type 93 and ST15. Conclusion: Here, we have documented the characteristics of KPC- and NDM-1-coproducing isolates that harbored SHV, CTX-M, and rmtC and were typed as wzi 93 and ST15. We conclude that continuous monitoring of carbapenemases for unusual carbapenemase production is crucial to prevent the spread of these powerful isolates.

Research paper thumbnail of Kan Kültürü Uygulamalarının Değerlendirilmesi: İşletim Sistemi (Epicenter) Verilerinin Kullanımı

Mikrobiyoloji Bulteni, 2019

Research paper thumbnail of Deep fungal infection caused by Trichophyton rubrum after heart transplantation: A case report with dermoscopy

Australasian Journal of Dermatology, 2019

Deep fungal infection caused by Trichophyton rubrum after heart transplantation: A case report wi... more Deep fungal infection caused by Trichophyton rubrum after heart transplantation: A case report with dermoscopy Dermatophytosis is usually restricted to the cornified layer of the epidermis. The most prevalent dermatophyte species

Research paper thumbnail of The Antibacterial Effect of Propolis against Clinical Isolates

Propolis, an old and a new natural product collected from beehives by honeybees (Apis mellifera) ... more Propolis, an old and a new natural product collected from beehives by honeybees (Apis mellifera) has been used from ancient times. The aim of this study is to determine the antibacterial activity of Propolis against gram positive and negative clinical isolates besides standard bacterial strains. Two different crude Propolis samples obtained from Konya-Turkey and Moscov-Russian Federation (2012 October) were used in this study. Methicillin sensitive Staphylococcus aureus (MSSA), methicillin resistant Staphylococcus aureus (MRSA), extended spectrum beta lactamases producing (ESBL) Escherichia coli and multi-drug resistant (MDR) Acinetobacter baumannii clinical isolates were tested. Thirty isolates from each bacterium enrolled. S.aureus ATCC 29213, MRSA ATCC 43300, E.coli ATCC 25922, P.aeruginosa ATCC 27853 strains were also tested as standard strains. The MICs of the strains were determined by broth dilution method. MSSA and MRSA clinical isolates’ MIC ranges of Turkish Propolis extra...

Research paper thumbnail of In vitro activity of fosfomycin in combination with imipenem, meropenem, colistin and tigecycline against OXA 48–positive Klebsiella pneumoniae strains

Diagnostic Microbiology and Infectious Disease, 2013

Carbapenem resistance due to OXA-48 enzymes in Klebsiella pneumoniae is increasing particularly i... more Carbapenem resistance due to OXA-48 enzymes in Klebsiella pneumoniae is increasing particularly in the Middle Eastern and European regions. Treatment options are limited. The aim of this study was to evaluate the in vitro synergistic activity of fosfomycin in combination with imipenem, meropenem, colistin and tigecycline against OXA-48 producing K. pneumoniae strains. Twelve carbapenem-resistant OXA-48 producing K. pneumoniae isolates were enrolled in this study. Synergistic activity of fosfomycin combined with imipenem, meropenem, colistin, and tigecycline was assessed by chequerboard method. The combination of fosfomycin was synergistic with imipenem, meropenem and tigecycline with the ratios of 42%, 33%, and 33%, respectively. Whilst the combination of fosfomycin with colistin was fully antagonistic against all of the strains, there was no statistically significant difference between the in vitro synergistic activities of fosfomycin in combination with imipenem, meropenem and tigecycline combinations (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; 0.05). Fosfomycin in combination with other agents can be preferred against multidrug resistant K. pneumoniae strains.

