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Objective: Lung cancer, one of the most important health problems today, is the most common type of cancer that causes death in both women and men.Although A549 lung cells originating from human alveolar carcinoma cells match the type II alveolar cell phenotype, it also has many characteristics that human primary alveolar epithelial cells have.Noscapine consists of the components in the poppy somniferum (opium). It was first isolated from Papaver somniferum (opium) in 1817. It consists of the most abundant opioids found in the opium plant (up to 10% of the total composition) after morphine. It is also known as Narcotine, Nectodon, Nospen, Anarcotine and (archaic) Opiane, and S is an (-) isomer with R stereochemistry (S stereochemistry in phthalid-carbon and R in isoquinoline-carbon). Noscapine is structurally and chemically different from other opium alkaloids such as morphine, codeine, thebaine, papaverine and narcein.The aim of the study the ınvestıgatıon of the apoptotıc and antıangıogenıc effects of noscapine ın human lung cancer (A549) cells.Materials and Methods: In the study, concentrations of 10 ppm, 15 ppm, 20 ppm, 25 ppm, 40 ppm, 50 ppm, 60 ppm, 65 ppm, 70 ppm, 75 ppm, 80 ppm, 90 ppm and 100 ppm were used in the proliferation experiment proportion of vitality values. It was observed that it decreased and the LD50 value was determined as 40 ppm. Statistical analysis used: Statistical analysis of the analyzes was performed using SPSS Statistics 20,0 program.Results: VEGF values decreased at 20 ppm, 40 ppm and 80 ppm noscapine concentrations compared to the control group. There was a significant decrease in PARP values at 80 ppm.Conclusions: As a result of the findings; It is thought that concentrations of noscapine 10 ppm, 20 ppm and 40 ppm can reduce angiogenesis and prevent metastasis by lowering VEGF levels. PARP levels decreased at all noscapine concentrations but the most significant difference was seen at 80 ppm noscapine concentration., Giriş ve Amaç: Günümüzün en önemli sağlık sorunlarından biri olan akciğer kanseri hem kadınlarda hem de erkeklerde en sık ölüme neden olan kanser türüdür.İnsan alveolar karsinom hücrelerinden kaynaklanan A549 akciğer hücreleri, tip II alveolar hücre fenotipiyle eşleşmesine rağmen, insan primer alveolar epitel hücrelerinin sahip olduğu birçok özelliğe de sahiptir.Noskapin, haşhaş somniferum (afyon) içindeki bileşenlerden oluşur. İlk olarak 1817'de Papaver somniferum'dan (afyon) izole edilmiştir. Morfinden sonra afyon bitkisinde (toplam bileşimin %10'una kadar) bulunan en bol opioidlerden oluşur. Narcotine, Nectodon, Nospen, Anarcotine ve (arkaik) Opiane olarak da bilinir ve S, R stereokimyasına sahip bir (-) izomerdir (fitalid-karbonda S stereokimyası ve izokinolin-karbonda R). Noskapin yapısal ve kimyasal olarak morfin, kodein, tebain, papaverin ve narsein gibi diğer afyon alkaloidlerinden farklıdır. Bu çalışmanın amacı, insan akciğer kanseri (A549) hücrelerinde noskapin'in apoptotik ve antianjiogenik etkilerinin araştırılmasıdır.Gereç ve Yöntemler: Çalışmada 10 ppm, 15 ppm, 20 ppm, 25 ppm, 40 ppm, 50 ppm, 60 ppm, 65 ppm, 70 ppm, 75 ppm, 80 ppm, 90 ppm ve 100 ppm konsantrasyonları kullanılmıştır. Bulgular: Canlılık değerlerinin çoğalma deneyi oranı. Düştüğü gözlendi ve LD50 değeri 40 ppm olarak belirlendi. Kullanılan istatistiksel analiz: Analizlerin istatistiksel analizi SPSS Statistics 20,0 programı kullanılarak yapıldı. Bulgular: VEGF değerleri 20 ppm, 40 ppm ve 80 ppm noskapin konsantrasyonlarında kontrol grubuna göre azaldı. 80 ppm'de PARP değerlerinde önemli bir düşüş oldu.Sonuç: Bulgular sonucunda; Noskapin konsantrasyonlarının 10 ppm, 20 ppm olduğu düşünülmektedir. 40 ppm, VEGF seviyelerini düşürerek anjiyogenezi azaltabilir ve metastazı önleyebilir. PARP seviyeleri tüm noskapin konsantrasyonlarında azaldı, ancak en önemli fark 80 ppm'de görüldü.

Introduction: The assessment of the clonal spread of methicillin resistant Staphylococcus aureus (MRSA) in nosocomial and community-acquired infections through characterization of the isolates is critical for tracking the evolution of the epidemics, implementing effective control measures, and preventing future outbreaks of MRSA. In this context, it is aimed with this study to determine the clonal relationships between the S. aureus isolates obtained from the patients receiving treatment in the intensive-care units of a state hospital in Turkey. Methodology: A total of 80 MRSA isolates obtained from the patients receiving treatment in three different intensive-care units were analyzed for their antibiotic susceptibilities, pulsed-field gel electrophoresis profiles, and multilocus sequence types. Results: The dendrogram of the pulsed-field gel electrophoresis profiles revealed two major pulsed-field gel electrophoresis pulsotypes: A and B, which were further divided into two (A1 and A2) and four (B1-B4) subgroups, respectively. Multilocus sequence typeanalysis indicated that all isolates belonged to a single MRSA clone, sequence type 239. No significant difference was found between the antibiotic sensitivity profiles of strains isolated from different intensive-care units. All of the strains were sensitive to linezolid and vancomycin. Conclusions: It was concluded that the MRSA strains isolated from the patients receiving treatment at the intensive-care units of the hospital constituted two major pulse-field types and belonged to the ST239 lineage, one of the most extensively distributed MRSA lineages throughout the world.

From the family Enterobacteriaceae is Escherichia coli ( E. Coli) is a pathogenic bacterium that is becoming increasingly important, especially in hospitals, common social areas. Thanks to the broad-spectrum beta-lactams (ESBL) they produce, they are usually multi-resistant and are common in intestinal and urinary tract infections. It is of great importance to reduce cross-contamination from public areas and to examine and reveal the genotype structure of the bacteria in question, i.e. to reach fingerprints, subtype sequences of strains. 50 E. Coli strains selected in the study were typified by Pulse field gel electrophoresis.

A novel coronavirus (SARS-CoV-2) outbreak, responsible for a pneumonia-associated respiratory disorder (COVID-19), has started in early December 2019 in Wuhan, China, and has rapidly spread around the world. Rapid and accurate diagnostic testing plays a crucial role in tackling the COVID-19 pandemic. In this study, it was aimed to compare 5 primer sets designed to amplify different regions for the detection of SARS-CoV-2 and to perform sequence analysis. Conventional RT-PCR was carried out using primers targeting different regions of the virus genome including ORF1ab, Envelope (E), RNA-dependent RNA polymerase (RdRp), Spike (S) and Nucleocapsid (N) genes for the diagnosis of COVID-19. DNA sequence of ORF1ab gene from each sample were compared with the DNA sequence data of SARS-CoV-2 stored in the GenBank and ORF1ab phylogenetic tree was constructed. The amplicon sizes of ORF1ab, S, E, N and RdRp genes were 588 bp, 440 bp, 145 bp, 323 bp and 196 bp, respectively. The SARS-CoV-2 RNA was detected from 74% of total samples from RdRp gene, 87% for N gene, 74% for S gene, 61% for E gene and 82% for ORF1ab region. The ORF1ab sequences of SARS-CoV-2 from 82 patients were had 100% identity to the sequence of Wuhan isolate and among themselves. The phylogenetic analysis revealed that all isolates formed a cluster. The results of this study suggest that the N region is the best for SARS-CoV-2 identification.

The aim of this study is to determine the relationship between the job satisfaction levels of public sector health workers and their organizational commitment. The research was conducted with the participation of health sector employees. Job Satisfaction Scale and Organizational Commitment Scale were used. In the study, job satisfaction and organizational commitment levels were also investigated in terms of demographic variables. The obtained data were analyzed by statistical methods. Descriptive Statistics, ANOVA, t test, correlation and regression analysis were used. According to the findings; there is a negative relationship between emotional continuance and external satisfaction. There is positive correlation between continuance commitment internal satisfactions, and negatively significant relationship between continuance commitment and external satisfaction. In addition, a significant negative correlation was founded between normative commitment and internal satisfaction, positive significant relationship between normative commitment and external satisfaction. It was determined that continuance commitment and normative commitment variables had a significant effect on the internal job satisfaction of helthcare personnel, while emotional commitment, continuance commitment and normative commitment variables had a significant effect on external job satisfaction. It was found that demographic factors are also effective on job satisfaction and organizational commitment. ​Extended English summary is in the end ofFull TextPDF (TURKISH)file. Özet Bu çalışma ile kamu sektörü sağlık çalışanlarının iş tatmin düzeyleri ile örgütsel bağlılık düzeyleri arasındaki ilişkinin belirlenmesi amaçlanmıştır. Araştırma sağlık sektörü çalışanlarının katılımı ile gerçekleştirilmiştir. İş tatmini ölçeği ve örgütsel bağlılık ölçeği kullanılmıştır. Çalışmada ayrıca iş tatmini ve örgütsel bağlılık düzeyleri demografik değişkenler açısından da araştırılmıştır. Elde edilen veriler istatistiki yöntemler ile analize edilmiştir. Tanımlayıcı İstatistikler, ANOVA, t testi, korelasyon ve regresyon analizi kullanılmıştır. Araştırma sonucunda elde edilen bulgulara göre; duygusal bağlılık ile dışsal tatmin arasında negatif yönlü bir ilişki vardır. Devam bağlılığı ile içsel tatmin arasında pozitif yönlü, devam bağlılığı ile dışsal tatmin arasında negatif yönlü anlamlı bir ilişki bulunmaktadır. Ayrıca normatif bağlılık ile içsel tatmin arasında negatif yönlü anlamlı bir ilişki ve normatif bağlılık ile dışsal tatmin arasında pozitif yönlü anlamlı bir ilişki bulgulanmıştır. Sağlık personellerinin içsel iş tatminlerine devam bağlılığı ve normative bağlılık değişkenlerinin anlamlı birer etkisi olduğu, dışsal iş tatminlerine duygusal bağlılık, devam bağlılığı ve normatif bağlılık değişkenlerinin anlamlı birer etkisi olduğu tespit edilmiştir. Demografik faktörlerin de iş tatmini ve örgütsel bağlılık üzerinde etkili olduğu bulgulanmıştır.

