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outcomes of stapled and hand-sewn Roux-en-Y intestinal anastomoses in childhood. Materials and Methods: At a university hospital, the records of the children who underwent roux-en-Y anastomosis between December 2007 and December 2014 were reviewed. The data were compared according to the roux-en-Y anastomosis technique used (stapled versus hand-sewn). Results: A total of 52 patients had undergone roux-en-Y anastomosis. All had biliary atresia or choledochal cyst. Thirty-one of the patients were diagnosed with biliary atresia and 21 with choledochal cysts. Staple anastomosis technique was used in 16 of the patients with biliary atresia and 9 of the patients with choledochal cyst. Both in biliary atresia and choledochal cyst cases; operations with stapled anastomosis were significantly shorter than the ones with hand-sewn anastomosis. Among the biliary atresia cases, post-operative oral feeding was initiated significantly earlier in the stapled group, with its lower risks of post-operative cholangitis and longer hospital stay than 7 days. Conclusion: This is the first study in children, confirming the time-saving advantage of stapled anastomosis over hand-sewn, during roux-en-Y anastomosis for biliary atresia and choledochal cyst; along with the safety of stapler use, including the neonates. Stapled anastomosis yields lower complication rates, faster function gain with earlier feeding and hospital discharge.

Aim Non-operative treatment approach is another method used in the treatment of uncomplicated appendicitis, in which the infection in the appendix is suppressed and treated with antibiotics. Our study aims to investigate the clinical outcomes and the risk factors for recurrence in our pediatric patients with suspected uncomplicated appendicitis, who underwent non-operative treatment. Methods The medical data of the patients who underwent non-operative treatment with the diagnosis of suspected uncomplicated appendicitis between January 2016 and January 2021 in a tertiary pediatric surgery center were analyzed. Demographic data, treatment process, and clinical results of the patients were recorded. Statistical evaluation was made by comparing the two groups with and without recurrence after non-operative treatment. Results The median age of 41 patients whose data were evaluated was 13 (6-17) years. Eight patients (19.5%) had appendicolith. The median duration of IV antibiotic treatment was 4 (3-7) days, and the patients' abdominal tenderness disappeared in a median of 2 (1-4) days. Recurrence developed in 8 (19.5%) patients after a median of 7 (1-14) months after non-operative treatment. It was found that the time to the disappearance of abdominal tenderness was statistically longer in the group that developed recurrence than that in the group that did not (p=0.01). Conclusion Our study revealed that appendicolith was not a risk factor for the development of recurrence. The time to the disappearance of abdominal tenderness may be useful for detecting patients at a higher risk of recurrence.

Çalışan kişiye uyacak şekilde iş, ekipman ve işyeri tasarlama bilimi "ergonomi" olarak adlandırılır. Ergonomi, endüstriyel şirketler tarafından işçilerin görevlerini ve çalışma alanlarını tasarlamak için yaygın olarak kullanılır. Ergonominin amacı, insan-makine etkileşimini geliştirerek sistemlerin performansını artırmaktır. Bu bağlamda kullanıcı arayüzü tasarlanarak, bunun yanısıra ilgili sistemler geliştirilerek görev ve kullanıcı ile daha uyumlu hale getirilebilir. Ergonomi; antropometri, biyomekanik, genel mühendislik, fizyoloji, psikoloji ve fizik gibi çeşitli disiplinleri içerir. Burada değinilmesi gereken önemli konulardan biri; başta boyun, sırt, bilek, kol, omuz ve bacaklar olmak üzere bazı vücut bölgelerinin riske maruz kalma düzeyini belirleyen risk değerlendirmesidir. Olumsuz etkilerini önlemek için risk düzeyini belirlemek önemlidir. Bu amaçla, risk seviyelerini belirlemek için Hızlı Tüm Vücut Değerlendirmesi (REBA), Hızlı Üst Ekstremite Değerlendirmesi (RULA) ve Hızlı Maruziyet Değerlendirme (HMD) gibi çeşitli yöntemler kullanılır. Ancak risk seviyesi sektörlere göre değişmektedir. İnşaat sektörü en riskli sektörlerden biridir ve önemine göre bu çalışmada ele alınmıştır. İnşaat endüstrisindeki bazı yaygın süreçler seçilmiştir ve üç ergonomi risk değerlendirme yöntemi; bir Türk inşaat firmasındaki riskleri ortaya çıkarmak için REBA, RULA ve HMD uygulanmıştır. İlgili sonuçlar karşılaştırmalı olarak sunulmuş ve yorumlanmıştır.

Bu çalışmada, yükseköğretim ek ders ücret yönetim süreçlerinde yaşanan sorunların çözümü için geliştirilen bir bilişim sisteminin kullanılabilirliğinin belirlenmesine odaklanılmıştır. Bu amaçla araştırmacılar tarafından bir bilişim sistemi geliştirilmiştir. Bilişim sistemi uygulamaya konulmadan önce bir öntest yapılarak kullanıcıların ek ders süreçleriyle ilgili karşılaştıkları sorunlar tespit edilmiş ve memnuniyet düzeyleri ölçülmüştür. Sistem devreye alındıktan iki yıl sonra bir sontest uygulanarak mevcut sorunların azalıp azalmadığı belirlenmiş ve bilişim sisteminin kullanılabilirlik düzeyi ölçülmüştür. Elde edilen bulgulardan bilişim sisteminin kullanılabilirlik skorunun kabul edilebilir bir düzeyde olduğu tespit edilmiştir. Sistemin kullanımıyla birlikte sorunların azaldığı ve memnuniyet düzeyinin arttığı görülmüştür. Kullanılabilirlik düzeyi yüksek ürün ve hizmetlerin özellikleri açısından geliştirilen bilişim sistemi değerlendirilmiş ve gelecek araştırmalar için önerilerde bulunulmuştur.

