The Isolates of Bacteriuria and Fungiuria: Single Center Laboratory-Based 14-Year Analysis

Introduction: Developing and changing medical practices may cause a change in the frequency, variety and susceptibility of infection agents over years. Therefore, the analysis reports of the isolates in urinary tract infections (UTIs) will provide significant contributions to the correct management of these infections. We aimed to analyze the trends of frequency, distribution and antimicrobial susceptibility of agents isolated from urine cultures of both ambulatory patients and inpatients in this study. Materials and Methods: We evaluated the results of urine cultures for a 14-year period, retrospectively. Results: A total of 49.034 isolates from 46.626 culture positive nonrepetitive specimens were included. The most common isolate was E. coli (46.2%), followed by Enterococcus species (12.2%). Significant differences in species distribution were observed based on gender and the units where patients were treated, including ambulatory care, inpatient units, and intensive care units. The highest susceptibility rates for E. coli were observed with imipenem (≥99%) and amikacin (≥86%). The susceptibility of E. coli to cefazolin decreased over the years (from 70% to 32%). Enterococcus spp. were susceptible to vancomycin and linezolid with high rates (≥92% and ≥95%, respectively). A prominent decrease was observed in the susceptibility rate for Enterococcus spp. against ampicillin in years; from 94% to 68%. A continuous decreasing trend was detected in the susceptibility of Klebsiella spp. Conclusion: E. coli continues to be the most common urinary isolate. The distribution and frequency of isolates may show difference among centers and units. Continuous monitoring of antimicrobial susceptibility is important for accurate management of UTIs

The Distribution of Hepatitis C Virus Genotypes of Patients with Chronic Hepatitis C Infection in the Eskisehir Region of Turkey

Aim:Chronic Hepatitis C is a serious disease than can result in long-term health problems. It is known that different genotypes in HCV infections account for differences in disease courses and treatment responses. Our study aimed to determine the HCV genotype distribution of patients with chronic hepatitis C infection. Material and Method: This study investigated the anti-HCV, HCV RNA viral loads, and HCV genotypes of 203 patients who were followedup in Eskisehir Osmangazi University Medical Faculty from 2009-2014. Anti-HCV was tested by microparticle ELISA (Abbott AxSYM System HCV 3.0). HCVRNA viral loads were determined by Artus HCV RG PCR kit (QIAGEN) on a Rotor-Gene 6000 (Corbett Research) instrument between 2009-2011, and by Cobas TaqMan 48 (Roche) between 2011-2014 by Real Time PCR. Genotyping of HCV RNA positive patients was performed by HCV genotype Pyrosequencing test and PCR based assay Abbott Real Time Genotype II (USA). Results: The distribution of HCV genotypes was as follows: In 151 (74.4%) patients genotype 1; in 36 genotype 1b (17.7%), in 5 type 1a (2.4%), in 3 genotype 2(1.4%); in 4 genotype 3(1.9%); and in 4 genotype 4(1.9%). HCV viral loads were between 1.25x10(3)-8.35x10(7). In 191 (94.0%) patients, anti-HCV was positive and in 12 (6.0%), anti-HCV was negative. Discussion: The most common HCV genotype in the Eskisehir region was genotype 1, and the most common subtype in this group was genotype 1b. Treatment protocols should be reevaluated by taking into consideration that sustained viral response in these patients might be weak. In Turkey, approximately 90% of HCV infections are of type 1 (most are type 1b), although types 2, 3, and 4 HCV infections are also seen

Investigation of Human Papillomavirus Prevalence in Women in Eskişehir, Turkey by Pap Smear, Hybrid Capture 2 Test and Consensus Real-Time Polymerase Chain Reaction and Typing with Pyrosequencing Method