Carbapenemase-producing and colistin resistant Klebsiella pneumoniae has become a worldwide healthcare problem. This study describes molecular characterization of carbapenemase-producing and colistin resistant clinical K. pneumoniae isolates.A total of 93 non-replicate carbapenem and colistin resistant K. pneumoniae were recovered from clinical specimens in a university hospital during 2017–2019. Detection of blaOXA-48, blaKPC, blaNDM-1, blaIMP, blaVIM-1 and mcr-1, -2, -3, -4, -5, -6, -7, and -8 genes was performed by PCR. The bacterial isolates were assigned to clonal lineages by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).All isolates harbored blaOXA-48 and only two isolates harbored blaOXA-48, and blaNDM-1 genes together. In colistin resistant K. pneumoniae, mcr-1 was detected in two (2.1%) isolates. Ninety three isolates of K. pneumoniae were categorized into three clusters and five pulsotypes. MLST revealed two different sequence types, ST101 (89/93) and ST147 (4/93).In our study ST101 was found to be a significantly dominant clone carrying blaOXA-48 and among our strains a low frequency of mcr-1 gene was determined. The emergence of colistin resistance was observed in K. pneumoniae ST101 isolates. ST101 may become a global threat in the dissemination of carbapenem and colistin resistance.

Objectives Appropriate antibiotic therapy and prevention of cross-contamination are the most important subjects in tuberculosis (TB) control. The aim of this study was to investigate the major phylogenetic clades and transmission rate of multidrug-resistant (MDR) Mycobacterium tuberculosis isolates (n = 200) from patients with TB in Sivas and Konya Provinces of Turkey. Methods The phylogenetic relationship among the isolates was investigated by spoligotyping method. In addition, the 24-locus mycobacterial interspersed repetitive unit–variable-number tandem repeat (MIRU-VNTR) typing method was used to reveal cross-contamination. Results Spoligotyping revealed 13 different spoligotypes. A total of 188 strains (94.0%) were included in the cluster. The most prominent spoligofamily was the T family (43.0% of strains), followed by LAM (26.0%), H (8.0%), X and S (both 6.0%) and U (5.0%). Also, 12 strains (6.0%) belonged to the Beijing profile. MIRU-VNTR results showed 176 (88.0%) different genotypes among the isolates. In total, 24 strains (12.0%) were in the cluster. Conclusions According to spoligotyping, there is a heterogeneous M. tuberculosis population in Turkey. MIRU-VNTR results showed that cross-contamination observed between MDR M. tuberculosis isolates in Turkey is controllable.

Amaç: Bu çalışma ile, yoğunbakım ünitelerinde yatan hastalardan izole edilen A. baumannii suşlarının antibiyotiklere direnç oranının saptanması ve hastane enfeksiyonu etkeni çoklu ilaç direncine sahip izolatların klonal ilişkisinin, pulsed-field jel elektroforez (PFGE) yöntemi kullanılarak gösterilmesi amaçlandı.Materyal ve Metod: Bir üniversite hastanesi; Anesteziyoloji ve Reanimasyon Yoğunbakım Ünitesi (AYBÜ), Göğüs Hastalıkları Yoğunbakım Ünitesi ve Pediatri Yoğun Bakım Ünitesi’ nde Ocak 2010-Ekim 2011 tarihleri ve AYBÜ’de Temmuz-Kasım 2012 tarihleri arasında takip edilen, A. baumanii ile oluşan, Ventilatör İlişkili Pnömoni (VİP) ve Primer Kan Dolaşımı Enfeksiyonu (PKDE) tanısı alan 69 hasta ve aynı sayıda izolat çalışmaya alındı.Bulgular: Hastaların 63 (%91) tanesi VİP, 6 (%9) tanesi ise PKDE tanısı almıştı. Tüm hastalara YBÜ yatışı boyunca en az iki invaziv girişim uygulanmıştı. Üriner kateterizasyon (%100), mekanik ventilasyon (%94,2) ve periferik venöz kateterizasyon (%91,3) en sık uygulanan invaziv girişimlerdi. Antibiyotik duyarlılıkları imipenem, kolistin ve tigesiklin için E-test, diğer antibiyotikler için disk difüzyonla çalışıldı. Tüm suşlar için en etkili antibiyotik kolistin (%98,6) idi. Daha sonra tigesiklin (%97,1) ve levofloksasin (%69,6) gelmekteydi. Suşların tamamı seftriakson, piperasilin/tazobaktam, meropenem ve imipeneme dirençli bulundu. A. baumannii izolatlarının ApaI ile kesilen genomik DNA’sına yapılan PFGE analizi ile, 69 A. baumannii suşunun 62 (%89,9)’sinin küme içinde olduğu saptandı. Bu suşlar 16 küme içinde yer almakta idi. Suşların 7 (%10,1)’si özgül PFGE profili gösterdi ve suşlar arasında 23 pulsotip saptandı.Sonuç: Çoğul ilaç dirençli A. baumannii izolatlarının kümeleşme oranının yüksek bulunması ve benzer genotipteki izolatların farklı ünitelerdeki hastalardan izole edilmesi bu bakterinin hastanemiz YBÜ’ lerinde endemik duruma geçtiğinin göstergesidir. Önlem alınmadığı takdirde A. baumannii uzun yıllar boyunca hastanelerde kalabilmekte ve hastalar arasında kolaylıkla bulaş olabilmektedir. Özellikle çapraz bulaşın önlenmesi için enfeksiyon kontrol programlarının gerekliliği ve önemi bir kez daha vurgulandı., Aim: With this study, the detection of the resistance rates of A. baumannii strains isolated from the patients in the intensive care units to the antibiotics and the demonstration of the clonal relationship of the isolates with multi-drug resistant of the factor of nosocomial infection were aimed by using the method of pulsed-field gel electrophoresis (PFGE).Material and Methods: A university hospital, 69 patients followed between January 2010-October 2011 at the Intensive Care Unit of Anesthesiology and Reanimation (ICUAR), Intensive Care Unit of Chest Diseases and Pediatric Intensive Care Unit and July-November 2012 at ICUAR and the same number of isolates formed with A. baumannii, Ventilator-Associated Pneumonia (VAP) and diagnosis of Primary Bloodstream Infection (PBI) were enrolled to the study.Findings: 63 (91%) of the patients were diagnosed with VAP and 6 (9%) of them with PBI. At least two invasive interference had been performed to all patients during the staying at the ICU. Urinary catheterization (100%), mechanical ventilation (94.2%), and peripheral venous catheterization (91.3%) were the most frequently performed invasive interferences. Antibiotic susceptibilities to imipenem, colistin and tigecycline were studied with the E-test and to the other antibiotics with the disk diffusion. Colistin was the most effective antibiotic for all of the strains (98.6%). Then, tigecycline (97.1%) and levofloxacin (69.6%) were in second place. All of the strains were resistant to ceftriaxone, piperacillin/tazobactam, meropenem, and imipenem. With the PFGE analysis of A. baumannii isolates performed to the genomic DNA cut with ApaI, it was found that 62 of the 69 A. baumannii strains (89.9%) were within the cluster. These strains were located within 16 clusters. 7 of the strains (10.1%) showed the profiles of specific PFGE and 23 pulsotypes were detected among the strains.Result: Being high of clustering rate of multidrug-resistant A. baumannii isolates and isolating the isolates in similar genotypes from the patients in different units is the indicator of these bacteria to be an endemic situation in the ICUs of our hospital. If precautions are not taken, A. baumannii has been able to remain in the hospitals for many years and can be easily transmitted among the patients. Especially for the prevention of cross-contamination, the necessity and importance of infection control programs have once again emphasized.

Bacillus cereus is an aerobic and facultatively anaerobic, spore-forming bacterium, and it is found naturally in soil and poses a risk factor for the contamination of food and foodstuffs including cereals, vegetables, spices, ready-to-eat (RTE) foods, meats, milk, and dairy products. This study determined the prevalence of B. cereus in raw poultry meat, raw cow’s milk, cheese, spices, and RTE foods in Hatay province. The study also analysed the psychrotrophic properties, toxigenic characteristics, and pulsed-field gel electrophoresis (PFGE) profiles of the isolates. The levels of contamination with B. cereus determined for cheese, raw milk, RTE foods, spices, and raw poultry meat were 16.6%, 34.2%, 42.8%, 49%, and 55.5%, respectively. B. cereus was isolated from 84 (42%) of the 200 samples analysed and the 84 isolates were verified by PCR analysis targeting the haemolysin gene specific for B. cereus. Of the total isolates, 64 (76.1%) were psychrotrophic. The toxin gene profiling of B. cereus isolates was determined by amplifying the four genes nhe, hbl, cytK, and ces. The nhe and cytK genes were most frequently detected in the isolates, while the hbl and ces genes were not found. In addition, a high genetic relationship between the isolates was detected at a 92% similarity level by PFGE analysis. In conclusion, the occurrence of both psychrotrophic and toxigenic B. cereus strains in this study indicated a potential risk for food spoilage and food poisoning.

Weeksella virosa is an atypical Gram-negative bacterium that does not grow on MacConkey agar. In this report, we present a 4-year-old female patient with Addison’s disease and end-stage renal failure secondary to focal sclerosing glomerulosclerosis. Continuous ambulatory peritoneal dialysis had been performed, and 3 months later, the patient developed fever, diarrhea, and vomiting. Peritoneal fluid culture and dialysis fluid culture were positive for W. virosa. It was identified with Phoenix (BD, USA) and confirmed via 16S rRNA sequencing. It cannot be identified by Maldi Biotyper (Bruker). The isolate was found to be resistant to cephalosporins, ciprofloxacin, and amikacin by gradient test. Intraperitoneal cefepime was initiated but since antimicrobial susceptibility testing revealed cephalosporin resistance, therapy was changed to intraperitoneal meropenem. Following the removal of peritoneal dialysis catheter, fever, abdominal distention, and vomiting were resolved. Piperacillin, aztreonam, and carbapenems can be used for empirical therapy. Antimicrobial susceptibility testing should be performed to guide the choice of treatment. Removal of peritoneal dialysis catheter is an important step of management of this infection. To our knowledge, this is the first report of W. virosa in a pediatric patient and first report from Turkey.

