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Antimicrobial resistance (AMR) is one of the most important problems threatening human health worldwide. The impact of the Coronavirus disease-2019 (COVID-19) pandemic on AMR continues to be discussed. Some researchers argue that the pandemic will increase AMR rates, while others suggest the opposite. The aim of this study was to investigate the change in AMR of Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus strains in three cross-sectional periods in Türkiye, the first one before the COVID-19 pandemic, the second and the third one during the pandemic. The change in antibiotic susceptibility in Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus strains isolated from urine, blood, and lower respiratory tract samples of patients hospitalized in intensive care units and wards of hospitals before (November 2019) and during the COVID-19 pandemic (November 2020 and July 2021) was investigated in this study. A total of 17 voluntary hospitals, members of the Antibiotic Susceptibility Surveillance Study Group (ADSI) of the Society for Clinical Microbiology Specialists (KLIMUD), participated in the study. Identification of bacteria was performed with automated bacterial identification systems (VITEK2, bioMérieux, France or Phoenix, BD, USA). Antibiotic susceptibility tests were performed in one center with the Kirby-Bauer disc diffusion method and in other centers with automated antibiotic susceptibility test systems (VITEK2, bioMérieux, France or Phoenix, BD, USA), and the results were evaluated according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. Antibiotic susceptibility ratios were statistically analyzed using either the chi-square or Fisher's exact test. A p-value of < 0.05 was considered statistically significant. Antibiotic susceptibility test results of a total of 4030 strains; 1152, 1139, and 1739 belonging to November 2019, November 2020, and July 2021, respectively; were examined. While cefotaxime and ceftazidime susceptibility rates in E.coli strains increased during the pandemic period compared to previous period (p= 0.04, p= 0.001, respectively); nitrofurantoin sensitivity (p= 0.02) and extended-spectrum beta-lactamase (ESBL) ratios (p< 0.001) were found to be decreased. It was determined that the susceptibility rates of all other examined antimicrobials did not change statistically. It was observed that the susceptibility rates of all antibiotics in K.pneumoniae isolates decreased during the pandemic period, but the ESBL rates increased between 2019-2020 (p= 0.01) and decreased between 2020-2021 (p= 0.02). It was found that ESBL rates increased before and after the pandemic. It was observed that the susceptibility to ciprofloxacin (p= 0.0001), levofloxacin (p= 0.003), and gentamicin (p= 0.005) in S.aureus strains increased during the pandemic period. No significant changes were observed in other antibiotic susceptibility rates. Methicillin resistance of S.aureus (MRSA) strains decreased between 2019-2020 (p= 0.03) and increased again in 2021 (p= 0.04) and returned to the pre-pandemic rate. Our study results suggest that the measures taken to reduce the spread of COVID-19 with the pandemic (such as quarantine practices, increased hand hygiene, mask use, and national/international travel restriction) may reduce the spread of bacteria such as ESBL-producing E.coli and the rate of MRSA, which is considered as a hand hygiene indicator. The increase in the later stages of the pandemic recalls the relaxation in compliance with hand hygiene rules. The decrease in the susceptibility rate of K.pneumoniae isolates to antibiotics and the increase in the ESBL rate may be due to inappropriate and excessive use of antibiotics during the pandemic period. However, we believe that these data should be supported by studies to be conducted nowadays when all the rules and measures are back as if the pandemic has ended.

Objectives : To determine the serotype distribution of pneumococcus causing invasive pneumococcal disease (meningitidis, bacteremia and empyema) in children in Turkey, and to observe potential changes in this distribution in time to guide effective vaccine strategies. Methods : We surveyed S. pneumoniae with conventional bacteriological techniques and with real-time polymerase chain reaction (RT-PCR) in samples of cerebrospinal fluid (CSF), blood and pleural fluid. S. pneumoniae strains were isolated from 33 different hospitals in Turkey, which are giving health services to approximately 60% of the Turkish population. Results : A total of 167 cases were diagnosed with invasive pneumococcal disease between 2015 and 2018. We diagnosed 52 (31.1%) patients with meningitis, 104 (62.2%) patients with bacteremia, and 11 (6.6%) patients with empyema. Thirty-three percent of them were less than 2 years old and 56% less than 5 years old. Overall PCV13 serotypes accounted for 56.2% (94/167). The most common serotypes were 19 F (11.9%), 1 (10.7%) and 3 (10.1%). Conclusions : Besides the increasing frequency of non-vaccine serotypes, vaccine serotypes continue to be a problem for Turkey despite routine and high-rate vaccination with PCV13 and significant reduction reported for the incidence of IPD in young children. Since new candidate pneumococcal conjugate vaccines with more serotype antigens are being developed, continuing IPD surveillance is a significant source of information for decision-making processes on pneumococcal vaccination.

Colistin resistant Acinetobacter baumannii strains are of great concern worldwide. However, the role of efflux pumps in colistin resistance needs to be elucidated. We investigated the changes in colistin MICs of 29 colistin resistant A. baumannii isolates in response to resistance-nodulation-division (RND)-type efflux pump inhibitor (EPI) and the alterations in AdeR and AdeS two-component regulatory proteins previously associated with the overproduction of AdeAB. The EPI, 1-(1-naphthylmethyl)-piperazine (NMP), led to significant reductions in colistin MICs. At least one of the following amino acid substitutions was found in AdeS proteins from 18 of the isolates: L172P, A94V, V27I, V32I, G186V, and G164A. Besides, A136V and V120I alterations were identified in AdeR from five isolates. Therefore, EPI-responsive colistin resistance in our isolates is most likely due to the action of an RND-type efflux system. The underlying mechanism of resistance might be the result of certain AdeRS alterations, leading to AdeAB overexpression.

Urinary tract infections are one of the most common bacterial infections and rapid diagnosis of the infection is essential for appropriate antibiotic therapy. The goal of our study was to identify urinary pathogens directly by MALDI-TOF MS and to perform antibiotic susceptibility tests in order to shorten the period spent for culturing.Urine samples submitted for culture to the Clinical Microbiology Laboratory were enrolled in this study. Urine samples were screened for leukocyte and bacteria amount by flow cytometry. Samples with bacterial load of 106-107/mL were tested directly by MALDI-TOF MS and antibiotic susceptibility tests (AST) were performed.In total, 538 positive urine samples were evaluated in our study. MALDI-TOF MS identified the microorganism directly from the urine sample in 91.8% of these samples and the concordance rate of conventional identification and direct detection was 95.8% for Gram-negatives at the genus and species level. Escherichia coli (n:401) was the most frequently isolated microorganism, followed by Klebsiella pneumoniae (n:57). AST results were generated for 111 of these urine samples and the concordance was 90% and 87% for E. coli and K. pneumoniae, respectively.Our results showed that screening of urine samples with flow cytometry to detect positive samples and identification of uropathogens directly by MALDI-TOF MS with an accuracy of over 90% can be a suitable method particularly for Gram-negative bacteria in clinical microbiology laboratories.

Gram-positive anaerobic cocci (GPAC), a large group of anaerobic bacteria, are the members of the normal microbiota that colonizes the skin and mucosal surfaces of the human body. However, in case of a wound or when the host becomes immunocompromised, GPAC can cause invasive and most frequently mixed infections. GPAC are the second most frequently isolated bacteria in anaerobic infections. Although the studies are limited, GPAC have been reported to develop resistance to antimicrobial drugs. The resistance of the pathogens to the antimicrobials and improper therapy can cause poor clinical outcomes. Therefore, monitoring of the resistance trends of regional clinically important anaerobic bacteria periodically is recommended. In our study, we aimed to determine the antimicrobial susceptibility profiles of clinically important GPAC. A total of 100 non-duplicated pathogenic GPAC isolates were collected from Marmara University Hospital between 2013 and 2015. The isolates were identified by using conventional methods, "matrix-assisted laser desorption ionization-time of flight mass spectrometry system (MALDI-TOF MS)" (VITEK MS; v3.0, bioMerieux, France) and 16S rRNA gene sequencing. Antimicrobial susceptibility test was carried out by the agar dilution method according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. The following antimicrobials were tested: penicillin, amoxicillin/ clavulanic acid (AMC), cefoxitin, meropenem, clindamycin, erythromycin, tetracycline, tigecycline, chloramphenicol, moxifloxacin and metronidazole. The minimum inhibitory concentration (MIC) results were interpreted according to the breakpoints described by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Breakpoints recommended by CLSI for cefoxitin, tetracycline and moxifloxacin, and breakpoint recommended by Food and Drug Administration (FDA) for tigecycline were used since there were no EUCAST breakpoints for these antimicrobials. MIC50 and MIC90 values were determined for erythromycin since the breakpoint was not described by EUCAST, CLSI or FDA guidelines. The identification results showed that the strains (n= 100) consisted of five different GPAC genus; Parvomonas (40%), Finegoldia (34%), Peptoniphilus (14%), Peptostreptococcus (10%) and Anaerococcus (1%). All of the organisms were susceptible to meropenem, tigecycline and metronidazole. The isolates were highly susceptible to penicillin, AMC, cefoxitin, and chloramphenicol, since the resistance rates against these antimicrobials were 5% or less. The resistance rates against clindamycin, tetracycline and moxifloxacin were 14%, 31% and 24%, respectively. In total, 11% of the isolates were multidrug resistant. Metronidazole and tigecycline displayed high in vitro activity against GPAC and both are appropriate antimicrobials for the selection of empiric therapy. The effectiveness of meropenem was also found high, but it was observed that this antimicrobial would be more appropriate to use in the treatment of severe mixed infections accompanied by other microorganisms with the resistance potential. Detection of penicillin and AMC resistant isolates, which are frequently used in the treatment of GPAC infection, requires periodic monitoring of the antimicrobial susceptibility patterns of GPAC. The high rates of resistance against clindamycin, tetracycline and moksifloxacin indicated that these antimicrobials should not be used for empirical treatment of infections without prior antimicrobial susceptibility testing. This study is one of the largest susceptibility studies specifically carried out on GPAC to date in Turkey. We believe that our results will provide good surveillance data both for our hospital and our country.

