[Comparison of Three Different Methods in Investigating the Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates]. / Karbapeneme Dirençli Acinetobacter baumannii Klinik Izolatlarinin Moleküler Epidemiyoloji Açisindan Arastirilmasinda Üç Farkli Yöntemin Karsilastirilmasi.

The aim of the study was to evaluate the relationship between carbapenem-resistant Acinetobacter baumannii isolates carrying oxacillinase-type carbapenemase genes with "international high-risk clones" (IC I, II, and III) by different molecular epidemiological methods and to statistically compare the concordance and discrimination power of the methods. Carbapenem-resistant and moderately susceptible A.baumannii isolates from non-repeating blood cultures of 72 patients were included in the study. The presence of "blaOXA-23 , blaOXA-24 , blaOXA-51 ve blaOXA-58 " genes within OXA-type carbapenemases was detected by polymerase chain reaction (PCR) method and confirmed by DNA sequence analysis. Pulsed f ield gel electrophoresis (PFGE), multilocus sequence typing (MLST) and matrix-assisted laser desorption/ ionization time- of-flight mass spectrometry (MALDI-TOF MS) analyses were performed to evaluate the clonal relations of IC I, II and III clones together with clinical isolates. In the statistical comparison of the methods, discrimination power was evaluated by Simpson index of diversity (SID) and concordance by "Wallace coefficient". All of the isolates were found to carry blaOXA-23 and blaOXA-51 genes. As a result of the bioinformatic analysis of the four isolates selected for sequence analysis; blaOXA-23 and blaOXA-51 genes were detected in the selected isolates, and the analysis of two isolates carrying blaOXA-51 gene showed 99% similarity with blaOXA-92 gene. The isolates were clustered into five pulsotypes (A, B, C, D and E) according to ≥ 85% similarity coefficient by PFGE. The isolates and RUH 875, RUH 134, LUH 5875 strains belonging to high-risk clones ICI, ICII and ICIII, respectively, were divided into five main groups [A (n= 58), B (n= 8), C (n= 4), D (n= 4) and E (n= 1)] and 10 subgroups (A1, A2, A4, A5, A6, A9, B1, B4, C3, D1) by PFGE. IC clone III (E1) and seven strains showed singleton PFGE profiles (A3, A7, A8, B2, B3, C1, C2). ICII was found in A5 subtype, ICI in C1 subtype and ICIII in E1 subtype. By PFGE subtype groups, 18 pulsotypes were determined and ST1, ST2, ST81, ST157 and ST604 sequence types were found in 20 isolates randomly selected from pulsotypes according to MLST Pasteur scheme (cpn60, fusA, gltA, pyrG, recA, rplB, rpoB). Principal component analysis (PCA) of the spectra of 72 A. baumannii isolates and ICI, ICII and ICIII clones was performed by MALDI-TOF MS. In PCA analysis, the cluster distance level was defined as 1.5 and the isolates were divided into three clusters. IC clone I, II and III together with 70 clinical isolates were grouped in one cluster, while two clinical isolates (AB083 and AB0115) formed singleton clusters. There was no significant agreement between MALDI-TOF MS; MLST and PFGE data according to Wallace coefficient. It was found that PFGE method gave significant results in terms of discrimination power with SID coefficient, MALDI-TOF MS PCA analysis had the lowest discrimination power value, and the Wallace coefficient result of PFGE and MLST was concordant. In conclusion, MALDI-TOF MS may not function as a gold standard method like PFGE and MLST for epidemiological analysis in A.baumannii species and the epidemiological typing protocols used for MALDI-TOF MS need to be improved and developed.

Neutralization of Wild-Type and Alpha SARS-CoV-2 Variant by CoronaVac® Vaccine and Natural Infection- Induced Antibodies.

One of the immune responses desired to be achieved by SARS-CoV-2 vaccination is to create neutralizing antibodies (nAbs), thus preventing the development and spread of infection. The aim of this study was to investigate the seropositivity rate, anti-spike antibody levels, and neutralizing capacity of these antibodies against wild type (WT) and alpha variants in serum samples of individuals who had been naturally infected or vaccinated with CoronaVac®. Total anti-spike antibody levels were determined in all samples. Neutralization assays were performed by the reduction of the cytopathic effect in Vero-E6 cells with infectious WT and alpha SARS-CoV-2 variants. Although both naturally infected and vaccinated individuals were all seropositive for antispike antibodies, 84.8% of the vaccinated group, and 89.3% of the naturally infected group had detectable nAbs. The nAbs titers were significantly higher in the naturally infected group for both WT and alfa variant of the virus as compared to the vaccinated individuals. In this study, it was observed that all individuals became seropositive six weeks after exposure to the vaccine or the virus. Moreover, naturally infected individuals had higher levels of nAbs than those vaccinated. The presence of nAbs against the alpha variant in both naturally infected and vaccinated individuals suggests that these antibodies may also be protective against infections, which may be caused by other variants, such as delta and omicron.