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.

WOS: 000484847800013, The purpose of this study was to determine the phenotypic antibiotic susceptibility patterns, extended-spectrum beta-lactamase (ESBL) genes and genotypic profiles of ESBL-positive Escherichia coli strains isolated from urine samples obtained from outpatients with urinary tract infection in Turkey. A total of 120 E. coli strains during 2017, 2018, and 2019 (40 patients per year) were examined for antibiotic susceptibility patterns by disc diffusion method, for ESBL genes using PCR and sequencing and for molecular typing by pulsed-field gel electrophoresis (PFGE) method. The isolates were evaluated for their sensitivity to 21 different antibiotics. Four different antimicrobial resistance patterns were determined according to antibiotic susceptibility status of the isolates. The beta-lactamase genes detected in the isolates were CTX-M-15 + OXA-1 (n = 14), CTX-M-15 (n = 24), TEM-1 + CTX-M-15 (n = 52), TEM1 + SHV-12 (n = 6), SHV-12 1 (n = 6), TEM-1 + CTX-M-1 (n = 6), TEM-1 + CTX-M-16 (n = 6) and TEM-1 + CTX-M-9 (n = 6). The CTX-M-15 was the most prevalent ESBL enzyme in the isolates. As a result of PFGE analysis performed by XbaI enzyme restriction process, one major PFGE profile and three main groups (Group I-I-III) were observed. While antibiotic resistance profiles of the strains showed four groups (RI-RII-RIII-RIV), PFGE band profiles showed a major group (90% similarity ratio). High ESBL production and decreased susceptibility to broad-spectrum cephalosporins were observed in E. coli strains. In addition, PFGE analysis showed high clonal similarity among E. coli isolates.

Vancomycin-Resistant E. faecium (VRE) strains from clinical specimens were identified by conventional methods before. Following the phenotype-based identification, all strains were also identified using both BD Phoenix and VITEK MS bioMerieux System. Strains were typed with the Bruker MALDI-TOF MS system, pulsed field gel electrophoresis (PFGE) and 16S rRNA gene sequencing analysis and then the sensitivity compared for each. A cut off value of 850 assigned with Bruker MALDI-TOF MS system was found to give equal sensitivity to that of PFGE. Results obtained were compared with those of molecular typing. The main advantage of MALDI-TOF MS technology over the others was the much shorter analysis time which lasted only a few hours rather than days or a whole week. Also, the Bruker MALDI-TOF MS system was used for typing and compared with the gold standard method and this study is first to report the determined cut off level for typing of VRE strains.

Background: Researching carbapenem-resistant isolates and the use of antibiotics and following infection control policies enable the identification of carbapenemase-producing bacteria and prevent their spread.Methods: P. aeruginosa isolates were recovered from Medicine Faculty of Recep Tayyip Erdoğan University between April 2015 and October 2016 and identified by conventional methods and the automated Vitek 2 Compact (BioMerieux, France) system. Antimicrobial susceptibility experiments were performed in accordance with CLSI criteria and the automated Vitek 2 Compact system. The PCR method was investigated for the presence of β-lactamase resistance genes. PFGE typing was performed to show clonal relation among samples.Results: Seventy P. aeruginosa strains were isolated from seventy patients. The median age of 70 cases was found 66 with minimum 17 and maximum 92 years old. 67.1% of the patients had contact with the health service in the last 90 days and 75.7% of the patients had received antimicrobial therapy in the previous 90 days. The most common comorbidity was cardiovascular diseases. Twenty-four (34.3%) strains were carbapenem resistant, 2 strains were multidrug-resistant except colistin, and none of the samples had colistin resistance. The gene encoding β-lactamase or metallo-β-lactamase was found in a total of 36 strains. The bla VEB gene was identified in only 1 strain alone, but in combination with other resistance genes in a total of 17 strains. While the bla PER gene was detected in 5 samples alone, it was found in 13 samples in combination with other genes. Among the genes encoding metallo-β-lactamase, the most bla NDM positive was detected (n=22), followed by 14 positive samples of bla KPC . bla IMP and bla VIM were detected in 5 and 1 samples, respectively. Also, the association of bla VEB - bla PER and bla VEB - bla KPC - bla NDM was found to be very high. Much more resistance genes and associations were detected in hospital-acquired samples than community-acquired samples, both proportionally and in terms of co-occurrence. Most of the community-associated strains were collected in the F2 clade, while most of the hospital-associated strains were collected in the G1 clade. However, no difference was found between the community and hospital-associated strains according to PFGE results. Simultaneously, other microorganisms were also isolated from patients from which these 6 P. aeruginosa strains were isolated. Of these patients, 5 patients died, except the number 70.Conclusions: The median length of stay (days) was found to be significantly higher in the group with HAI than in the group with CAI. Compared to sample 28 and 37, which carried 5 β-lactamase coding genes, the death of these 5 patients with fewer or no resistance genes showed that the coexistence of other factors - especially other microorganisms in addition to resistance genes, was important.

Mortality due to K. pneumoniae bacteremia is on rise, particularly in regions with high rates of carbapenem and colistin resistance. We aimed to define risk factors for colistin resistance and its impact on mortality. Patients diagnosed with "carbapenem-resistant K. pneumoniae (CRKp)" bacteremia between 2014 and 2018 were divided into two groups as "colistin susceptible (ColS)" and "colistin resistant (ColR)" based on broth microdilution method. Retrospective case-control study was conducted to compare characteristics and outcomes. Multiple logistic regression model was used to define independent risk factors for acquired colistin resistance and Cox proportional hazard model for 28-day mortality. A total of 82 patients (39 ColS and 43 ColR) were included. Mean age was 61.5 years, and 50 (61%) were male. Colistin resistance was significantly increased with duration of hospital stay (p = 0.007) and prior colistin use (p = 0.007). Overall, the 28-day mortality rate was 66%. Age (p = 0.014) and colistin resistance significantly increased 28-day (p = 0.009) mortality. Microbiological response to treatment within 7 days favors survival. PFGE analysis revealed an outbreak with K. pneumoniae ST78 and ST45 clones. Patients treated with combined antimicrobials had significantly lower 28-day mortality (p = 0.045) in comparison to monotherapy. However, types of combinations did not show significant superiority on each other. Colistin resistance increases 28-day mortality in CRKp bacteremia. Although combined regimens are more effective than monotherapy, existing antibacterial combinations have no apparent superiority to each other. New treatment options are pivotal.

The objectives of this study were: i) to detect the presence of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) in raw milk, cheese, beef minced meat, and chicken meat samples; ii) to evaluate the antimicrobial susceptibility of the isolates; and iii) to determine clonal relation among the isolates by using pulsed-field gel electrophoresis (PFGE) method. Therefore, a total of 160 food samples were randomly collected between August 2014 and May 2015 in Hatay province, located in the southern Turkey. Twenty (12.5%) of the samples were found to be contaminated with S. aureus. A total of 40 isolates from the 20 positive samples were confirmed to be S. aureus by multiplex PCR based on 16S rRNA and nuc gene. The mec A gene was not detected in any of the S. aureus strains. In the present study, 39 out of 40 (97.5%) isolates were found to be resistant to one or more antibiotics. All of isolates were susceptible to gentamicin, oxacillin, and vancomycin. The highest resistance rate was detected in penicillin (95%) and ampicillin (92.5%), followed by tetracycline (30%), erythromycin (20%), ciprofloxacin (12.5%). Nine major patterns were determined by PFGE. In 6 of these patterns, thirty-six strains (90%) had identical PFGE profiles.

Avian chlamydiosis, is a highly contagious, systemic disease occuring in domestic and wild birds. Chlamydia psittaci, the causative agent of the disease, is a gram-negative bacterium in the Chlamydiaceae family that can only live within the cell. The agent can be transmitted directly to humans by contact with infected animals or feces of infected animals. It can also be transmitted by inhalation of fecal dust. Since the disease has a zoonotic character, it is also important in terms of public health. By using the monoclonal antibodies against cell wall proteins (OMP) of C.psittaci, six (A-F) and two (WC and M56) serotypes were determined in mammals. The aim of this study was to investigate and genotype the presence of C.psittaci ompA gene in domestic pigeon feces grown in family management style in ten different districts in Ankara in winter and summer seasons. Within the scope of the study, 100 pigeon stool samples were collected from birdhouses in 10 different districts of Ankara (Beypazari, Haymana, Kizilcahamam, Cubuk, Pursaklar, Bala, Cankaya, Polatli, Golbasi and city center) in two different seasons. DNA extraction from fecal samples was performed by classical methods. The presence of the agent in the extracted DNA samples was investigated by polymerase chain reaction (PCR) analysis of the ompA gene. Two-way sequence analysis of the ompA gene was performed with the primers used in the study from the target DNA products amplified by PCR. The results of sequence analysis were compared with the international database and serotyping/genotyping was performed. In the study, C.psittaci ompA gene was detected in 6 (6%) samples of 100 pigeon stool samples. Among these positive samples, two were from Bala (one sample from winter, one sample from summer), two were from Haymana (one sample from winter, one sample from summer) and two were from Golbasi (one sample from winter, one sample from summer); where the same agent was isolated in the same aviaries in different seasons. In this study, no difference was found between the presence of C.psittaci in pigeon droppings and season. In addition when the sequence analysis of the isolated samples were compared with the World database; all isolates were found to be 100% genotype B and 99% genotype E. In this study, the sequence analysis of the ompA gene of C.psittaci from domestic pigeon feces was determined for the first time in Turkey. Although the presence of C.psittaci in domestic pigeons is low, it is a zoonotic bacterium and is important for the public health.

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.