Clostridioides difficile, a gram-positive, anaerobic, spore forming bacillus known as Clostridium difficile according to the previous taxonomy, is the most important agent of antibiotic-associated diarrhea. C.difficile infections have become a major health problem for many countries. The rate of antimicrobial resistant C.difficile isolates is rapidly increasing all around the world. Yet there is limited data on this subject in our country. The aim of this study was to determine the antimicrobial susceptibility profiles of C.difficile strains isolated from stool samples in Marmara University Pendik Training and Research Hospital Microbiology Laboratory. A total of 93 toxigenic C.difficile, defined by serological and molecular techniques, were included in this study. Antimicrobial susceptibility profiles of isolates were determined by using agar dilution method according to the Clinical and Laboratory Standards Institute (CLSI; M11-A7). The following antimicrobials commonly used for the treatment of C.difficile infections or applied previously in C.difficile epidemiological studies were tested: metronidazole, vancomycin, meropenem, ceftriaxone, ampicillin-sulbactam, clindamycin, erythromycin, moxifloxacin, tetracycline, doxycycline, tigecycline and linezolid. The minimum inhibitory concentration (MIC) results were interpreted according to the breakpoints described by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Breakpoints recommended by CLSI were applied for ceftriaxone, clindamycin, tetracycline and moxifloxacin since there were no EUCAST breakpoints for these antimicrobials. MIC50 and MIC90 values were determined for three antimicrobials (linezolid, erythromycin, doxycycline) whose breakpoints were not described by EUCAST or CLSI guidelines. All isolates were susceptible to metronidazole, vancomycin, ampicillin-sulbactam, meropenem and tetracycline. Susceptibility to ceftriaxone, clindamycin and moxifloxacin was found in 58.1%, 35.5% and 20.4% of the isolates, respectively. MIC50 and MIC90 values of tigecycline, erythromycin linezolid, doxycycline were 0.125-0.25 mg/L, 1-2 mg/L, 2-2 mg/L, 0.062- 0.125 mg/L, respectively. This study shows the current antimicrobial susceptibility patterns of C.difficile isolates in our hospital and will also be the reference data for clinical laboratories in our country where anaerobic culture and susceptibility tests are not performed in routine practice. In conclusion, two main antimicrobial agents commonly used in the treatment of C.difficile infections, metronidazole and vancomycin, seem to be effective. However, high resistance rates against to the certain tested antimicrobials highlight the need for further surveillance to monitor the emergence of resistance.

Prevotella species, being members of the human microbiota, are obligate anaerobic gram-negative bacteria. These organisms may cause opportunistic infections, including specific oral infections, local or systemic infections. A significant increase of resistance to some antimicrobials has been detected among Prevotella species. The frequency of resistance vary among isolates from different infection sources and between geographic locations. The knowledge about the antimicrobial susceptibility patterns of different Prevotella species is limited in Turkey. Providing the antimicrobial susceptibility data of these bacteria is very important for effective empirical treatment. In this study, we aimed to determine susceptibility data for 12 antimicrobial agents against Prevotella strains originating from human infections, collected in two centers in Turkey. A total of 118 Prevotella strains, isolated from different clinical samples in Marmara University Faculty of Medicine Medical Microbiology and Istanbul University Faculty of Dentistry Oral Microbiology Laboratories between January 2014-December 2017, were tested. Organisms were identified by using MALDI-TOF MS and by 16S rRNA gene sequencing. Minimal inhibitor concentrations of ampicillin, ampicillin-sulbactam, piperacillin-tazobactam, cefoxitin, meropenem, imipenem, clindamycin, tetracycline, tigecycline, moxifloxacin and metronidazole were determined using gradiyent test methodology (E-test; bioMerieux, France) and the European Committee on Antimicrobial Susceptibility Testing, Clinical and Laboratory Standards Institute and Food and Drug Administration guidelines were used for interpretation. Thirteen different Prevotella species were identified, Prevotella bivia and Prevotella nigrescens were the most prevalent species (n= 21) followed by Prevotella buccae (n= 19). All Prevotella strains were susceptible to piperacillin-tazobactam, cefoxitin, meropenem, imipenem and tigecycline. A total of 2 (1.7%) isolates were resistant to metronidazole and 1 (0.8%) isolate was intermediately resistant to ampicillin/sulbactam. The frequency of resistant isolates against ampicillin, clindamycin, tetracycline and moxifloxacin were 57.6%, 36.4%, 18% and 16.3%, respectively. In conclusion, piperacillin/tazobactam, cefoxitin, and tigecycline displayed high in vitro activity against Prevotella spp. and they all remained good candidates for empiric therapy. Imipenem and meropenem were also found to be very active, but the usage of carbapenems should be reserved for serious mixed infections, potentially accompanied by other resistant organisms. Intermediate resistance to ampicillinsulbactam and the resistance against metronidazole emphasized the need of periodic monitoring of their susceptibility patterns. The high rates of non-susceptibility to ampicillin, clindamycin, tetracycline and moxifloxacin indicated that these antimicrobials should not be used for treatment of infections without prior antimicrobial susceptibility testing.

The aim of this study was to evaluate the prevalence of nasopharyngeal (NP) carriage and the serotype distribution and antimicrobial resistance of Streptococcus pneumoniae in children with chronic diseases, which predisposes them to invasive pneumococcal disease in comparison with that in healthy children. A cross-sectional prevalence study was performed between February 2015 and February 2016 in Istanbul, Turkey. We enrolled 1,024 children with chronic diseases and 394 healthy children aged 0-18 years. The overall prevalence of S. pneumoniae NP (SPNP) carriage was 9.8%, with 8.4% in healthy children and 10.3% in children with chronic diseases. The prevalence rates of SPNP carriage were 17.5%, 13.5%, 10.5%, 9.3%, 8.6%, 8.6%, 8%, 6.7%, and 4%, respectively, in each of the following risk groups: primary immunodeficiency, asthma, chronic renal failure, congenital heart disease, chronic lung disease, leukemia, nephrotic syndrome, solid organ tumors, and type 1 diabetes mellitus. In the multivariate analysis, a history of otitis media within the last year, a history of pneumonia within the last year, and more than one sibling under 8 years of age were found to be independent risk factors for SPNP carriage.

In this study, the performance of the "RESIST-3 O.K.N. K-SeT" (Coris BioConcept, Gembloux, Belgium) immunochromatographic assay was evaluated in 132 Klebsiella pneumoniae comprising 102 carbapenem resistant and 30 carbapenem susceptible isolates. Genotypically known isolates of Gram negative bacteria (n=22) including various species were also tested by the assay as controls. The isolates tested by the immunochromatographic assay and also were run PCR for bla KPC , bla IMP , bla VIM , bla NDM , and bla OXA-48 . The rates of bla NDM , bla OXA-48 , and bla KPC in carbapenem resistant isolates were found at 52.9%, 39.2%, and 2.0%, respectively. Both bla NDM and bla OXA-48 were found in six (5.9%) isolates. The results of the assay showed 100% concordance with those obtained by PCR in 132K. pneumoniae. The agreement between the two methods was found to be identical at the isolate level. The assay also correctly detected all genotypically known isolates of Escherichia coli, Serratia marcescens, Citrobacter freundii, Enterobacter cloacae, K. pneumoniae carrying bla KPC , bla NDM , and/or bla OXA-48 . On the other hand, the assay did not exhibit any cross-reaction in control isolates harboring bla IMP and bla VIM . We conclude that the RESIST-3 O.K.N. K-SeT is a reliable, rapid, and user friendly test and we recommend it for routine diagnostic laboratories., (Copyright © 2018 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.)

Background: The aim of the present study was to determine the diagnostic and prognostic values of suPAR and to compare them to CRP and PCT in pediatric patients with systemic inflammatory response syndrome (SIRS)., Material-Methods: A prospective case-control study was performed.The study was performed in a tertiary university hospital which has a 649-bed capacity. Patients included 27 children with SIRS and 27 control subjects without any infection or immunosuppressive condition. Blood samples were obtained on the day of admission and on the 4-7th days of the hospital stay., Results: The median (min-max) serum levels of suPAR obtained on the first day of the admission were 10.06 (2.7-57.46) and 2.22 (1.08-5.13) ng/Ml for the SIRS group and control group, respectively. The median serum levels of suPAR in the SIRS group was significantly higher than that in the control group (p < 0.05). The serum suPAR levels was significantly higher in nonsurvivors than in survivors in SIRS group (p < 0.05). In the SIRS group, the area under the receiver operating characteristics curve (AUC ROC ) for suPAR revealed an optimum cut-off value, sensitivity, specificity, NPV and PPV of 0.978, 3.8 ng/mL, 96%, 96%, 96%, and 96%, respectively., Conclusions: We conclude that suPAR does have diagnostic value in children with SIRS. Additionally, persistent high serum suPAR level predicts mortality in SIRS in children., (Copyright © 2016 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.)