Research paper thumbnail of Cell counting chamber vs. Sysmex XN-1000 for determining white blood cell count and differentiation for body fluids

Turkish Journal of Biochemistry

Objectives Sterile body fluids (BFs) include key information for the diagnosis and monitoring of ... more Objectives Sterile body fluids (BFs) include key information for the diagnosis and monitoring of a variety of diseases. A cornerstone test is the total white blood cell (WBC) count, which comprises the differential of WBC of body fluid analysis. It is important to test automated hematology analyzers that should be verified using patient samples. The aim of this study is to compare both the performance of the Sysmex XN-1000 system’s body fluid module for cell counting and differentiation to the results of a cell counting chamber. Methods This study was performed on 200 routinely laboratory sent BFs. Cell counts and differentiation were determined with both bright-lined Neubauer Cell Counting Chamber and Sysmex XN-1000 system body fluid mode. Results The correlation coefficients of WBC count by two methods indicated very strong correlation (r≥0.90, p<0.0001) for any specimen except pleural fluid. According to Passing Bablok regression analysis, Sysmex XN-1000 showed acceptable perf...

Research paper thumbnail of İn Vitro Activity of Plazomicin and Underlying Resistance Mechanisms in Enterobacteriaceae İsolated From Blood İsolates From Hospitalized Patients in Turkey

Research paper thumbnail of Repurposing Sitagliptin for COVID-19 in Adults: Clinical Benefits and An Approach for the Mechanism

Flora the Journal of Infectious Diseases and Clinical Microbiology

Research paper thumbnail of Sensitivity Affected by Disease Severity and Serum Sampling Time: a Performance Evaluation of Six SARS-CoV-2 Antibody Immunoassays

Japanese Journal of Infectious Diseases

Comparative validation and clinical performance data are essential for the reliable interpretatio... more Comparative validation and clinical performance data are essential for the reliable interpretation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antibody test results. This study aimed to assess the performance of six SARS-CoV-2 IgG immunoassays in the context of different disease severities. Four automated chemiluminescence immunoassays (Access [Beckman Coulter], Architect [Abbott], Atellica-IM [Siemens], and Elecsys [Roche]) as well as two ELISA assays (SARS-CoV-2 IgG-S1-based and NCP IgG [Euroimmun]) were evaluated using samples from 143 patients as well as 50 pre-pandemic control serum samples. Accuracy and precision tests were performed for validation purposes. Overall sensitivity ranged between 73.38-88.65% and was higher in spike protein-based assays, while the specificity was ≥98% in all immunoassays. The clinical performance of the immunoassays differed depending on disease severity and target antigen. For instance, the IgG response was lower for samples taken <20 days post-symptom onset (87.30%) compared with those taken ≥20 days post-symptom onset (94.80%). Moreover, moderate disease levels led to the highest levels of IgG. Higher levels of antibodies were detected in the clinically moderate disease group. In asymptomatic and mild groups, more antibody positivity was detected with spike protein-based assays. All the assays tested could be used to detect SARS-CoV-2 IgG. However, spikebased assays revealed relatively higher sensitivity rates than nucleoprotein-based assays, particularly in cases of asymptomatic and mild disease.

Research paper thumbnail of Medically important Candida spp. identification: an era beyond traditional methods

Turkish Journal of Medical Sciences

Background/aim: Candida infections are gaining more attention for the last few decades so diagnos... more Background/aim: Candida infections are gaining more attention for the last few decades so diagnostic tools are very important for early diagnosis. Conventional identification of yeasts is time-consuming, molecular methods are more complicated and relatively expensive gold-standard methods. Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) was put into the market due to its speed and high accuracy. The aim of this study was to evaluate the performance of corn meal tween-80 agar (CMTA), CHROMagar Candida medium, and MALDI-TOF MS and to compare the obtained results with DNA sequencing. Materials and methods: The CHROMagar Candida medium, CMTA, and MALDI-TOF MS Biotyper System were used to test 416 isolates. The isolates with discrepant results by at least one of the three methods were subjected to sequence analysis. Results: The identification results of the 351 (%84.4) were compatible with all three methods. When compared to the sequencing results, the most accurate results were obtained by the MALDI-TOF MS, especially for rare Candida species. Conclusion: MALDI-TOF MS is found to be the most accurate identification tool for clinically important Candida strains. CMTA alone should not be used for the final identification of Candida species and the chromogenic medium should always be considered presumptive.