Identification and antifungal susceptibility of Saprochaete clavata from invasive infections in Turkey.

Saprochaete clavata is an emerging opportunistic pathogen, that causes life-threatening infections, but there are limited evidence and information about the evaluation of in vitro antifungal susceptibility test results. The aim of this study was to determine S. clavata isolates from clinical specimens and to investigate their in vitro antifungal susceptibility. S. clavata was identified by API ID20C AUX (BioMérieux, Brussels, Belgium), MALDI TOF (Bruker Daltonik, Germany), and ITS gene region sequencing. In vitro susceptibility tests were performed using Sensititre YeastOne (TREK Diagnostic System, East Grinstead, UK). During the study period, 4,736 fungi were isolated from various clinical samples and, S. clavata was identified in eight patients with underlying diseases namely, pancreatic neoplasma, acute myeloid leukaemie, follicular lymphoma, cholelithiasis. Anidulafungin and micafungin minimum inhibitory concentration values were 1-2 and 1-4 mg/L, respectively, while those of the azole group antifungals were much lower. This is the first study in Turkey reporting isolation, identification and antifungal susceptibilities of S. clavata from clinical specimens. Higher MIC values seen in some isolates suggest that continuous monitoring of sensitivity rates and observation of regional differences will thus be useful guides in determining infection control and antifungal use policies.

[Investigation of Plasmid Mediated mcr Colistin Resistance Gene in Clinical Enterobacterales Isolates]. / Klinik Enterobacterales Izolatlarinda Plazmit Aracili mcr Kolistin Direnç Geninin Arastirilmasi.

Carbapenems are used in the treatment of infections caused by multidrug-resistant bacteria and colistin (polymyxin E) is used as the last choice of antimicrobial agent in those resistant to carbapenems. The worldwide and increased use of colistin, which causes cell death by disrupting the permeability of the cytoplasmic membrane of gram-negative bacteria, raised the problem of resistance. The transferable colistin resistance enzyme mcr, is a phosphoethanolamine transferase that adds phosphoethanolamine to lipid A and modifies lipopolysaccharides, leading to polymyxin resistance. The aim of this study was to investigate some of the most prevalent plasmid mediated colistin and carbapenemase resistance genes in colistin resistant Enterobacterales isolates. Enterobacterales isolates which were isolated in the samples of patients treated in the clinical units between October 2016 and September 2018 in the Karadeniz Technical University Faculty of Medicine Farabi Hospital Medical Microbiology Laboratory were included in the study. In addition to conventional methods, isolates were identified to the species level by MALDI-TOF MS (Bruker Daltonics, Germany). The antibiotic susceptibilities of Enterobacterales isolates were studied by an automated microbiology system (Phoenix, Becton Dickinson, USA) and evaluated according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. In isolates that are resistant to colistin, and the isolates that are found to be sensitive but should be included in the patient report of the colistin susceptibility test, colistin susceptibility tests were repeated with liquid microdilution method in accordance with EUCAST standards. The presence of extended spectrum beta-lactamase (ESBL), AmpC beta-lactamase and carbapenemase were determined by phenotypic methods according to EUCAST recommendations in colistin resistant Enterobacterales isolates. Furthermore, resistance genes of mcr-1-5, blaOXA-48, blaKPC, blaNDM, blaVIM, blaIMP were detected by polymerase chain reaction (PCR) method, followed by nucleotide sequence analysis of the amplified products. In our study, 14657 Enterobacterales isolates belonging to 7535 patients treated in different clinical units were examined retrospectively. Escherichia coli 61.2% (n= 8968), Klebsiella pneumoniae 22.7% (n= 3334) and Enterobacter cloacae 6.9% (n= 1005) were the most prevalent isolates. Carbapenem resistance was detected in 894 isolates, and 5.8% (n= 412) of 7135 isolates isolated between October 2016 and September 2017; 6.4% (n= 482) of 7522 isolates between October 2017 and September 2018 were found to be resistant. Considering all isolates, colistin resistant isolates were 65 (0.9%) between October 2016 and September 2017 and 97 (1.3%) between October 2017 and September 2018. By including only the first isolates in the study for the same agent growths in different samples of the same patient, 46 colistin resistant isolates were selected. Six isolates which could not be cultivated from stock cultures were excluded from the study material. Thirteen (32.5%) of the 40 colistin resistant Enterobacterales isolates were isolated in 2017 and 27 (67.5%) were isolated in 2018. ESBL was detected in 22, AmpC beta-lactamase was detected in 6, carbapenem resistance was detected in 15 of them by phenotypic methods. As a result of PCR analysis, mcr-1 gene detected in 2 isolates, blaOXA-48 in 2 isolates, blaVIM in 1 isolate, blaKPC and blaOXA-48 in 1 isolate, blaNDM and blaOXA-48 in 5 isolates. These results were confirmed by sequencing of the PCR products. The mcr-1 genes were found in E.coli isolates grown in urine culture samples of 2 women over 65 years of age treated in our hospital. Among the antibiotics tested, only ampicillin resistance was observed in 1 of the patients, whereas ampicillin, amoxicillin-clavulanate and ciprofloxacin resistance were detected in the other. In conclusion, as far as we can reach in the literature our publication is the first study showing the presence of mcr-1 gene in clinical samples in our country and confirmed by DNA sequence analysis. The detection of mcr gene in isolates without multidrug resistance showed once again the importance of colistin susceptibility testing in the laboratories. In addition, the presence of isolates containing more than one resistance genes in our study, suggests that the spread of carbapenem and colistin resistance may be faster than expected.