Background: Chryseobacterium indologenes is an uncommon organism that has been documented to cause a variety of invasive infections mostly in hospitalized patients with severe underlying diseases., Case Presentation: A three-month-old female infant born at term by caesarean section with meningomyelocele and congenital diaphragmatic hernia had two surgeries for the repair of meningomyelocele and diaphragmatic hernia on her 3rd and 14th day, respectively. On the 3rd month of her life, she deteriorated clinically with fever, leukocytosis and increase of acute-phase reactants. Gas exchange condition became worse than it was before. Respiratory secretions, oxygen requirements and ventilator demand increased. Chest X-ray showed bilateral pulmonary infiltrates. Bacteriological blood, urine and cerebrospinal fluid culture test results were negative. C. indologenes was isolated from tracheobronchial secretion sample obtained by endotracheal aspiration. Although susceptible to ciprofloxacin (MIC:0.5 gr/L), levofloxacin and piperacillin-tazobactam, the isolate was resistant to meropenem, imipenem and colistin. She was treated with ciprofloxacin successfully. Her fever resolved and gas exchange condition improved after 72 h of the treatment. The antibiotic treatment was given for a course of 14 days., Conclusion: Chryseobacterium indologenes may emerge as a potential pathogen in infants with the factors such as invasive equipment, having underlying diseases and prolonged hospitalization.

Background: Clostridium difficile is a major cause of antibiotic-associated diarrhea and frequently results in healthcare-associated infections. The aim of this study was to determine the incidence and potential risk factors for C. difficile infection (CDI) in hospitalized children who developed diarrhea. A retrospective study was performed at a university hospital in İstanbul over a three-year period (2012-2014)., Results: During the study period 12,196 children were hospitalized, among them 986 (8 %) children with diarrhea were investigated for CDI and 100 (0.8 %) children were diagnosed with CDI. The incidence of CDI in hospitalized children was 4/1000, 9/1000 and 9/1000 patients per year in year 2012, 2013 and 2014, respectively (p = 0.008, p < 0.01). The mean age of children with CDI (2.6 ± 2.6 months) was lower than children without CDI (57.5 ± 63.5 months) [p = 0.001]. In the multivariate analysis, the presence of underlying chronic diseases [presence of malnutrition (OR 7, 95 % CI 1.33-36.7, p = 0.021), presence of solid organ tumors (OR 6, 95 % CI 2.4-15.7, p < 0.00), presence of congenital heart diseases (OR 4.6, 95 % CI 1.13-18.7, p = 0.03), hospitalization in PICU (OR 15.6, 95 % CI 3.2-75.8, p = 0.001) and hospitalization in hematology and oncology ward (OR 7.8, 95 % CI 2-29.9, p = 0.002)] were found to be independent risk factors for CDI., Conclusion: This is the first description of the incidence and associated risk factors of CDI in Turkish children. One of the most important risk factor was prior antibiotic exposure which emphasizes the importance of antibiotic stewardship programs.

Background: The 7-valent conjugate pneumococcal vaccine (PCV7) was introduced by the Turkey National Immunization Program in 2008 and replaced by the PCV13 in 2011. We assessed the impact of PCV vaccination on the nasopharyngeal (NP) carriage, serotype distribution and antimicrobial resistance of Streptococcus pneumoniae (SP) among healthy Turkish children., Methods: A prospective surveillance study was performed between September 2011 and September 2013 in Istanbul, Turkey. NP swabs, demographic data, and vaccination statuses were obtained from 2165 healthy children aged 0-18years. Pneumococcal carriage was defined by a positive culture; serotyping was performed via multiplex conventional PCR, and the antibiotic susceptibilities of the isolates were determined based on the minimum inhibitory concentration (MIC) values of the Clinical Laboratory Standards Institute (CLSI)., Results: The prevalence of pneumococcal carriage was 6.4%. The carriage rates were 8%, 7%, and 5% in the following age groups: 0-24months, 25-60months, and >60months, respectively. The carriage rate was significantly higher in the 0-24month age group than in the >60months age group (p=0.03). Sixty percent of the children were not vaccinated with any PCV; 4%, 2%, and 4% received at least 1, 2 or 3 doses and 30% children received the full schedule (4 doses) of either PCV7 or PCV13. Among the isolated S. pneumoniae strains, 45% were of the non-vaccine type (NVT) and 55% were of the vaccine type (VT). The children who received at least a single PCV dose had significantly lower odds of colonization via VT serotypes than the non-vaccinated children [odds ratio: 0.61 (95% confidence interval=0.41-0.91), p=0.01]. The percentages of the serotypes covered by PCV7 and PCV13 were 51% and 56%, respectively. The most frequently isolated serotypes were 6A/B/C (n=22, 16.5%), 19F (n=18, 13.5%), 23F (n=15, 11.2%), serotype 9V/A (n=10, 7.5%), 12F (n=5, 4.5%), 15A/F (n=7, 4.5%) and 22 A/F (n=6, 4.5%). Using the meningitis criteria and the MIC, 62% of the isolates were resistant to penicillin and 13% were non-sensitive to ceftriaxone. Erythromycin and clindamycin resistance were 43% and 31%, respectively., Conclusion: We shown that following nation-wide PCV vaccination, S. pneumoniae NP carriage was decreased., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Introduction: The human nasopharynx is the main reservoir of Neisseria meningitidis, and asymptomatic carriage is common. N. meningitidis one of the common causes of bacterial meningitis in Turkey, especially after the implementation of the national immunization program that includes conjugated pneumococcal and Haemophilus influenzae type b vaccines. The purpose of this study was to evaluate the prevalence of meningococcal carriage and determine the leading serogroup, which may help authorities to adapt appropriate meningococal vaccine into the national immunization programme., Methodology: The prevalence of oropharyngeal carriage of N. meningitidis in 1,000 healthy subjects, 0-79 years of age, was investigated. Oropharyngeal swabs were collected during an 18-month period. Samples obtained were inoculated onto Thayer-Martin agar. The API-NH test and VITEK-MS system were used for identification of colonies. Multiplex real-time polymerase chain reaction assay was used to determine serogroups with serogroup-specific genes., Results: N. meningitidis was isolated from 6 of 1,000 subjects (0.6%). Meningoccocal carriers were between 21 and 40 years of age. All isolates were serogrouped as B, except one that did not survive on subculture. N. lactamica was isolated from 13 of 1,000 subjects (1.3%)., Conclusions: Carriage rate of meningococci in our study was relatively low. However, we detected that serogroup B was the leading strain in meningococcal carriage in Istanbul; choosing an appropriate meningococcal vaccine containing serogroup B should therefore be considered. High absolute humidity throughout the year in Istanbul may explain the low prevalence of carriage in our study. This should be verified with a multicenter national survey.

The aim of the present study was to determine the diagnostic value of soluble urokinase plasminogen activator receptor (suPAR) in pediatric patients with febrile neutropenia. A prospective case-control study was performed. Patients included 29 children with febrile neutropenia (FN) and 27 control subjects without any infection or immunosuppressive condition. Blood samples were obtained on the day of admission and on the 4th to 7th days of the hospital stay. The median (minimum-maximum) serum levels of suPAR obtained on the first day of the admission were 2.08 (0.93-9.42) and 2.22 (1.08-5.13) ng/mL for the FN group and the control group, respectively. The median serum levels of suPAR in the FN and control groups were not significantly different (P = .053). The mean serum suPAR level was significantly higher in nonsurvivors than in survivors in the FN group (P < .05). In the FN group, the area under the receiver operating characteristics curve (AUCROC) for suPAR was 0.546, but no optimum cutoff value, sensitivity, specificity, negative predictive value (NPV), or positive predictive value (PPV) was obtained. We conclude that suPAR is not useful as a diagnostic biomarker in children with febrile neutropenia; however, persistent high serum suPAR level may predict mortality in FN in children.

Introduction: Healthcare-associated infections (HAIs) are important causes of morbidity and mortality, especially in critically ill patients in intensive care units. The aim of this study was to assess the rate and distribution of HAIs, pathogens, and antimicrobial susceptibility patterns in a newly opened pediatric intensive care unit (PICU)., Methodology: The infection control team detected and recorded HAI cases according to the Centers for Disease Control and Prevention's criteria in the PICU of Marmara University Pendik Training and Research Hospital over a four-year period following its opening. Laboratory-based HAIs surveillance was performed prospectively from 1 January 2011 to 30 November 2014., Results: During the study period, 1,007 patients hospitalized in the PICU and 224 HAIs were identified. The overall HAI rate was 22.24%, and the incidence density was 20.71 per 1,000 patient-days. The most commonly observed HAIs were bloodstream infection (35.7%), pneumonia (21.4%), and urinary tract infection (20.5%), and the three most common HAI pathogens were Klebsiella spp. (19.4%), Pseudomonas aeruginosa (13.8%), and Acinetobacter baumanii (12%). Methicillin resistance was detected in 78% of coagulase-negative Staphylococcus. Presence of extended-spectrum beta-lactamases was determined in 45% and 54% of Klebsiella spp. strains and Escherichia coli isolates, respectively., Conclusions: Our rate of HAIs is higher than the mean rates reported in PICU studies from developed countries. Active surveillance studies of HAIs is an essential component of infection control, which may contribute to improving preventive strategies in developing countries.