Q fever is a zoonosis caused by Coxiella burnetii. In this report, a case of chronic Q fever endocarditis with pancytopenia and hypergammaglobulinemia mimicking a lymphoproliferative disease was presented. A 39-years-old male living in Çatalca and whose family is engaged in animal husbandry admitted with the complaints of weakness and fatigue. The patient had aortic valve replacement 29 years ago and had aortic valve re-replacement, and ascending aorta grafting because of endocarditis three years ago. It was revealed that the second operation of the patient was due to possible infective endocarditis, but no definitive agent could be identified. He was evaluated for massive hepatosplenomegaly, pancytopenia, hypergammaglobulinemia, presence of M-spike and elevated β-2 microglobulin levels and was referred to our hematology clinic with a preliminary diagnosis of lymphoproliferative disease. Lymphoplasmacytic lymphoma was excluded with the result of bone marrow biopsy and he was referred to our clinic for the investigation of possible infectious etiologies. We detected hepatosplenomegaly and finger clubbing. His blood analyses were normal except for the following: leukocyte count 3800/μl, platelet count 148000/μl, gamma globulin 5.9 gr/dl, rheumatoid factor (RF) and antinuclear antibody (ANA) positivity. Chronic Q fever endocarditis was suspected and C.burnetii Phase I IgG test was found positive in 1/132071 titers. Although transesophageal echocardiography showed no lesion of endocarditis, positron emission tomography/computed tomography revealed increased fluorodeoxyglucose uptake around the prosthetic heart valve and graft. The patient was diagnosed as having Q fever endocarditis and graft infection. He refused hospitalization and was started on hydroxychloroquine and doxycycline treatment. The patient stopped taking these antibiotics by himself seven days after the diagnosis. He was admitted with a headache to another hospital and operated for an intracranial hemorrhage and died shortly after. Apart from unfamiliarity, wide range of clinical presentations of disease could also lead to delayed diagnosis. Among patients with chronic Q fever, continuous bacteremia and antigenic stimulus causes inflammatory syndrome with hepatosplenomegaly, hypergammaglobulinemia and, presence of autoantibodies which leads to misdiagnoses of rheumatologic, autoimmune or hematologic diseases Chronic Q fever should be investigated in patients with known valvulopathy and chronic hepatomegaly or splenomegaly, pancytopenia, hypergammaglobulinemia, and unexplained autoantibody positivity.

Introduction: Q fever is a zoonotic disease with high morbidity and low mortality with multisystemic involvement. It is transmitted to humans through inhalation and gastrointestinal system. The disease is known to be asymptomatic in the acute and may result in mortality with complications in the chronic phase. 26 Q fever cases with neurological involvement were examined demographically. Materials and Methods: Q fever cases we have observed in the last five years were evaluated retrospectively in terms of neurological involvement. The diagnosis of the patients was made clinically and radiologically according to the serological indicators. The diagnosis was decided according to clinic and blood seropositivity. The process of acute and chronic identification was made according to the complaints, increased titration in phase II and phase I antibody positivity. The cases with neurological complaints were included in the study. Cases with neurological symptoms related to other causes were excluded from the study. Results: Out of 26 patients, 21 were male and 5 were female, and their mean age was 56.38 ± 16.93 and 41.20 ± 30.57, respectively. 22 patients had definite acute, 3 patients had possible, and 1 patient had chronic diagnosis. Two patients were mortal in acute fatal encephalitis. Despite one of our cases was in the encephalitis picture, he died in intensive care unit due to the lower respiratory tract infection. A total of 23 cases responded well to antibiotic therapy. Doxycycline, ciprofloxacin, and ceftriaxone were used in the treatment of patients. While improvement was observed in all patients using doxycycline, mortality was observed in two of the late diagnoses due to atypical neurological involvement. Conclusion: It is known that Q fever is a zoonotic disease that has been overlooked in recent years. Considering q fever in patients with neurological involvement in endemic regions and evaluating early treatment and serological indicators can be lifesaving.

Myiasis is a disease caused by tissue invasion of diptera larvae and eggs. Oral myiasis is mostly related to old age, poor oral hygiene, suppurative lesions, anatomical disorders and cancer cases. Oral squamous cell carcinoma (OSCC) is an important risk factor for myiasis. This report presents the case of an 82-year-old woman who presented with gingival myiasis developing on the background of OSSC. The patient was diagnosed with OSSC in the hospital. Myiasis larvae were identified and sent to the National Parasitology Reference Laboratory for identification. Thus, development of myiasis on OSCC background was shown in Turkey for the first time. Myiasis larvae have been identified as the 3rd phase of the larvaeMiyaz, diptera larva ve yumurtalarının doku istilasından kaynaklanan bir hastalıktır. Oral miyaz nadir görülen, yaşlılık, zayıf ağız hijyeni, süpüratif lezyonlar ve kanser olguları ilgili bir durumdur. Oral skuamöz hücreli karsinom (OSCC) miyazda önemli bir risk faktörüdür. Bu raporda, 82 yaşında bir kadın hastada OSCC zemininde gelişen miyaz sunulmuştur. Hasta, ağız içinde ovoid bir lezyon ile diş hekimine müracaat etmiş, sonra hastanede OSSC tanısı konmuş ve bu zeminde miyaz larvaları tespit edilmiştir. Larvalar Ulusal Parazitoloji Referans Laboratuvarı’na gönderilmiştir. Laboratuvar çalışmaları ile tespit edilen larvaların üçüncü dönem

Background Brucellosis is a worldwide zoonotic disease that causes serious public health problems. This study aimed to identify Brucella strains isolated from various clinical samples by conventional and molecular methods and to determine antimicrobial susceptibilities against doxycycline (DOX), streptomycin (STR), ciprofloxacin (CIP) and rifampicin (RIF) by the gradient strip (E test) test method. Methods A total of 87 Brucella strains isolated from various clinical specimens between 2004 and 2018 were included in this study. While four of the 87 strains included in the study were identified only at the genus level, the remaining 83 strains were identified at the species level by the Real-Time Multiplex PCR (M-RT-PCR) method and conventional methods were used for biotyping. Results According to molecular identification results, 83 strains were identified as B. melitensis by the M-RT-PCR method, with 82 strains identified as Brucella melitensis biovar (bv) 3 and one as B. melitensis bv 1 according to the conventional biotyping method. Among the antibiotics studied, CIP was found to be the most active agent according to the minimum inhibitory concentrations (MIC)90 values. This was followed by DOX and STR, respectively. While all of the isolates were sensitive to CIP, DOX and STR, 18 (20.7%) strains were found to be moderately susceptible to RIF, with the highest values of MIC50 and MIC90. Conclusions In our study, all strains were identified as B. melitensis. DOX, STR, CIP and RIF used in the treatment of brucellosis were found to be effective.

