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

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

Proteins associated with neutrophil degranulation are upregulated in nasopharyngeal swabs from SARS-CoV-2 patients.

COVID-19 or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appeared throughout the World and currently affected more than 9 million people and caused the death of around 470,000 patients. The novel strain of the coronavirus disease is transmittable at a devastating rate with a high rate of severe hospitalization even more so for the elderly population. Naso-oro-pharyngeal swab samples as the first step towards detecting suspected infection of SARS-CoV-2 provides a non-invasive method for PCR testing at a high confidence rate. Furthermore, proteomics analysis of PCR positive and negative naso-oropharyngeal samples provides information on the molecular level which highlights disease pathology. Samples from 15 PCR positive cases and 15 PCR negative cases were analyzed with nanoLC-MS/MS to identify the differentially expressed proteins. Proteomic analyses identified 207 proteins across the sample set and 17 of them were statistically significant. Protein-protein interaction analyses emphasized pathways like Neutrophil degranulation, Innate Immune System, Antimicrobial Peptides. Neutrophil Elastase (ELANE), Azurocidin (AZU1), Myeloperoxidase (MPO), Myeloblastin (PRTN3), Cathepsin G (CTSG) and Transcobalamine-1 (TCN1) were found to be significantly altered in naso-oropharyngeal samples of SARS-CoV-2 patients. The identified proteins are linked to alteration in the innate immune system specifically via neutrophil degranulation and NETosis.

Risk factors and clinical responses of pneumonia patients with colistin-resistant Acinetobacter baumannii-calcoaceticus.

BACKGROUND: Nosocomial infections with carbapenem-resistant Acinetobacter baumannii-calcoaceticus complex (ABC) strains are great problem for intensive care units. ABC strains can develop resistance to all the antibiotics available. Carbapenem resistance is common and colistin resistance is rare in our country. Knowing the risk factors for colistin resistance is important since colistin seems to be the only remaining therapeutic option for the patients with pneumonia due to extensively drug resistant ABC for our country. AIM: To investigate the comparison of clinical responses and outcomes between pneumonia patients with colistin-susceptible and -resistant Acinetobacter sp. Strains. METHODS: During the study period, 108 patients with pneumonia due to colistin-susceptible strains and 16 patients with colistin-resistant strains were included retrospectively. Continuous variables were compared with the Mann-Whitney U test, and categorical variables were compared using Pearson's chi-square test or Fisher's Exact chi-square test for two groups. A binary logistic regression model was developed to identify the potential independent factors associated with colistin resistance in patients with colistin-resistant strains. RESULTS: High Acute Physiology and Chronic Health Evaluation II scores (OR = 1.9, 95%CI: 1.4-2.7; P < 0.001) and prior receipt of teicoplanin (OR = 8.1, 95%CI: 1.0-63.3; P = 0.045) were found to be independent risk factors for infection with colistin-resistant Acinetobacter sp. Different combinations of antibiotics including colistin, meropenem, ampicillin/sulbactam, amikacin and trimethoprim/sulfamethoxazole were used for the treatment of patients with colistin-resistant strains. Although the median duration of microbiological cure (P < 0.001) was longer in the colistin-resistant group, clinical (P = 0.703), laboratory (P = 0.277), radiological (P = 0.551), microbiological response (P = 1.000) and infection related mortality rates (P = 0.603) did not differ between the two groups. Among the patients with infections due to colistin-resistant strains, seven were treated with antibiotic combinations that included sulbactam. Clinical (6/7) and microbiological (5/7) response rates were quite high in these patients. CONCLUSION: The optimal therapy regimen is unclear for colistin-resistant Acinetobacter sp. infections. Although combinations with sulbactam seems to be more effective in our study patients, data supporting the usefulness of combinations with sulbactam is very limited.

The Prevalence of Mixed Genotype Infections in Turkish Patients with Hepatitis C: a Multicentered Assessment.