Background: Multidrug-resistant Gram-negative bacilli are responsible for more than 50% of healthcare-associated infections. Colonization dynamics, characteristics, and risk factor data for CR-GNB are scarce in children., Aim: To examine the molecular characteristics of, and risk factors for nosocomial colonization with, carbapenem-resistant Gram-negative bacilli (CR-GNB) in hospitalized paediatric patients in a tertiary university hospital's paediatric units in Turkey., Methods: A prospective case-control study was performed at a university hospital in Istanbul, Turkey., Findings: A total of 1840 rectal swab specimens were collected from all 762 hospitalized children between March 2013 and October 2013. Among them, 176 (23%) patients were colonized with CR-GNB. Of these, 72 (9%) patients were colonized with carbapenem-resistant Enterobacteriaceae, 138 (18%) with CR-non-fermenter Gram-negative bacilli (CR-NF) and 34 (4%) with both. The median CR-GNB colonization time was 10 days (range: 1-116). The median duration of rectal colonization with CR-GNB was 8 days (range: 1-160). NDM (31%) was the second most frequent carbapenemase identified in Acinetobacter baumannii isolates, and has not previously been detected in Turkey. All of the 17 patients colonized with NDM-producing A. baumannii were newborns in the neonatal intensive care unit. Independent risk factors for CR-GNB colonization were: age <1 year, nasogastric tube placement, presence of underlying chronic diseases, ampicillin usage, surgical intervention, and carbapenem use., Conclusion: This is the first description of NDM in A. baumannii in newborn units in Turkey. Carbapenem usage is a common independent risk factor for both CRE and CR-NF colonization, which underscores the importance of antibiotic stewardship programmes., (Copyright © 2015 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.)

Lactococcus lactis is a gram-positive coccus that is nonpathogenic in humans. Herein, we present the case of a 1-year-old boy with Down syndrome and Hirschprung's disease (HD) who developed a catheter-related bloodstream infection with L. lactis after gastrointestinal surgery. The patient had been hospitalized in the pediatric surgery unit from birth because of HD, and had undergone the Duhamel-Martin procedure which caused recurrent diarrhea episodes and feeding intolerance. On the infant's 430th day of life, he had an episode of gastroenteritis and feeding intolerance. Because of clinical suspiction of sepsis, blood cultures were taken both from the central venous catheter and peripheral vein, and evidence of a growing microorganism was detected in 2 different central venous catheter blood cultures taken 2 days apart. The colonies were then identified by both the Vitek 2 and Vitek MS systems (bioMérieux, Marseille, France) as L. lactis spp. lactis. The central venous catheter could not be removed because of the absence of a peripheral venous line, and the patient was subsequently successfully treated with vancomycin. Therefore, although Lactococcus species is generally thought to be nonpathogenic, it should still be kept in mind as a potential pathogen in infants.

Polymerase chain reaction-based surveillance for bacterial meningitis including 841 children revealed 246 with bacterial DNA in cerebrospinal fluid samples of which 53% were Streptococcus pneumoniae, 19% Neisseria meningitidis, and 16% Haemophilus influenzae type b. The most common S. pneumoniae serotypes/serogroups were 1, 19F, 6A/6B, 23F, 5, 14, 18 and 19A. Among 47 meningococci, 86% were serogroup B, 6% serogroup C, 3% serogroup A, 3% serogroup X and 3% serogroup W.

Background: The aim of this study was to determine the distribution of vancomycin and daptomycin MICs among methicillin-resistant Staphylococcus aureus (MRSA) blood isolates, the prevalence of heterogeneous vancomycin-intermediate S. aureus (hVISA) and the relationship between hVISA and vancomycin MIC values., Methods: A total of 175 MRSA blood isolates were collected from seven university hospitals in Turkey. All isolates were tested for susceptibility to vancomycin and daptomycin by reference broth microdilution (BMD) and by standard Etest method. BMD test was performed according to CLSI guidelines and Etest was performed according to the instructions of the manufacturer. All isolates were screened for the presence of the hVISA by using macro Etest (MET) and population analysis profile-area under the curve (PAP-AUC) methods., Results: The vancomycin MIC50, MIC90 and MIC ranges were 1, 2, and 0.5-2 μg/ml, respectively, by both of BMD and Etest. The daptomycin MIC50, MIC90 and MIC ranges were 0.5, 1 and 0.125 -1 μg/ml by BMD and 0.25, 0.5 and 0.06-1 μg/ml by Etest, respectively. The vancomycin MIC for 40.6% (71/175) of the MRSA isolates tested was >1 μg/ml by BMD. No vancomycin and daptomycin resistance was found among MRSA isolates. Percent agreement of Etest MICs with BMD MICs within ±1 doubling dilution was 100% and 73.1% for vancomycin and daptomycin, respectively. The prevalence of hVISA among MRSA blood isolates was 13.7% (24/175) by PAP-AUC method. MET identified only 14 of the hVISA strains (sensitivity, 58.3%), and there were 12 strains identified as hVISA that were not subsequently confirmed by PAP-AUC (specificity, 92.1%)., Conclusions: Agreement between BMD and Etest MICs is high both for vancomycin and daptomycin. Daptomycin was found to be highly active against MRSA isolates including hVISA. A considerable number of isolates are determined as hVISA among blood isolates. As it is impractical to use the reference method (PAP-AUC) for large numbers of isolates, laboratory methods for rapid and accurate identification of hVISA need to be developed.

This study aimed to investigate serotype distribution and antimicrobial resistance of Streptococcus pneumoniae isolates obtained from children with chronic respiratory diseases admitted to hospital with a diagnosis of acute exacerbations between 2008-2010 at Marmara University Hospital, Istanbul, Turkey. Sixty one S.pneumoniae strains isolated from the respiratory samples of patients were studied for erythromycin, clindamycin, tetracyline, trimethoprim-sulphametoxazole (TMP-SMX), vancomycin, levofloxacin susceptibilities by disk diffusion method; MIC values of penicillin and ceftriaxone were determined by E-test (AB Biodisk, Sweden). Results were evaluated according to the CLSI standards. The erythromycin-clindamycin double disc method was applied for the detection of macrolide resistance phenotypes. The presence of macrolide resistance genes, ermB, mef(A)/(E), ermTR were determined by PCR using specific primers for each gene. The serotypes were determined by multiplex PCR using specific primers for 40 different serotypes. According to CLSI criteria, penicillin resistance in S.pneumoniae isolates were found to be 8.2% (5/61) and intermediate resistance rate was 54% (33/61) for oral penicillin. Penicillin resistance were found to be only 1.6% (1/61) for parenteral penicillin. Resistance rates of erythromycin, clindamycin, tetracyline, TMP-SMX were detected as 55.8%, 46%, 47.5% and 67.2%; respectively. No resistance was detected to vancomycin and levofloxacin. Constitutive macrolide-lincosamide-streptogramin B (cMLSB) phenotype and M phenotype were observed in 82.4% (n= 28) and 17.6% (n= 6) of the macrolide resistant isolates, respectively. Inducible macrolide-lincosamide-streptogramin B (iMLSB) phenotype was not detected. The macrolid resistance genotypes, ermB, mef(A)/(E), were positive 50% and 14.7%; respectively. Both ermB and mef(A)/(E) genes were detected 35.3% of the macrolid resistant isolates. None of the isolates were positive for ermTR gene. The most common S.pneumoniae serotypes were determined as serotype 19F, 23F and 6, furthermore penicillin (34%, 15.7% and 18.4%, respectively) and macrolide (38.2%, 20.6% and 14.7%, respectively) resistance rates of those serotypes were found relatively high. Serotype covarage of 7-, 10-, 13-valent conjugated pneumococcal vaccines and 23-valent pneumococcal vaccine were 65%, 67%, 69%, and 78.6%, respectively. In our country, use of the vaccines with these coverage rates has been observed to be effective in children exposed to intensive use of antibiotics with chronic lung disease.