Shortly after the first detection of human immundeficiency virus (HIV) infection in USA in 1981, the number of cases have increased gradually from all around the world. Turkey’s high capacity for tourism and the unique geographic location extending between Europe and Asia, provides convenience for the passage of individuals across the countries and sexually transmitted infections including HIV, as well. According to the official data of the Ministry of Health; there are 25809 HIV positive and 1958 AIDS cases as of November 30, 2020, after the epidemic started in 1985 in Turkey. Despite the decrease in the number of newly detected HIV cases as a result of serious measures taken for the transmission of infection worldwide, the increase in the number of cases still continues in our country. Shortening the reporting period and starting treatment as soon as possible in the diagnosis of infection is critical for the control of the epidemic. For this purpose, Centers for Disease Control and Prevention (CDC) published a new test algorithm in 2010, which suggested the use of the Geenius™ HIV ½ supplemental assay test instead of western blot tests, which have been used for many years to verify HIV screening test positivity. In this study, we aimed to report the experience of the National HIV-Acquiner Immundeficiency Syndrome (AIDS) and Viral Hepatitis Reference Laboratories of Turkey in the first year of transition to the new HIV algorithm and to evaluate the diagnostic performance of Geenius™ HIV ½ and line immunassay (LIA) s. A total of 2090 anti-HIV positive patient sera sent to National HIV-AIDS and Viral Hepatitis Reference Laboratories of Turkey, Ankara for HIV confirmation were included in the study. All samples were retested with a fourth-generation enzyme linked immunosorbent assay (ELISA) test (VIDAS® HIV-1/2 Duo Ultra assay, BioMerieux, France) followed by the confirmatory tests; Geenius™ HIV 1/2 confirmatory assay (BioRad, Redmond, WA) and Line-immunoassay (INNO-LIA HIV ½ Score, Fujirebio, Belgium). Indeterminate/negative test results or discrepancies between the confirmatory tests were resolved with HIV-1 RNA reverse transcriptase polymerase chain reaction (RT-PCR) (artus HI Virus-1 RT-PCR, Qiagen, Germany) test and in-house HIV-2 RNA and proviral DNA PCR. The sensitivity, specificity, and the agreement of the each assay were compared. Cohen’s Kappa analysis was used for the evaluation of the agreement between the tests. According to the new algorithm which recommended Geenius™ test besides HIV-1 RNA test, 1707 (81.7%) HIV-1 positive samples were identified. Of these samples; 95.9% and 95.02% were identified as HIV-1 positive by GeeniusTM and INNO-LIA, respectively. However, 2.5% of the positive samples were negative with Geenius™ and 3.5% with INNO-LIA. One and a half percentage (1.5%) of these samples were detected with Geenius™ and 1.4% with INNO-LIA as indeterminant. When all the positive samples determined with ELISA were evaluated; it was detected that,1.3% were indeterminate by Geenius™ test and 2.4% by the INNO-LIA test. When the INNO-LIA test was regarded as the gold standard method; sensitivity, specificity, positive predictive and negative predictive values of the Geenius™ test were as follows; 99.7%, 96.1%, 98.9%, and 99.1%. The agreement between INNO-LIA and Geenius™ tests was found to be 98.95% (κ= 0.969; very good). When the Geenius™ and HIV-1 PCR tests were evaluated together for the confirmation; the sensitivities of Geenius™ and INNO-LIA tests were 99.8% and 98.3%, specificities were 89.8% and 85.3%, respectively. Slight positive bands were detected in the gp36 or gp140 bands, the HIV-2 specific envelope proteins, were detected in seven samples, However, the positivity disappeared after the dilution of the samples and it was accepted as false positivite reaction due to the absence of HIV-2 RNA and proviral DNA in these samples. In conclusion; we concluded that Geenius™ and INNO-LIA tests have a perfect agreement in HIV diagnosis and due to the rapid and reliable results provided for the HIV test protocol, Geenius™ test can be used safely as an alternative to the immunoblot tests. HIV-1 RNA testing must be performed in all HIV confirmation centers in order to detect acute HIV cases in the fast and early period which are the main reason for the updates in HIV diagnosis.

Objective: The aim of this study was to evaluate the results of examination for intestinal parasites in fecal samples sent to our laboratory by obtaining from patients applied to the hospital because of various complaints.

Amaç: İnfluenza rutin tanısında yüksek duyarlılık ve özgüllüğü nedeniyle real-time PCR testi tercih edilmektedir. Ancak PCR testlerinin yüksek maliyet ve deneyimli personel gereksinimi, laboratuvar ortamına ve cihazlarına ihtiyaç duyulması, numune transferi ve hekime sonucun ulaşmasında geçen süre gibi nedenlerle hasta başı kullanılan hızlı influenza tanı testlerinin kullanımı gündeme gelmiştir. Bu çalışmanın amacı, influenza enfeksiyonu tanısında kullanılan 3 farklı hızlı tanı testinin gerçek zamanlı RT-PCR yöntemi ile karşılaştırılması ve tanısal performansının belirlenmesidir.Yöntem: Çalışmamıza 2017-2018 influenza sezonunda laboratuvarımıza gönderilen toplam 209 solunum yolu örneği dahil edilmiştir. Örnekler Humasis Influenza antigen card plus (Kore), SD Biosensor Standard-Q Influenza A/B (Kore) ve SD Biosensor Standard-F Influenza A/B FIA (Kore) hızlı antijen tanı kitleri ile üretici firmaların önerileri doğrultusunda test edilmiştir.Bulgular: Çalışmamızda Humasis kiti ile İnfluenza A için duyarlılık %80,99, İnfluenza B için %68,66 hesaplanmıştır. SD Biosensor Standard Q Influenza A/B ve SD Biosensor Standard F Influenza A/B FIA kiti ile her iki virüs için de duyarlılık %70’in altında bulunmuştur. Humasis kitinin duyarlılığı diğer kitlere oranla daha yüksek saptanır- ken özgüllük tüm kitlerde %90’ın üzerinde belirlenmiştir.Sonuç: Bu çalışma ile hızlı antijen testlerinin, influenza virüs aktivitesinin yoğun olduğu influenza sezonu dönemi veya salgın durumlarında influenza virüs enfeksiyonu tanısında tarama testi veya destekleyici test olarak kullanılabileceği sonucuna varılmıştır., Aim: Due to its high sensitivity and specificity, real-time PCR testing is preferred for routine diagnosis. However, for PCR tests, the use of rapid influenza diagnostic tests at bedside due to reasons such as high cost, experienced personnel, laboratory conditions and equipment requirement, sample transfer and test time has come to the fore. Purpose of the study was to compare three different diagnostic tests used in the diagnosis of influenza infection with the real-time RT-PCR method and to determine the diagnostic performance.Methods: A total of 209 respiratory tract samples sent to our laboratory during the 2017-2018 influenza season were included in our study. The samples were tested with Humasis Influenza antigen card plus, SD Biosensor Standard-Q Influenza A/B, and SD Biosensor Standard-F Influenza A/B FIA rapid antigen diagnostic kits according to the recommendations of the manufacturers.Results: In our study, susceptibility was calculated 80.99% for influenza A and 68.66% for influenza B with Humasis kit. With the SD Biosensor Standard Q Influenza A/B and the SD Biosensor Standard F Influenza A/B FIA kit, the sensitivity for both viruses was below 70%. While the sensitivity of the humasis kit was higher than the other kits, the specificity was higher than 90% in all kits.Conclusion: n this study, it was concluded that rapid antigen tests can be used as a screening test or supportive test for the diagnosis of influenza virus infection during the influenza season period or epidemic conditions during which influenza virus activity is intense.