[Molecular epidemiology, antimicrobial resistance and characterization of extended-spectrum beta-lactamases of Salmonella enterica serotype Paratyphi B clinical isolates]. / Salmonella enterica serotip Paratyphi B klinik izolatlarinin moleküler epidemiyolojisi, antimikrobiyal direnci ve genislemis spektrumlu beta-laktamazlarinin karakterizasyonu.

Although Salmonella enterica serotype Paratyphi B is the less frequently isolated serotype worldwide and in Turkey, it is the most common serotype in our hospital, with a marked increase in 2007. The purpose of this study was to investigate the antibiotic susceptibility and the extended spectrum beta-lactamase (ESBL) profile, and molecular epidemiology of S. Paratyphi B isolates detected in our hospital microbiology laboratory. Seventy isolates identified as S. Paratyphi B from 109 Salmonella isolates obtained from clinical specimens from different patients between October 2005 and December 2012, were included in the study. In addition to conventional methods, isolates were identified using the Phoenix automated microbiology system (Becton Dickinson, USA). Serotyping of the isolates was performed on the basis of slide agglutination and the Kauffmann-White scheme. The antibiotic susceptibility of the isolates was determined using the BD Phoenix' automated system and disk diffusion test. ESBL enzymes were investigated using the combined disk test, isoelectric focusing, polymerase chain reaction (PCR) and sequence analysis. The molecular epidemiology of the 51 isolates obtained between October 2005 and August 2008 was examined with pulsed-field gel electrophoresis (PFGE) using the XbaI enzyme. S. Paratyphi B isolates were obtained from 70 specimens (46 blood, 16 fecal, 4 bone marrow, 2 urine and 2 wound) each from different patients. Resistance to nalidixic acid was determined in 18.6%, resistance to ampicillin, cefotaxime and cefepime in 2.9% and to ceftazidime and co-trimoxazole in 1.4% of the isolates. ESBL production was detected only in two isolates; in one TEM-1 was accompanied by CTX-M-15 and in the other isolate CTX-M-3 was found. Forty-six of the 51 isolates (90%) were found to be genetically related by PFGE and were placed in cluster A. The distribution of the isolates in cluster A revealed six subtypes as A1 (n= 7), A2 (n= 11), A3 (n= 7), A4 (n= 18), A5 (n= 2) and A6 (n= 1). Three different patterns not related to the cluster A were determined in the remaining five isolates (two were B, one of each was C, D and E). In conclusion, although the rate of antibiotic resistance was low in the S. Paratyphi B isolates in our hospital, rare types of ESBLs such as CTX-M-3 and CTX-M-15 were detected in Salmonellae. As far as the current literature is considered, this is the first report in Turkey of blaCTX-M-15 in Salmonella spp. and blaCTX-M-3 genes in S. Paratyphi B. The results may indicate a possible future threat to the treatment of Salmonella infections. Since most of the isolates were genetically related, this might suggest an epidemic in our region.

