[Detection of Virulence Genes in Pseudomonas aeruginosa Isolates by Polymerase Chain Reaction and Investigation of High-Risk Clones by Matrix Assisted Laser Desorption/ Ionization Time-of-Flight Mass Spectrometer Method]. / Pseudomonas aeruginosa Izolatlarinda Virülans Genlerinin Polimeraz Zincir Reaksiyonuyla Tespiti ve Yüksek Riskli Klonlarin Matriksle Desteklenmis Lazer Desorpsiyon/Iyonizasyon Uçus Zamani Kütle Spektrometresi Yöntemi ile Arastirilmasi.

Pseudomonas aeruginosa is a non-fermentative gram-negative bacillus. Many virulence factors play a role in the pathogenesis of P.aeruginosa. The aim of this study was to early detection of ST111, ST175, ST235, ST253, ST395 which are named high-risk clones with increased epidemic potential due to multidrug resistance in P.aeruginosa isolates by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method and to evaluate the relationship between high-risk clones and the presence of P.aeruginosa virulence factors and carbapenemase production genes.P.aeruginosa isolates (n= 100) found to be resistant to at least imipenem or meropenem antibiotics isolated from the various clinical samples in the medical microbiology laboratory between 01.01.2021 and 07.06.2022 were included in the study. For the detection of virulence genes uniplex polymerase chain reaction (PCR) for toxA and multiplex PCR for algD, plcN, lasB, plcH were performed in P.aeruginosa isolates. In the detection of carbapenemase genes, two separate multiplex PCRs used for blaKPC , blaNDM , blaVIM , blaOXA-48 and for blaIMP , blaSPM , blaSIM , blaGIM , blaGES . Investigation of the peaks specific to high-risk clones was performed by using VITEK®-MS (bioMérieux, France) system. P.aeruginosa isolates were mostly isolated from intensive care units (45%) and respiratory tract samples (46%). The antibiotic to which the isolates were found to be most susceptible was amikacin, while highest resistance was detected for piperacillin. In PCR results, toxA, lasB, plcH, plcN and algD were detected as 89%, 99%, 98%, 100%, 100%, respectively. When the presence of characteristic peaks belonging to high-risk clones was evaluated with MALDI-TOF MS, ST253 (7%) and ST175 (2%) were detected. The peaks specific to ST235 and ST395 clones were not detected in our study. blaVIM was detected in two isolates and blaGES-5 carbapenemase was detected in two isolates. Virulence factors were detected at high rates in both high-risk clones and other strains and no significant relationship was found between high-risk clones and virulence factors. Early detection of high-risk clones, identification of antimicrobial resistance mechanisms will help to develop strategic treatment options and prevent their worldwide spread.

Determination of amphotericin B antifungal susceptibility in Candida strains using an inverted microscope.

INTRODUCTION: Invasive Candida infections have recently shown a significant increase in prevalence and are associated with high mortality rates. Initiating early antifungal treatment in patients with candidemia is vital. The aim of our study was to compare the antifungal susceptibility results of a new method called Flat Plate Method modified from reference "Clinical and Laboratory Standards Institute (CLSI) microdilution method by us with Sensitititre Yeast One colorimetric method and the reference CLSI method. METHODOLOGY: We tested 100 Candida isolates from blood cultures. We followed the CLSI M27-A3 (reference method for broth dilution antifungal susceptibility testing of yeasts; third edition) guidelines for testing in vitro susceptibility to amphotericin B. In the Flat Plate method, 96-well plates were used for evaluation with an inverted microscope. Minimum inhibitory concentration (MIC) values in the SYO method were measured following the manufacturer's instructions. The MIC values obtained by all three methods were considered compatible if they were within ± 2 dilution limits. RESULTS: The SYO method detected C. albicans and C. glabrata with 100% essential agreement, whereas there was 96.29% essential agreement in the case of C. parapsilosis. In the Flat Plate method, the essential agreement with amphotericin B was 91.42%, for C. albicans isolates and 89.47%.for C. glabrata strains. CONCLUSIONS: When determining early antifungal susceptibility using the Flat Plate method, the results are obtained quickly, with high accuracy, and without incurring additional costs. However, there is a need for comprehensive studies comparing different antifungals.