It has been reported that direct identification from blood culture bottles with positive signals and reporting the results to the clinics earlier has positive effects on mortality and morbidity. Extraction methods especially using detergents are used for the direct identification from the bottles which give positive signal. For this purpose, in-house methods developed based on the usage of saponin are widely available in the literature. In this study, it was aimed to develop a simple, easy-to-apply and reliable protocol for identifying the agent directly from the blood culture bottle that gives positive signal with the use of detergent Tween® 80, and to study the obtained protocol in clinical samples in a routine microbiology laboratory and to evaluate the results. The study was carried out in two stages, the experimental stage where the method was developed and the clinical stage where the method was applied. In the experimental stage, blood culture bottles were created with standard strains and isolates previously diagnosed with the 16S rRNA method. 10% solution of Tween® 80 was prepared with distilled water. 1 ml sample was transferred from the bottle that gave positive signal to the microcentrifuge tube, 100 µl of 10% solution of Tween® 80 was added, vortexed for 10 seconds and then incubated for 5 minutes at room temperature. The tubes were centrifuged for 5 min at 14.000 rpm, the supernatant was discarded and the pellet was washed with 1 ml of distilled water and centrifuged at 14.000 rpm for 5 minutes in three times. Samples taken from the pellets were rubbed on the slide and dried on air. Firstly, 1 µl of 70% formic acid, then 1 µl, of matrix solution was added and it was used after drying. In the second stage of the study, the method was applied to the 502 vials giving positive signal in the Microbiology Laboratory of Ankara University Faculty of Medicine Ibni Sina Hospital between 17 April 2018-31 August 2018 and the results were compared with the subculture results. The results obtained at the end of extraction in the experimental stage were compared with the subculture results and no statistical difference was found. In 383 (82.9%) bottles among 462 (92.1%) bottles with monomicrobial positive cultures, compatible results with the subculture results were obtained. Of the microorganisms correctly identified, 350 (91.3%) were bacteria and 33 (8.7%) were fungi. On the other hand, 216 (56.4%) of the bacteria were gram positive and 134 (34.9%) of them were gram negative bacteria. At least one microorganism was correctly identified in 19 (47.5%) of 40 (7.9%) bottles with polymicrobial blood cultures. Their distribution was gram negative (n= 10) and gram positive (n= 8) and yeast (n= 1). No microorganisms were identified in six bottles with polymicrobial cultures. According to the results, we believe that this in-house method developed using Tween® 80 will be a routinely applicable method for blood culture bottles that give positive signal in microbiology laboratories and it will contribute to the early diagnosis.

Francisella tularensis is a gram-negative, coccobasillus, facultative intracellular bacteria and causes a zoonotic disease, tularemia in humans. F.tularensis has four subspecies, which have different virulences for humans as F.tularensis subsp. tularensis, F.tularensis subsp. holarctica, F.tularensis subsp. mediasiatica and F.tularensis subsp. novicida. F.tularensis subsp. tularensis is the most virulent subspecies and mortality rate is high in human cases. F.tularensis subsp. holarctica, which has been reported in our country to date, has lower virulence than that of subsp. tularensis, and causes rare lethality among untreated patients. According to the erythromycin resistance and the properties of glucose-glycerol fermentation, F.tularensis subsp. holarctica has three biovar as biovar I, biovar II and biovar japonica. F.tularensis subsp. mediasiatica has been reported only in a few central asian countries and its virulence is similar to the F.tularensis subsp. holarctica F.tularensis subsp. novicida is avirulent for immunocompetent individuals but has been observed to cause infection in immunocompromised individuals. The aim of this study was to determine the F.tularensis subspecies in 259 F.tularensis strains isolated from clinical specimens, drinking water and a rodent sample and 517 F.tularensis PCR-positive DNA isolated from clinical specimens between years 2009 and 2014. Conventional PCR was performed using primers specific for the RD1 (Region Difference) region of F.tularensis. Subspecies were differentiated depending on the difference in PCR amplification product size. In our study, F.tularensis subsp. holarctica was detected in 764 samples yielding 922 base pair (bp) amplification product. The DNA samples obtained from one water and 11 lymph aspirates were determined as F.tularensis subsp. holarctica biovar japonica. The DNA sequence analysis of the amplification product of the RD1 region of the isolate from water sample was determined. The 1136 bp nucleotide sequence obtained from the DNA sequence analysis was 100% similar to F.tularensis subsp. holarctica biovar japonica (FCS075 strain-accesion number AF469618) when compared with GenBank data. The whole genome sequence of this isolate was also determined and recorded to GenBank with accesion number CP007148. None of the samples used in our study belonged to other sub-species. F.tularensis subsp. holarctica biovar japonica positive 11 lymph aspirate samples were sent to our center from Ankara (n= 1), Kayseri (n= 1) and Afyon (n= 9) provinces. The results of the current study revealed that F.tularensis subsp. holarctica biovar japonica caused a tularemia outbreak in a village in Afyon province at first time and it was observed sporadically in two other different provinces.

Background/aim: This prospective study aimed to determine the presence of the most common carbapenemase genes, blaOXA-48, blaKPC, blaIMP, blaVIM and blaNDM on carbapenem resistant clinical K.pneumoniae and E.coli isolates. Materials and methods: Isolates were selected according to EUCAST guideline; gradient test and disc diffusion with both meropenem and ertapenem discs. Resistance rates of these isolates to other antimicrobial agents were also examined by disc diffusion method. Carbapenem resistance gene were investigated by using Real-Time PCR. Results: A total of 3845 E. coli and 1689 K.pneumoniae isolates from clinical samples between January 2015 and April 2017 were evaluated. The 419 isolates were found as carbapenem resistant but only the first resistant isolate (n=155; 126 K.pneumoniae and 29 E.coli) of each patient were included. Carbapenem resistant isolates were most frequently isolated from intensive care units (48.8%). Colistin was the most effective antibiotic (91.0%). The 121 (78.1%) of the tested isolates were positive for OXA-48 (103 K.pneumoniae and 18 E.coli) and 9 K. pneumoniae carrying blaNDM were also positive for blaOXA-48. VIM, IMP and KPC type carbapenemases were not detected in any isolates. Conclusion: Carbapenem-resistant pathogens have been shown to be able to develop resistance mechanisms with more than one carbapenemase encoding gene.