Distribution, virulence attributes and antifungal susceptibility patterns of Candida parapsilosis complex strains isolated from clinical samples.

It was recently proposed that Candida parapsilosis represents a complex composed of three closely related species, i.e., C. parapsilosis sensu stricto, C. orthopsilosis, and C. metapsilosis. The aim of this study was to describe the distribution of C. parapsilosis complex isolates among clinical samples. We also evaluated antifungal susceptibility profiles, in vitro presence of lipase and secreted aspartyl proteinase, as well as their ability to grow in total parenteral nutrition (TPN) solution, and biofilm production. A total of 413 non-C. albicans Candida isolates were obtained from various clinical samples between 2010 and 2011 in a Turkish Tertiary Care Hospital. Of them, 42 were identified as members of the C. parapsilosis complex. Among these, 38 (90.5%) were C. parapsilosis sensu stricto, 3 (7.1%) C. metapsilosis, and 1 (2.4%) C. orthopsilosis. All isolates recovered from blood were found to be C. parapsilosis sensu stricto and C. metapsilosis. In phenotypic tests, all 42 isolates grew in TPN solution and, although 26.2% of C. parapsilosis sensu stricto-isolates were capable of forming biofilms in vitro, neither C. orthopsilosis nor C. metapsilosis isolates were able to do so. Acid proteinase activity was detected in 31% of isolates and lipase activity in 33%. All isolates were sensitive to voriconazole, caspofungin, and anidulafungin, with only a single C. parapsilosis sensu stricto isolate showing dose-dependent susceptible to fluconazole. While the number of C. metapsilosis and C. orthopsilosis isolates remained low, there were no significant differences in antifungal MIC as compared to C. parapsilosis sensu stricto.

[Investigation of Pneumocystis jirovecii in Respiratory Samples of Immunocompromised Patients with PCR, IFA and Giemsa Staining Methods]. / Immün Yetmezligi Olan Hastalarin Solunum Yolu Örneklerinde PCR, IFA ve Giemsa Boyama Yöntemleriyle Pneumocyctis jirovecii'nin Arastirilmasi

Pneumocystis jirovecii is an important opportunistic agent leading to pneumonia in immunocompromised patients. In this study, the presence of P.jirovecii were investigated by using Giemsa stain, indirect fluorescent antibody (IFA) test and two different nested polymerase chain reaction (nPCR) assays in respiratory samples obtained from 50 immunocompromised patients presenting with respiratory symptoms. The target genes used for nested PCR were mitochondrial large subunit ribosomal RNA (MtLSUrRNA) and internal transcribed spacer (ITS) region. P.jirovecii was detected in 7 (14%) and 11 (22%) respiratory samples by IFA and PCR, respectively, although all samples were negative with Giemsa stain. As a result, IFA and PCR were found to be rapid and reliable tests for the diagnosis of P.jirovecii infections and they should better be used together for accurate diagnosis.

[Determination of hepatitis C virus genotypes among hepatitis C patients in Eastern Black Sea Region, Turkey]. / Dogu Karadeniz Bölgesi Hepatit C Hastalarinda Hepatit C Virusu Genotiplerinin Belirlenmesi.

Hepatitis C virus (HCV), the major cause of transfusion-associated hepatitis, is an important public health problem in the world as well as in Turkey. HCV is grouped as six distinct genotypes and a large number of closely-related subtypes. Genotyping of HCV is an important tool for providing epidemiological data, prediction of prognosis, and optimization of antiviral therapy. This study was carried out to determine the distribution of HCV genotypes in hepatitis C patients residing in different provinces of the Eastern Black Sea Region, Turkey. A total of 304 HCV-RNA positive cases (151 male, 153 female; age range: 11-93 years, mean age: 55.2 ± 13.3 years) who were admitted to the Molecular Microbiology Unit of Department of Medical Microbiology, Karadeniz Technical University Faculty of Medicine, between January 2009 to December 2012, were included in the study. HCV genotypes were detected in plasma samples of the patients by using commercial assays [INNO-LiPA HCV II (Innogenetics, Belgium) or Abbott RealTime HCV Genotype II (Abbott Molecular Inc, USA)]. Due to the ambiguous genotyping results in some samples with these methods, an in-house multiplex polymerase chain reaction (PCR) assay with genotype-specific primers was also used in the study. Similar to the previous reports from Turkey, our results showed that four HCV genotypes (1, 2, 3, and 4) prevailed in the Eastern Black Sea Region and the predominant genotype and subtype were genotype 1 (92.8%) and 1b (87.5%), respectively. Distribution of genotypes were observed to vary according to the province. Prevalences of subtype 1a, genotype 2, 3, and 4 were noted as 5.3%, 1.6%, 4.9%, and 0.7%, respectively. Furthermore, the samples from Giresun, Gumushane and Bayburt provinces, which are relatively less immigrated, had higher genotype 1, and the prevalence rates in the region was affected by the presence of non-citizen residents. This study is the first report on distribution of HCV genotypes in chronic hepatitis C patients living in the provinces of Eastern Black Sea Region. Moreover, genotype-specific multiplex PCR assay could be useful in resolving certain methodological problems such as "ghost bands" encountered in line probe assay (LiPA) and multiple genotypes (including genotype 4) observed in real-time PCR during the characterization of HCV genotypes seen in Turkey.