Kanatlı klamidiyozisi evcil ve yabani kanatlılarda görülebilen, oldukça bulaşıcı ve sistemik bir hastalıktır. Hastalık etkeni Chlamydia psittaci, Chlamydiaceae familyasında, gram-negatif ve sadece hücre içerisinde yaşayabilen bir bakteridir. Etken insanlara, enfekte hayvanla temas ve dışkı aracılığıyla bulaşabileceği gibi etkeni içeren dışkı tozlarının solunmasıyla da bulaşabilir. Hastalık zoonoz bir karakter taşıdığı için halk sağlığı yönüyle de önemlidir. C.psittaci etkeninin hücre duvarı proteinlerine (OMP) karşı monoklonal antikorların kullanımıyla kanatlılarda altı (A-F), memelilerde iki (WC ve M56) serotip belirlenmiştir. Serotiplerde konak özgüllüğü vardır. Moleküler genotiplendirmede hücre duvarı proteinlerini kodlayan “major outer membrane protein/MOMP” ompA geni kullanılmaktadır. Bu çalışmada, Ankara’da on farklı ilçede bulunan aile işletmeciliği tarzında yetiştirilen, evcil güvercin dışkılarında C.psittaci ompA geni varlığının kış ve yaz mevsimlerinde araştırılması ve ompA geninin dizi analizi ile genotiplendirilmesi amaçlanmıştır. Çalışma kapsamında Ankara ilinde 10 farklı ilçede (Beypazarı, Haymana, Kızılcahamam, Çubuk, Pursaklar, Bala, Çankaya, Polatlı, Gölbaşı ve Merkez) bulunan kuşhanelerden iki farklı mevsimde 100 güvercin dışkı örneği toplanmıştır. Toplanan dışkı örneklerinden DNA eldesi klasik yöntemlerle yapılmıştır. Dışkıdan elde edilen DNA örneklerinde etkenin varlığı ompA geninin polimeraz zincir reaksiyonu (PCR) analizi ile araştırılmıştır. PCR ile çoğaltılan hedef DNA ürünlerinden çalışmada kullanılan primerler ile ompA geninin çift yönlü dizi analizi yapılmıştır. Dizi analizi sonuçları uluslararası veri tabanı ile karşılaştırılarak serotiplendirme/ genotiplendirme yapılmıştır. Çalışmada 100 güvercin dışkı örneğinden altı örnekte C.psittaci ompA geni tespit edilmiştir. Bu pozitif örneklerin ikisi Bala (bir kış ve bir yaz dönemi numunesi), ikisi Haymana (bir kış, bir yaz dönemi numunesi), ikisi Gölbaşı (bir kış, bir yaz dönemi numunesi) ilçelerinden olmak üzere aynı kuşhanelerden farklı mevsimlerde izole edilmiştir. Bu çalışma ile güvercin dışkılarında C.psittaci’nin varlığı ile mevsim arasında bir fark belirlenmemiştir. Ayrıca, bu çalışmada pozitif örneklerde ompA geni dizi analiz sonuçlarının Dünya veri bankası ile karşılaştırıldığında bütün izolatların %100 oranında genotip B, %99 oranında da genotip E ile uyumlu olduğu görülmüştür. Türkiye’de, ompA geninin dizi analizi ile evcil güvercin kökenli C.psittaci genotipi ilk kez bu çalışmada belirlenmiştir. C.psittaci’nin zoonoz bir bakteri olması ve evcil güvercinlerde düşük oranda da olsa bulunması halk sağlığı açısından önemlidir., Avian chlamydiosis, is a highly contagious, systemic disease occuring in domestic and wild birds. Chlamydia psittaci, the causative agent of the disease, is a gram-negative bacterium in the Chlamydiaceaefamily that can only live within the cell. The agent can be transmitted directly to humans by contact with infected animals or feces of infected animals. It can also be transmitted by inhalation of fecal dust. Since the disease has a zoonotic character, it is also important in terms of public health. By using the monoclonal antibodies against cell wall proteins (OMP) of C.psittaci, six (A-F) and two (WC and M56) serotypes were determined in mammals. The aim of this study was to investigate and genotype the presence of C.psittaci ompA gene in domestic pigeon feces grown in family management style in ten different districts in Ankara in winter and summer seasons. Within the scope of the study, 100 pigeon stool samples were collected from birdhouses in 10 different districts of Ankara (Beypazari, Haymana, Kizilcahamam, Cubuk, Pursaklar, Bala, Cankaya, Polatli, Golbasi and city center) in two different seasons. DNA extraction from fecal samples was performed by classical methods. The presence of the agent in the extracted DNA samples was investigated by polymerase chain reaction (PCR) analysis of the ompA gene. Two-way sequence analysis of the ompA gene was performed with the primers used in the study from the target DNA products amplified by PCR. The results of sequence analysis were compared with the international database and serotyping/genotyping was performed. In the study, C.psittaci ompA gene was detected in 6 (6%) samples of 100 pigeon stool samples. Among these positive samples, two were from Bala (one sample from winter, one sample from summer), two were from Haymana (one sample from winter, one sample from summer) and two were from Golbasi (one sample from winter, one sample from summer); where the same agent was isolated in the same aviaries in different seasons. In this study, no difference was found between the presence of C.psittaci in pigeon droppings and season. In addition when the sequence analysis of the isolated samples were compared with the World database; all isolates were found to be 100% genotype B and 99% genotype E. In this study, the sequence analysis of the ompA gene of C.psittaci from domestic pigeon feces was determined for the first time in Turkey. Although the presence of C.psittaci in domestic pigeons is low, it is a zoonotic bacterium and is important for the public health.

MALDI-TOF MS provides fast, easy to perform and cost-effective diagnosis in clinical microbiology laboratories, however in some cases results of MALDI-TOF MS should be confirmed with additional tests. This confirmation is especially important for causes of life-threatening infections like Neisseria meningitidis. In our laboratory, three isolates were identified as N. meningitidis by Bruker MALDI Biotyper (BD, USA) between April 2018 and March 2019 from clinical specimens of blood, sputum, and urine. 16S rRNA sequencing was performed for further investigation. Two of the isolates were identified as Neisseria subflava and only one was confirmed as N. meningitidis by sequencing. These results show that MALDI-TOF MS is not always reliable in the diagnosis of N. meningitidis and clinical microbiologists should confirm these results with additional tests. Also, clinical correlations should be determined. Accurate identification of this microorganism is very important because of the necessity of prophylactic antimicrobial usage and biosafety precautions. Enlarged databases of Neisseria species are needed to overcome this problem.

Vancomycin-resistant enterococcus (VRE) is a global threat to public health. Knowledge about the occurrence of vanA-carrying enterococci in broiler and environmental samples is important as antibiotic resistance can be transferred to human bacteria. The aim of this study was to investigate the presence of VRE in broiler cloacal and environmental (house) samples and to genotype the isolates. In this study, 350 swabs were collected from broiler farms. All samples were plated onto enterococcus selective agar containing 6 mg/L vancomycin and 64 mg/L ceftazidime. Minimum inhibitory concentration (MIC) values were determined for vancomycin and teicoplanin. Vancomycin-resistant Enterococcus faecium (VREfm) was isolated from 6 out of 300 (2%) broiler cloacal samples and 13 out of 50 (26%) house samples. All E. faecium isolates had vanA genes. All VREfm isolates (19 isolates) were confirmed to be 95% similar to each other. In conclusion, although 20 years have passed since the ban on avoparcin in Turkey, the present study shows that VREfm isolates are still present in broiler production and especially in broiler houses, and most importantly, a major VREfm clone was isolated from broiler cloacal and house samples.

We report a rare case of necrotizing fasciitis of the abdominal wall caused by Hungatella effluvii and Streptococcus constellatus. Necrotizing fasciitis has high mortality, so early diagnosis and aggressive treatment are essential for good clinical outcome. Identification of the microbial contribution to these infections is crucial for targeted antibiotic treatment.

Acinetobacter baumannii, an aerobic, non-motile, gram-negative bacterium is an important nosocomial pathogen which shows resistance to the most antibiotics. Carbapenems are the most commonly used antibiotics for the treatment of infections caused by this pathogen. However the emergence of resistance against carbapenems in an increasing rate generates serious problems for antimicrobial therapy. The aims of this study were to detect the antibiotic susceptibility, and the presence of blaOXA resistance genes of clinical A.baumannii isolates and to determine the clonal relationship between these isolates. A total of 79 A.baumannii strains isolated from various clinical specimens (37 respiratory tract samples, 11 wound, 10 blood, 8 catheters, 6 tissue, 5 urine, 2 abscess) of the patients admitted to Mersin University Medical School Hospital between May 2012-January 2013, were included in the study. The isolates were identified by conventional methods and Vitek®2 Compact automated system. Antibiotic susceptibilities of the isolates were determined by Kirby-Bauer disk diffusion method and evaluated according to CLSI criteria. The presence of blaOXA-51, blaOXA-23, blaOXA-24, blaOXA-48 and blaOXA-58 genes were detected by an in-house polymerase chain reaction (PCR), and the clonal relationship between the isolates were identified by pulsed-field gel electroforesis (PFGE) using the ApaI restriction enzyme. In our study, all of the isolates were susceptible to colistin, while the resistance rates against piperacillin-tazobactam, ciprofloxacin, imipenem, meropenem, cefoperazone/sulbactam, trimethoprim-sulfamethoxazole, ceftazidime, levofloxacin, gentamicin, tetracycline, ampicillin-sulbactam, amikacin, netilmicin and tigecycline were 97.5%, 96.2%, 94.9%, 94.9%, 93.6%, 91.1%, 88.6%, 86%, 83.6%, 77.2%, 69.6%, 55.7%, 27.8% and 3.8%, respectively. All the isolates were identified as A.baumannii with the OXA-specific PCR and OXA16S rDNA sequence analysis. All of the isolates (100%) harboured blaOXA-51 and 71 (89.9%) harboured blaOXA-23 gene, however they were all negative for blaOXA-24, blaOXA-48 and blaOXA-58 genes. According to PFGE results 10 pulsotypes were identified, of these eight pulsotypes formed 77 (97.5%) similar strains with indistinguishable PFGE profiles ranging between 3-30 [A (n= 30), B (n= 20), C (n= 9), D (n= 5), E (n= 4), F (n= 3), G (n= 3), H (n= 3)]. When compared with the other clones, clones A and B were dominant among the samples and they have exhibited high level of antibiotic resistance. The rest two pulsotypes [I (n= 1), J (n= 1)] were in close relation with the main cluster. No common outbreak isolate was detected, but the relationship between the majority of the strains pointed out that there was a cross contamination problem in our hospital. In conclusion blaOXA-51 and blaOXA-23 were detected as predominant genes responsible from carbapenem resistance in our clinical A.baumannii strains, and it was considered that the high prevalence of clones A and B may constitute a threat in terms of hospitalized patients.