Research paper thumbnail of Comparison of a novel antigen detection test with reverse transcription polymerase chain reaction assay for laboratory diagnosis of SARS-CoV-2 infection

Infection

Molecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time ... more Molecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction (RT-PCR) in respiratory specimens is considered the gold standard method. This method is highly sensitive and specific but it has some limitations such as being expensive and requiring special laboratory equipment and skilled personnel. RapidFor™ Antigen Rapid Test Kit is a commercially available Ag-RDT which is produced in Turkey and designed to detect the nucleocapsid antigen of SARS-CoV-2 in nasopharyngeal swab samples. The aim of this study was to evaluate the performance of this novel SARS-CoV-2 antigen detection considering the RT-PCR method as the gold standard. Four hundred forty-four nasopharyngeal swab samples which were collected from the patients who met clinical criteria of COVID-19 from ten centers in Turkey between September 2020 and February 2021 were included in the study. All the nasopharyngeal swab samples were tested for SARS-CoV-2 RNA using commercial RT-PCR kits (Bioeksen and A1 Lifesciences, İstanbul, Turkey) according to the manufacturer's instructions. Viral loads were assessed according to the cycle threshold (Ct) values. RapidFor™ SARS-CoV-2 antigen test (Vitrosens Biotechnology, Istanbul, Turkey) was used to investigate the presence of SARS-CoV-2 antigen in all samples following the manufacturer's instructions. Out of 444 nasopharyngeal swab samples tested, 346 (77.9%) were positive and 98 (22.1%) were negative for SARS-CoV-2 RNA by RTPCR. Overall sensitivity of the RapidFor™. Antigen Rapid Test Kit was 80.3% whereas specificity was found to be 87.8%. Positivity rate of rapid antigen test in samples with Ct values over 25 and below 30 was 82.7%, while it increased to 95.7% in samples 20 ≤ Ct < 25 and reached 100% in samples with Ct values below 20. RapidFor™ SARS-CoV-2 Ag test might be a good choice in the screening of symptomatic and asymptomatic patients and their contacts for taking isolation measures early, with advantages over RT-PCR as being rapid, easy and being applicable in every laboratory and even at point of care.

Research paper thumbnail of Retrospective Evaluation of Risk Factors for Invasive Candida Infections in a Medical Intensive Care Unit

Infectious Diseases and Clinical Microbiology, 2022

Objective: We aimed to detect the risk factors for invasive candida infections by evaluating the ... more Objective: We aimed to detect the risk factors for invasive candida infections by evaluating the fungal strains cultivated from samples taken in a medical intensive care unit (ICU). Materials and Methods: We investigated fungal growths between January 1, 2016, and December 1, 2018, retrospectively. All reported fungal growths and demographic characteristics, clinical features, treatments and outcomes of the patients with fungal growths were recorded. Results: Fungal growths were reported from 384 different samples obtained from 179 ICU patients. The most common strain was determined to be C. albicans (47.9%). The incidence of non-albicans Candida strains was increased over the years (2016-44%, 2017-52.5%, 2018-49%), most significantly C. glabrata (7.7% to 14.6%). The most common strain was C. parapsilosis (57.9%) in patients with candidemia, and infection was more severe among them. Fluconazole resistance was rare. When patients with and without fungal growth were compared, a significant difference was found between groups in terms of age, acute physiology and chronic health evaluation II (APACHE II) score, length of ICU and hospital stay, ICU and hospital mortality (p<0.001, p=0.011, p<0.001, p=0.031, p=0.016). Candida score was significantly higher in candidemic patients (3.0 vs 0.0 p<0.001). Conclusion: Among fungal growths in samples from critically ill patients, the incidence of non-albicans Candida strains was gradually increasing. Older age, higher APACHE II score, and longer hospital and ICU stay were associated with fungal growths.