Bacteroides species, the predominant constituents of the human intestinal microbiota can cause serious intraabdominal and postoperative wound infections and bacteremia. Moreover, these bacteria are more resistant to antimicrobial agents than the other anaerobes. The limited number of the antimicrobials, such as carbapenems, beta-lactam/beta-lactamase inhibitors and nitroimidazoles are highly effective in eliminating Bacteroides. However, a few metronidazole-resistant isolates have been reported from several countries recently. The nim genes (nim A-G) are suggested to be responsible for the majority of the metronidazole resistance. Here, we describe a metronidazole-resistant Bacteroides thetaiotaomicron isolated from a blood culture. A gram-negative obligate anaerobic rod was isolated from the postoperative 5th day blood culture of a 62-year-old male patient with adenocarcinoma of the pancreas head. The strain was identified as B.thetaiotaomicron by using a combination of conventional tests and commercially available biochemical kits. Antimicrobial susceptibility testing was performed by agar dilution method. The resistance genes were investigated by means of PCR using specific primer pairs for nim gene. The purified PCR product was sequenced and analyzed by comparison of the consensus sequences with GenBank sequences. The MIC for metronidazole was 16 mg/L. Although the strain was intermediate according the CLSI criteria, it was resistant (> 4 mg/L) according to EUCAST criteria. The isolate was nim gene positive, and nucleotide sequencing of the PCR product shared 100% similarity with nimE gene (emb |AM042593.1 |). On the other hand the isolate was susceptible to carbapenems and sulbactam-ampicillin. Following administration of ampicillin-sulbactam, the patient's fever disappeared after 24 hours. The clinical condition improved considerably and he was discharged at day 8. The patient was followed up at the medical oncology clinic; however he died due to disease progression six months after surgery. Since anaerobic bacteremia is associated with high mortality rate, prompt diagnosis and proper management are critical. The studies on Bacteroides bacteremia have revealed adverse outcomes in patients receiving antibiotics to which the bacterium was resistant. In the present case, the metronidazole-resistant organism would be reported as susceptible according to CLSI breakpoint value and on account of this result the treatment might lead to clinical failure. Therefore EUCAST MIC values seem to be more rational in case of Bacteroides antibiotic susceptibility testing.

Objective: To investigate the effect of tonsil size reduction using temperature controlled radiofrequency on the number of pathogenic bacteria in the tonsil tissue., Materials and Methods: This study was performed on 25 patients who had undergone tonsillectomy under general anesthesia at our clinic. Immediately after the cold knife tonsillectomy both tonsils were removed, one was included in the control and the other one was included in the study group. In vitro radiofrequency was applied to the tonsil in the study group at eight distinct points, each lasting 15s. Biopsy materials were taken under sterile conditions from the center of each tonsil for further culturing., Results: The difference in bacterial number was investigated between the two groups. The bacterial number following radiofrequency administration was found to be significantly very lower compared to the control group (p<0.01). Radiofrequency administration significantly reduced growth of all types of bacteria., Conclusion: The radiofrequency tonsil ablation technique, which is used safely and effectively in the management of obstructive tonsil hypertrophy, currently has no indication for the treatment of patients with chronic and recurrent tonsillitis. However, when the right conditions are provided, the radiofrequency tonsil ablation technique may be applied to patients with chronic and recurrent tonsillitis and further studies investigating the differences in the frequency of patients' tonsillitis episodes should be undertaken., (Crown Copyright © 2012. Published by Elsevier Ireland Ltd. All rights reserved.)

Bacteroides fragilis, which is found in normal colon flora, is the most commonly encountered pathogen in anaerobic infections and more resistant to antimicrobial agents than the other anaerobes. Limited number of antibiotics; such as carbapenems, beta-lactam/beta-lactamase inhibitors and nitroimidazoles are the most effective antibiotics against Bacteroides, however resistant isolates to these antimicrobials have been reported recently. Resistance against carbapenems occurs due to a metallo-beta-lactamase enzyme expressed by cfiA gene. While agar dilution method is used to test the antimicrobial susceptibility of anaerobic organisms, E-test is recommended for susceptibility testing of anaerobes associated with life-threatening infections with high mortality and morbidity. In this study, meropenem E-test was used to determine the carbapenem resistance of B.fragilis strains and to estimate the presence of cfiA gene. A total of 63 B.fragilis strains that were previously isolated from clinical samples (of which 16 were from stool samples) in our laboratory, were enrolled in the study. Minimum inhibitory concentration (MIC) values were determined by meropenem E test (AB Biodisk, Sweden) and presence of cfiA genes were investigated by in-house polymerase chain reaction. The MIC ranges of meropenem were < 0.002 - > 32 µg/ml and the resistance rate was 9.5% (6/63). Thirty-three percent (21/63) of strains harboured cfiA gene. A statistically significant relation (p< 0.0001) was determined between presence of cfiA gene and high MIC value (MIC 0.5 µg/ml). The proportion of cfiA-positive isolates detected in this study was substantially higher than that reported in other countries. This might be attributed to the frequent use of carbapenems in our hospital. The results of this study indicated that meropenem E-test method could be useful to estimate the presence of cfiA gene in B.fragilis strains and thus to detect the resistant strains.

The aim of this study was to determine the in vitro activities of doripenem, imipenem, and meropenem against clinical gram-negative isolates. A total of 596 clinical isolates were obtained from intensive care unit (ICU) and non-ICU patients in 10 centers over Turkey between September-December 2008. The origin of the isolates was patients with nosocomial pneumonia (42.4%), bloodstream infections (%40.4), and complicated intraabdominal infections (17.1%). Of the isolates, 51.8% were obtained from ICU patients. The study isolates consisted of Pseudomonas spp. in 49.8%, Enterobacteriaceae in 40.3%, and other gram-negative agents in 9.9%. The minimum inhibitory concentrations (MIC) for doripenem, imipenem and meropenem were determined for all isolates in each center using Etest® strips (AB Biodisk, Solna, Sweden). Of the isolates, 188 (31.5%) were resistant to at least one of the carbapenems. MIC50 of doripenem against Pseudomonas spp. Was 1 mg/L which was similar to that of meropenem and two-fold lower than imipenem. Susceptibility to carbapenems in P.aeruginosa was 64% for doripenem at an MIC level of 2 mg/L, 53.9% and 63% for imipenem and meropenem at an MIC level of 4 mg/L, respectively. Doripenem and meropenem showed similar activity with the MIC90 of 0.12 mg/L whereas imipenem was four-fold less active at 0.5 mg/L. Against other gramnegative pathogens, mostly Acinetobacter spp., MIC50 was 8 mg/L for doripenem and 32 mg/L for other two carbapenems. P.aeruginosa isolates were inhibited 84.2% with doripenem and 72.1% with meropenem at the MIC level of 8 mg/L. Doripenem generally showed similar or slightly better activity than meropenem and better activity than imipenem against pathogens collected in this study. Against Pseudomonas spp., doripenem was the most active of the three carbapenems. Doripenem and meropenem were equally active against Enterobacteriaceae and at least four-fold more active than imipenem. It was concluded that doripenem seemed to be a promising agent in the treatment of nosocomial pneumonia, blood stream infections and intraabdominal infections particularly in patients who were under risk of developing antimicrobial resistance.

Although necrotizing fasciitis (NF) is a rapidly progressive infection, recurrent NF is very rare. Herein we report a rare case of recurrent NF due to Streptococcus pyogenes. A 12-year-old female with hereditary sensory and autonomic neuropathy (HSAN) type IV presented with fever and swelling on her left knee. NF was diagnosed and she was treated successfully. Two years later she was readmitted with NF of the right knee and limb. Despite treatment, progressive tissue necrosis developed and proximal femur amputation was performed. Eight months following the second attack she was readmitted with NF of her left knee and her entire leg. Despite a wide surgical debridement and antibiotic treatment, the clinical status of the patient failed to improve and she subsequently died. Although many conditions have been reported to be predisposing factors for NF, this is the first report of an association between HSAN type IV and recurrent NF due to S. pyogenes. We recommend antibiotic prophylaxis for patients with NF due to S. pyogenes, especially for those with predisposing factors.

Toxigenic Clostridium difficile strains cause a spectrum of antibiotic-associated diseases ranging from self-limited diarrhea to severe life-threatening colitis. Pathogenesis primarily involves the action of two important cytotoxins, namely toxin A and toxin B. However, epidemics of C.difficile-associated disease due to the novel, highly virulent strains of C.difficile (binary toxin positive and toxin A variant) have been recognised in hospitals of some countries. The aim of this study was to investigate the toxin gene profiles of C.difficile strains isolated from hospitalized patients with diarrhea. The stool specimens collected from 633 inpatients at Marmara University Hospital, Istanbul, Turkey, between September 2006-March 2008, were included to the study. The presence of C.difficile toxins in the samples has been screened by a commercial enzyme immunoassay kit (ImmunoCard Toxins A&B EIA; Meridian Diagnostics, Belgium). Stool samples were also cultivated on cycloserin-cefoxitin-fructose agar (CCFA; BioMerieux, France) at anaerobic conditions, and the isolates were identified by conventional methods and Rapid ID 32A (BioMerieux, France) system. Toxin production of C.difficile strains isolated from stool cultures have been detected by commercially available "Triage C.difficile Panel" (Biosite Diagnostics, Italy) and "ImmunoCard Toxins A&B EIA" (Meridian Diagnostics, Belgium) kits. In-house polymerase chain reaction (PCR) was performed to investigate the presence of genes for toxin A (tcdA), toxin B (tcdB) and binary toxin (cdtA and cdtB). Stool specimens from 50 (7.9%) patients (age range: 2-> 65 years; mean age: 35.9 ± 27.6 years; 26 were male) yielded C.difficile in culture. All of 50 isolates were found positive for glutamate dehydrogenase enzyme and 28 (56%) were found positive for toxin A with "Triage C.difficile Panel" kit. Toxin positivity rate was detected as 4.7% (30/633) with EIA test performed in stool samples directly, however this rate was 5.7% (36/633) in culture filtrates of the isolates (n= 50), with the same test. Since EIA test yielded false negative results in six samples, the sensitivity of this test was estimated as 85.7% by means of the detection of toxin in direct stool samples. All of the 36 toxin-producing C.difficile isolates were found positive for toxin A and toxin B genes (tcdA+/tcdB+), however there were neither variant strains (tcdA-/tcdB+) nor binary toxin gene positive isolates among tested bacteria. Our results have also indicated that 77.8% (28/36) of patients who harbored toxigenic C.difficile strains have the history of beta-lactam antibiotic (penicillin, cephalosporin and imipenem) use. It was thought that the data of this study would constitute a database on the toxin gene profiles of C.difficile in hospitalized patients with diarrhea both in our hospital and Turkey. The current data have indicated that for the time being there were no risk for isolates producing new toxin variants or binary toxin, however, continuous monitorization of such C.difficile strains is of crucial importance in order to detect the emergence of those strains and establish necessary control and preventive measures.