BACKGROUND: HCV virus infections are one of the major health problems in the world that can cause cirrhosis and liver cancer at a higher rate than other hepatitis data. The aim of this study was to determine the prevalence of mixed infections with different HCV genotypes in Turkey and also to evaluate the current HCV genotype and sub-type distributions by a multicentered assessment. METHODS: The HCV genotype data of 17,578 hepatitis C patients collected from 23 centers from different geographic regions covering all Turkey were collected. The data included information about the HCV genotypes in the last 10 years (between 2007 and 2016), demographic properties of the patients and the methods/systems used to determine the genotypes. RESULTS: Two hundred twenty-eight of the patients (1.3%) had mixed genotype. The most common mixed genotype combination was 1b + 4 (0.83%) followed by 1a + 1b (0.26%). Genotype distribution varies according to geographical regions. However, genotype 1 (82.92%) was the most common genotype in all regions and all years. This was followed by genotype 3 (7.07%) and genotype 4 (5.43%). A variety of methods were used by the centers including sequencing, pyrosequencing, real-time PCR, in-house RFLP, reverse hybridization (LIPA), and hybridization. CONCLUSIONS: Infection with mixed HCV genotypes in Turkey is uncommon. Genotype distribution varies according to geographic regions; the most common genotype 1 is encountered all over the country, while genotypes 3 and 4 are only in some of the centers. Since there is limited information about mixed HCV infection, further investigations are needed to determine the clinical importance of mixed HCV infection.

Fecal carriage of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella spp. in a Turkish community.

BACKGROUND/AIM: The aim of this study was to determine the prevalence of fecal carriage of extended-spectrum beta-lactamase (ESBL)-producing bacteria, enzyme types, and risk factors affecting colonization. MATERIALS AND METHODS: A total of 576 stool samples from outpatients were examined between October 2012 and May 2013. Screening was done with selective EMB plates. ESBL were detected by double-disk synergy and confirmed agar strip gradient methods. Enzyme types were determined by PCR. RESULTS: The prevalence of fecal carriage was found as 30% (173 of 576). Recent use of antibiotics, hospitalization and surgical operation, diabetes, crowded household populations, and old age were associated with higher carriage rates. Of the ESBL-producing bacteria, 87.5% were positive for blaCTX-M genes. Of the blaCTX-M gene-positive isolates, 95.2% were positive for blaCTX-M-1 genes; among these, 82.2% were positive for blaCTX-M-3 and 67.7% were positive for blaCTX-M-15 genes while 62.5% isolates were positive for both blaCTX-M-3 and blaCTX-M-15 genes Conclusions: A high rate (30%) of fecal carriage of ESBL bacteria was found in an adult population. The predominant beta-lactamase enzyme types were CTX-M-3 and CTX-M-15.

Evaluation of the Carbapenem Inactivation Method for Detection of Carbapenemase-Producing Gram-Negative Bacteria in Comparison with the RAPIDEC CARBA NP.

Timely detection of carbapenemases by both phenotypic and genotypic methods is essential for developing strategies to control the spread of infections by carbapenem-resistant isolates and related morbidity and mortality. The aim of this study was to compare the performance of a commercial kit, the RAPIDEC® CARBA NP, and an in-house technique, the carbapenem inactivation method (CIM), against a panel of 136 carbapenemase- and noncarbapenemase-producing Enterobacteriaceae, Acinetobacter baumannii, and Pseudomonas aeruginosa isolates. RAPIDEC CARBA NP displayed 99% sensitivity and 100% specificity, whereas the sensitivity and specificity were 78% and 100% for the CIM test, respectively. A slight modification of the CIM test, a prolonged incubation time of 4 hours instead of two, increased the sensitivity of the test to 90% by diminishing false negativity particularly for A. baumannii. In conclusion, both tests possess a high performance and are practical for the detection of carbapenemases. Although RAPIDEC CARBA NP is a more rapid and reliable method, the CIM test may represent a useful tool for microbiology laboratories due to its simplicity and availability at any laboratory with low cost.

Effects of polymer-based, silver nanoparticle-coated silicone splints on the nasal mucosa of rats.