Introduction: Stenotrophomonas maltophilia, which is able to form a biofilm, has mostly been related to catheters when it is the agent in hospital infections; these infections generally present as bacteremia and pneumonia, which may progress with complications and result in death. Methodology: The study included 153 S. maltophilia strains isolated from clinical samples sent to our hospital laboratory between 1 January 2014 and 30 June 2018. The bacteria were identified and their antibiotic sensitivity was determined using the VITEK-2 automated system. PFGE (Pulsed Field Gel Electrophoresis): The strains isolated from 34 patient clinical samples and from 1 patient bedcover were taken for PFGE examination. Results: The TMP/SXT and levofloxacin sensitivity of 153 S. maltophilia strains was examined. TMP/SXT resistance was determined to be 39% and levofloxacin resistance at 5%. Among 35 S. maltophilia strains, seven genotypes were identified using the PFGE method. While three strains showed a specific genotype profile, the other 32 were determined to consist of four clusters. The cluster rate was therefore 91.4% (32/35). Conclusions: There was a clonal relationship between the vast majority of the 35 S. maltophilia isolates, which suggests that there was a cross-contamination problem in the hospital. One strain (#4) was identified by dendrogram analysis showed a high rate of similarity to the other strains and was determined to be the common source of the cross-contamination.

WOS: 000469890500001, PubMed: 30853450, Many reports have been published on the suspected vertical transmission of Encephalitozoon cuniculi; however, prior to 2003, these reports were based on circumstantial evidence, such as histopathological, immunohistochemical, or serological diagnosis of the infection. In 2003, vertical transmission of the parasite was confirmed by detection of E. cuniculi DNA in fetuses with the nested polymerase chain reaction (PCR) technique. However, the passage of the parasite to eyes of fetus during the intrauterine stage still requires verification. In the current study, natively infected with parasite spores female rabbits were mated with non-infected males. All resulting offspring that died before ten postpartum days were investigated using molecular techniques to confirm the intrauterine transmission of the parasite to the offspring' eyes. In total, 119 DNA samples from rabbit offspring tissues were collected from blood, kidney, brain, eye (both eyes were used as single samples), lung, placenta, liver and heart were used for PCR. Parasitic DNA in the eyes of offspring was detected (54%) 6 of 11 naturally seropositive mother rabbits. PCR results were found to be positive for the eyes of 63% (19/30) of the offsprings from seropositive rabbits. Therefore, mother rabbits naturally infected with E. cuniculi showed the molecular presence of the parasite in their offspring' eyes. Sequence analysis confirmed the partial DNA sequence data of E. cuniculi and blast analysis identified the agent as genotype I. These results confirm transmission of E. cuniculi to rabbit offspring' eyes in the intrauterine period. This is the first molecular evidence to show ocular transmission of the infection via an intrauterine route in rabbits.

The most effective method for monitoring country-level drug resistance frequency and to implement the necessary control measures is the establishment of a laboratory-based surveillance system. The aim of this study was to summarize the follow up trend of the drug-resistant tuberculosis (TB) cases, determine the load of resistance and evaluate the capacities of laboratories depending on laboratory quality assurance system for the installation work of National Tuberculosis Laboratory Surveillance Network (TuLSA) which has started in Ankara in 2011. TuLSA studies was carried out under the coordination of National Tuberculosis Reference Laboratory (NRL) with the participation of TB laboratories and dispensaries. Specimens of TB patients, reported from health institutions, were followed in TB laboratories, and the epidemiological information was collected from the dispensaries. One isolate per patient with the drug susceptibility test (DST) results were sent to NRL from TB laboratories and in NRL the isolates were rechecked with the genotypical (MTBDRplus, Hain Lifescience, Germany) and phenotypical (MGIT 960, BD, USA) DST methods. Molecular epidemiological analysis were also performed by spoligotyping and MIRU/VNTR. Second-line DST was applied to the isolates resistant to rifampin. A total of 1276 patients were reported between January 1st to December 31th 2011, and 335 cases were defined as "pulmonary TB from Ankara province". The mean age of those patients was 43.4 ± 20 years, and 67.5% were male. Three hundred seventeen (94.6%) patients were identified as new cases. The average sample number obtained from pulmonary TB cases was 3.26 ± 2.88, and 229 (68.3%) of them was culture positive. DST was applied to all culture positive isolates; 90.4% (207/229) of cases were susceptible to the five drugs tested (ethambutol, isoniazid, pyrazinamide, rifampicin, streptomycin). Eight (3.5%) of the isolates were multidrug-resistant (MDR-TB), while no extensively drug-resistant strains were detected. MDR-TB is likely to occur in 63.3 times more among previously treated cases, and 73.3 times more in legal aliens. The achievement of therapy among pulmonary TB cases was 91.9%. Spoligotyping performed for 221 M.tuberculosis complex isolates, showed that all strains were clustered in nine groups. SIT 41 (105/221; 47.5%) was the most frequent spoligotype detected, and clustering rate based on MIRU-VNTR results were found as 16.3%. All of the clustered strains were sensitive while all of MDR-TB isolates showed specific MIRU-VNTR profiles. In conclusion, TuLSA studies started in Ankara in 2011 and the system is still expanding in the country. Our data obtained with TuLSA have been published as a regional surveillance data in the WHO Global Tuberculosis Report 2011, and as a national surveillance data in Global Tuberculosis Report 2012.

Background: Production of extended-spectrum beta-lactamase (ESBL) is one of the antibiotic resistance strategies in the bacteria. Extended spectrum beta-lactamase producing Escherichia coli (E. coli) infections alarmingly increased in recent years in Turkey. Objectives: The current study aimed at determining antibiotic resistance and genotypic profiles of ESBL-positive E. coli isolates. Methods: Forty-five ESBL-positive E. coli species were isolated from a variety of units both at the Mevlana University Foundation Hospital and the Mevlana University Medical Center at Konya province in Turkey from December 2013 to December 2014. Antibiotic resistance profile was determined by the Kirby-Bauer disk diffusion method. Genotypic profile was determined by pulsed-field gel electrophoresis (PFGE) Results: The rate of ESBL production in E. coli strains was 13.1%. The isolates were highly resistant to penicillins, cephalosporins, and monobactams, while very low resistant to carbapenems. Four PFGE profiles were identified: profile A (2%), profile B (2%), profile C (67%), and profile D (29%). Profile C, the most commonly identified profile, possessed 6 subprofiles (profiles C1-C6) with more than 85% clonal similarity; Profile C2 was the commonest identified subprofile of profile C (27%). Conclusions: Extended spectrum beta-lactamase producing E. coli strains were highly resistant to beta-lactam antibiotics. WOS:000428203400004 Q4

Summary Introduction Trichosporon asahii is the most common species that causes trichosporonosis. Materials and methods In the present study, a collection of 68 T. asahii strains recovered from hospitalized patients urine samples between 2011 and 2016 was examined. T. asahii strains were identified by sequencing the intergenic spacer 1 region (IGS1) and genotyped. In addition, proteinase, phospholipase, esterase, haemolytic activity, and biofilm formation of a total of T. asahii strains were investigated. Results The predominant genotype was 1 (79.3%) and followed by 5 (8%), 3 (6.9%), 6 (3.4%), 4 (1.1%), 9 (1.1%). In none of the 68 strains, proteinase and phospholipase activities could be detected, while all were found to be esterase positive. Biofilm production and hemolytic activity were detected in 23.5 and 97% respectively. Discussion Our results indicated that six genotypes were (1, 5, 3, 6, 4, 9) present among T. asahii strains and no property was found to associate with a genotype, in terms of virulence factors.

Background: Brucellosis is a zoonotic disease caused by Brucella species. Although brucellosis is considered as an occupational disease in adults, recently it has become an infectious disease affecting all age groups, including children. Molecular epidemiological studies are crucial for control and treatment of disease in children. Objectives: This study aimed at identifying Brucella species, to detect antibiotic susceptibilities and define transmission dynamics between the Brucella isolates in children. Methods: A total of 77 Brucella isolates were identified by conventional and polymerase chain reaction methods. Anti - biotic susceptibilities were investigated by E - test strips. The isolates were genotyped by using multiple locus variable number tandem repeat analysis (MLVA) (MLVA - 16 Orsay), including 8 mini - satellite (panel 1) and 8 microsatellite (panel 2A and 2B) markers. Results: The mean age was 9.14 ± 3.4 years. All patients had been consuming unpasteurized milk. All isolates were Brucella melitensis biovar 3. Only 2 isolates were resistant to ceftriaxone, while the other isolates were susceptible to other antimicrobial agents. The MLVA - 16 typing revealed 42 MLVA profiles. Eighteen profiles included 2 or more isolates, indicating a clustering rate of 66.7%. Twenty - four isolates showed a unique profile. Single locus, double locus, and 3 locus variants were detected in 32, 26, and 15 isolates, respectively. Bruce 30, Bruce 16, Bruce 9, Bruce 7, and Bruce 4 were highly discriminatory loci, respectively. All strains were defined as genotype 122, according to MLVA - 11, and genotype 43 according to MLVA - 8, and were in the Eastern Mediterranean genotype. Conclusions: High clustering rate revealed that brucellosis among the children mainly resulted from common sources. Controlling animal movements and avoiding contaminated milk products have an importance to interrupt spread of brucellosis in children.