Research paper thumbnail of The role of galactomannan test results in the diagnosis of pediatric invasive aspergillosis

Infectious Diseases, 2021

Abstract Background Invasive aspergillosis (IA) is an important cause of morbidity and mortality ... more Abstract Background Invasive aspergillosis (IA) is an important cause of morbidity and mortality in immunosuppressed children. Early detection of the infection can improve prognosis in this patient population. Objectives To investigate the utility of Aspergillus galactomannan antigen assay (GM-EIA) as a diagnostic tool for IA in at-risk paediatric patients. Patients/Methods For the study, 659 GM-EIA results from 59 patients diagnosed with IA and 3368 GM-EIA results from 351 subjects without evidence for IA (controls) were reviewed retrospectively. Three cut-off values (i.e. ≥0.5, ≥1, ≥1.5) were specified to determine GM-EIA positivity. Results The median age was 6.3 years for boys and 14.5 years for girls. There was a significant difference between the girls and boys in terms of age (p < 0.01). For proven/probable/possible IA patients, sensitivity of 67.8% and specificity of 59.8% were detected when the ≥0.5 cut-off value was used for GM-EIA-positivity. The specificity increased to 80% at the cut-off of ≥1 and to 88% at the cut-off of ≥1.5. False positivity rates were 9.14, 3, and 1.45% at the ≥0.5, ≥1 and ≥1.5 cut-offs respectively. In the proven/probable IA group, sensitivity and negative predictive values were 86.9 and 97.2% at the ≥0.5 cut-off, 85.7 and 97.9%, at the ≥1 cut-off and 84.2 and 98.1% at ≥1.5 cut-off respectively. The positive likelihood ratio was 7.57 and the odds ratio was 42.67 at ≥1.5 cut-off. Conclusion The GM-EIA may be used for both screening and diagnostic purposes in paediatric patients using a cut-off value of ≥1.5 for GM-EIA positivity.

Research paper thumbnail of COVID-19 ve Bakteriyel Ko-İnfeksiyon: Fusobacterium Bakteriyemisi

Flora the Journal of Infectious Diseases and Clinical Microbiology, 2021

Coronavirus Disease 2019 (COVID-19) is a viral infection first seen in Wuhan, China, in December ... more Coronavirus Disease 2019 (COVID-19) is a viral infection first seen in Wuhan, China, in December 2019 and then affected the whole world by causing a pandemic. The disease may be asymptomatic, and symptoms such as fever, cough, shortness of breath, weakness, headache, and sore throat can be seen. Various bacterial infections may accompany the process in some COVID-19 patients. In this case, accompanying Fusobacterium nucleatum bacteremia in a patient diagnosed with COVID-19 was examined.

Research paper thumbnail of Lökosit ve Trombositten Zengin Fibrinin Escherichia Coli ve Enterococcus Faecalis'e Karşı Antibakteriyel Etkileri

Acta Medica Alanya, 2021

Bu çalışmanın amacı, lökosit ve trombositten zengin fibrinin (TZF) Escherichia coli'ye (E. Coli) ... more Bu çalışmanın amacı, lökosit ve trombositten zengin fibrinin (TZF) Escherichia coli'ye (E. Coli) ve Enterococcus faecalis'e (E. Faecalis) karşı in vitro antibakteriyel etkilerini araştırmaktır. Gereç ve yöntemler: Çalışma 21 hasta (10 kadın, 11 erkek, yaş aralığı 21-32 yaş) üzerinde yürütülmüştür. Katılımcılardan elde edilen kan örnekleri kullanılarak TZF hazırlanmıştır. TZF'nin E. coli ve E. faecalis ATCC standart suşlarına antibakteriyel aktivitesi Kirby Bauer disk difüzyon yöntemi kullanılarak test edilmiştir. Bulgular: Beklenen sonuçlar kontrol diski ile elde edilmesine rağmen, TZF'nin değerlendirilen bakterilere karşı inhibisyon zonu göstermediği tespit edilmiştir Sonuç: TZF, E.coli'ye ve E. faecalis'e karşı inhibisyon bölgesi göstermemiştir.