Infection is a serious complication after nasal packing that otolaryngologists seek to avoid. The aim of this study is to investigate the use of silver (Ag) nanoparticle, which serves as antimicrobial agents, with nasal tampons. The study design is an experimental animal model and the setting is tertiary referral center. Twenty-four rats were randomized into the following four groups: (1) control group (n = 6); (2) silicone nasal splint (SNS) group (n  =  6); (3) polypropylene-grafted polyethylene glycol (PP-g-PEG) amphiphilic graft copolymer-coated SNS group (n  =  6); and (4) Ag nanoparticle-embedded PP-g-PEG (Ag-PP-g-PEG) amphiphilic graft copolymer-coated SNS group (n  =  6). These tampons were applied to rats for 48 h, after which they were removed in a sterile manner, and the rats were sacrificed. The nasal septa of the rats were excised, and assessments of tissue changes in the nasal mucosa were compared among the groups. The removed tampons were microbiologically examined, and quantitative analyses were made. When the groups were compared microbiologically, there were no significant differences in bacterial colonization rates of coagulase-negative Staphylococcus spp. among the three groups (p = 0.519), but there was a statistically significant difference among bacterial colonization rates of Heamophilus parainfluenzae and Corynebacterium spp. (p = 0.018, p = 0.004). We found that H. parainfluenzae grew less robustly in the Ag-PP-g-PEG than the PP-g-PEG group (p = 0.017). However, we found no significant difference between the Ag-PP-g-PEG and SNS groups, or between the SNS and PP-g-PEG groups. The growth of Corynebacterium spp. did not differ significantly between the Ag-PP-g-PEG and SNS groups (p = 1.000). When Group 4 was compared with Group 2, the former showed less inflammation. Compared with other tampons, Ag-PP-g-PEG amphiphilic graft copolymer-coated silicone nasal tampons caused less microbiological colonization and inflammation. Therefore, the use of these tampons may prevent secondary infections and reduce the risk of developing complications by minimizing tissue damage.

Investigation of OprD Porin Protein Levels in Carbapenem-Resistant Pseudomonas aeruginosa Isolates.

BACKGROUND: The Pseudomonas aeruginosa porin OprD is a substrate-specific porin that facilitates the diffusion of basic amino acids, small peptides, and carbapenems into the cell. OprD-mediated resistance occurs as a result of decreased transcriptional expression of oprD and/or loss of function mutations that disrupt protein activity. OBJECTIVES: In this study, we examined the level of oprD expression in P. aeruginosa clinical isolates to determine the contribution of OprD porins in carbapenem resistance. MATERIALS AND METHODS: Included strains were divided into two groups, comprised of multidrug-resistant (MDR) and isolated carbapenem-resistant (ICR) strains. The transcription product level of oprD was identified using real-time polymerase chain reaction (qPCR). RESULTS: Of the 18 clinical isolates, a decrease in the oprD level was found to be significant in 13 isolates. Nine of eighteen isolates with a significant decrease were determined in the first group and comprised MDR isolates that showed a statistically significant difference compared with the ICR group (P = 0.001). In the ICR group, oprD levels were found to be significantly low in 4 isolates. Six different patterns were determined by comparing band profiles in AP-PCR. CONCLUSIONS: Although the data support the idea that the basic mechanism of imipenem resistance could be via the loss of oprD, they do not fully explain the role of oprD and indicate that other mechanisms may play an important role. Additionally, the significant decrease in the oprD levels in MDR strains suggests that oprD also plays a role in the emergence of both carbapenem and non-carbapenem resistance.

The effects of active efflux pumps on antibiotic resistance in Pseudomonas aeruginosa.

In this study, we investigated the roles of active efflux pumps in antibiotic resistance. The transcription efflux pump genes were analyzed by real-time polymerase chain reaction (qPCR) to determine their role in drug resistance. Antibiotic sensitivity testing was carried out using the Vitek 2 automated system (bioMérieux, France). Isolates were divided into four groups according to their resistance status: multiple-drug resistant (MDR), isolated carbapenem resistant (ICR), isolated quinolone resistant (IQR), and carbapenem and quinolone resistant (CQR). Transcript levels of mexB, mexD, mexF, and mexY were analyzed by qPCR using a LightCycler instrument (Roche, Germany). The genetic similarity between isolates was determined using arbitrarily primed PCR (AP-PCR). Among the 50 isolates investigated, the frequency of genes classified as overexpressed were 88 % for mexD, 76 % for mexB, 46 % for mexF, and 40 % for mexY. Within the MDR group, mexB was overexpressed in 15 of 22 isolates, mexD in 20 of 22, mexF in 15 of 22, and mexY in 19 of 22. In the ICR group, isolates mexB and mexD were each overexpressed in five isolates. mexD overexpression was observed in all seven CQR isolates. Within the IQR group, mexB and mexD were overexpressed in all 12 isolates. mexF overexpression was detected in 7 of 12 isolates in this group. 18 distinct banding patterns were determined by AP-PCR. Increased transcription of mexB was directly correlated with meropenem resistance in the majority of isolates tested, while MexCD-OprJ and MexEF-OprN were related to quinolone resistance; the MexCD-OprJ efflux pump was also related to multidrug resistance. Increased transcription of mexY may contribute to the gentamicin resistance.