Serum MUC3 Protein as a Novel Marker of Gestational Hypertensive Disorders.

Background: This study aimed to investigate the serum levels of mucoprotein 3 in hypertensive diseases of pregnancy. Methods: In total, 60 consecutive women with gestational hypertensive diseases (gestational hypertension (n = 20), severe preeclampsia (n = 20), HELLP syndrome (n = 20)) and 20 pregnant women without any gestational hypertensive diseases were included for this prospective controlled study. Serum MUC3 protein levels were measured with commercially available ELISA kits. Results: Serum MUC3 protein level was the lowest in normal pregnant women (0.1047 ± 0.0295 ng/ml); while the severity of the disease increases, it significantly increased in severe preeclampsia (0.2700 ± 0.0199 ng/mL) and HELLP syndrome group (0.3494 ± 0.0455 ng/mL), but less in the gestational hypertension (0.2172 ± 0.0354 ng/mL) group. Mean serum MUC3 protein level differences were found the least in gestational hypertension (0.1125 ± 0.0107, p < 0.001), the most in HELLP syndrome (-0.2546 ± 0.0107, p < 0.001) compared with the pregnant control group. Conclusion: The increase in serum MUC3 protein concentration in these women supported the argument that serum MUC3 protein may be used as a marker indicating the severity of the gestational hypertensive diseases.

Bloodstream yeast infections in a university hospital in Northeast Turkey: a 4-year survey.

This study presents data on species distribution and antifungal susceptibility profiles of Candida bloodstream isolates obtained from a Turkish Tertiary Care Hospital during a 4-year period. All hospitalized patients who had ≥ 1 blood culture positive for yeast during their hospital stay from January 2005 through 2009 were included in this study. All isolates were identified to species level using CHROMagar and ID 32 C. Fluconazole and voriconazole antifungal susceptibility testing was performed using the disk diffusion method according to CLSI M44-A. In vitro activity of amphotericin B was determined by the Etest. Of all 166 yeast isolates, C. albicans was the dominant species (34.3%), followed by Candida parapsilosis (28.9%) and C. tropicalis (8.4%). All of the 48 C. parapsilosis strains were identified as C. parapsilosis sensu stricto. Resistance to fluconazole was more common among C. krusei isolates. Voriconazole resistance was absent. One C. lusitaniae strain showed a high amphotericin MIC (4 µg/ml). Our survey indicated an increase of some non-C. albicans Candida species in our hospital while antifungal resistance was uncommon.

Fungemia and renal fungus ball formation with Candida norvegensis in a child with acute lymphoblastic leukemia.

Invasive fungal infections cause significant morbidity and mortality in pediatric cancer patients. Candida species are the most frequently isolated pathogen. Candida species may cause bloodstream and deep-seated infection in neutropenic children with cancer. The gastrointestinal system, lung, liver and spleen are the most frequently involved organs. Isolated renal involvement presented as abscess formation has been reported rarely in children with cancer. Herein, we report a patient with acute lymphoblastic leukemia (ALL) who presented with renal abscess and fungus ball formation due to Candida norvegensis, which is an unusual cause of infection.

[Genotypic identification and distribution patterns of Candida parapsilosis complex species (C.parapsilosis sensu stricto, C.metapsilosis and C.orthopsilosis) isolated from clinical samples]. / Klinik Örneklerden Izole Edilen Candida parapsilosis Kompleks Türlerinin (C.parapsilosis sensu stricto, C.metapsilosis ve C.orthopsilosis) Genotipik Olarak Tanimlanmasi ve Dagilimlarinin Belirlenmesi.