Effect of antinuclear antibody positivity on antineutrophil cytoplasmic antibody results by indirect immunofluorescence assay.

BACKGROUND: The indirect immunofluorescence assay (IIFA) utilizing antineutrophil cytoplasmic antibodies (ANCA) is widely used as a diagnostic test for autoimmune vasculitis. The presence of antinuclear antibodies (ANA) might lead to a misleading interpretation of ANCA. This study aims to explore the impact of the presence of ANA on the interpretation of ANCA. METHODS: This retrospective research examined samples negative for antiMPO and antiPR3 ANCA by IIFA and explored correlations between the ANA-IIFA results and the ANCA interpretation frequencies. Our analysis involved the use of suitable statistical methods, including Chi-square and kappa statistics. RESULTS: Up to 75.2% of the ANCA-IIFA-positive samples exhibited a positive p-ANCA pattern when using the ethanol-fixed substrate, with c-ANCA positivity at 24.8%. In the ANA-IIFA-positive samples, ~77.3% displayed p-ANCA patterns on ethanol-fixed substrates. A comparison between the ANA-IIFA titers and the p-ANCA results revealed that p-ANCA positivity was notably more common in samples with higher titers, and this correlation was found to be statistically significant. CONCLUSION: Positive ANA results by IIFA tests are linked to a higher incidence of p-ANCA interpretation, particularly in cases with higher titer patterns. This insight aids laboratories in establishing effective workflows to investigate potential p-ANCA interference.

Evaluation of outbreak persistence caused by multidrug-resistant and echinocandin-resistant Candida parapsilosis using multidimensional experimental and epidemiological approaches.

Candida parapsilosis is known to cause severe and persistent outbreaks in clinical settings. Patients infected with multidrug-resistant C. parapsilosis (MDR Cp) isolates were identified in a large Turkish hospital from 2017-2020. We subsequently identified three additional patients infected with MDR Cp isolates in 2022 from the same hospital and two echinocandin-resistant (ECR) isolates from a single patient in another hospital. The increasing number of MDR and ECR isolates contradicts the general principle that the severe fitness cost associated with these phenotypes could prevent their dominance in clinical settings. Here, we employed a multidimensional approach to systematically assess the fitness costs of MDR and ECR C. parapsilosis isolates. Whole-genome sequencing revealed a novel MDR genotype infecting two patients in 2022. Despite severe in vitro defects, the levels and tolerances of the biofilms of our ECR and MDR isolates were generally comparable to those of susceptible wild-type isolates. Surprisingly, the MDR and ECR isolates showed major alterations in their cell wall components, and some of the MDR isolates consistently displayed increased tolerance to the fungicidal activities of primary human neutrophils and were more immunoevasive during exposure to primary human macrophages. Our systemic infection mouse model showed that MDR and ECR C. parapsilosis isolates had comparable fungal burden in most organs relative to susceptible isolates. Overall, we observed a notable increase in the genotypic diversity and frequency of MDR isolates and identified MDR and ECR isolates potentially capable of causing persistent outbreaks in the future.

Investigation of Anti-SARS-CoV-2-specific IgG Levels in Breast Milk after Vaccination or COVID-19 Infection.