Rickettsia species are gram negative, small pleomorphic coccobacilli, obligate intracellular bacteria. The majority of these bacteria are transported by the ticks. Rickettsia slovaca and Rickettsia raoultii are among the Rickettsia species in the spotted fever group and carried by Dermacentor species ticks, that cause tick-borne lymphadenopathy (Tickborne Lymphadenopathy-TIBOLA or Dermacentor-borne necrotic erythema and lymphadenopathy- DEBONEL). Rickettsia species are obligate intracellular bacteria and they can be cultivated in cell cultures. The chance of isolation of Rickettsia species from clinical and tick specimens has been increased by the shell-vial centrifugation cell culture method. The aim of this study was to isolate R.slovaca from two Dermacentor marginatus species ticks which were detected in humans by the use of shell-vial centrifugation cell culture method using VERO cell. Before proceeding to the culture stage, an algorithm including description, disinfection, dissection of ticks and methods of hemolymph, homogenization, DNA extraction and real-time PCR was performed. Iodine-alcohol disinfection was performed following identification of the ticks with the use of a stereo microscope. Ticks hemolymph were obtained with extremity dissection of ticks and indirect fluorescence antibody (IFA) test was performed with Rickettsia positive sera. Ticks identified as containing Rickettsia like bacteria in hemolymph were homogenized and DNA extraction was performed from homogenate of ticks. By real-time PCR, using Rickettsia genus-specific PanR8 primers and probes, PCR positive Rickettsia spp. were determined among the ticks. Vero cells that have formed monolayer in vials were used for Rickettsia culture. Homogenized tick samples which were positive for Rickettsia in hemolymph and real-time PCR methods were inoculated to cell culture vials. Suspended bacteria in the inoculum were allowed to approach the cells by the shell-vial centrifugation method. Cells were scraped after five days of incubation in 5% CO2 at 36°C. An aliquot of the determined cell suspension was fixed to the slides and then IFA was performed using Rickettsia positive sera. In fluorescence microscopy examination, adhered and proliferated bacteria were observed on Vero cells. This cell suspension was again inoculated into the Vero cell cultures to increase bacterial replication and taken for 5-7 days of incubation. DNA was extracted from the suspension of the cultivated bacteria. Conventional PCR of citrate synthase (gltA) and outer membrane protein A (ompA) gene regions were used to identify Rickettsia species. DNA sequence analysis of PCR amplification products were determined. DNA sequence results were compared to Genbank data and found that the gltA sequence was 100%, similar to R.slovaca with accession number AY129301.1 and the ompA sequence was 100%, similar to R.slovaca with accession number KF791242.1. In addition, the two strains isolated in phylogenetic analysis were found to be R.slovaca. As a result, R.slovaca isolation from of D.marginatus type ticks has been reported for the first time in our country by the cell culture method.

The first aim of this study is to determine all the problems experienced by teaching staff in the course of additional course management process. The second aim is to introduce a new process design for the solution of the problems identified and the functioning of an information system that can be used in the process. As no basis was found in the literature for the identification of the problems faced by the teaching staff about the additional course processes, mixed method research paradigm has been utilized and the explanatory sequential design was applied as research design. Qualitative data were gathered on the opinions of the teaching staff about the possible problems they encountered in the additional course processes and their ideas about an information system proposal believed to be able to solve the problems. These data were analyzed in terms of the occurrence conditions, environment, frequency of encounter and results. A quantitative data collection tool has been developed by considering the result categories as a form. This tool was then used to evaluate the validity of these forms on more teaching staff. The problems experienced in the current situation and the possible solutions from the participants were presented by supporting the qualitative and quantitative findings with findings of the observations. It was proposed to develop an automation system for the solution of the problems and information was given about the process steps of the system., Bu çalışmanın ilk amacı öğretim elemanlarının ek ders yönetim süreçlerinde yaşadıkları problemleri tüm detaylarıyla tespit etmektir. İkinci amacı ise, tespit edilen problemlerin çözümüne yönelik yeni bir süreç tasarımını ve süreç içerisinde kullanılabilecek bir bilişim sisteminin işleyişi tanıtmaktır. Ek ders süreçleriyle ilgili öğretim elemanlarının karşılaştıkları problemlerin tespiti için alanyazında herhangi bir dayanak bulunmadığı için karma yöntem bir araştırma tasarımı ve desen olarak da keşfedici sıralı desen uygulanmıştır. Öğretim elemanlarının ek ders süreçlerinde karşılaştıkları olası problemler ve problemleri çözebileceğine inanılan bir bilişim sistemi önerisine yönelik düşünceleri üzerine nitel olarak veri toplanmıştır. Bu veriler, ortaya çıkma şartları, ortam, karşılaşma sıklığı ve sonuçlar yönünden çözümlenmiştir. Bulunan sonuç kategorilerini birer biçim olarak kabul ederek nicel bir veri toplama aracı geliştirilmiştir. Daha sonra bu araç daha fazla öğretim elemanı üzerinde bu biçimlerin ne kadar geçerli olduğunu değerlendirmek amacıyla kullanılmıştır. Elde edilen nitel ve nicel bulgular, gözlemler sonucunda elde edilen bulgularla desteklenerek mevcut durumda yaşanan problemler ve olası katılımcılardan gelen olası çözüm önerileri ortaya konulmuştur. Yaşanan problemlerin çözümüne yönelik bir bilişim sistemi geliştirilmesi önerisi yapılmış ve sistemin işleyişi hakkında bilgi verilmiştir.

Pertussis is an important cause of morbidity and mortality in infants under two months of age and these high risk babies are dependent on maternally derived antibodies until completion of their first immunization series. This study aimed to evaluate the vaccine response of late preterm and term newborns as well as their mothers who underwent combined tetanus-diphtheria toxoid and acellular pertussis (Tdap) vaccination during pregnancy.A total of 70 pregnant women were administered Tdap vaccine (Boostrix®, GSK) between 27 and 33 gestational weeks of pregnancy. The IgG antibodies against pertussis toxin (PT) and filamentous hemagglutinin (FHA) in maternal blood before vaccination and in both maternal and umbilical cord blood after vaccination were evaluated using the in-house ELISA method. The geometric mean concentrations (GMC) and placental transfer ratios of antibodies were measured.Participants' with a mean age of 29.59 ± 4.70 years received Tdap vaccine at an average 28.6 ± 1.31 gestational weeks. Average pre and post vaccination levels of anti-PT IgG GMCs and anti-FHA IgG GMCs were 8.01 IU/ml vs 39.48 IU/ml (p = 0.001) and 122.24 IU/ml vs 183.97 IU/ml (p 0.001), respectively. The anti-PT and anti-FHA IgG GMCs of cord blood after vaccination was 25.15 IU/ml and 118.77 IU/ml, respectively (p 0.001 and p = 0.064). Placental transfer ratios of anti-PT ve anti-FHA IgG antibodies were detected as 0.65 and 0.62, respectively.Immunization of pregnant women with Tdap at the third trimester results in high maternal and infant antibody levels. Maternal immunization during each pregnancy seems to be the best strategy in revealing the highest maternal and infant antibodies and in narrowing the gap between birth and immune system maturation in infants. Pregnant women in our country should also get the Tdap vaccine during pregnancy especially in the early third trimester.