Objective: Enterococci are the second most common cause of nosocomial urinary tract and wound infections, also third most common cause of nosocomial bacteremia. Currently, especially vancomycin-resistant enterococci (VRE) are one of the significant pathogens that cause nosocomial infections and increase mortality, morbidity, and healthcare costs. Therefore prevention and control of the nosocomial VRE outbreaks and epidemiological analysis of the infection are important. Pulsed-Field Gel Electrophoresis (PFGE) is accepted as a “gold standard” method in the molecular epidemiological analysis of enterococcal infections. The aims of this study are to determine the clonal relationship among the nosocomial enterococcal isolates and the rate of cross-contamination between them. Method: Thirty-six Enterococcus strains isolated from hospitalized patients with nosocomial infection in different clinics of Dicle University Hospital between November 2010 and June 2012 were included in this study. A total of 36 isolates were obtained from various clinical samples including urine (n=18), blood (n=6), bronchoalveolar lavage (BAL) fluid (n=5), wound biopsy sample (n=5), vaginal smear (n=1) and catheter tip (n=1). Nine of the thirty-six isolates were VRE. Isolation and identification of the isolates were conducted in the OZET Amac: Enterokoklar hastaneden kaynaklanan uriner

Accurate identification of viridans group streptococci (VGS) frequently encountered as a causative agent of infective endocarditis is always a challenge for the clinical microbiology laboratory. Clinical microbiology laboratories generally use semi automatic/full automatic systems, molecular methods and also conventional methods for the identification of these bacteria. There are recent published studies that have used MALDI-TOF (Matrix Assisted Laser Ionization Mass Spectrometry-Time of Flight) systems in the identification of VGS. The aim of the study was to compare the performance of the conventional methods, semi automatic and MALDI-TOF MS system used in identification of VGS in oral microbiota of persons under the risk of infective endocarditis, with the gold standard method 16S rRNA sequence analysis and to create a diagnosis algorithm for the identification of VGS in clinical microbiology laboratories according to the obtained data. The study was conducted with 51 VGS strains isolated from oral microbiota of the patients with rheumatologic cardiac, valve and/or prosthetic valve diseases, under the risk of development of infective endocarditis, who have admitted to Ankara Numune Training and Research Hospital, Department of Cardiology, between February-June 2015. Standard microbiology procedures, optochin susceptibility and bile solubility tests were done for the isolation of bacteria. Bacteria were also identified with APISTREP (bioMerieux, France) and MALDI-TOF MS Bruker Microflex (Bruker Biotyper; Bruker Daltonics, Bremen, Germany) methods. BSF-8 (5'-AGAGTTTGATCCTGGCTCAG-3') and BSR-534(5'-ATTACCGCGGCTGCTGGC-3') primers were used in the 16S rRNA sequence analysis of bacteria. ABI PRISM 3100 Avan t Genetic Analyzer (Applied Biossytems, Foster City, CA, USA) were used for the sequence analysis. Electropherograms were analyzed in SeqScape Software (Applied Biosystems, Foster City, CA, USA) and compared with the reference sequences in GenBank with BLASTN (NCBI). According to the result of optochin and bile solubility tests, with API STREP system, 16 (31,37%) of the isolates were identified as Mitis group, 15 (29.41%) as Anginosus group, 9 (17.5%) as Salivarius group, 7 (13,73%) as Sanguinis group and 4 (7.84%) as Bovis group among optochin and bile resistant alpha hemolytic streptococci. Moreover, of the same isolates 20 (39.22%) were identified as Mitis group, 14 (27.45%) as Anginosus group, 13 (25.49%) as Salivarius group and 4 (7.84%) as Sanguinis group with MALDI-TOF system. In the identification with 16S rRNA, 25 (49.02%) of the isolates were identified as Mitis group, 13 (25.49%) as Anginosus group, 12 (23.53%) as Salivarius group and 1 (1.96%) as Sanguinis group. According to the results, it was determined that 33 (64.70%) of the isolates identified in MALDI-TOF MS system and 31 (60.78%) of the isolates identified in API STREP system were compatible with 16S rRNA sequence analysis method. For Mitis group, API STREP test sensitivity was 48.00% and specificity was 84.62% and MALDI-TOF system sensitivity was 80.00% and specificity was 100%. As VGS identification is a complicated process, we believe a single method will be insufficient for the identification of these isolates in clinical microbiology laboratories. We suggest that MALDI-TOF system can be used for VGS diagnosis, however, optochin test and/or molecular methods should also be included in the diagnosis algorithm when necessary.

Acinetobacter baumannii which is a significant cause of nosocomial infections, increases the rate of morbidity and mortality in health care settings especially in intensive care units (ICUs). The aim of this study was to determine the antibiotic resistance profiles of A.baumannii strains isolated from blood cultures of inpatients from different ICUs, wards and hospital environment and evaluate their clonal relationships and epidemiologic features. A total of 54 A.baumannii strains (47 from the blood cultures and 7 from the hospital environment), identified between 01 January 2012-28 December 2012 at the Clinical Microbiology Laboratory of Ankara Numune Training and Research Hospital, Turkey, were included in the study. Identification of A.baumannii isolates and their antimicrobial [sulbactam-ampicillin (SAM), piperacillin (PIP), piperacillin-tazobactam (TZP), ceftazidime (CFZ), cefoperazone-sulbactam (SCF), cefepime (CEF), imipenem (IMP), meropenem (MER), amikacin (AMK), gentamicin (GEN), netilmicin (NT), ciprofloxacin (CIP), levofloxacin (LVF), tetracycline (TET), tigecycline (TG), colistin (COL), trimethoprim-sulfamethoxazole (SXT)] susceptibility testing were performed by Vitek 2 (bioMérieux, France) system. The clonal relationship between the A.baumannii isolates was analysed by pulsed-field gel electrophoresis (PFGE). In our study colistin, tigecycline and netilmicin were found to be the most effective agents against A.baumannii isolates. All of the clinical isolates (n= 47) were found susceptible to COL, however all were resistant to SAM, PIP, TZP, CEF, IPM, CFZ, MER and CIP. While 1.85%, 14.8%, 14.8%, 16.6%, 59.2% and 22.2% of the isolates were susceptible to SCF, AMK, NT, GEN, TG and SXT, respectively; 1.85%, 1.85%, 9.2%, 16.6%, 38.8% and 27.7% of the isolates were intermediate to SCF, TET, AMK, NT, LVF and TG, respectively. Similarly, all of the environmental A.baumannii isolates (n= 7) were resistant to SAM, PIP, TZP, CFZ, CEF, IPM, MER and CIP, and all were susceptible to TG and COL. The resistance rates of the environmental isolates to SCF, AMK, GEN, NT, LVF, TET and SXT were determined as 57.1%, 85.7%, 85.7%, 28.8%, 28.6%, 85.7% and 57.1%, respectively. PFGE analysis done by the use of ApaI enzyme revealed the presence of one major clone. Dendogram analysis indicated that environmental and clinical isolates were in the same clone indicating that the outbreak was possibly originated from the same internal ICUs. Our data emphasized that multidrug resistant A.baumannii isolates were quite common in our hospital, and enviromental cross-contamination throughout the year was confirmed by molecular methods. Despite the precautions such as continous education on effective hand washing, use of gloves and hospital cleaning, established in our hospital, this single clonal spread was attributed to staff shortage and poor adherence to infection control rules. In conclusion, for the prevention of dissemination of multidrug resistant A.baumannii strains and control of nosocomial infections, infection control strategies should be established and strict compliance to these rules should be provided.

This study was made for defining some microbiological and chemical properties of mechanically deboned broiler meats. For this; a hundred mechanically seperated broiler meat were used, as a material. Mean value of dry matter, humidity, protein, lipid, ash and pH of deboned chicken meats were; 36.10%, 63.89%, 14.04%, 20.18%, 1.09% and 6.6 respectively. At research, calcium and phosphorus analysis have been made by Inductively Coupled Plasma, ICP and mean calcium and phosphorus values were 674.01 mg/kg and 503.38 mg/kg. According to microbiological analysis results; mean aerob mesophile total viable count 6.64 log cfu/g, Enterobacteriaceae spp. 3.95 log cfu/g, Micrococcus/Staphylococcus 5.12 log cfu/g, Pseudomonas spp. 4.24 log cfu/g, yeast/mold 2.19 log.cfu/g. Analysis of coliform group bacteria and E.coli has been made according to MPN techniques. Number of coliform bacteries were, Bu çalışma, mekanik olarak ayrılmış broiler etlerinin (MABE) bazı mikrobiyolojik ve kimyasal özelliklerinin belirlenmesi amacıyla yapılmıştır. Bu amaçla materyal olarak 100 adet mekanik olarak ayrılmış kanatlı eti kullanılmıştır. Mekanik olarak ayrılmış broiler etlerinin kuru madde, rutubet, protein, yağ, kül ve pH ortalama değerleri sırasıyla % 36.10, % 63.89, % 14.04, % 20.18, % 1.09 ve 6.6 olarak saptanmıştır. Araştırmada, kalsiyum (Ca) değeri 674.01 mg/kg ve fosfor (P) değeri ise 503.38 mg/kg olarak ölçülmüştür. Mikrobiyolojik analiz sonuçlarına göre aerob mezofil genel canlı sayısı 6.64 log kob/g, Enterobacteriaceae spp. 3.95 log kob/g, mikrokok/stafilokok 5.12 log kob/g, Pseudomonas spp. 4.24 log kob/g, maya/küf 2.19 log kob/g olarak saptanmıştır. Koliform bakteri ve E.coli sayısı

Pseudomonas aeruginosa is an important nosocomial pathogen that causes opportunistic infections and hospital outbreaks. During October 2012, carbapenem-resistant P.aeruginosa strains with similar antibiotic resistance patterns, were isolated from specimens sent from the intensive care and plastic surgery units in our hospital. Thus a hospital outbreak was suspected. The microbiology laboratory database was retrospectively searched and all strains of P.aeruginosa isolated during the four month period, starting with the initial carbapenem-resistant strain in August 2012, was evaluated as a hospital outbreak. The aim of this study was to define the outbreak by investigating the clonal relationship between the strains, to detect the potential environmental sources and to evaluate the period of the outbreak, risk factors and the efficiency of infection control measures. The study was conducted between August-November 2012. Twenty patients with carbapenem-resistant P.aeruginosa (CRPA) positive cultures were included in the study. The control group consisted of 22 patients with carbapenem-susceptible P.aeruginosa (CSPA) positive cultures. The clonal relationship between 26 CRPA strains was studied by pulsed-field gel electrophoresis (PFGE). The PFGE results indicated that CRPA strains in our hospital were not related to a single clone, however, there were four major clones composed of four to eight strains. Logistic regression analysis indicated that the risk increased 15.7 fold (95% CI: 1.19-207.76) by the use of carbapenem, 76.8 fold (95% CI: 2.03-2901.30) by surgical procedures and 0.787 fold (95% CI: 0.63-0.97) by the duration of hospital stay. Surveillance cultures from health-care personel and the environment performed in course of the outbreak, yielded no growth of a strain with the similar antibiotic resistance pattern. The spread of CRPA has been controlled by the use of effective precautionary measures, regressing the isolate number to 0-1 strain/month. Since CRPA infections have high mortality and lack therapeutic alternatives, they should be regarded among the priorities of the infection control programmes. This study has enabled to test the effectiveness of the infection control program, to make plans for the possible future outbreaks and to train the staff.