OBJECTIVE: Newborns are vulnerable to all types of infections due to their developing immune system. To compensate for their immune immaturity, newborns rely on the passive transfer of antibodies through the placenta and own mother's breast milk (BM). In the present study, we investigated whether vaccination against SARS-CoV-2 leads to the presence of antibodies in BM. Furthermore, we compared the levels of SARS-CoV-2-specific anti-spike (anti-S) IgG antibodies in the BM of mothers who were vaccinated against Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or had coronavirus disease 2019 (COVID-19) infection naturally or were vaccinated after natural infection. STUDY DESIGN: This was a prospective cohort study conducted in the Ondokuz Mayis University Faculty of Medicine. Forty-six mothers who had at least two doses of the BNT162b2 messenger RNA-based vaccine and/or had a history of symptomatic COVID-19 infection were included in the study. BM samples were analyzed by the Abbott Architect SARS-CoV-2 IgG II Quant kit following the manufacturer's instructions. RESULTS: Forty-six mothers with an average age of 29.7 ± 5.7 years participated the study: 18 (39.1%) had COVID-19 infection + BTN162b2 vaccine, 17 (37.0%) had BTN162b2 vaccine, and 11 (23.9%) had natural infection. The highest SARS-CoV-2-specific anti-S IgG antibody titers in BM were found in mothers who were vaccinated following the infection (anti-SARS-CoV-2 IgG: 32.48 ± 57.1 arbitrary units AU/mL). However, no significant difference in anti-SARS-CoV-2 antibody levels was observed between the three groups (p = 0.641). No antibody was detected in 15.2% of BM samples. CONCLUSION: Both vaccination and natural COVID-19 infection during pregnancy leads to the passive transfer of specific anti-SARS-CoV-2 IgG antibodies to BM. These results are important to overcome vaccine hesitancy and increase vaccination levels in expectant mothers. KEY POINTS: · We investigated the levels of SARS-CoV-2 antibodies in BM after natural infection and vaccination.. · Anti-SARS-CoV-2 IgG antibodies were detected in 39 (84.8%) BM samples.. · The highest titers in BM were found in mothers who were vaccinated following natural infection..

[Investigation of O25b-ST131 Clone Frequency and Presence of Carbapenem and Fosfomycin Resistance Genes in Escherichia coli Isolates: First Detection of fosA3 from Escherichia coli O25bSTf131 Clone from Türkiye]. / Escherichia coli Izolatlarinda O25b-ST131 Klonu Sikligi ile Karbapenem ve Fosfomisin Direnç Genlerinin Varliginin Arastirilmasi: Escherichia coli O25b-ST131 Izolatlarinda Türkiye'den Ilk fosA3 Tespiti.

Escherichia coli ST131 clone was first reported in 2008 and defined as a 'high-risk pandemic clone'. This clone plays a critical role in the spread of antimicrobial resistance worldwide. It was reported in many studies that the E.coli ST131 clone is widespread worldwide and can carry virulence and antibiotic resistance genes. E.coli ST131 clone is associated with a fluoroquinolone and broad-spectrum cephalosporin resistance. The agents used in the treatment of infections caused by the E.coli ST131 clone are limited. For this reason, monitoring the resistance status of these limited agents is crucial. In this study, we aimed to investigate the prevalence of the O25b-ST131 clone, and the presence of carbapenem and fosfomycin resistance genes in fluoroquinolone-resistant E.coli isolates isolated from mid-stream urine samples. For the detection of the O25b-ST131 clone in fluoroquinolone-resistant E.coli isolates, amplification was performed with primers O25pabBspe-F and O25pabBspe-R. For the determination of resistance genes, carbapenem resistance genes blaNDM, blaVIM, blaKPC, blaIMP, and blaOXA-48 in carbapenem resistant isolates and plasmid-mediated fosfomycin resistance genes fosA3 and fosC2 in fosfomycin resistant isolates were investigated by multiplex PCR method. According to PCR results, the prevalence of E.coli O25b-ST131 isolates was 51.2%. Carbapenem resistance rate was 3.41%, and fosfomycin resistance rate was 3.41% in fluoroquinolone-resistant E.coli isolates. Carbapenem and fosfomycin resistance rates in E.coli O25bST131 isolates were determined as 0.83% and 2.5%, respectively. At least one of the carbapenem-resistance genes (blaNDM and/or blaOXA-48) was detected in six of the eight carbapenem-resistant isolates. Fosfomycin resistance gene fosA3 was seen in four of eight fosfomycin-resistant isolates. fosC2 gene was not detected in any of the isolates. In addition, the plasmid-mediated fosfomycin resistance gene fosA3 was detected in an E.coli O25b-ST131 isolate, and this result was confirmed by sequence analysis. To the best of our knowledge, this is the second report about fosA3 positivity in E.coli ST131 isolates from the world and the first reported from Europe and Türkiye. As a result, approximately half of the fluoroquinolone-resistant E.coli isolates were identified as E.coli ST131 clones. Despite the high rate of this clone, the carbapenem and fosfomycin resistance rates are still relatively low, which is pleasing for the future of treatment. However, it should not be forgotten that resistance rates and the prevalence of resistance genes should be constantly monitored.