Objective: Antibiotic resistance is one of the most significant problems of human-animal and environmental ecosystems. It is crucial to establish integrated surveillance systems and monitor resistance for the management of antibiotic resistance. Standardization of antibiotic resistance data obtained from various disciplines is the critical point in enhancing the data quality. To realize this objective, a common antibiotic susceptibility testing training program was prepared and performed for professionals from various disciplines to standardize the resistance data to be obtained from the human, animal, and environmental sectors in our country. Method: A total of 48 individuals participated in a five-day training program in three terms. In each period, four small groups, each consisting of four people from a group of different professions, were generated. Participants were trained on quality control, phenotypic tests, genotypic tests, and the use of resistance data in antibiotic susceptibility testing. Pre-test and post-tests were applied to the participants. Results: Individuals with a postgraduate degree who studied antibiotic susceptibility testing in the fields of medicine, veterinary medicine, pharmacy, food, and environment participated in the training. The average number of correct answers in the pre-test and post-test increased from 4.8 to 10.5 in April, from 4 to 9 in June and from 3.4 to 8.5 in September. They studied phenotypic and genotypic tests in the supplied isolates under the supervision of the educators. Conclusion: We presume that dissemination of the training at graduate and postgraduate levels will also enable the One-Health approach to become widespread. In addition, worldwide application of similar trainings will help standardization of resistance data, as well as one health approach.

Meningococcal conjugate vaccine was administered for the first time to pilgrims in 2018 in Turkey prior to their departure to the Hajj. This study aimed to determine the effect of vaccination on the prevalence of Neisseria meningitidis carriage among the pilgrims returning to Turkey. This prospective paired (departing and arriving) cohort study included pilgrims aged 10–80 years and compared N.meningitidis carriage before and after pilgrimage. Oropharyngeal samples were collected from 229 pilgrims before departing for Mecca, Kingdom of Saudi Arabia (KSA) and after their return to Turkey. Meningococcal carriage was detected in 3.9% (n = 9) at the time of departure; all positive samples were serogroup B. Upon returning to Turkey,1 (0.4%) pilgrim, who was not a carrier before pilgrimage, was positive for serogroup B. This study is the first to examine meningococcal carriage following the administration of conjugate vaccine to Hajj pilgrims from Turkey.

Background Serological methods have great importance for the detection of Treponema pallidum antibodies in syphilis diagnosis. The goal of the present study is to evaluate various commercially available screening assays in comparison with the FTA-abs test. Methods A total of 363 serum samples were enrolled in the study. Following routine testing including RPR and TPHA tests, each sample was tested by treponemal immunoassays (Chorus Syphilis Screen Recombinant, Architect Syphilis TP, Syphilis Virclia Monotest, Siemens Advia Centaur Syphilis, Euroimmun Treponema pallidum Screen ELISA, Vircell Syphilis ELISA IgG + IgM, SD Bioline Syphilis). The result obtained from each test was compared with the confirmatory FTA-abs test. Kappa (κ) coefficients were used to compare the concordance of the tests. Results When the various tests were evaluated in comparison with the FTA-abs test, the sensitivity, specificity and percent agreement of each test were as follows: Architect Syphilis TP, 92.3%, 94.5%, 92.8%; Chorus Syphilis Screen Recombinant, 87.9%, 91.2%, 88.7%; Syphilis Virclia Monotest, 80.5%, 97.8%, 84.9%; Siemens Advia Centaur Syphilis, 87.5%, 89%, 87.9%; Euroimmun Treponema pallidum Screen ELISA, 87.5%, 85.7%, 87.1%; Vircell Syphilis ELISA IgG + IgM, 73.2%, 62.6%, 70.5%; TPHA, 89%, 63.7%, 82.6%; SD Bioline Syphilis, 58.1%, 94.5%, 67.2%; RPR test, 57.7%, 57.1%, 57.6%. Conclusion The results of the present study show that Treponema pallidum specific immunoassays with a performance similar or better than TPHA test generally performed well with the confirmatory FTA-abs test and may be an alternative for screening total antibodies in syphilis infection.

Background/aim: Limited data on syphilis coinfection in human immunodeficiency virus (HIV) positive cases exist in Turkey. Our aim is to investigate syphilis coinfection and to evaluate the compatibility of the screening Architect Syphilis Tp ELISA with the fluorescent treponemal antibody absorption (FTA-abs) confirmation test in HIV positive cases. Materials and methods: Totally 519 HIV positive patients were included in the study. Enzyme linked fluorescent assay (ELFA) was used as a screening test and positive samples were confirmed by line immunassay (LIA). In order to discriminate acute HIV infection and false ELISA positivity, HIV-1 RNA PCR was performed in ELFA positive and LIA negative samples. Architect Syphilis TP ELISA was used for the detection of total antibodies against Treponema pallidum in HIV positive patients. Positive results were confirmed by the FTA-abs test. Results: Out of 519 HIV-1 positive patients, IgG and IgM positivity, and only IgG positivity was detected as 1.9% and 11.4% in all the samples, respectively. A total of 79 (15.2%) sera were positive with Architect Syphilis Tp ELISA test and 69 (13.3%) were positive with FTA-abs test. Statistically significant, almost perfect agreement was found between Architect Syphilis Tp ELISA and FTA-abs tests (kappa = 0.921 and P < 0.001). Conclusion: Implementation of syphilis and HIV screening tests together among risk groups is considered to be appropriate.