İnsan papillomavirus (HPV) enfeksiyonları, subklinik veya asemptomatik enfeksiyonlardan anogenital kanserlere kadar değişen geniş bir klinik spektruma sahiptir. Önlenebilir bir hastalık olarak düşünülen servikal kanser (SK), dünyada, kadınlarda üçüncü en sık görülen kanser türü olduğundan, SK taramalarında HPV-DNA'sının saptanması ve risk grubunun belirlenmesi büyük önem taşımaktadır. Bu çalışmada, Eskişehir'de, kadınlarda HPV-DNA varlığının iki farklı moleküler yöntemle araştırılarak, moleküler yöntem sonuçlarının hem birbirleriyle hem de sitoloji sonuçlarıyla karşılaştırılması amaçlanmıştır. Araştırmaya, Eskişehir Kanser Erken Teşhis, Tarama ve Eğitim Merkezi'ne (KETEM) tarama amaçlı başvuran, 30-65 yaş arası 1081 kadın dahil edilmiştir. Katılımcılardan Pap yayması ve moleküler yöntemler için, eş zamanlı üç ayrı servikal sürüntü örneği alınmıştır. Araştırmanın ilk aşamasında, tüm servikal örneklerde HPV-DNA varlığı Hybrid Capture 2 (HC2; Qiagen, Almanya) yöntemiyle araştırılmış; ikinci aşamada ise HPVDNA'sı pozitif bulunan kadınların dahil edildiği, geri kalanının ise rastgele seçildiği toplam 152 kadının örnekleri konsensus gerçek zamanlı polimeraz zincir reaksiyonu (RT-PCR) ile tekrar çalışılmış (Takara Bio Inc., Japonya) ve HPV-DNA varlığı saptanan örneklerde pirodizilemeye dayalı ticari sistem (Diatech Pharmacogenetics S.R.L, İtalya) ile genotip tayini yapılmıştır. Çalışmanın ilk basamağında; kadınların %3 (32/1081)'ünde HC2 testi, 47 (%4.4)'sinde ise sitoloji sonucu tek başına ve/veya birlikte pozitif olarak raporlanmıştır. Beş (%0.5) örnekte her iki test ile de pozitif sonuç alınmış, bunların dördünde yüksek riskli HPV-DNA saptanmıştır. HC2 testi ile yüksek riskli HPV varlığı saptanan 23 (23/1081, %2.1) kadının 19'unda sitoloji sonuçları negatif olarak raporlanmıştır. Sitoloji sonucu pozitif olarak saptanan 42 (42/1081, %3.9) örnekte ise HC2 testi ile HPV-DNA varlığı saptanmamıştır. Çalışmanın ikinci aşamasına dahil edilen 152 örnekten 32 (%21.1)'si HC2 testi ile, 40 (%26.3)'ı Pap yayması ile, 53 (%34.9)'ü de konsensus RT-PCR ile tek başına ve/veya birlikte pozitif bulunmuştur. HC2 testi ile pozitif saptanan 32 örneğin tamamı konsensus RT-PCR ile de pozitif olarak saptanmış; ancak RT-PCR ile pozitif saptanan 21 örnek HC2 testi ile negatif sonuç vermiştir. Sitolojisinde anomali saptanan 40 örneğin ise dokuzunda (%22.5) RT-PCR ile ve beşinde (%12.5) HC2 ile HPV-DNA varlığı gösterilirken 31 (%77.5) örnekte her iki yöntemle de HPV-DNA saptanmamıştır. Genotip tayini yapılabilen 44 örnekte en sık saptanan tip, HPV tip 16 (n=15, %34.1) olmuş, bunu tip 90 (n=11, %25) ve tip 18 (n=4, %9.1) izlemiştir. Çalışmamızda, FDA (U.S. Food and Drug Administration) onaylı HC2 testi esas alındığında, Pap yaymasının duyarlılık, özgüllük, pozitif ve negatif prediktif değerleri, sırasıyla %16.1, %96, %10.6 ve %97.5 olarak saptanmıştır. HC2 ve konsensus RT-PCR yöntemleri arasında ise önemli derecede uyumluluk (Cohen's kappa: 0.665) bulunmuştur. Sonuç olarak, ülkemizdeki sitopatolog sayısının yetersizliği ile birlikte, ASCCP (American Society for Colposcopy and Cervical Pathology) ve FDA'nın da önerileri göz önüne alındığında; SK taramasının tam ve etkin şekilde yapılabilmesi için, Pap testine ilave olarak moleküler tanı yöntemlerinin uygulanmasına ihtiyaç olduğu bir kez daha ortaya konmuşturHuman papillomavirus (HPV) infections have a broad range of clinical spectrum from subclinical or asymptomatic infection to anogenital carcinoma. The detection of HPV-DNA and determination of the risk groups in cervical cancer (CC) screening is very important because CC is considered to be a preventable illness which is the third most common cancer type of women in the world. The aims of this study were to investigate the presence of HPV-DNA in women by two different molecular methods and to compare their results together with the results of cytology, in Eskişehir, Central Anatolia, Turkey. A total of 1081 women aged between 30-65 years, who applied to Eskişehir Early Diagnosis, Screening and Training of Cancer Center (KETEM) for screening were included in the study. Three separate cervical samples were collected simultaneously from the participants for cytologic examination and molecular studies. In the fi rst step of the study, all cervical samples were investigated for the presence of HPV-DNA by Hybrid Capture 2 (HC2; Qiagen, Germany) method. In the second part of the study, consensus real-time polymerase chain reaction (RT-PCR) (Takara Bio Inc., Japan) was performed in 152 samples which included HC2 positive and randomly selected negative samples, and then the HPV genotypes were detected by using a commercial kit based on pyrosequencing method (Diatech Pharmacogenetics S.R.L, Italy). In the fi rst part of the study, HC2 test was found positive in 3% (32/1081) of the women, while in 4.4% (47/1081) Pap smear was positive alone or with HC2 test. Five (0.5%) samples yielded positive results with both of the methods, and four of them were positive for high risk HPV types. Cytology results were negative in 19 out of 23 (23/1081, 2.1%) samples that were reported as high risk HPV by HC2 test. On the other hand, 42 (42/1081, 3.9%) samples that were positive by cytology yielded negative results by HC2 test. In the second part of the study, 32 (21.1%) of 152 selected samples were positive by HC2 test, 40 (26.3%) were positive by Pap smear, and 53 (34.9%) were positive by consensus RT-PCR. All of the 32 samples that were positive by HC2 were also positive by RT-PCR, however 21 samples that were positive by RT-PCR were negative by HC2 test. Among 40 samples that were positive (abnormal) by Pap smear, HPV-DNA was positive in nine (22.5%) by RT-PCR and in fi ve (12.5%) by HC2 test, but HPV-DNA was not detected in 31 (77.5%) samples by both of the tests. Genotyping of the strains could be performed in 44 samples, and the most common type detected was HPV type 16 (n=15, 34.1%), followed by type 90 (n=11, 25%) and type 18 (n= 4, 9.1%). In our study, the sensitivity, specifi city, positive and negative predictive values of Pap smear method were estimated as 16.1%, 96%, 10.6% and 97.5%, respectively, based on the HC2 results which was approved by U.S. Food and Drug Administration (FDA). In addition, a signifi cant degree of concordance was detected between HC2 and concensus RT-PCR methods (Cohen's kappa: 0.665). In conclusion, regarding the insuffi cient number of cytopathologists in our country and according to the recommendations of American Society for Colposcopy and Cervical Pathology (ASCCP) and FDA, it was once again demonstrated that, the implementation of molecular diagnostic methods in addition to the Pap smear for effective screening of CC are neede

