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ObjectiveUrinary tract infections (UTIs) due to extended-spectrum beta-lactamase (ESBL) producing Escherichia coli and Klebsiella pneumoniae are among the leading causes of morbidity and mortality in older adults. Identifying associated factors for ESBL production may contribute to more appropriate empirical treatment.Materials and methodsThis was a prospective observational study. Hospitalized patients of age > 65 with community-onset or hospital-acquired upper UTI due to E. coli or Klebsiella pneumoniae were included. A multivariate analysis was performed.ResultsA total of 97 patients were included. ESBL prevalence among UTIs with E. coli or Klebsiella pneumoniae was 69.1% (n = 67). CRP values at the time of UTI diagnosis were found to be significantly higher in the ESBL-producing group (p = 0.004). The multivariate analysis revealed that male gender (OR: 2.72, CI: 1.02–7.25), prior recurrent UTI (OR: 3.14, CI: 1.21–8.14), and the development of secondary bacteremia (OR: 4.95, CI: 1.03–23.89) were major associated factors for UTI in older adults due to ESBL-producing E. coli and Klebsiella pneumoniae.ConclusionSevere UTI in older men with a history of recurrent UTI may be a warning to the clinician for ESBL production in the setting of high ESBL prevalence. Carbapenems may be prioritized in the empirical treatment of patients with known risk factors for ESBL.

Candida auris has emerged as a significant fungal threat due to its rapid worldwide spread since its first appearance, along with its potential for antimicrobial resistance and virulence properties. This study was designed to examine virulence characteristics, the efficacy of ceragenins, and biofilm-derived drug resistance in seven C. auris strains isolated from Turkish intensive care patients. It was observed that none of the tested strains exhibited proteinase or hemolysis activity; however, they demonstrated weak phospholipase and esterase activity. In addition, all strains were identified as having moderate to strong biofilm formation characteristics. Upon determining the minimum inhibitory concentrations (MIC) of ceragenins, it was discovered that CSA-138 exhibited the highest effectiveness with a MIC range of 1–0.5 µg/mL, followed by CSA-131 with a MIC of 1 µg/mL. Also, antimicrobial agents destroyed mature biofilms at high concentrations (40–1280 µg/mL). The investigation revealed that the strains isolated from Türkiye displayed weak exoenzyme activities. Notably, the ceragenins exhibited effectiveness against these strains, suggesting their potential as a viable treatment option.

Objectives: To evaluate the bacterial colonization and associated risk factors in patients with bronchiectasis. Methods: A total of 121 patients followed at the Bronchiectasis Unit, between 1996 and 2013 and diagnosed as having noncystic fibrosis bronchiectasis with high resolution computed tomography or multi-slice computed tomography were included in this retrospective study. The following definition of colonization was used for study purposes: Detection of at least two isolates of an organism separated by at least 3 months in a year. Results: Of these 121 patients, 65 (54%) were female and 56 (46%) were male. Mean age was 50.6 ± 16.1 years. Mean duration of illness was 20.3 ± 15.5 years. 43 (35.5%) cases had colonization. The major pathogens responsible for colonization were Pseudomonas aeruginosa (n = 25; 20.6%) and Haemophilus influenzae (n = 14, 11.5%). The stepwise logistic regression analysis showed a significant association between colonization and a low percentage of forced vital capacity (FVC%) and the presence of cystic bronchiectasis (P < 0.05). Conclusion: The following factors have been found to be associated with colonization in patients with bronchiectasis: Low FVC% and the presence of cystic bronchiectasis.

Background: Emerging carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) (CRKP) bacteremias are presenting significant public health risks due to limited treatment options and increased mortality. K. pneumoniae isolates exhibit carbapenem resistance rates that vary from 25% to 50% throughout the European continent, including our country. Aims: To assess the characteristics of CRKP bacteremia, a condition that has recently demonstrated an increasing prevalence in our center. We sought to ascertain the resistance rates of isolated strains to antibiotics other than carbapenems, identify the responsible carbapenemase genes, evaluate the efficacy of antibiotics, determine mortality rates, explore clonality among strains, and investigate the influence of the COVID-19 pandemic on all these factors. Study Design: Retrospective observational study. Methods: This study included patients aged 18 and older who had experienced meropenem-resistant K. pneumoniae bacteremia. Meropenem resistance was confirmed by employing the Kirby-Bauer disk diffusion method. Meropenem minimum inhibitory concentration (MIC) levels were determined using the gradient test, while colistin MIC levels were ascertained using the disk elution technique. Carbapenemase genes were evaluated via colony polymerase chain reaction (PCR), and clonality analysis was performed using the arbitrarily primed PCR technique. Results: The study comprised 230 patients, with a mean age of 63.1 ± 15.9 years, of whom 58.7% were male. Oxacillinase-48 (OXA-48) was detected in 74.8% of the patients, New Delhi metallo-beta-lactamase (NDM) in 12.6%, OXA-48 + NDM in 7.8%, and KPC in 4.8%. The 14-day and 30-day mortality rates were 57% and 69.6%, respectively. Multivariate analysis of the 30-day mortality revealed several crucial factors, including bacteremia development in the intensive care unit, the occurrence of bacteremia during the COVID-19 pandemic, polymicrobial bacteremia, the use of indwelling intravenous catheters, a platelet count of ≤ 140,000/µl, procalcitonin levels of ≥ 6 µg/l, and a Charlson comorbidity score ≥ 3. Notably, the OXA-48 and KPC genes were upregulated significantly during the COVID-19 pandemic, while the NDM gene groups were downregulated. Additionally, both 14-day and 30-day mortality rates increased significantly. Conclusion: In this study, the most prevalent carbapenemase gene was OXA-48; however, there has been a recent increase in KPC genes. No dominant epidemic strain was identified through clonality analysis. The clustering rate was 68% before the pandemic, increasing to 85.7% during the pandemic. The significance of infection control measures is underscored by the rise in both clustering and mortality rates during the COVID-19 pandemic.