Although a significant decrease has been reported in the incidence of diphteria in many regions of the world following the routine diphtheria immunization programs, the emergence of new cases indicated that toxigenic strains are still circulating in the community. Diphtheria vaccine does not provide protection against asymptomatic carriage and colonization of non-toxigenic Corynebacterium diphtheriae. It is a known fact that invasive infections may arise from non-toxigenic C.diphtheriae strains that the non-toxigenic strains can become toxigenic strains leading to diphteria. It is also known that there is a risk of diphteria outbreaks due to decreased antitoxin level and inadequate adult immunization programs. In our country, there is no routine surveillance of toxigenic and non-toxigenic C.diphtheriae. In the present study we aimed to investigate the presence of C.diphtheriae, Corynebacterium ulcerans and Corynebacterium pseudotuberculosis in children presenting with the symptoms of upper respiratory tract infections that might be confused with those moderate diphteria, in order to highlight the requirement of microbiological surveillance and to create awareness about these microorganisms among public health experts, microbiologists and clinicians. Throat swab specimens were obtained from children who were admitted to the pediatric outpatient clinics, in Dr. Sami Ulus Obstectrics, Children Health and Diseases Educational and Research Hospital, with upper respiratory tract infections between 1 February 2016-22 March 2016. The specimens were inoculated in 5% sheep blood agar plates. The plates that were incubated in appropriate conditions, were evaluated for Group A beta hemolytic streptococcocci. Subsequently, culture plates were sent to the Public Health Institution of Turkey, National Respiratory Pathologens Reference Laboratories for the investigation of the presence of C.diphtheriae, C.ulcerans and C.pseudotuberculosis. The growth in each plate were collected with a sterile swab and inoculated in tryptic soy broth. Following 2 hours of incubation at 37oC, subcultures were inoculated in cystine-tellurite-blood agar (CTBA) and 5% sheep-blood agar plates; after an overnight incubation tellurite-reducing colonies were inoculated in Tinsdale agar plates. The suspected colonies with positive cystinase activity were identified by conventional methods and also with Coryne API (Biomerieux, France) systems. Toxicity tests (ELEK, PCR) were performed to investigate whether the C.diphtheriae strains were producing toxins. A total of 500 patients were involved in the study. Of these 260 (52%) were girls and 240 (48%) were boys with a mean age of 76 (range, 21-213) months. All patients except one were fully vaccinated with boosters. Most common presenting symptoms of the patients were fever (19.8%), sore throat (52.6%), cough (49.2%), tonsillar hyperemia (97.6%), presence of crypt (24.6%), and membrane over tonsils (1%). Group A beta-hemolytic streptococcocci were detected in the throat swab cultures of 66 (%13.2) patients. Genotypically toxin negative C.diphtheriae biovar gravis was identified in the throat swab cultures of 3 patients (2 girls and 1 boy). The tonsils were hyperemic and hypertrophic in all the patients with C.diphtheriae biovar gravis. C.ulcerans and C.pseudotuberculosis were detected in none of the patients. It is considered that similar regular cross-sectional studies or routine screening programs are expected to raise awareness about this forgotten microorganism both epidemiologically and microbiologically.

Background: Viral conjunctivitis are the most frequent infections in ophthalmology clinics. The diagnosis is usually relying on clinical findings and medical history. However, topical antibiotics are often used unnecessarily addition to symptomatic treatment because of unsure agents. We aimed to detect the Adenovirus, Coxsackievirus and Enterovirus from conjunctiva and pharyngeal samples of patients. Methods: The conjunctiva and pharyngeal samples of the patients with conjunctivitis were taken by Virocult transport media and kept at −80 ̊C up to study day. Adenovirus spp, Enterovirus 70 and Enterovirus 71, Coxsackie A24 and Coxsackie A16 were detected by real-time PCR. Samples from healthy health care workers of ophthalmology clinic were used for control group. Results: A total of 176 samples (conjunctival and pharyngeal samples of 62 patient and 26 healthy subjects) were included. The mean age of 34 (55.7%) male and 27 (44.3%) female patients was 34 ± 17. Twenty five (40.3%) of the patients were receiving antibiotic drops at first visit. The main etiologic agent in conjunctival samples was found to be Adenovirus (46/62, 74.2%) followed by Enterovirus 70 (4/62, 6.4%) and Enterovirus 71 (4/62, 6.4%). Coxsackievirus 16 and 24 were also found in 2 patients (1/62 each, 1.6%). Pharyngeal samples were also positive for Adenovirus (20/62, 32.3%), Enterovirus 70 and 71 (7/62, 11.3% and 5/62, 8.1% respectively), Coxsackievirus 16 and 24 (2/62, 3.2% and 1/61, 1.6%). Conclusions: It is very difficult in viral conjunctivitis to make clinical differentiation caused by different agents because of common clinical signs and symptoms. In routine clinical work, the viral conjunctivitis usually related with Adenovirus. But almost one fourth of the patients’ conjunctivitis were not related to Adenovirus, which shows the importance of the laboratory diagnostics. True diagnosis plays an important role on prevention of contamination and unnecessary use of antibiotics in viral conjunctivitis. Keywords: Adenovirus, Conjunctivitis, Viral, PCR

Tularemia is a zoonotic disease caused by Francisella tularensis. Humans can acquire the infection through bites from arthropods, contact with animal tissues, consumption of the infected water and inhalation of aerosolized bacteria. The oropharyngeal form is the most common presentation in Turkey, reflecting the consumption of contaminated water. While the most common complication of the disease is the suppuration of the lymph nodes, abscess formation can be a very rare complication. In this study, we report a glandular tularemia case with bilateral inguinal lymphadenopathy and intra-abdominal abscess. A 51-year-old woman came to the infectious diseases clinic with fever and swelling in the groin ongoing for two months. She had been started on a treatment of amoxicillinclavulanic acid at another hospital for two weeks and had a history of watering her garden bare feet with natural pool water. She had fever and bilateral inguinal lymph nodes in her physical examination. One of her lymph nodes was extracted for diagnosis. The pathological examination result was granulomatous lymphadenitis. The sample’s culture and PCR results were negative for tuberculosis and tularemia but the F. tularensis microagglutination test (MAT) was positive. She had received treatment for Tularemia but her clinical and laboratory findings had not improved. Pelvic lymphadenopathies and an intra-abdominal abscess were observed in an MRI. Percutaneous drainage was done and the patient’s condition improved. This tularemia case was presented to emphasize that in regions, like our country, where tularemia is epidemic, if specific treatment is late, rare complications can be seen.

Background: In Turkey, pneumococcal conjugated vaccine (PCV) was introduced to the national immunization program as PCV7 in 2008, and was replaced with PCV13 in 2011. The aims of this study wereto investigate the effects of PCV13 on nasopharyngeal pneumococcal carriage (NPC) by determining theserotype distribution, and to identify risk factors for carriage, in healthy Turkish children. Methods: This prospective study was conducted on 500 healthy children aged 0-13 years between Apriland November 2014. Nasopharyngeal swab samples were taken, and molecular method for capsularserotyping was performed by multiplex PCR. Results: Of 500 children, 43.4% were unvaccinated with a PCV (7- or 13-valent), 56.6% were vaccinatedand The NPC rate was found to be 9.8%. Of 49 positive Streptococcus pneumoniae isolates, 26 (53%) werePCV13 vaccine strains (VSs), and 17 (34.7%) were non-VS. Six isolates (12.2%) were not typeable by themethod applied. The most common serotypes detected were serotype 3 (18.3%), serotype 19F (14.2%), serotype 6A/B (8.1%), serotype 11A (8.1%), and serotype 15B (8.1%). The total coverage rate of the PCV13serotypes was 60.4%. Conclusion: A significant decrease in carriage rate was detected within three years after the introductionof PCV13 in Turkey. However, the nasopharyngeal carriage of PCV13 strains was found to be interestinglyhigh. (c) 2019 The Authors. Published by Elsevier Ltd on behalf of King Saud Bin Abdulaziz University forHealth Sciences. This is an open access article under the CC BY-NC-ND license (http://creativecommons. org/licenses/by-nc-nd/4.0/).