Research paper thumbnail of Ceftazidime – Avibactam susceptibility among carbapenem-resistant Enterobacterales in a pilot study in Turkey

Acta Microbiologica et Immunologica Hungarica, 2021

This study aimed to detect carbapenemase genes and to determine the in vitro susceptibility of Ce... more This study aimed to detect carbapenemase genes and to determine the in vitro susceptibility of Ceftazidime-Avibactam (CZA) in Enterobacterales isolates. Carbapenemase genes were detected by polymerase chain reaction. CZA sensitivity of isolates was evaluated with broth microdilution (BMD) and disk diffusion methods. A total of 318 carbapenem-resistant Enterobacterales isolates were included. Most of the isolates (n = 290, 91.2%) were identified as Klebsiella pneumoniae. The most common carbapenemase type was OXA-48 (n = 82, 27.6%). CZA susceptibility was evaluated in 84 isolates with OXA-48 and KPC carbapenemase activity. Both BMD and disk diffusion methods revealed that 95.2% of the isolates were sensitive to CZA; whereas, 4 (4.76%) isolates were resistant to CZA. Among colistin resistant isolates, 96.5% (n = 80) of them were susceptible to CZA. Our study demonstrated high in vitro efficacy of CZA in Enterobacterales isolates producing OXA-48 carbapenemase. High susceptibility rate...

Research paper thumbnail of Antibody response to two doses of inactivated SARS‐CoV‐2 vaccine (CoronaVac) in kidney transplant recipients

Transplant Infectious Disease, 2021

Background: Coronavirus Disease-19 (COVID-19) has high mortality in kidney transplant recipients ... more Background: Coronavirus Disease-19 (COVID-19) has high mortality in kidney transplant recipients (KTR), and vaccination against severe acute respiratory syndromecoronavirus-2 (SARS-CoV-2) is vital for this population. Although the humoral response to messenger RNA vaccines was shown to be impaired in KTR, there is a lack of data regarding the antibody response to inactivated vaccines. We investigated the antibody response to two consequent doses of the inactivated SARS-CoV-2 vaccine (CoronaVac; Sinovac Biotech, China). Methods: A total of 118 patients from two centers were included. The levels of anti-SARS-CoV-2 immunoglobulin-G antibodies against the nucleocapsid and spike antigens were determined with enzyme immunoassay (DIA.PRO; Milano, Italy) before the vaccine and one month after the second dose of the vaccine. Thirty-three patients were excluded due to antibody positivity in the serum samples obtained before vaccination. Results: Eighty-five patients, 47 of whom were female, with a mean age of 46 ± 12, were included in the statistical analysis. The maintenance immunosuppressive therapy comprised tacrolimus (88.2%), mycophenolate (63.6%), and low-dose steroids (95.3%) in the majority of the patients. After a median of 31 days following the second dose of the vaccine, only 16 (18.8%) patients developed an antibody response. The median (IQR) antibody level was 52.5 IU/ml (21.5-96). Age (48 vs. 38, p = .005) and serum creatinine levels (1.14 vs. 0.91, p = .04) were higher in non-responders and were also found to be independently associated with the antibody response (odds ratio (OR): 0.93, p = 0.012 and 0.15, p = 0.045, respectively) in multivariate analysis. Conclusion: In this study, we found the antibody response to the inactivated vaccine to be considerably low (18.8%) in KTR. Increased age and impaired renal function were associated with worse antibody response. Based on the knowledge that mRNA vaccines yield better humoral responses, this special population might be considered for additional doses of mRNA vaccination.

Research paper thumbnail of Response to SARS-CoV-2 associated GuillainBarre syndrome after awaking on the ICU: Consider differentials

Research paper thumbnail of An unusual course of SARS-CoV-2 infection: Challenging diagnosis of Guillain-Barré Syndrome

Tuberk Toraks, 2021

An unusual course of SARS-CoV-2 infection: Challenging diagnosis of Guillain-Barré Syndrome COVID... more An unusual course of SARS-CoV-2 infection: Challenging diagnosis of Guillain-Barré Syndrome COVID-19, caused by severe acute respiratory syndrome coronavirus-2, typically presents with respiratory symptoms and fever, but still a variety of clinical presentations have been reported. In this study, it was aimed to report a case of COVID-19 with an atypical presentation and an atypical course. As well, the recovery phase was complicated with GBS and consequently cytomegalovirus infection. It should be kept in mind that patients with COVID-19 severe disease need to be followed for neurological and other complications which may arise during the course of critical illness.