Serotype distribution of Streptococcus pneumoniae and pneumococcal vaccine coverage in adults in Turkey between 2015 and 2018.

OBJECTIVE: To evaluate the serotype distribution and antibiotic resistance in pneumococcal infections in adults and to provide a perspective regarding serotype coverage of both current and future pneumococcal vaccines. PATIENTS AND METHODS: This passive surveillance study was conducted with the Streptococcus pneumoniae strains isolated from the specimens of patients with pneumonia (materials isolated from bronchoalveolar lavage), bacteraemia, meningitis, pleuritis and peritonitis between 2015 and 2018. Serogrouping and serotyping were performed by latex particle agglutination and by conventional Quellung reaction using commercial type-specific antisera, respectively. The strains were analysed for penicillin, cefotaxime, erythromycin and moxifloxacin susceptibilities by E-test. RESULTS: In the whole study group (410 samples from adults aged ≥18 years), the most frequent serotypes were 3 (14.1%), 19 F (12%) and 1 (9.3%). The vaccine coverage for PCV13, PCV15, PCV20 and PPV23 was 63.9%, 66.6%, 74.1% and 75.9%, respectively, in all isolates. Penicillin non-susceptibility in invasive pneumococcal disease (IPD) was 70.8% and 57.1% in the patients aged <65 and ≥65 years, respectively. About 21.1% and 4.3% of the patients with and without IPD had cefotaxime resistance. Non-susceptibility to erythromycin and moxifloxacin was 38.2% and 1.2%, respectively. CONCLUSIONS: The results revealed that novel PCV vaccines may provide improved coverage as compared with the currently available vaccine, PCV13. The significant antibiotic resistance rates imply the need to extend the serotype coverage of the vaccines. Continuing the surveillance in pneumococcal diseases is critical to explore the serotype distribution and incidence changes of IPD cases in the population and to inform policy makers to make necessary improvements in the national immunization programmes.Key messagesThis multicentre study demonstrated the most recent serotype distribution and antibiotic resistance in adult population in Turkey.Shifting from PCV13 to novel conjugated vaccines will significantly increase the coverage.Continuing the surveillance in pneumococcal diseases is critical to explore the serotype distribution changes and the incidence of cases with invasive pneumococcal disease in the population.

The Relationship Between COVID-19 Disease Severity and Zonulin Levels.

Introduction Zonulin is a protein that plays a role in the reversible regulation of epithelial permeability. As zonulin is released in large amounts into the intestinal lumen, it disrupts the integrity of the tight junctions and causes continuous migration of antigens to the submucosa. Consequently, it can trigger inflammatory processes and severe immune reactions. In severe cases, SARS-CoV-2 may have a major impact on the clinical manifestations of the disease by directly or indirectly affecting intestinal cells and triggering systemic inflammation. Therefore, our study aimed to investigate the role of one of the possible mediators, zonulin, in the severity of the COVID-19 infection. Methods  Thirty COVID-19 patients and 35 healthy controls were included in the study. Blood samples were taken from the patients on the 1st, 4th, and 8th days of hospitalization. Serum zonulin levels were determined by enzyme-linked immunosorbent assay (ELISA). Complete blood count (white blood cell [WBC], neutrophil, lymphocyte, and platelet), biochemical parameters (serum lactic acid dehydrogenase [LDH], erythrocyte sedimentation rate [ESR], C-reactive protein [CRP], D-dimer, ferritin, fibrinogen levels) were determined and chronic systemic disease states of the patients were assessed. Results  Serum zonulin levels were notably higher in the healthy control group compared to the patient group (p=0.003). Although there was an increase in the zonulin values by time in hospitalization, this rising was not significant. Conversely, ESR and CRP levels were significantly higher in the patient group (p<0.001). There was no significant difference between the two groups regarding gender, age, and WBC counts. Conclusion  The serum zonulin levels of COVID-19 patients with the mild clinical course were lower than the healthy control group. Moreover, serum zonulin levels were not correlated with ESR, CRP, and other inflammation markers. Our results suggest that low serum zonulin levels in COVID-19 patients might represent a mild disease course.