This study was aimed to follow up the antibiotic resistance trends in Streptococcus pneumoniae and Haemophilus influenzae isolated from clinical specimens between 2003-2006 at Marmara University Hospital, Istanbul, Turkey. Antibiotic susceptibilities were performed by disk diffusion method, and penicillin susceptibility was determined by E-test (AB Biodisk, Sweden). Results were evaluated by CLSI standards. During this period a total of 258 S. pneumoniae and 548 H. influenzae were isolated in our laboratory. According to the 2006 CLSI penicillin breakpoints, overall resistance of S. pneumoniae isolates to penicillin was 39.9% and intermediate and high level penicillin resistance rates were 30.2% and 9.7%, respectively. The rates of high level penicillin resistant pneumococci by years were 11.1% in 2003; 10.9% in 2004; 6% in 2005, 12.1% in 2006 and except for 2005 no significant change in resistance rates was detected. However, according to the 2008 CLSI penicillin breakpoints, resistance was found to be 3.5%, intermediate and high level penicillin resistance being 3.1% and 0.4%, respectively. While penicillin resistance rates by years were as 4.4% in 2003, 5.5% in 2004, 0% in 2005 and 4.4% in 2006, high level penicillin resistance was detected only in 2003 as 2.2%. Resistance rates of chloramphenicol, erythromycin, tetracyline and trimethoprim-sulphametoxazole (TMP-SMX) were detected as 10.1%, 19%, 26.8% and 49.2%, respectively while erythromycin, tetracycline and TMP-SMX multi-drug resistance was detected in 12.4% of the isolates. No resistance was detected to vancomycin. Beta-lactamase production rate in H. influenzae isolates was 3.3%, being 1.6% in 2003 with a raise up to 4% in 2006. No beta-lactamase negative ampicillin-resistant isolate was detected. Although chloramphenicol and cefaclor resistance were in low levels (2.2% and 0.7%, respectively), TMP-SMX resistance was detected as 25.5%. TMP-SMX resistance was two fold more in beta-lactamase producers compared with the non-producers, whereas chloramphenicol resistance revealed a significant increase in beta-lactamase producers (1% versus 44.5%). In conclusion, doubling of beta-lactamase production rate in H. influenzae within years indicates the importance of continuous follow-up of antibiotic resistance in specific pathogens. The evaluation of penicillin results obtained for pneumococci according to modified 2008 CLSI criteria revealed that penicillin can still be used effectively in the treatment of pneumococcal respiratory tract infections. Continuous active surveillance of resistance rates provides important data for the determination of the empirical therapy protocols for S. pneumoniae and H. influenzae infections.

We investigated the performance of a seminested PCR (snPCR) assay carried out directly from overnight incubated blood culture bottles of 50 newborn intensive care unit (NICU) patients with suspected candidemia and compared these, for sensitivity, specificity and reliability with results from blood cultures. All positive blood cultures (n = 17) yielded positive results for snPCR, which detected the same Candida species, as did the yeast isolates of which 13 were C. parapsilosis and 4 were C. albicans. With both assays showing 32 negative samples and one sample positive with snPCR but negative with blood culture, sensitivity and specificity of snPCR were 100% and 97%, respectively. The patient with contradictory results exhibited a positive blood culture one week later yielding the same species as identified by snPCR. These are the first data demonstrating that snPCR from overnight blood culture bottles can be a potential tool for rapid detection and identification of Candida species, allowing follow-up of the "gold standard" blood culturing, as well.

Increasing resistance due to extended-spectrum beta-lactamases (ESBLs) and multiple resistance mechanisms in gram-negative hospital isolates restrict the role of beta-lactam antibiotics in empirical treatment of serious infections. As the prevalence of ESBL producing strains and resistance rates to antimicrobial agents can vary in each center, local surveillance studies are required to guide therapy. In this study, in vitro rates of resistance to ceftriaxone, ceftazidime, cefepime, imipenem, cefoperazone/sulbactam and piperacillin/tazobactam were evaluated in 1196 gram-negative hospital isolates in a multicenter in vitro study with the participation of six different centers in Turkey between the period of June 2004-January 2005. The isolates included Escherichia coli (n= 457), Klebsiella pneumoniae (n= 390), Pseudomonas aeruginosa (n= 194) and Acinetobacter boumannii (n= 155). In addition, frequency of ESBL production and types of enzymes were determined in blood isolates of E. coli and K. pneumoniae. MICs and ESBL production were investigated by E-test (AB Biodisk, Solna) and the results were evaluated by using CLSI breakpoints. PCR analysis was used for typing of the ESBLs. In E. coli, 26% and in K. pneumoniae 32% of the isolates were ESBL producers. Among the blood isolates of E. coli and K. pneumoniae, 31.7% and 33.3% produced ESBLs, respectively. CTX-M (71.4%) was the most prevalent enzyme, followed by TEM (49.4%) and SHV (46.7%) derived enzymes. CTX-M-15 (69.4%) was the most frequent CTX-M type in blood isolates followed by CTX-M-3 (28.6%) and CTX-M-1 (2%). Resistance to imipenem was not observed in E. coli isolates, however it was 1.3% in K. pneumoniae, 28.9% in P. aeruginosa and 52.2% in A. baumannii strains. Resistance to cefoperazone/sulbactam was found as 6%, 17.7%, 27.9% and 41.3% in E. coli, K. pneumoniae, P. aeruginosa and A. baumannii isolates, respectively, whereas resistance rates to piperacillin/tazobactam were 10.2%, 22.3%, 22.7% and 78.7%, respectively. These results indicate that ESBL production and rates of resistance to beta-lactam antibiotics are high in hospital isolates of gram-negative bacteria in Turkey, however, they show variations in different hospitals and CTX-M enzymes are prevalent in these isolates.

Streptococcus pneumoniae carriage is a risk factor for the development of respiratory system infections and the spread of penicillin-resistant strains. The aim of this study was to investigate nasopharyngeal carriage of S. pneumoniae in healthy children and resistance to penicillin and other antimicrobials and to assess related risk factors. Nasopharyngeal specimens collected from healthy children less than six years of age, visiting a Mother and Child Health Center for health control, were investigated microbiologically between February-March 2004. Carriage rate was 37.2% (n=112/301); 33.9% intermediate and 5.4% high penicillin resistance were detected. According to multivariate analysis, carriage rate was inversely related to number of rooms (OR:0.574) and child age (OR:0.978), while penicillin resistance was correlated well with antibiotic use in the last two months (OR:2.193). Decreased sensitivity plus resistance to other antimicrobials were: trimethoprim-sulfamethoxazole (TMP-SMX) 45.6%; erythromycin 16.1%, tetracycline 16.1%; clindamycin 9.8%, and ofloxacin 3.6% in pneumococcal isolates, which increased significantly (p<0.05) to 72.7%, 31.8%, 27.3%, 20.5%, and 6.8%, respectively, in penicillin non-sensitive S. pneumoniae (PNSSP) except for ofloxacin. Overall multidrug resistance was 17.9%, while PNSSP exhibited a resistance rate of 38.6%. In conclusion, S. pneumoniae carriage rates determined in healthy children were high and PNSSP strains also showed increased resistance to other antimicrobials.