Background: Monitoring the longevity of immunoglobulin G (IgG) responses following severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections is vital to understanding the role of antibodies in preventing infection. Aims: To determine the quantitative IgG responses specific to the Spike-S1 (S1) receptor-binding domain (S1/RBD) region of the virus in serum samples taken between 4 weeks and 7 months after polymerase chain reaction (PCR) positivity in patients who are diagnosed with coronavirus disease-2019 (COVID-19). Study Design: A longitudinal study. Methods: This study included 113 patients with a clinical and molecular diagnosis of COVID-19. The first and second serum samples were taken 1 and 7 months, respectively, after the PCR positivity. S1/RBD-specific IgG antibody response was assayed using anti-SARS-CoV-2 QuantiVac ELISA (IgG) kit (Euroimmun, Lübeck, Germany). The neutralizing antibodies were investigated in 57 patients whose IgG test results were above the cut-off value. Results: In 57 patients with SARS-CoV-2 IgG, the anti-SARS-CoV-2 IgG quantitative antibody levels significantly decreased after 7 months (Z = −2.197, p = 0.028). A correlation was detected between the anti-SARS-CoV-2 IgG and nAb percent inhibition (IH%) levels detected in 1 month (rs = 0.496, p < 0.001), but without significant correlation in serum samples taken on 7 months. The nAb IH% levels of the first and second were compared for COVID-19 severity and revealed no statistical difference (p = 0.256). In the second serum sample, the nAb IH%s of patients with moderate COVID-19 showed a statistically significant difference from patients with mild COVID-19 (p = 0.018), but without significant differences between severe and moderate or mild COVID-19. Conclusion: SARS-CoV-2 quantitative IgG antibody titers are significantly reduced at long-term follow-up (> 6 months). Due to the limited information on seroconversion, comprehensive studies should be conducted for long-term follow-up of the immune response against SARS-CoV-2.

Background: Widespread and effective use of molecular diagnostic tests is indispensable for protecting public health and containing the severe respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. More than 1 year into the pandemic, as resources have reached a point of depletion, grouping samples in pools of certain sizes appears to be a reasonable method to reduce both the costs and the processing time without necessitating additional training, equipment, or materials. Aims: To assess whether the pooling strategy that was used in past outbreaks and is used in blood tests prior to transfusion for screening large populations can also be used in SARS CoV-2 tests. Study Design: Diagnostic accuracy study. Methods: This prospective study was conducted with 2815 samples, sent to the coronavirus disease 2019 (COVID-19) Laboratory of our hospital between February 12 and 21, 2021, to be tested for the presence of SARS-CoV-2. The samples were examined individually and in pools of five 100 µl taken from each sequential sample, using 3 different SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) kits, the Allplex™ 2019-nCoV Assay kit (Seegene, Republic of Korea), the GeneMAP™ 2019-nCoV detection V.3 kit (GenMark, Türkiye), and the Bio-Speedy™ SARS-CoV-2 Double Gene™ RT-qPCR kit (Bioeksen, Türkiye) on the BioRAD CFX96™ Touch (Bio-Rad Laboratories Inc., Hercules, CA, USA) platform available in our laboratory. Results: Following the extraction of serial dilutions prepared from the SARS-CoV-2 RNA positive (cycle of threshold: 20) sample, the standard curves of RT-PCR were analyzed. By evaluating the efficiency (E) values, all 3 kits showed high sensitivity and similar results; while the highest level was detected with the Allplex™ 2019-nCoV Assay kit in the nucleocapsid (N) gene (E: 124%), the lowest was detected with the Double Gene™ RT-qPCR kit in the N and ORF 1ab genes (E: 90%). Of the samples included in the study, only 1 positive sample with low viral load was found to be negative when studied by pooling. The total number of kits to be used in pooled tests and then to individually retest the 5 samples in positive pools was calculated as 827 and the savings rate as 69.91% (1968/2815). Conclusion: The pooling strategy is an effective approach to extend the impact of limited testing resources and reagents available in certain periods of the COVID-19 pandemic. Testing by pooling samples requires improvement of RNA extraction methods and careful monitoring of RT-PCR test sensitivity to avoid missing low-positive entities. Therefore, based on the prevalence of COVID-19 in their regions, laboratories should conduct their own validation of pooling studies for RNA extraction and amplification methods they use.