Evaluation of emm gene types, toxin gene profiles and clonal relatedness of group A streptococci.

The aim of this study is to evaluate antibiotic susceptibilities, emm gene types, toxin gene profiles and clonal relatedness of group A streptococci (GAS) isolates obtained from patients and carriers. A total of 79 clinical isolates from patients and 60 isolates from carriers were included in the study. Emm typing, toxin gene detection for speA, speB, speC, speG and smeZ genes and pulsed-field gel electrophoresis (PFGE) was performed. Twenty-one distinct emm types were detected; the most common types were emm12, emm89, emm1, emm77, emm4 and emm3. The detection rates of both emm types and the toxin genes didn't differ significantly between patients and carriers. The presence of speA and smeZ was significantly higher in emm1 and speG was significantly lower in emm4 when compared to the other emm types. The rate of clustering obtained with PFGE wasn't significantly different in patients and carriers. As a result, twelve of the 21 emm types detected in this study were covered by the 26-valent vaccine, constituting 77.7% of the emm typeable isolates; however the emm4 type which is one of the most common types in the present study is not among this coverage.

Evaluation of hepatitis C virus RNA stability in room temperature and multiple freeze-thaw cycles by COBAS AmpliPrep/COBAS TaqMan HCV.

To assess the stability of various sample types and storage conditions for quantitative detectability of hepatitis C virus (HCV) RNA viral loads, we studied serum and EDTA/citrate plasma samples obtained from 10 patients known to be positive for HCV RNA. Samples were subjected to the following conditions: 1) 10 freeze-thaw (FT) cycles, and 2) storage at room temperature for 24, 48, and 72 h. Detection of HCV RNA was performed by COBAS AmpliPrep/COBAS TaqMan HCV. The following conclusions were reached: 1) no significantly different viral loads were observed in different blood compartments; 2) no significantly different viral loads were observed after 24, 48, and 72 h at room temperature; 3) no significantly different viral loads were observed after 10 FT cycles in serum and plasma samples; and 4) HCV RNA is quite stable in serum and plasma (EDTA/citrate) samples.

Activity of a dry mist-generated hydrogen peroxide disinfection system against methicillin-resistant Staphylococcus aureus and Acinetobacter baumannii.

BACKGROUND: The aim of this study was to evaluate the activity of a dry mist-generated hydrogen peroxide (DMHP) system (Sterinis; Gloster Sante Europe, Labege cedex, France) against methicillin-resistant Staphylococcus aureus (MRSA) and Acinetobacter baumannii. METHODS: McFarland 0.5 suspensions of 2 test bacteria, either pure or containing 5% sterile serum, were prepared and inoculated onto sterile stainless steel disks. Each disk in a Petri dish-with the Petri dish cover either closed or open-was placed in different locations in an intensive care unit room. Quantitative cultures were performed after the cycle. RESULTS: No growth occurred on the disks in the absence of a barrier, except 1 disk containing serum. Existence of a barrier, as a drawer or a covered Petri dish, caused failure in the disinfection activity. The mean reduction in initial log(10) bacterial count was lower for both of the test bacteria in presence of a barrier: 4.44- to 4.70-log(10) colony-forming units (cfu) decrease was observed in absence of a barrier, whereas 1.49- to 3.79-log(10) cfu decrease was observed in presence of a barrier. When the culture results were compared according to organic load content, the mean (±standard deviation) reduction of initial contamination in pure and in serum containing MRSA suspensions was 4.25 ± 1.20- and 3.34 ± 1.89-log(10) cfu, respectively. The mean (±standard deviation) reduction in pure and in serum containing A baumannii suspensions was 4.34 ± 0.89- and 3.87 ± 1.26-log(10) cfu, respectively. The differences were statistically significant (P < .001). CONCLUSION: Sterinis was capable of killing MRSA and A baumannii on open surfaces; however, it was not effective in closed or semiclosed areas. Presence of serum also caused failure in the disinfection activity of the system.