Candida parapsilosis, which has recently gained increasing importance, is the second most common fungal pathogen isolated from clinical specimens. C.parapsilosis strains exhibiting genetic heterogeneity were previously considered as a complex of three genetically different groups (group I, II, III). However, they have recently been reclassified as new species and named as C.parapsilosis sensu stricto (Grup I), C.orthopsilosis (Grup II) and C.metapsilosis (Grup III). In the present study we aimed to identify C.parapsilosis complex species by PCR-RFLP (Polymerase chain reaction-Restriction fragment lenght polymorphism) method and to determine the distribution of new species isolated from clinical specimens. A total of 68 samples (44 blood, 10 urine, 5 wound, 2 paracentesis fluids, 2 tympanocentesis samples and one of each cerebrospinal fluid, peritoneal fluid, surgical material, oral lesion and nail sample) in which C.parapsilosis had been isolated and identified with API 20C AUX (bioMérieux, France) between October 2005 - July 2009 in the Microbiology Laboratory of Karadeniz Technical University Hospital, in Trabzon, Turkey, were included in the study. Yeast genomic DNA was extracted using the "High Pure PCR Template Preparation Kit" (Roche Diagnostic, USA) and amplification of SADH gene was performed by using specific primers (S1-F sense; 5'-GTTGATGCTGTTGGATTGT-3' ve S1-R antisense; 5'-CAATGCCAAATCTCCCAA-3') with PCR. RFLP method was then applied by digesting PCR product (716 bp) with BanI enzyme (Fermentas, USA). In our study 98.5% (67/68) of the isolates were identified as C.parapsilosis sensu stricto, and 1.5% (1/68) was identifed as C.orthopsilosis, whereas no C.metapsilosis strains were detected. The strain identified as C.orthopsilosis was from a urine specimen and all the blood culture isolates were C.parapsilosis sensu stricto. In conclusion, the inability to differentiate C.parapsilosis complex species by phenotypical and routine tests leads to lack of knowledge in the clinical importance, isolation rates and geographical distribution of these species. Thus, genotypical identification of C.parapsilosis complex species will be the initial step for the arrangement of further studies in that area.

[Comparison of COBAS AmpliPrep/COBAS TaqMan 48 and VERSANT HCV-RNA 3.0 systems for the determination of hepatitis C virus load]. / Hepatit C virus yükünün belirlenmesinde COBAS AmpliPrep/COBAS TaqMan 48 ve VERSANT HCV-RNA 3.0 sistemlerinin karsilastirilmasi.

The aim of this study was to investigate the concordance between COBAS Taqman 48 (Roche Molecular Systems, Pleasanton, CA, USA) and VERSANT HCV RNA 3.0 (Bayer Diagnostics, Terrytown, NY) test systems for the detection of hepatitis C virus (HCV) load. Plasma samples taken from 42 patients with chronic HCV infection between 15 May-15 June 2006, were included to the study, and HCV-RNA levels have been searched with the use of the two above mentioned systems. Thirteen of the samples (30.9%) yielded negative and 26 (61.9%) samples yielded positive results by both of the systems. Two samples that were found negative by COBAS system, displayed 3.38 and 3.41 log10 IU/ml HCV-RNA by VERSANT system, respectively, while one sample that was found negative by VERSANT system, displayed 2.52 log10 IU/ml HCV-RNA by COBAS system. The correlation and linearity of the tests were found high according to Pearson correlation analysis [(r = 0.904, p < 0.0005), (R2 = 0.817)]. The viral load values detected by COBAS AmpliPrep/COBAS Taqman 48, were higher than the values obtained by VERSANT HCV-RNA 3.0, with a mean of 0.33 log10 IU/ml. In conclusion, both of the systems yielded similar results, however, since HCV viral load values may differ in different systems, the follow-up of viral load should be done by the same system for a particular patient.

Asymptomatic Chlamydia trachomatis infection and predictive criteria among low-risk women in a primary care setting.

The aim of this study was to estimate the prevalence and predictors of Chlamydia trachomatis infection among young adult low-risk women attending either of two inner-city family planning clinics in Trabzon, the most densely populated city in Turkey's Black Sea region. The study group comprised 150 sexually active women attending either of two family planning clinics. Two endocervical swabs were collected from each woman and tested for the presence of C. trachomatis by tissue culture and a commercially available enzyme immunoassay (ELISA). Multivariable logistic regression analysis was used to identify the associations of clinical factors for predicting C. trachomatis infection. C. trachomatis was detected in 19 of the samples (12.7%) by cell culture and in 15 (9.9%) by ELISA. None of the demographic characteristics could be associated with the state of infection, but the women preferring the withdrawal method for contraception accounted for a significantly higher percentage of the C. trachomatis-positive cases than women who used other contraceptive methods. The most frequent signs of cervical infection were vaginal discharge (RR = 4.86, 95% CI 1.60 and 14.79, P = 0.005) and cervical erosion (RR = 3.26, 95% CI 0.97 and 10.90, P = 0.056).