Background: Blood stream infections (BSIs) due to carbapenem-resistant Enterobacteriaceae (CRE) are associated with high hospital mortality rates and present a tremendous challenge to clinicians. The optimal treatment remains undefined. We aimed to investigate the risk factors for mortality and the correlation between different treatment modalities and outcomes. Methods: The clinical characteristics and treatment outcomes of a cohort of 36 patients with BSIs due to CRE were investigated and a retrospective nested case–control study of surviving and non-surviving patients was conducted. Results: Fifty percent of the cases were male and the mean patient age was 54.9 ± 15.8 years. Klebsiella pneumoniae was the etiological agent in 26 cases (72.2%), Escherichia coli in eight (22.2%), and Enterobacter aerogenes in two (5.5%). All strains were phenotypically positive for carbapenemase activity and all except two (one E. coli and one K. pneumoniae) yielded both blaOXA-48 carbapenemases and blaCTX-M-type extended-spectrum beta-lactamases (ESBLs) in PCR products. The 14-day, 28-day, and all-cause in-hospital mortality rates were 41.6%, 50%, and 58.3%, respectively. The median time to death was 8 days (range 2–52 days). No significant differences were observed between survivors and non-survivors in terms of baseline characteristics, comorbid conditions, etiologies, or sources of bacteremia, however hematological malignancies (p = 0.015) and prolonged neutropenia (p = 0.044) were more common in non-survivors. Microbiological eradication and clinical response within 7 days were two major determinants of 28-day attributable mortality (p = 0.001 and p = 0.001, adjusted r2 = 0.845). Colistin-based dual combinations, and preferably triple combinations, were associated with significantly better outcomes when compared to non-colistin-based regimens (p

Even though recurrent tonsillitis is one of the most frequently encountered problems of childhood, its etiology and treatment are points of debate. We aimed to determine pathogenic bacteria of the tonsil core, the diagnostic ability of surface swab cultures to show the core pathogenic bacteria. The study group consisted of 58 children between ages 3 and 12 who had problems with recurrent tonsillitis and tonsillectomy was planned as treatment. Surface and core swabs were taken during tonsillectomy and aerobe and anaerobe cultures were performed. Pathogens could be detected in core cultures in 50 (86%) of 58 patients. In core cultures 26 (52%) isolates of Staphylococcus aureus,13 (26%) isolates of Haemophilus influenzae, 10 (20%) isolates of group A beta hemolytic streptococci, and small numbers of other organisms were detected. Surface swabs could detect pathogenic bacteria in 19 (33%) patients. Overall penicillin resistance was 48%. S. aureus and H. influenzae should be considered as pathogens for recurrent tonsillitis as well as group A beta hemolytic streptococci. We believe that the antibiotic decision should be made with keeping penicillin resistance in mind.

Introduction: The aim of this study was to determine the causative agents of community-acquired lower urinary tract infections (CALUTIs) in primary care. We also aimed to evaluate the antimicrobial susceptibility rates of urinary Escherichia coli isolates to various oral antibiotics and to assist primary care physicians with antibiotic selection. Materials and Methods: The study was performed in 55 primary care centers in 13 cities between May and July 2009. Adult patients with at least two of dysuria, pollakiuria, nocturia, suprapubic tenderness, or blurred urine symptoms, but not fever, were included in the study. Urinary samples were obtained and patient data were recorded at the primary care centers. Results: Totally, 400 patients were enrolled. In 175 (43.8%) patients, urine cultures yielded a urinary pathogen. The most frequently encountered pathogen was E. coli (62.8%). Among E. coli isolates, the lowest resistance rates were detected for nitrofurantoin (0.9%) and fosfomycin (3.6%) and the highest for trimethoprim/sulfamethoxazole (43.6%) and amoxicillin/clavulanate (41%). Resistance rates to quinolones were 23.6% for ciprofloxacin and 21% for levofloxacin. Minimum inhibitory concentration (MIC)50 and MIC90 values for ciprofloxacin and levofloxacin were 0.015 and 32 μg/mL and 0.06 and 16 μg/mL, respectively. Quinolone resistance was significantly higher in patients who received an antimicrobial treatment within the last three months (p< 0.001). Extended spectrum beta-lactamase (ESBL) positivity was detected in 15 of 110 (13.6%) E. coli isolates. Quinolone resistance was significantly higher among ESBL positive than ESBL negative strains (53.3% vs. 15.8%, p= 0.002). Conclusion: In conclusion, the most frequent causative agent in CALUTIs was E. coli. The lowest resistance rates among E. coli isolates were detected for nitrofurantoin and fosfomycin. Resistance rates to quinolones were over 20% in our study. Our identifikasyostudy provides important data about the causative agents and their antibiotic susceptibilities and also contains valuable data for rational antibiotic usage in the treatment of CALUTI in Turkey.