Investigation of Human Papillomavirus Prevalence in Women in Eskisehir, Turkey by Pap Smear, Hybrid Capture 2 Test and Consensus Real-Time Polymerase Chain Reaction and Typing with Pyrosequencing Method

Human papillomavirus (HPV) infections have a broad range of clinical spectrum from subclinical or asymptomatic infection to anogenital carcinoma. The detection of HPV-DNA and determination of the risk groups in cervical cancer (CC) screening is very important because CC is considered to be a preventable illness which is the third most common cancer type of women in the world. The aims of this study were to investigate the presence of HPV-DNA in women by two different molecular methods and to compare their results together with the results of cytology, in Eskisehir, Central Anatolia, Turkey. A total of 1081 women aged between 30-65 years, who applied to Eskisehir Early Diagnosis, Screening and Training of Cancer Center (KETEM) for screening were included in the study. Three separate cervical samples were collected simultaneously from the participants for cytologic examination and molecular studies. In the first step of the study, all cervical samples were investigated for the presence of HPV-DNA by Hybrid Capture 2 (HC2; Qiagen, Germany) method. In the second part of the study, consensus real-time polymerase chain reaction (RT-PCR) (Takara Bio Inc., Japan) was performed in 152 samples which included HC2 positive and randomly selected negative samples, and then the HPV genotypes were detected by using a commercial kit based on pyrosequencing method (Diatech Pharmacogenetics S.R.L, Italy). In the first part of the study, HC2 test was found positive in 3% (32/1081) of the women, while in 4.4% (47/1081) Pap smear was positive alone or with HC2 test. Five (0.5%) samples yielded positive results with both of the methods, and four of them were positive for high risk HPV types. Cytology results were negative in 19 out of 23 (23/1081, 2.1%) samples that were reported as high risk HPV by HC2 test. On the other hand, 42 (42/1081, 3.9%) samples that were positive by cytology yielded negative results by HC2 test. In the second part of the study, 32 (21.1%) of 152 selected samples were positive by HC2 test, 40 (26.3%) were positive by Pap smear, and 53 (34.9%) were positive by consensus RT-PCR. All of the 32 samples that were positive by HC2 were also positive by RT-PCR, however 21 samples that were positive by RT-PCR were negative by HC2 test. Among 40 samples that were positive (abnormal) by Pap smear, HPV-DNA was positive in nine (22.5%) by RT-PCR and in five (12.5%) by HC2 test, but HPV-DNA was not detected in 31 (77.5%) samples by both of the tests. Genotyping of the strains could be performed in 44 samples, and the most common type detected was HPV type 16 (n=15, 34.1%), followed by type 90 (n=11, 25%) and type 18 (n=4, 9.1%). In our study, the sensitivity, specificity, positive and negative predictive values of Pap smear method were estimated as 16.1%, 96%, 10.6% and 97.5%, respectively, based on the HC2 results which was approved by U.S. Food and Drug Administration (FDA). In addition, a significant degree of concordance was detected between HC2 and concensus RT-PCR methods (Cohen's kappa: 0.665). In conclusion, regarding the insufficient number of cytopathologists in our country and according to the recommendations of American Society for Colposcopy and Cervical Pathology (ASCCP) and FDA, it was once again demonstrated that, the implementation of molecular diagnostic methods in addition to the Pap smear for effective screening of CC are needed