Horizontol dissemination of TEM- and SHV-typr beta-lactamase genes-carrying resistance plasmids amongst clonical isolates of Enterobacteriaceae.

The extended-spectrum ß-lactamase (ESBL)-producing bacteria have been isolated at increasing frequency worldwide. Expression of ESBL is often associated with multidrug resistance and dissemination by resistance plasmids. During a two-month period in 2000, 133 clinical isolates of enterobacterial strains were randomly collected from outpatients and inpatients at a university hospital in Turkey. The ESBL producing strains were determined by double-disk synergy (DDS) testing. Twenty ESBL producing strains (15%) including Escherichia coli (n = 9), Klebsiella pneumoniae (n = 7), Klebsiella oxytoca (n = 2) and Enterobacter aerogenes (n = 2) were detected and further analyzed for their resistance transfer features, plasmid profile and nature of the resistance genes. Plasmid transfer assays were performed using broth mating techniques. TEM- and SHV- genes were analyzed by polymerase chain reaction (PCR) and hybridization using specific probes. EcoRI restriction enzyme analyses of R plasmids were used in the detection of epidemic plasmids. Fourteen plasmid profiles (A, B1, B2, C1, and C2 to L) were obtained with EcoRI restriction enzyme analysis. Most of these plasmids were detected to carry both TEM- and SHV-derived genes by PCR, and confirmed by localizing each gene by hybridization assay. Epidemiological evidence indicated that there was an apparent horizontal dissemination of conjugative R plasmids among multidrug-resistant enterobacterial genera and species in this hospital.

Molecular epidemiology of clinical Pseudomonas aeruginosa isolates carrying IMP-1 metallo-beta-lactamase gene in a University Hospital in Turkey.

Pseudomonas aeruginosa isolates carrying IMP- or VIM-type metallo-beta-lactamase (MBL) have been increasingly reported in hospitals worldwide. One hundred P. aeruginosa clinical isolates from unrelated inpatients hospitalized at a Turkish university hospital were screened for the presence of bla(IMP) and bla(VIM) genes by polymerase chain reaction (PCR). One (1%) isolate was found to carry a VIM-type MBL gene, whereas nine (9%) carried an IMP-1 MBL gene carried on a cassette inserted into a class 1 integron. Only four of the IMP producers were detected as MBL producers according to E-test MBL. Minimum inhibitory concentrations (MICs) of imipenem for the IMP-1 and VIM-type MBL-producers were highly variable (MIC values, 8-128 mug/ml). Imipenem resistance was not plasmid-mediated according to the transformation assays. Piperacillin/tazobactam was the only effective drug in antimicrobial susceptibility testing. No aztreonam-resistant IMP and VIM producers were detected to produce an extended-spectrum beta-lactamase (ESBL). Three class 1 integrons of approximately 2,300 bp, 1,800 bp, and 1,500 bp in size were detected in each of the nine IMP-positive isolates. Sequencing revealed three novel gene cassette arrays, aac(3)-1c-cmlA5, bla(IMP-1)-aadA7-like, and aacA7-smr-2-orfD. Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) indicated that a clonal spread of IMP-1-producers had occurred in this hospital.

[Biotypes and antibiotic resistance patterns of Gardnerella vaginalis strains isolated from healthy women and women with bacterial vaginosis]. / Saglikli ve bakteriyel vajinozlu kadinlardan izole edilen Gardnerella vaginalis suslarinin biyotiplendirilmesi ve antibiyotik direnç durumlarinin belirlenmesi.