Objectives: To determine the prevalence of antimicrobial resistance among Streptococcus pneumoniae and Haemophilus influenzae isolated in Turkey as part of Survey Of Antibiotic Resistance, a surveillance programme in the Africa and Middle East region examining the antimicrobial susceptibility of key bacterial pathogens involved in community-acquired respiratory tract infections (CARTIs)., Methods: Susceptibility was evaluated against a range of antimicrobial agents using disc diffusion and Etest methods., Results: Six centres in five cities collected 301 S. pneumoniae and 379 H. influenzae isolates between October 2004 and November 2005. Among S. pneumoniae, the prevalence of isolates with intermediate susceptibility (MICs 0.12-1 mg/L) and resistance to penicillin (MICs >or=2 mg/L) was 24.6% and 7.6%, respectively; there was a wide variation between cities (2.4% to 36.9% intermediate and 0% to 23.8% resistant phenotypes). Macrolide-azalide resistance rates exceeded those of penicillin resistance in all cities. Overall, 5.0% of isolates were co-resistant to penicillin and erythromycin and 10.0% were multidrug-resistant (joint resistance to erythromycin, co-trimoxazole and tetracycline). Agents tested to which over 90% of countrywide S. pneumoniae isolates remained susceptible were amoxicillin/clavulanate (98.7%), chloramphenicol (94.7%) and cefprozil (90.6%). Overall, the percentage of H. influenzae isolates producing beta-lactamase was 5.5%, differing widely across the country with the highest prevalence of beta-lactamase production detected in Trabzon (14.0%) and no beta-lactamase-positive isolates found in Izmir. H. influenzae had the highest per cent susceptibility to amoxicillin/clavulanate (99.5%) and ofloxacin (99.2%) while >20% were resistant to co-trimoxazole., Conclusions: Prevalence of penicillin and macrolide-azalide resistance among S. pneumoniae appears to be on the increase in Turkey while overall beta-lactamase production in H. influenzae remains relatively low. To adequately monitor the spread of drug-resistant phenotypes among these two important CARTI pathogens, ongoing collection of resistance surveillance data is required-where possible locally as resistance patterns can vary substantially between cities and institutions.

The objectives of the study were to investigate and compare the susceptibility profiles of preoperative and postoperative intestinal Bacteroides fragilis and Bacteroides thetaiotaomicron strains against antimicrobials to evaluate their resistance development patterns due to prophylactic antibiotic administration. Preoperative and postoperative stool samples were obtained from patients undergoing elective abdominal surgery with a "clean-contaminated" wound categorization. All patients received cefoxitin 2 g as prophylaxis. Isolates of Bacteroides species were identified. Susceptibility tests against ampicillin, piperacillin, cefoxitin, clindamycin, chloramphenicol, metronidazole, imipenem, and amoxicillin-clavulanate were performed. Stool samples were collected from 40 patients at two settings: before and after the operation. Most of the patients (53%) were operated on because of colorectal carcinoma and underwent surgery that included colectomy or anterior resection. Bacteroides fragilis and Bacteroides thetaiotaomicron were isolated in both samples obtained from 22 and 34 patients, respectively. In the present study 95% to 100%, 50% to 74%, 46% to 64%, and 18% to 35% of preoperatively isolated Bacteroides species were resistant to ampicillin, cefoxitin, clindamycin, and piperacillin, respectively. Although there were no statistically significant difference, postoperative strains were more resistant than preoperative isolates, and the resistance rates were found to be 95% to 100%, 55% to 82%, 46% to 86%, and 37% to 41%, respectively. Both Bacteroides species isolated from all specimens before and after the surgery were uniformly susceptible to amoxicillin-clavulanate, imipenem, metronidazole, and chloramphenicol.Our data revealed that Bacteroides strains revealed high resistance to ampicillin, cefoxitin, piperacillin, and clindamycin. Metronidazole, imipenem, and amoxicillin-clavulanate seem highly effective against both Bacteroides species. Cefoxitin prophylaxis did not significantly increase the resistance patterns against antimicrobial agents.

Some of the Bacteroides fragilis strains produce enterotoxin named fragilysin which is accepted as a virulence factor. In this study, the presence of enterotoxin genes (bft) in clinical B. fragilis strains has been investigated and the antimicrobial resistance patterns of bft positive and negative isolates have been compared. B. fragilis strains isolated from different clinical samples were identified by conventional methods and API 20A system, and the presence of bft genes were searched by using BF3/BF4 primers in polymerase chain reaction. A total of 100 B. fragilis strains of which 50 bft gene positive and 50 bft gene negative were included to the study, and their antimicrobial susceptibilities were determined by agar dilution method as recommended by NCCLS (M11-A4). Of 100 strains, 71 (34 bft negative, 37 bft positive) have been isolated from the stool, and 29 (16 bft negative, 13 bft positive) have been isolated from other specimens (blood, abscess, pleural and peritoneal fluids). beta-lactamase production was detected in 96% of enterotoxigenic B. fragilis (ETBF) and 95% of non-toxigenic strains, and all tested strains were found to be susceptible to amoxicillin/clavulanic acid, imipenem and metronidazole. The resistance rates (with MIC90 values) of bft positive isolates against the other antibiotics were as follows; 96% (256 microg/ml) for ampicillin, 16% (256 microg/ml) for piperacillin, 8% (32 microg/ml) for cefoxitin, 24% (> 256 microg/ml) for clindamycin, 74% (64 microg/ml) for tetracycline and 0% (8 microg/ml) for chloramphenicol. These rates were found as follows for bft negative strains; 95% (256 microg/ml) for ampicillin, 6% (64 microg/ml) for piperacillin, 6% (32 microg/ml) for cefoxitin, 38% (> 256 microg/ml) for clindamycin, 64% (64 microg/ml) for tetracycline and 4% (8 microg/ml) for chloramphenicol. Although the resistance rates and MIC90 values of bft positive strains against the antimicrobials seemed to be higher, there were no statistically significant differences between resistance rates of bft positive and negative strains (P > 0.05; 0.12 and 0.28, respectively).

In this study, alginate, elastase and alkaline protease production of Pseudomonas aeruginosa, which are accepted as virulence factors, have been investigated in the strains isolated from 60 lower respiratory tract samples of cystic fibrosis patients, together with the strains isolated from 59 lower respiratory tract, 62 urine and 32 blood samples of non-cystic fibrosis patients, in order to evaluate the relationship between the virulence factors and infected body sites. Our results indicated that all isolates including the ones from cystic fibrosis patients produced similar levels of alginate ranging between 1.830+/-1.666 and 1.305+/-1.690 microg/ml with the exception of urinary isolates for which the alginate amount was 0.9655+/-1.386 (p<0.05). Elastase levels exhibited no statistically significant difference among groups of isolates; and finally alkaline protease levels, although not statistically significant, was greater in urine isolates than blood and respiratory isolates; however, it was significantly lower in cystic fibrosis isolates compared to the remaining three groups (p<0.05). It can be concluded that alginate, elastase and alkaline protease levels do not differ when different body sites are considered. However, it was observed that alkaline protease was the least produced virulence factor in terms of different body sites. Alginate was found to be the most commonly produced virulence factor in respiratory tract isolates, regardless of presence of cystic fibrosis.

In order to find the distinctive features of Salmonellae and Salmonella infections in Turkey, 620 Salmonellae strains, isolated from various clinical samples (481 stool, 108 blood, 12 urine, 3 bone marrow, 3 cerebrospinal fluid, 9 pus, and one from each of the bile, pleural fluid, wound, catheter samples) in 13 clinical microbiology laboratories of 10 provinces in Turkey (Ankara, Antalya, Bursa, Edirne, Eskişehir, Istanbul, Izmir, Kayseri, Konya and Trabzon) between July 1, 2000 and June 30, 2002, were serotyped. Among the patients 43% were female, 57% were male, 63.2% were from outpatient clinics and 36.8% were hospitalized patients. Seventy eight percent of the patients had gastroenteritis, 10.7% had septicemia/local infection, 9.8% had typhoid/paratyphoid fever and 1.5% were carriers. Incidence of gastroenteritis was higher in 0-5 years age group (p<0.001). Of the 620 Salmonella enterica isolates, 47.7% were S. Enteritidis, 34.7% S. Typhimurium, 6% S. Paratyphi B, 2.9% S. Typhi, 0.2% S. paratyphi A, 6.1% serogroup C1, and 2.4% serogroup C2. S. Enteritidis was the most common serotype in all provinces except for Kayseri, where S. Typhimurium was found to be the most common serotype (68.2%). Overall, the most frequently isolated serotype was S. Enteritidis, also being the most common serotype in stool and blood cultures. During the surveillance period two outbreaks have occurred, the first one by S. Enteritidis strains in Edirne, and the second one by S. Typhimurium strains in Kayseri. As a result, Salmonella infections are still a common health problem in Turkey, and active surveillance of Salmonella infections has vital importance.

Nasopharyngeal swab specimens from 324 children with respiratory tract infections were evaluated to detect the rate of Streptococcus pneumoniae colonisation. S. pneumoniae was detected in 92 (28%) of the subjects. Forty three (46.7%) of the isolates were serotyped by the capsular swelling tests. The most common serotypes were 19F, 6B, 3 and 23F. The 7, 9 and 11 valent conjugate pneumococcal vaccines covered 35.8%, 40% and 46.7% of all the S. pneumoniae isolates, respectively. Thirty two (34.8%) isolates exhibited penicillin MIC values between 0.1 and 1 microg/ml, only 1 isolate had MIC > or = 2 microg/ml. Penicillin resistant pneumococcal colonisation was most frequently detected in children with viral upper respiratory tract infections (12.5%). Resistance rates of trimetoprim-sulfamethoxazole, erythromycin, chloramphenicol, clindamycin, ceftriaxone, rifampin were 31.5%, 9.8%, 6.5%, 4.3%, 1%, 0%, respectively. Being a children of a family with low income was the only risk factor for colonisation with S. pneumoniae, whereas having a sibling attending to a day care center, antibiotic use in the last three months and use of more than one antibiotic were significant risk factors for colonisation with penicillin resistant S. pneumoniae (p < 0.05).