[Causative agents of intravenous catheter-related infections and their antibiotic susceptibilities]. / Damar Içi Kateter ile Iliskili Enfeksiyon Etkenleri ve Antibiyotik Duyarliliklari

Intravenous catheterization can lead to colonization as well as a broad spectrum of infections ranging from catheter site infections to catheter-related blood stream infections (CRBSIs). The aim of this study was to evaluate the distribution of causative agents and their antibiotic susceptibility patterns in CRBSIs and catheter site infections along with the colonization rates and colonizing microorganisms in Zonguldak Karaelmas University Hospital, Turkey. The results of cultures from catheter tips and/or intracatheter blood cultures and simultaneously taken peripheral blood cultures were sent to medical microbiology laboratory and were retrospectively investigated for 201 patients hospitalized between September 2007 and September 2009. The catheter tips were cultured by semi-quantitative and quantitative culture methods. Blood cultures from the catheters and peripheral veins were performed in BACTEC 9120 (Becton Dickinson, USA) blood culture systems. The antibiotic susceptibility tests were done by Kirby-Bauer disk diffusion method according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). Out of 201 patients included, 28 (13.9%) had CRBSIs and 13 (6.4%) had catheter site infections while colonization was defined for 55 (27.3%) patients. Of 28 patients with CRBSIs, Acinetobacter spp. were isolated from 11 including five carbapenem-resistant strains, methicillin-resistant coagulase-negative staphylococci (MRCNS) from eight, methicillin-susceptible coagulase-negative staphylococci (MSCNS) from two, Klebsiella pneumoniae from two patients and one of each patient's cultures yielded methicillin-resistant Staphylococcus aureus (MRSA), carbapenem-resistant Pseudomonas aeruginosa, Enterococcus spp., Escherichia coli and MRCNS + Enterococcus faecium. Of 13 patients with catheter site infections, five MSCNS, two methicillin-susceptible S.aureus (MSSA), two E.coli, and one of each K.pneumoniae, MRCNS, Enterococcus spp., K.pneumoniae + P.aeruginosa were isolated. No resistance to vancomycin and teicoplanin were detected among the staphylococci isolated from CRBSIs and catheter site infections. The distribution of the 55 colonizing microorganisms were as follows; 18 MSCNS, 18 MRCNS, four Acinetobacter spp., five K.pneumoniae, three E.coli, two MSSA, and one of each MRSA, P.mirabilis, P.aeruginosa, Corynebacterium spp., Candida albicans. In this study, the predominant microorganism isolated from CRBSIs was Acinetobacter spp., followed by coagulase-negative staphylococci. This unexpected distribution of the agents was related to the Acinetobacter spp. that have gained endemic potential following an Acinetobacter outbreak in our hospital in 2006. We emphasize that it is critical for any individual hospital to assess periodically the distribution and susceptibility profiles of isolates obtained from catheter-related infections to set out rational empirical treatment strategies.

Determination of Staphylococcus aureus carriage in hemodialysis and peritoneal dialysis patients and evaluation of the clonal relationship between carriage and clinical isolates.