As Gardnerella vaginalis is accepted as a member of normal vaginal flora, it is one of the dominant species which has been related to bacterial vaginosis (BV). The aim of this study was to determine the isolation rate, biotypes and antibiotic resistance patterns of G.vaginalis from the vaginal swab samples of 408 women who were admitted to the outpatient clinics of Family Planning Center. Hippurate hydrolysis, lipase and beta-galactosidase tests were performed for biotyping the isolates, and agar dilution (for metronidazole) and disk diffusion (for clindamycin) tests were used for the detection of antibiotic resistance patterns. As a result, by Nugent's BV scoring protocol, 122 (29.9%), 20 (29.4%), 137 (33.6%), and 18 (4.4%) of the women were diagnosed as BV, intermediate form, normal vaginal flora (NVF) and mycotic vaginosis, respectively. The overall isolation rate of G.vaginalis was found as 23% (94/408). Of them, 56.4% (53/94) and 8.5% (8/94) were isolated from samples of BV cases and subjects with NVF, respectively, and the difference was statistically significant (p<0.05). The biotyping results showed that the most frequently detected types were biotype 1 (44%), 5 (20%) and 4 (18%). There was no statistically significant difference between the biotype distribution of BV patients and the subjects who have NVF (p=0.687). The results of antibiotic susceptibility tests indicated that 70% and 53% of the isolates were resistant to metronidazole and clindamycin, respectively. It was of interest that MIC values for metronidazole was > or =128 microg/ml in 57% of resistant strains. The data of this study has emphasized that the metronidazole resistance is very high in our population, and the large scale studies are needed to clarify the relationship between BV and G.vaginalis biotypes, which can be found in the normal vaginal flora.

Determination of Seroprevalence of Borrelia burgdorferi IgG in Adult Population Living in Trabzon.

BACKGROUND: Lyme borreliosis is a tick-borne, multi-systemic infectious disease that is thought to be wide spread in Turkey even though studies on its seroprevalence are limited. AIMS: To determine the seroprevalence of Lyme borreliosis in part of north-eastern Tur-key (in the city of Trabzon), and to identify possible relationships between seropositivity and various factors such as location, gender, age group, occupation, income, and educational level. STUDY DESIGN: Retrospective cross-sectional study. METHODS: A total of 884 blood samples collected from provincial and district health centers serving a population of about 800,000 were included in this study. ELISA was used to determine the anti-Borrelia IgG antibody levels in the samples. Samples that yielded positive results by ELISA were further subjected to western blot (WB). RESULTS: IgG antibodies were found in 128 samples (14.5%). Statistical analysis revealed significant differences between age groups and educational levels in terms of the incidence of seropositivity, whereas location, gender, occupational group and income level had no effect (p<0.001, p<0.001, p=0.948, p=0.645, p=0.131, p=0.080 respectively). CONCLUSIONS: The risk of contracting Lyme borreliosis in Trabzon is high, and necessary measures need to be taken to avoid the spread of disease.

Investigation of Chlamydia pneumoniae DNA, chlamydial lipopolisaccharide antigens, and Helicobacter pylori DNA in atherosclerotic plaques of patients with aortoiliac occlusive disease.

BACKGROUND AND INTRODUCTION: It has been suggested that chronic infections may have a role in both the initiation and progression of atherosclerosis. While the majority of available data are focused on coronary artery disease, our aim was to investigate the presence of Chlamydia pneumoniae and Helicobacter pylori in samples from aortoiliac occlusive disease. METHODS: Aorta-iliac atherectomy specimens were collected under sterile conditions from 21 patients (19 male, 2 female) undergoing surgery for aortoiliac occlusive disease. Seventeen macroscopically healthy vessels (12 internal mammary arteries, 3 radial arteries, prepared for coronary artery bypass graft, and 2 traumatic artery specimens, one of which was a superficial femoral artery and the other was a radial artery) were used as control. Blood samples for serological assays were obtained immediately before surgery. The polymerase chain reaction (PCR) was employed to search for H. pylori and C. pneumoniae DNA in atherosclerotic plaques and healthy vessel samples. Group-specific chlamydial lipopolysaccharide (LPS) antigens in atherosclerotic plaques and in healthy vessel samples and serum IgG antibodies to chlamydial LPS were determined by using a commercially available enzyme-linked immunosorbent assay (ELISA). Antibodies to H. pylori were also tested in all cases by means of an in-house ELISA. RESULTS: Chlamydial LPS and DNA were detected in 6 of 21 (28.57%) atherosclerotic lesions using ELISA or PCR, respectively. There was no evidence of H. pylori DNA in any plaque specimens. All cases in which C. pneumoniae DNA was positive were also seropositive for antichlamydial LPS. Neither C. pneumoniae DNA nor antigen nor H. pylori DNA was found in the macroscopically healthy samples. CONCLUSION: Our results suggest that C. pneumoniae but not, as proposed, H. pylori may be involved in the pathogenesis of aortoiliac atherosclerosis.