Acinetobacter baumannii, an aerobic, non-motile, gram-negative bacterium is an important nosocomial pathogen which shows resistance to the most antibiotics. Carbapenems are the most commonly used antibiotics for the treatment of infections caused by this pathogen. However the emergence of resistance against carbapenems in an increasing rate generates serious problems for antimicrobial therapy. The aims of this study were to detect the antibiotic susceptibility, and the presence of bla

Background: Colistin-resistant Pseudomonas aeruginosa (P. aeruginosa) has been defined as pandrug-resistant (PDR) strain. Outbreaks of PDR P. aeruginosa especially in pulmonary tract infections due to contaminated bronchoscopes have rarely been reported. The emergence of pandrug-resistant strains in both CF (Cystic Fibrosis) and non-CF clinical isolates over recent years remains of a great concern. Hospital wards contaminated with PDR P. aeruginosa infection, must be shot down until their eradication. Health Authorities must be informed immediately and infection control strategies must be implemented. Aim: To report such an outbreak and modify the infection control strategy in an academic hospital in Ankara Turkey. Methods: From October to December 2013, PDRPseudomonas aerogionsa were identified from bronchial cultures of 15 patients who had undergone bronchoscopy prior to the infection. Three batches of surveillance cultures were obtained from the environmental objects and healthcare workers related to the procedures. Pulsed-field gel electrophoresis (PFGE) was used for bacterial typing. Antimicrobial susceptibility was assessed by disc diffusion and E-test methods. Findings: A total of 70 specimens were obtained during the first surveillance operation. One Colistin-resistant P. aeroginosa was isolated from a bronchoscope. Although the disinfection protocols for bronchoscope were revised and implemented, seven additional bronchial cases were identified thereafter. The pathogen was identified from two subsequent surveillance cultures and was not eliminated until Ethylene oxide sterilization was added to the disinfection protocol. PFGE revealed that all 15 isolates from the patients and the three isolates from the bronchoscope shared a common pattern with minor variance. XbaI restriction enzyme turned out better than SpeI in interpreting bacterial pulse types with BioNumerics 6.0. The most suitable cut off value for SpeI was above 80% Dice similarity while for XbaI above 95%Dice similarity with BioNumerics 6.0. Conclusion: The outbreak of “Colistin” pan drug-resistant Pseudomonas aeroginosa was caused by a contaminated bronchoscope and was terminated by the implementation of a revised disinfection protocol for bronchoscope.

WOS: 000394568600011 The aim of this study was to determine the prevalence and clonal typing of extended-spectrum beta-lactamase (ESBL)producing Escherichia coli in healthy broilers in Turkey. Three hundred broiler cloacal samples were collected from various broiler slaughterhouses and inoculated on Levine agar plates supplemented with 2 mu g/mL cefotaxime. Suspected strains were identified using a BBL Crystal Enteric/Nonfermenter ID Kit (Becton Dickinson, USA) and ESBL production was confirmed using an ESBL phenotypic confirmatory test. ESBL types were analyzed using PCR and sequencing. Pulsed field gel electrophoresis (PFGE) was performed with XbaI for the clonal typing of ESBL-producing E. coli isolates. While 33 phenotypic ESBL-producing E. coli isolates were identified, eight of them had only the blaTEM-1. Twenty-five ESBL-producing isolates were detected. This research is the first on the investigation and detection of ESBL-producing E. coli isolates from broilers in Turkey. In this study, 8.3% ESBL-producing E. coli were isolated from the cloacal samples of broilers collected from slaughterhouses in Turkey. CTX-M-15 (80%) was the most frequently isolated ESBL type. Using PFGE analysis, it was determined that these isolates had clonal similarity. Kirikkale UniversityKirikkale University [2011/43] The authors thank Kirikkale University (project number: 2011/43) for supporting this research.

In this study, drug resistance of 28 ESBL-producing Escherichia coli isolates obtained from 144 patients hospitalized at the Yüzüncüyil University Hospital at Van (YUH), Turkey, between 2009 and 2012 were characterized by pulsed field gel electrophoresis and antibiotic susceptibility tests. Antibiotic resistance profile was determined by Phoenix automated system (BD, USA). The ratio of ESBL-producing E. coli strains was determined to be 19.4% (28 out of 144 E. coli isolates). It was determined that the anaesthesiology, paediatrics and thoracic medicine intensive care units in YUH were cross-contaminated between 2009 and 2012 by ESBL-producing E. coli strains, which is a sign of nosocomial infection in YUH. Analysis of PFGE results gave rise to two main PFGE profiles, profile-A with four subprofiles and profile-B with three subprofiles, where profile-A predominates over profile-B (14%). Comparison of the antibiotic resistance profile with the PFGE profile yielded similarities while some differences also exist due to either identical restriction enzyme cutting sites with slightly different genetic sequences in between the cutting sites or newly formed restriction enzyme cutting sites that do not affect antibiotic resistance genes. Enterobacteriaceae, particularly E. coli, have developed resistance in YUH by producing ESBLs against oxyimino and non-oxyimino cephalosporins, and penicillin-type antibiotics. Therefore, more effective antibiotics such as cefoxitin or cefoperazone-sulbactam should be used for the treatment of future nosocomial infections in YUH while hospital staff should take care with hygiene, such as hand washing.

WOS: 000365510300024 PubMed ID: 26775392 Background/aim: The purpose of the study was to evaluate the performance of the VITEK mass spectrometry (MS) (bioMerieux, France) system for the identification of Klebsiella spp. isolated from different sources. Moreover, while assessing the ability of the VITEK 2 automated expert system (AES) to recognize antimicrobial resistance patterns, the researchers have extended the study to compare VITEK 2 with the routine antimicrobial susceptibility testing method. Materials and methods: This study tested 51 Klebsiella spp. isolates that were isolated from environmental examples and clinical examples. Results of conventional methods and the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS were compared. Then, any differing results were compared against a reference 16S rRNA gene sequence, and when indicated, a recA sequencing analysis was done. Results: VITEK MS correctly identified 100% of the Klebsiella spp. isolates. There were two K. oxytoca isolates incorrectly identified to the species level with conventional methods according to the 16S rRNA gene sequencing analysis. In addition, a VITEK 2 AST-N261 card was used for the detection of extended spectrum beta-lactamases (ESBL). Using the VITEK 2 AES, ESBL positivity was found at the rate of 16.3% whereas this rate was 4.08% using the disk diffusion method. Conclusion: MALDI-TOF MS is a rapid and accurate method for the identification of Klebsiella spp. Moreover, the bioMerieux AES provides a useful laboratory tool for the interpretation of susceptibility results.

The most effective method for monitoring country-level drug resistance frequency and to implement the necessary control measures is the establishment of a laboratory-based surveillance system. The aim of this study was to summarize the follow up trend of the drug-resistant tuberculosis (TB) cases, determine the load of resistance and evaluate the capacities of laboratories depending on laboratory quality assurance system for the installation work of National Tuberculosis Laboratory Surveillance Network (TuLSA) which has started in Ankara in 2011. TuLSA studies was carried out under the coordination of National Tuberculosis Reference Laboratory (NRL) with the participation of TB laboratories and dispensaries. Specimens of TB patients, reported from health institutions, were followed in TB laboratories, and the epidemiological information was collected from the dispensaries. One isolate per patient with the drug susceptibility test (DST) results were sent to NRL from TB laboratories and in NRL the isolates were rechecked with the genotypical (MTBDRplus, Hain Lifescience, Germany) and phenotypical (MGIT 960, BD, USA) DST methods. Molecular epidemiological analysis were also performed by spoligotyping and MIRU/VNTR. Second-line DST was applied to the isolates resistant to rifampin. A total of 1276 patients were reported between January 1st to December 31th 2011, and 335 cases were defined as "pulmonary TB from Ankara province". The mean age of those patients was 43.4 ± 20 years, and 67.5% were male. Three hundred seventeen (94.6%) patients were identified as new cases. The average sample number obtained from pulmonary TB cases was 3.26 ± 2.88, and 229 (68.3%) of them was culture positive. DST was applied to all culture positive isolates; 90.4% (207/229) of cases were susceptible to the five drugs tested (ethambutol, isoniazid, pyrazinamide, rifampicin, streptomycin). Eight (3.5%) of the isolates were multidrug-resistant (MDR-TB), while no extensively drug-resistant strains were detected. MDR-TB is likely to occur in 63.3 times more among previously treated cases, and 73.3 times more in legal aliens. The achievement of therapy among pulmonary TB cases was 91.9%. Spoligotyping performed for 221 M.tuberculosis complex isolates, showed that all strains were clustered in nine groups. SIT 41 (105/221; 47.5%) was the most frequent spoligotype detected, and clustering rate based on MIRU-VNTR results were found as 16.3%. All of the clustered strains were sensitive while all of MDR-TB isolates showed specific MIRU-VNTR profiles. In conclusion, TuLSA studies started in Ankara in 2011 and the system is still expanding in the country. Our data obtained with TuLSA have been published as a regional surveillance data in the WHO Global Tuberculosis Report 2011, and as a national surveillance data in Global Tuberculosis Report 2012.