We conducted three prospective studies of Haemophilus influenzae in different groups of children. Pharyngeal swab samples were taken (i). from 1382 healthy infants and children between 0 and 10 years of age (group 1), attending well child clinics (n=438), day care centres (n=440) and elementary schools (n=504), and (ii). from 322 children aged 2-10 years (group 2), clinically diagnosed as having upper respiratory tract infection. Pharyngeal swab samples and sinus aspirates were obtained from 49 children between 2 and 9 years of age (group 3), clinically diagnosed as having sinusitis. H. influenzae was isolated in similar rates from 315 (22.7%) of children in group 1, 72 (22.3%) of children in group 2 and 12 (24.4%) of children in group 3. Serotype b comprised 7, 5.2 and 2% of all H. influenzae isolates for group 1, 2 and 3, respectively. Production of beta-lactamase was detected in 1.0% of H. influenzae type b isolates in group 1, 1.2 and 6.1% of all isolates in group 2 and 3, respectively. There were no beta-lactamase negative ampicillin-resistant strains.

The in vitro activities of several antimicrobial agents against clinical isolates of Streptococcus pneumoniae (283), Haemophilus influenzae (272), Moraxella catarrhalis (179) and Streptococcus pyogenes (256) were determined in a multicentre study with the participation of five hospitals from four cities in Turkey. Penicillin resistance in S. pneumoniae was evaluated using the E-test and the remaining agents by disk diffusion. For S. pneumoniae overall 25.8% of the isolates were intermediately and 3.9% were highly resistant to penicillin and resistance to chloramphenicol, azithromycin and trimethoprim/sulphamethoxazole (TMP/SMX) was 3.8, 2.1 and 55.4%, respectively. Seven percent of H. influenzae produced beta-lactamase and all were susceptible to cefotaxime and azithromycin; the highest rate of resistance, 23.5%, was for TMP/SMX. Eighty-one percent of M. catarrhalis isolates produced beta-lactamase, 18.4% were resistant to TMP/SMX and all were susceptible to sulbactam/ampicillin combination. Resistance to chloramphenicol and azithromycin of S. pyogenes was 2.2 and 1.9%, respectively.

In this study, the effect of hyperthermia on immune response and bacterial translocation from the gut in jaundiced rats was assessed. In hyperthermic (HP; N = 8) and normothermic (NP; N = 8) preconditioning groups, rats were preconditioned by hyperthermia for 15 min at 42 degrees C or 38 degrees C, respectively. After 8 hr, the common bile duct (CBD) of each animal was ligated. In thermal (TT; N = 8) and normothermic treatment groups (NT; N = 8) the CBD of the animals was ligated, and after seven days rats were treated by hyperthermia for 15 min at 42 degrees C and 38 degrees C, respectively. The rats in the preconditioning groups (HP and NP) were killed at day 7 and rats in the treatment groups (TT and NT) were killed 8 hr after they were put in a water bath. Determination of the immunophenotypes of lymphocytes and serum levels of bilirubin was done in serum samples taken just after death. The quantity and identify of translocated bacteria were determined in tissue samples of mesenteric lymph nodes, spleen, and liver. NK cell expression as well as CD4+/CD8+ ratio were elevated in HP group when compared to NP group. CD8+ expression was found to be low in HP group when compared to NP group. CD4+, CD11b+, and B cell expressions were not found to be different between HP and NP groups. All immunologic parameters were similar when TT and NT groups were compared to each other. In the TT group, half of the rats revealed bacterial translocation, whereas in all other groups, we determined translocation in only 1/8 rats. The application of hyperthermia as preconditioning rather than applying it after the establishment of jaundice seemed to be beneficial. Hyperthermic preconditioning led an improvement in immune responses whereas the latter resulted an increase in bacterial translocation with no favorable influence on immune system. Bacterial translocation was unrelated with the immune status.

Resistance of Streptococcus pneumoniae (750) to penicillin, erythromycin, chloramphenicol and trimethoprim/sulfamethoxazole isolated in 4 Turkish hospitals between 1996 and 1999 was evaluated according to year of isolation, patients' age groups and specimen. Penicillin susceptibility was determined by E-test strips and the other antibiotics were tested by disk diffusion test following the NCCLS guidelines in each center. Overall high and intermediate resistance to penicillin was 3% and 29%, respectively. There was a significant difference (p<0.001) between the centers with regard to penicillin resistance. However, there was no significant increase in resistance by year. Penicillin resistance varied significantly among children and adults (36% versus 25%) and according to the specimen. Highest rate of penicillin resistance was observed in respiratory specimens (36%) followed by ear exudates (33.5%). In blood isolates, resistance to penicillin was 28.6%. Overall resistance to erythromycin was 8%, to chloramphenicol 5% and to trimethoprim-sulfamethoxazole 47%. Although overall penicillin resistance in these Turkish S. pneumoniae isolates is high, resistance rates vary in each center and have not increased from 1996 to 1999.

Free radicals and reactive oxygen species have been implicated in the pathogenesis of a variety of hematologic diseases and erythrocyte aging. Aged erythrocytes are removed from the circulation primarily by the spleen. In this study, we aimed to determine the functional effectiveness of autotransplanted splenic tissue by its capacity to remove oxidatively modified erythrocytes from the circulation. Our experimental model in rats includes splenectomy with autotransplantation of 80% of the excised splenic tissue into the omental pouch. In this model, free radical damage was estimated by different parameters of lipid peroxidation such as carbonyl content and thiobarbituric acid reactive substances (TBARS), together with Heinz body formation. Our results have shown that splenic autotransplantation was effective in removing oxidatively modified, aged erythrocytes from the circulation.

Infection with Clostridium difficile can present with various clinical pictures ranging from an asymptomatic carrier state to pseudomembranous colitis and plays an important part in the etiology of nosocomial diarrhoea. To identify risk factors for C. difficile colonization and diarrhoea in hospitalized subjects, patients admitted to a general medicine ward at Marmara University hospital during a one year period were entered into the study. Of the 202 patients, nosocomial diarrhoea developed in 45 (22.3%). Fourteen patients (6.9%) were colonized with C. difficile during their hospitalization period. Ten of the colonized patients (71.4%) developed diarrhoea and were found to be positive by toxin assay. Pseudomembranous colitis was confirmed endoscopically in 3 of the patients with diarrhoea. Administration of beta lactam agents such as ampicillin and cephalosporins; gastrointestinal manipulations and admission to the intensive care unit were found as major risk factors for C. difficile colonization.

Male Wistar albino rats were allocated to three groups-sham operated (n: 10), splenectomized (n: 20) and splenic autotransplanted (n: 10). Twelve weeks after operation, all were challenged with 1.8 x 10(8) cfu/ml Pseudomonas aeruginosa intranasally. Half of the splenectomized rats received imipenem-cilastatin after 2 h of bacterial challenge. Mortality was then observed for the next 12 days. All animals were autopsied and liver, kidney, spleen and lung specimens were processed for microbiological culture and histopathological examination. In 80% of autotransplanted rats, splenic tissue regeneration was histopathologically verified. Hemoglobin oxidation of erythrocytes increased in splenectomized rats and remained close to control levels in the autotransplanted group. No significant difference was detected between IgM levels of splenectomized and autotransplanted groups. Mortality rates were the same for all groups, except that splenectomized animals given antimicrobial therapy had increased survival rates. In conclusion, it is likely that the spleen has no role in protection against pulmonary sepsis and that only appropriate antimicrobial therapy can protect the splenectomized host from Pseudomonas sepsis.

A study of the safety and immunogenicity of plasma-derived and yeast-derived recombinant hepatitis B vaccines administered by the intradermal route is reported. Three groups of medical students were inoculated intradermally at 0, 1 and 6 months with 2 micrograms of vaccine. Group 1 (n = 24) were administered plasma-derived vaccine (Green Cross HB-vaccine), group 2 (n = 21) yeast-derived recombinant vaccine (Engerix B), and group 3 (n = 13) two doses of plasma-derived vaccine with a third dose of yeast-derived vaccine. One month after administration of the third dose of vaccine, seroconversion rates in each of the three groups were 83, 100 and 92%, respectively, with anti-HBs geometric mean titres (GMT) of 329 IU l-1, 1390 IU l-1 and 1061 IU l-1. Although differences in seroconversion rates were not statistically significant, the GMT in group 1 was significantly lower than that in group 2 (p less than 0.01) and group 3 (p less than 0.05). The results presented show that intradermal administration of plasma-derived or yeast-derived vaccine, or a combination of the two, can provoke an effective immunogenic response to hepatitis B virus at approximately 10% of the cost of intramuscular vaccination. In this study administration of yeast-derived vaccine yielded better results than plasma-derived vaccine when administered by the intradermal route.

Two hundred and six serum samples collected from children in Hacettepe University and Marmara University, Faculty of Medicine Hospitals, aged between 0-15 were tested for the presence of Adenovirus group specific antibodies by complement fixation test. The frequency of Adenovirus group specific complement fixation antibodies were found to be 4.85%. Most of positive sera were detected in 0-2 age group.