Klasik ulaştırma sistemlerinin çevresel kaygıları göz önünde bulundurulduğunda, elektrikli araçlarla (EA) ilgili çalışmalar önem kazanmış ve son yıllarda sayıca artmıştır. Bu noktada ele alınması gereken sorunlardan biri EA’lar için şarj istasyonlarının uygun yerlerinin belirlenmesidir. Bu çalışmanın temel amacı, İstanbul'daki elektrik şarj istasyonlarına ilişkin en uygun konumları yolların akışını değerlendirmeye alarak bulmaktır. Şarj istasyonlarının konumları, yolların kapsanan akışını maksimize etmeyi amaçlayan akış-yakıt ikmal lokasyon modeline dayanan bir model kullanılarak belirlenmiştir. Matematiksel model farklı “p” değerli için çözülmüş ve en iyi lokasyonlar belirlenmiştir., The studies about Electric Vehicles (EV) have gained importance and increased in the last years depending on the environmental concerns of the classic transportation systems. One of the problems to consider at this point is locating the proper points of electric charging stations for EVs. The primary objective of this research is to locate the electric charging stations in Istanbul considering the flow of the paths. The locations of electric charging stations are determined by using a mathematical model based on the flow-refuelling location model with the aim of maximizing the captured flow. The mathematical model is run for various values of “p” and the optimum locations are obtained.

Purpose Toxoplasma gondii is an intracellular parasite that can affect all vertebrae and is the causative agent of toxoplasmosis. At present, the United States CDC (Centers for Disease Control and Prevention) recognizes this infection as a neglected disease. Toxoplasma gondii infection profiles exhibit differences because of the different regional and climatic responses to these parasites in Turkey, and these protozoan infections are notably common in this country. In this study, we attempted to obtain the whole-genome sequence of T. gondii using next-generation sequencing technology. Methods Toxoplasma gondii isolates were isolated from an infant with congenital toxoplasmosis by Ekmen et al. (1974) in Ankara, Turkey. Whole-genome sequencing (WGS) was performed using the Illumina HiSeq 2500 and HiSeq SBS Kit v2. A T. gondii library was created on this device in the initial stage. After the completion of the library phase, sequence analysis was begun with a next-generation sequencing device. The resulting fragments were combined using paired-end (PE) reading and converted into a single DNA fragment. Bioinformatic analysis was performed using the Geneious 2.1. program. Results In our study, WGS was successfully performed on T. gondii. The T. gondii whole-genome sequence has a coverage value of 50x, a size of 61,5763 Mb and a GC ratio of 52.6%. Data from this sequence were submitted to the National Center for Biotechnology Information (NCBI) GenBank ( www.ncbi.nlm.nih.gov ) database under the name Toxoplasma gondii TR01 (TG_TR01). The accession number of the genome obtained in this study is WOEV00000000.1. The biological sample access number is SAMN13338796. The genome of the T. gondii strain obtained in this study was compared with the reference genome, and 8312 CDSs (coding sequences), 183 tRNAs, 294 rRNAs and 8789 genes were identified. Among the 8312 CDSs, 4284 encoded hypothetical proteins (hypothetical protein CDSs/proteins of unknown function). The entire genome sequence of T gondii TR01 was compared with that of Toxoplasma gondii ME49. The results of this comparison demonstrate that the analyzed genome was 99,98% similar to the reference genome. The accession numbers of 14 chromosomes belonging to the genome sequences of T. gondii TR01 (TG_TR01) are CM019722.1, CM019723.1, CM019724.1, CM019725.1, CM019726.1, CM019727.1, CM019728.1, CM019729.1, CM019730.1, CM019731.1, CM019732.1, CM019733.1, CM019734.1, and CM019735.1. Conclusion In this study, a whole-genome sequences of T. gondii was conducted for the first time in Turkey. The analyzed strain was named T. gondii TR01. The data obtained from this study may contribute to a better understanding of T. gondii. T. gondii is an important pathogen with an unusual population structure. Although T. gondii is highly zoonotic and has a complicated life cycle, some strains of this parasite have exhibited high genetic sequence similarity, and our study supports this knowlegde. The characterization of this strain may be very useful for the scientific community of our country and may help to establish a foundation for further research investigating the genome of T. gondii.

Brucella melitensis and Brucella abortus account for almost all cases of brucellosis in Turkish population. We developed a fourplex quantitative real-time PCR (qPCR) assay for the electrophoresis-free, rapid and cost-effective differentiation of B. abortus and B. melitensis from the other Brucella spp. The 4-plex species differentiation assay was combined with a qPCR assay targeting 17 different single nucleotide polymorphism (SNP) loci in Brucella genomes. This combination resulted in a 21 Variable Genome Loci (21-VGL) qPCR assay for high resolution genotyping of B. abortus and B. melitensis. A total of 486 Brucella was analyzed using the qPCR assay to create a 21-VGL profile database. The database contained the profiles of 55 B. abortus, 352 B. melitensis, 3 B. ceti, 6 B. neotomae, 7 B. ovis, 6 B. pinnipedialis, 44 B. suis and 13 B. canis strains. The 21-VGL Brucella genotyping clearly distinguished B. abortus, B. melitensis, B. neotomae and B. ovis. The 21-VGL approach could not distinguish B. pinnipedialis from B. ceti and some B. suis genotypes from B. canis. The results revealed that more than 99% of the Brucella isolates in Turkey were B. melitensis and 21-VGL genotyping can be reduced to 8-VGL B. melitensis genotyping without any loss of genotyping resolution. To our knowledge, we introduced the fastest and the lowest-cost B. abortus and B. melitensis genotyping and species differentiation methodology in the literature.

In this study, we described the largest analysis to date conducted with VIDAS® HIV Duo Ultra assay. Additionally, we analyzed the diagnostic performance and cutoff values (TV) of HIV Duo Ultra assay and total cost analysis for HIV testing. Of 11,642 enzyme-linked immunosorbent assay (ELISA)-positive samples referred to our center for confirmation, 2000 were positive with HIV Duo Ultra, and of these, 87% were HIV-1 positive and 0.6% were HIV-1 indeterminate with the confirmatory test. Overall, the false-positivity rate was 1.75% for HIV Duo Ultra assay. The sensitivity and specificity were 100% and 99.1%, respectively, when the TV was set at the recommended cutoff value. Even increasing the cutoff value four times, sensitivity and specificity remained high, pointing out that a TV of 0.99 is highly indicative of HIV positivity. Retesting samples with HIV Duo Ultra assay decreased 80% of the confirmatory tests, revealing a significant decrease of 78% in the total costs and reporting time.