Research paper thumbnail of Traumatic Wound Infection Caused By Bacillus Cereus

Journal of Ankara University Faculty of Medicine, 2020

Bacillus cereus, doğada yaygın olarak bulunan, aerobik, sporlu, Gram-pozitif çomaktır (1). Virüla... more Bacillus cereus, doğada yaygın olarak bulunan, aerobik, sporlu, Gram-pozitif çomaktır (1). Virülansı genellikle düşüktür ve klinik örneklerden izole edildiğinde genellikle "kontaminant" olarak yorumlanır (2). Ancak, salgıladığı toksinlerle veya doku invazyonu yaparak besin zehirlenmesi yanı sıra, post-travmatik kutanöz ve subkütanöz enfeksiyonlar, nekrotizan fasiit, selülit, miyonekroz, akut ve kronik osteomiyelit gibi lokal ve sistemik enfeksiyonlara da neden olmaktadır (1,3). Bu yazıda B. cereus'un sebep olduğu post-travmatik bir yara enfeksiyonu olgusu sunularak konuyla ilgili literatür özetlenecektir. Olgu Sunumu 35 yaşında, Diabetes Mellitus'u olan erkek hasta, ateşli silah yaralanması sonrası sol ayak bileğinde tibia ve fibula kırığı nedeniyle acil servise getirildi. Muayenesinde; genel durumu orta, bilinci açık olan hastanın vital bulguları; nabız: 129/dak, solunum: 18/dak, kan basıncı: 83/65 mmHg olarak tespit edildi. Sol ayak bileğinde, geniş doku hasarı ve kemiğin ekspoze olduğu parçalı kırık mevcuttu. Yara distalinde nabızlar zayıf palpe edilmekteydi ve kapiller dolum mevcuttu. Yara yeri 3000 cc serum fizyolojikle (SF) yıkandıktan sonra kısa bacak atele alınarak hastaya kristalize insülin ve intravenöz hidrasyon başlandı. Ayak/ayak bileği grafisinde sol distal Bacillus cereus is an aerobic, endospore-forming Gram-positive rod found widely in nature, including soil, dust and mud, rotting organic matter, fresh and salt water, vegetables and fomites. When isolated from clinical specimens it is often interpreted as a "contaminant". However, it may present as an etiological agent in both gastrointestinal and extraintestinal infections. In this case report, we have presented a post-traumatic wound infection due to B. cereus in a 35 year-old, diabetic patient who have applied to hospital with gunshot injury and operated due to tibia and fibula fractures. B. cereus should not always be considered as a contaminant when cultured in the laboratory and should be kept in mind as a pathogen especially post-operative and post-traumatic wound infections.

Research paper thumbnail of Characterization of Klebsiella pneumoniae Coproducing KPC and NDM-1 Carbapenemases from Turkey

Microbial Drug Resistance, 2019

Aims: The emergence of multidrug-resistant and carbapenem-resistant Klebsiella pneumoniae has bec... more Aims: The emergence of multidrug-resistant and carbapenem-resistant Klebsiella pneumoniae has became a major public health threat. In this study, we describe the characteristics of isolates coproducing KPC and NDM-1 carbapenemases from patients hospitalized at an emergency unit in Ankara, Turkey, between January and August 2018. The isolates were characterized by antibiogram susceptibility, carbapenemase and extended-spectrum beta-lactamase production, plasmid-mediated colistin (COL) resistance, and high-level aminoglycoside resistance. Pulsed field gel electrophoresis (PFGE), sequencing, wzi typing, multilocus sequence typing, and plasmid analysis were used to investigate the epidemiological relationship between the isolates. Results: All isolates were found to be resistant to amoxicillin-clavulanic acid, piperacillin-tazobactam, cefotaxime, cefoxitin, cefuroxime, ceftazidime, cefepime, imipenem, meropenem, ertapenem, amikacin, gentamicin, ciprofloxacin, levofloxacin, and trimethoprim-sulfamethoxazole. The minimum inhibitory concentration values for imipenem, meropenem, and ertapenem were >32 μg/mL, and >256 μg/mL for amikacin and gentamicin, and two isolates were found to be susceptible to both tigecycline and COL. All strains were positive for SHV, CTX-M, and rmtC, and negative for mcr-1 genes. A/C and FIIAS plasmids were found in all isolates. All isolates had the same PFGE pattern: wzi type 93 and ST15. Conclusion: Here, we have documented the characteristics of KPC- and NDM-1-coproducing isolates that harbored SHV, CTX-M, and rmtC and were typed as wzi 93 and ST15. We conclude that continuous monitoring of carbapenemases for unusual carbapenemase production is crucial to prevent the spread of these powerful isolates.