Objective: In this study, “Pulsed-Field Gel Electrophoresis” (PFGE) protocol was optimized for use Providencia stuartii\'s typing in Molecular Microbiology Research and Application Laboratory, Public Health Agency of Turkey. Methods: This protocol compared with Gram-negative bacteria PFGE protocols, SpeI enzyme is suitable for this bacterium. Electrophoresis conditions should be revealed as 1. block: initial pulse duration 5 sec, ending pulse duration 40 sec, striking angle 120°, the current 6 V/cm2, temperature 14°C, time 19 hours; 2. block: initial pulse duration 35 sec, ending pulse duration 45 sec, striking angle 120°, the current 6 V/cm2, temperature 14°C, time 5 hours; TBE buffer pH=8.4. Phylogenetic analyzes were evaluated with Bionumerics software system (version 6.01; Applied Maths, Sint-Martens-Latem, Belgium). Results and conclusion: This procedure is simple, reproducible and suitable for P. stuartii. It has the potential evaluating the outbreaks due to bacteria performed, and providing useful information about the prevalence of nosocomial infections. This optimized protocol is allowed different centers\' PFGE results to compare with other laboratories results., Amaç: Bu çalışmada; Türkiye Halk Sağlığı Kurumuna bağlı Moleküler Mikrobiyoloji Araştırma ve Uygulama Laboratuvarında Providencia stuartii\'nin tiplemesinde kullanılmak üzere optimize edilmiş bir “pulsed-field jel elektroforezi” (PFGE) protokolü sunulmuştur. Yöntemler: Gram-negatif bakterilere ait daha önceki PFGE protokolleri ile kıyaslandığında; SpeI enziminin bu bakteri için uygun olduğu ve elektroforez koşullarının; 1. blok için başlangıç vuruş süresi 5 sn, bitiş vuruş süresi 40 sn, vuruş açısı 120°, akım 6 V/cm2, sıcaklık 14°C, süre 19 saat; 2. blok için başlangıç vuruş süresi 35 sn, bitiş vuruş süresi 45 sn, vuruş açısı 120°, akım 6 V/cm2, sıcaklık 14°C, süre 5 saat; TBE tamponu pH=8.4 şeklinde olması gerektiği ortaya konmuştur. Filogenetik analizler Bionumerics yazılım sistemi (version 6.01; Applied Maths, Sint-Martens-latem, Belgium) ile değerlendirilmiştir. Bulgular ve sonuç: Optimize edilen yöntem basit, tekrarlanabilir ve P. stuartii için kullanıma uygun bulunmuştur. Çalışılan bakterilere bağlı salgınları değerlendirme ve hastane enfeksiyonlarının yaygınlık derecesi hakkında yararlı bilgiler sunma potansiyeli vardır. Optimize edilen bu protokol, farklı merkezlere ait PFGE sonuçlarının birbirleriyle karşılaştırılmasına da olanak sağlayabilir.

Bartonella genusundaki türler insanlarda ve hayvanlarda uzun süreli bakteriyemiye neden olan hücre içi bakterilerdir. Bu çalışmada Batı Karadeniz Bölgesinde yakalanan Apodemus flavicollis , A. witherbyi, A. uralensis, A. mystacinus , Myodes glareolus, Crocidura suaveolens , Rattus rattus ve Rattus norvegicus türlerinin dahil olduğu 173 küçük memelide, kan kültürü ve moleküler yöntemlerle Bartonella türleri araştırıldı. Bartonella pozitifliği küçük memelilerde kan kültürü ile %63.6 (110/173) bulundu. Kültürde izole edilen Bartonella suşlarının, sitrat sentez gen bölgesi (gltA) DNA dizi analizi ile tür tanımlamaları yapıldı. İzolatlar Bartonella taylorii, B. birtlesii, B. coopersplainsensis ve zoonotik bir tür olan B. grahamii olarak tanımlandı. The species within the genus Bartonella are intracellular bacteria causing long -lasting bacteremia in humans and animals. In this study, Bartonella spp. in 173 small mammals, which were Apodemus flavicollis , A. witherbyi, A. uralensis , A. mystacinus , Myodes glareolus, Crocidura suaveolens , Rattus rattus and Rattus norvegicus species captured from Western Black Sea Region of Turkey, were investigated by blood culture and molecular methods. The positivity of Bartonella was 63.6% (110/173) by blood culture of small mammalian. The gltA gene regions for the isolated strains were identified by DNA sequencing analysis. Isolates were identified as Bartonella taylorii, B. birtlesii, B. coopersplainsensis and a zoonotic B. grahamii.

Objective: For the detection of outbreaks caused by Proteus mirabilis, strains clonal relations are determined methods as “pulsed-field gel electrophoresis (PFGE)”. The aim of this study was optimization of a pulsed-field gel electrophoresis for molecular typing of P. mirabilis. Methods: In this study, PFGE\' protocol is optimized for use in molecular typing of P. mirabilis. Phylogenetic analyzes of strains were evaluated with Bionumerics software system (version 6.01; Applied Maths, Sint-Martens-Latem, Belgium). Results: This protocol compared with Gram-negative bacteria PFGE protocols, NotI enzyme is suitable for this bacterium. Electrophoresis conditions should be revealed as; - block 1: initial pulse duration 1 sec, ending pulse duration 30 sec, striking angle 120°, the current 6 V/cm2, temperature 14°C, time 8 hours; - block 2: initial pulse duration 30 sec, ending pulse duration 70 sec, striking angle 120°, the current 6 V/cm2, temperature 14°C, time 16 hours; - TBE, pH=8.4. Conclusion: P. mirabilis strains were typed by PFGE and Bionumerics analysis program were determined clonal relationships. The procedure was simple, reproducible and suitable for these bacteria. Also it was evaluated, because of reducing time, the solution volumes and enzymes can be economically. Outbreaks of nosocomial infections due to bacteria studied assessment and the potential to provide useful information about the degree of prevalence. This optimized protocol is allowed different centers\' PFGE results to compare with other laboratories results. J Clin Exp Invest 2013; 4 (3): 306-312, Amaç: Proteus mirabilis ile oluşan salgınların saptanması için suşlar arasında klonal ilişkinin belirlenmesine yönelik “pulsed-field jel elektroforezi (PFGE)” gibi yöntemlere ihtiyaç vardır. Bu çalışmanın amacı; Proteus mirabilis’in moleküler tiplemesi için pulsed-field jel elektroforezinin optimizasyonudur. Yöntemler: Bu çalışmada; Proteus mirabilis tiplemesinde kullanılmak üzere optimize edilmiş bir pulsed-field jel elektroforezi protokolü sunulmuştur. Suşların filogenetik analizleri Bionumerics yazılım sistemi (version 6.01; Applied Maths, Sint-Martens-latem, Belgium) ile değerlendirilmiştir. Bulgular: Gram-negatif bakteriler için kullanılan PFGE protokollerinden farklı olarak NotI enziminin bu bakteri için uygun olduğu belirlendi ve elektroforez koşulları: - blok 1 için başlangıç vuruş süresi 1 sn, bitiş vuruş süresi 30 sn, vuruş açısı 120°, akım 6 V/cm2, sıcaklık 14°C, süre 8 saat; - blok 2 için başlangıç vuruş süresi 30 sn, bitiş vuruş süresi 70 sn, vuruş açısı 120°, akım 6 V/cm2, sıcaklık 14°C, süre 16 saat; - TBE pH=8.4 olarak saptandı. Sonuç: Bu PFGE protokolünün; P. mirabilis suşlarının tiplendirilmesi ve Bionumerics yazılım sistemi ile klonal ilişkilerinin belirlenmesi için uygun olduğu anlaşıldı. Optimize edilen yöntem basit, tekrarlanabilir ve bu bakteri için kullanıma uygundur. Ayrıca süreyi kısaltması, kullanı- lan çözelti ve enzimlerin düşük hacimleriyle çalışabilmesi nedeniyle, ekonomik olarak değerlendirilmiştir. Çalışılan bakterilere bağlı salgınları değerlendirme ve hastane enfeksiyonlarının yaygınlık derecesi hakkında yararlı bilgiler sunma potansiyeli vardır. Optimize edilen bu protokol, farklı merkezlere ait PFGE sonuçlarının birbirleriyle karşılaştırılmasına da olanak sağlayacaktır

Anthrax is a zoonotic infection caused by Bacillus anthracis. Although the incidence of disease has been decreasing in Turkey, it is still endemic in some regions of the country. The cutaneous form of disease is the most common clinical form, usually benign and rarely causes bacteriemia and sepsis. In this report, a case of cutaneous anthrax complicated with sepsis where B.anthracis was isolated from blood and wound cultures, was presented. A 53-years-old male living in Bursa province (northwestern Turkey), admitted to the emergency ward with high fever and a lesion on the right arm. His history indicated that he is dealing with livestock breeding and injured his arm during slaughtering of a sick lamb. The infection started as a black colored painless ulcer with 2 cm in diameter on his right elbow. The case was hospitalized and penicillin G therapy was started with the preliminary diagnosis of anthrax. Bullous lesions occurred around the wound, got necrosis and integrated with the first lesion. Gram stained slides from the bullous lesions revealed capsulated gram-positive bacilli under light microscope. Gram-positive bacilli were also isolated from bullous lesions and the blood cultures. The isolates were identified and confirmed as B.anthracis by conventional and molecular methods. Antibiotic susceptibility tests were performed by E-test method and the isolates were found to be susceptible to ampicillin, tetracyclin, tigecyclin, ciprofloxacin, levofloxacin, gentamycin, chloramphenicol, erythromycin, clarithromycin, vancomycin, linezolid, daptomycin and rifampicin. The lesion became surrounded by an extensive erythema and edema and expanded to the whole arm. Moxifloxacin was initiated due to the fact that clinical progress. During the second week of the therapy, a black colored scar was observed on the wound while hyperemia and edema regressed. The necrotic tissue debridated to accelerate healing and rest of the skin defect was planned for reconstruction. The patient who had septicaemia and disseminated cellulitis was discharged after his treatment continued for 14 days. Multiple-locus variable-number tandem repeat analysis method was used for molecular epidemiological investigation. The strains isolated from the patient were identified as genotype (GK) 43 classified in A3.a major cluster, and found to be identical to those strains isolated from animals in different provinces located at central and eastern Anatolia of Turkey. In conclusion, the risk of sepsis must be considered in patients with cutaneous anthrax with appropriate follow-up and treatment plan.

ERTURK, AYSE/0000-0001-6413-9165 WOS: 000320094900014 PubMed: 23698489 Acinetobacter baumannii is an important pathogen in hospitalized patients, particularly those in the intensive care unit (ICU). A total of 21 A. baumannii (6 from 5 patients and 15 from environmental samples) were isolated in the ICU and the isolation room of a state hospital in June 2011. The possible source of the outbreak was investigated. A. baumannii isolates were identified using conventional biochemical tests, BBL Crystal Identification Systems, OXA-51 specific PCR, and 16S rDNA sequencing. All the isolates were multidrug-resistant, showing resistance to cephalosporins, carbapenems, fluoroquinolones, and the aminoglycoside group of antibiotics. Pulsed-field gel electrophoresis suggested that all A. baumannii isolates were derived from a common source.