BACKGROUND: This study was conducted to investigate Staphylococcus aureus carriage in patients undergoing hemodialysis and peritoneal dialysis and to evaluate the clonal relationship between carriage and clinical isolates. METHODS: Surveillance for S aureus carriage was performed in 30 hemodialysis patients, 40 peritoneal dialysis patients, 13 workers in the unit, and 40 controls. The clonal relatedness of isolates was assessed by pulsed-field gel electrophoresis. RESULTS: Screening cultures yielded 8 (26.6%) isolates from the hemodialysis patients, 9 (22.5%) from the peritoneal dialysis patients, 4 (30.7%) from the staff, and 8 (20%) from the controls. All of the isolates were methicillin-susceptible except one from a hemodialysis patient. There was no significant difference in carriage rate among the study groups. A history of hospital admission in the previous 6 months and a history of infection was associated with an increased carriage rate. A total of 23 genotypes were established for the 28 isolates, demonstrating high clonal heterogenecity. Six clinical isolates from 4 hemodialysis patients and 4 clinical isolates from two peritoneal dialysis patients were molecularly evaluated to compare isolates obtained from infection with carriage isolates of the same patients. All but one of these clinical isolates were "indistinguishable/closely related" to the isolates obtained from the same patients as carriage isolates. CONCLUSION: Opur data show a clear association between S aureus carriage and S aureus infection. Determining the S aureus carriage state of patients undergoing dialysis can help guide infection prevention measures and treatment strategies.

[Hepatitis C virus genotypes in a province of western Black-Sea region, Turkey]. / Zonguldak bölgesinde hepatit C virusu genotipleri.

Hepatitis C virus (HCV) is one of the significant causes of hepatitis, cirrhosis and hepatocellular carcinoma all throughout the world. There are six genotypes and more than 50 subtypes of HCV. HCV genotyping is of crucial importance in the determination of the treatment protocols and the follow-up of the clinical course since treatment success is low and the duration of treatment is longer in HCV genotype 1 infected cases. The aim of the present study was to evaluate the HCV genotype profiles of the patients with chronic hepatitis C in Zonguldak, providing the first data about HCV genotypes from western Black-Sea region, Turkey. The HCV genotypes of 44 patients (26 female, 18 male; age range: 29-89 years, mean age: 60.05 ± 10.81 years) with positive anti-HCV antibody and HCV-RNA results, admitted to the hospital between May 2007 and July 2009, were retrospectively evaluated and included in the study. Alanine aminotransferase (ALT) levels of the patients were between 8-160 IU/L (mean 63.99 ± 37.15 IU/L) and the aspartate aminotransferase (AST) levels were between 17-160 IU/L (mean 62.77 ± 36.75 IU/L). HCV antibody was determined by ELISA method (Abbott Laboratories, USA), and HCV-RNA was determined by two commercial real-time polymerase chain reaction systems [Cobas Taqman (Roche Diagnostic, USA) and Rotor-Gene 6000 (Corbett Research, USA)]. The genotyping was performed by a reverse hybridization based method, Versant® HCV Genotype Assay (LiPA) 2.0 (Bayer Health Care, Belgium). HCV genotypes could not be determined for 5 (11.4%) patients since HCV-RNA levels were low. Genotyping could be performed for 39 (88.6%) patients and 38 (97.4%) had genotype 1b and one (2.6%) patient had genotype 1a. In conclusion, in concordance with the other studies conducted in our country, genotype 1b was found to be the most prevalent genotype in patients from our region.

Evaluation of the prevalence of enterotoxigenic Bacteroides fragilis and the distribution bft gene subtypes in patients with diarrhea.

The aim of this study was to determine the prevalence of enterotoxigenic Bacteroides fragilis (ETBF) in the patients with diarrhea in our region and to assess the association between diarrhea and bft gene subtypes. The presence of ETBF and bft gene subtypes were investigated in 200 stool samples from patients with diarrhea, diagnosed as gastroenteritis, which were sent to Clinical Microbiology Laboratory at Zonguldak Karaelmas University, Training and Research Hospital and in 200 stool samples from age-matched healthy subjects between April 14, 2009 and October 28, 2009. Nested - polymerase chain reaction was used to detect the presence of bft gene directly from stool samples. The bft gene subtypes were determined by PCR in case of ETBF detection. The presence of bft gene was detected in 29 (15%) of patients and 27 (14%) of control group. bft-1 and bft-2 were found in 24 and five stool samples from 29 diarrheic patients with ETBF, respectively. Among 27 control patients with ETBF, bft-1 and bft-2 were found in 24 and three samples, respectively. No bft-3 subtypes were identified in our study. ETBF was found as a single pathogen in 9% of the patients with diarrhea, while there was an accompanying pathogen in 6% of the patients. The proportion of coinfection with another pathogen among ETBF positive patients was 38%. Cooccurance with ETBF was present in nine of 18 patients with Rotavirus and two of five patients with Entamoeba histolytica. In conclusion; there was no statistically significant difference between the prevalence of ETBF in diarrheal patients and that of the control group. When the patients and controls were compared for each age group, no statistically significant difference in ETBF rates was found. There was no significant difference between groups with respect to bft subtypes; bft-1 was identified as the most common subtype. The rate of coinfection of ETBF and Rotavirus was high.