Research paper thumbnail of Kan Kültürü Uygulamalarının Değerlendirilmesi: İşletim Sistemi (Epicenter) Verilerinin Kullanımı

Mikrobiyoloji Bulteni, 2019

Research paper thumbnail of Deep fungal infection caused by Trichophyton rubrum after heart transplantation: A case report with dermoscopy

Australasian Journal of Dermatology, 2019

Deep fungal infection caused by Trichophyton rubrum after heart transplantation: A case report wi... more Deep fungal infection caused by Trichophyton rubrum after heart transplantation: A case report with dermoscopy Dermatophytosis is usually restricted to the cornified layer of the epidermis. The most prevalent dermatophyte species

Research paper thumbnail of The Antibacterial Effect of Propolis against Clinical Isolates

Propolis, an old and a new natural product collected from beehives by honeybees (Apis mellifera) ... more Propolis, an old and a new natural product collected from beehives by honeybees (Apis mellifera) has been used from ancient times. The aim of this study is to determine the antibacterial activity of Propolis against gram positive and negative clinical isolates besides standard bacterial strains. Two different crude Propolis samples obtained from Konya-Turkey and Moscov-Russian Federation (2012 October) were used in this study. Methicillin sensitive Staphylococcus aureus (MSSA), methicillin resistant Staphylococcus aureus (MRSA), extended spectrum beta lactamases producing (ESBL) Escherichia coli and multi-drug resistant (MDR) Acinetobacter baumannii clinical isolates were tested. Thirty isolates from each bacterium enrolled. S.aureus ATCC 29213, MRSA ATCC 43300, E.coli ATCC 25922, P.aeruginosa ATCC 27853 strains were also tested as standard strains. The MICs of the strains were determined by broth dilution method. MSSA and MRSA clinical isolates’ MIC ranges of Turkish Propolis extra...

Research paper thumbnail of In vitro activity of fosfomycin in combination with imipenem, meropenem, colistin and tigecycline against OXA 48–positive Klebsiella pneumoniae strains

Diagnostic Microbiology and Infectious Disease, 2013

Carbapenem resistance due to OXA-48 enzymes in Klebsiella pneumoniae is increasing particularly i... more Carbapenem resistance due to OXA-48 enzymes in Klebsiella pneumoniae is increasing particularly in the Middle Eastern and European regions. Treatment options are limited. The aim of this study was to evaluate the in vitro synergistic activity of fosfomycin in combination with imipenem, meropenem, colistin and tigecycline against OXA-48 producing K. pneumoniae strains. Twelve carbapenem-resistant OXA-48 producing K. pneumoniae isolates were enrolled in this study. Synergistic activity of fosfomycin combined with imipenem, meropenem, colistin, and tigecycline was assessed by chequerboard method. The combination of fosfomycin was synergistic with imipenem, meropenem and tigecycline with the ratios of 42%, 33%, and 33%, respectively. Whilst the combination of fosfomycin with colistin was fully antagonistic against all of the strains, there was no statistically significant difference between the in vitro synergistic activities of fosfomycin in combination with imipenem, meropenem and tigecycline combinations (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; 0.05). Fosfomycin in combination with other agents can be preferred against multidrug resistant K. pneumoniae strains.