Characterisation of carbapenem-resistant Acinetobacter baumannii outbreak strains producing OXA-58 in Turkey.

The aim of this study was to characterise the molecular epidemiology and mechanisms of carbapenem resistance of nosocomial Acinetobacter baumannii isolates in a new university hospital in Turkey. A total of 145 carbapenem-resistant A. baumannii (CRAB) isolates were collected during the period 2003-2006. All isolates were typed by amplified fragment length polymorphism (AFLP) analysis. AFLP analysis showed three predominant clusters consisting of 72, 20 and 12 clinical strains as well as some smaller clusters and 23 unique strains. The three main clonal AFLP types corresponded to three major antibiotic susceptibility patterns. One environmental isolate was found related to the major outbreak clone. The reference type strains of European clones I, II and III were also typed by AFLP and analysed for clonal similarity. Polymerase chain reaction (PCR) analysis of different carbapenem resistance genes showed that strains from each of the three main clusters as well as 79% of the remaining strains harboured the bla(OXA-58) gene. No genes encoding the metallo-beta-lactamases GIM-1, SIM-1, SPM-1, IMP-like and VIM-like or the oxacillinases OXA-24-like and OXA-23-like were detected. In conclusion, multiple clones of CRAB strains producing OXA-58-type oxacillinase were responsible for a sustained CRAB outbreak occurring in a hospital in Turkey. These isolates were not associated with A. baumannii strains of the major European clones I, II or III.

[Determination of hepatitis B virus genotypes by DNA sequence analysis in patients from Ankara, Turkey]. / Ankara bölgesindeki hepatit B virusu genotiplerinin DNA dizi analizi yöntemi ile belirlenmesi.

Hepatitis B virus (HBV) genotypes vary depending on the geographical region. The HBV genotype determined in Turkey has been genotype D which is found as the homogenously disseminated single genotype. The aim of this study was to determine HBV genotypes in a group of HBV infected patients who were admitted to a university hospital in Ankara, Turkey. Serum samples from HBsAg positive and anti-HBs negative 84 (52 male, 32 female) patients with HBV infection were included into the study. Anti-HBc was positive in 95.2%, HBeAg was positive in 47.6% and anti-HBe was positive in 11.9% of the patients. Mean HBV-DNA levels of the patients were 5.7 x 10(7) +/- 4.6 x 10(7) IU/ml; mean ALT levels were 131 +/- 171 IU/ml and mean AST levels were 98 +/- 170 IU/ml. HBV-DNA was extracted from serum by the phenol-chloroform method and PCR was performed to amplify the S gene region of HBV-DNA. Cycle sequencing of PCR products was performed by a commercial "Cy5/Cy5.5 Dye Primer Cycle Sequencing Kit" (Visible Genetics, Canada) based on dideoxy chain termination method. The sequences were read and analyzed in an automated fluorescence-based DNA-sequencing system (Long-Read Tower System, Visible Genetics, Canada). The nucleotide sequences of the patient samples were compared with the previously reported sequences in gene bank for each genotype. According to the comparative analysis of S-sequences of all patient samples with the published sequences of the genotypes in gene bank, all of the 84 hepatitis B strains (100%) were shown to be related to D genotypic group, subtype ayw. A phylogenetic analysis was performed and phylogenetic trees were constructed using programs in the PHYLIP phylogeny inference package. The patient samples clustered within the genotypic group D. According to these results, the main HBV genotype in our patients was genotype D in accordance with the previous molecular epidemiologic information on HBV in this geographic area. HBV genotype determination may help to establish more rational clinical approach in the evaluation of HBV infected patients.