Molecular epidemiology of Coxiella burnetii detected in humans and domestic ruminants in Turkey.

Q fever is a zoonotic disease that is known to be widespread throughout the world by many researches since its discovery in 1935 and it is important in terms of animal and public health. Coxiella burnetii, which is the etiological agent of the disease, is an obligate intracellular pathogen. While the disease generally manifests itself with abortion in animals, disease manifests as atypical pneumonia or granulomatous hepatitis in the acute form and as endocarditis in the chronic form in humans. Its presence in Turkey has been shown with a large number of studies. The aim of this study was to show the genotypic relationship with MLVA analysis of C. burnetii samples found in cattle, sheep and goat samples in Erzurum and Samsun Veterinary Control Institutes and blood samples collected from humans with atypical pneumonia findings. In the study, MLVA analyses of 100 positive samples from 50 cows, 41 sheep and 9 goats from Northeast Anatolia and Black Sea regions and C. burnetii positive samples found in 6 individuals with atypical pneumonia were performed. As a result of the study, it was found that 106 C. burnetii samples had belong to 16 genotype groups. It was found that genotype XVI was the most prevalent among these groups and it was seen in both regions. In addition to this, genotype IX profile was the second largest group with 83.3% (5/6) of human samples. In this study, the genotypes common in the regions were determined and a data source was created for possible outbreaks.

16s rRNA-based phylogenetic analyses of Elizabethkingia anophelis: Detection of Elizabethkingia anophelis, a rare infectious agent from blood and determination of antibiotic susceptibility in Turkey.

PURPOSE: Elizabethkingia anophelis was firstly isolated from the midgut of the Anopheles gambiae mosquito in 2011. After this year, it was isolated in some intensive care cases in Africa and Asia. This study, it was aimed to confirm the identification of E. anophelis in the blood of a pediatric patient. METHODS: After the suspicious bacteria were grown on blood agar, MALDI-TOF MS and 16s rRNA gene sequencing methods were used to identify and an antibiotic susceptibility test was carried out by Vitek 2 Compact system according to the EUCAST. Finally, a phylogenetic tree was created based on the 16s rRNA gene region. RESULTS: The isolate was identified as E. anophelis by both methods. It was found to be resistant to all beta-lactam antibiotics and also susceptible to ciprofloxacin and levofloxacin. According to the 16S rRNA-based phylogenetic tree, our isolate clustered within a branch containing other E. anophelis. CONCLUSION: These findings will guide clinicians in choosing which antibiotic to choose if they encounter this agent. Also, the clinicians should be vigilant against this agent, as it is a newly emerging infectious agent in Turkey.

[Invasive Mold Infections in Patients with Hematologic Malignities: The Effects of Environmental Factors]. / Hematolojik Maligniteli Hastalarda Invaziv Küf Enfeksiyonlari: Çevresel Faktörlerin Etkisi.

Invasive fungal infections (IFI) continue to be an important cause of morbidity and mortality in patients with hematological malignancies. Candida and Aspergillus species constitute most of the IFI in these patients.. It has been reported that most of the invasive aspergillosis epidemics are related to the construction works in the hospital. In this study, we aimed to investigate the frequency of IFI in the old and the new hospital building after relocation in patients with hematological malignancies. Of 8042 patients who were hospitalized in the Department of Hematology, Ondokuz Mayis University Faculty of Medicine between January 2015 and September 2019, 412 patients who were initiated antifungal therapy were included in the study. The patients in the hematology clinic, which were moved to the new oncology hospital building in January 2018, were grouped as prior and after relocation, and their demographical data, hematological diagnosis, chemotherapy regimens, mortality, IFI, focus of infection, presence of central venous catheter, antifungal prophylaxis and treatment, galactomannan level, fungal culture and computed tomography (CT) findings were evaluated retrospectively. It was determined that 55% of the patients were male and the median age was 58 (range:18-93). The rate of IFI development was 5.12% (n= 412) and the rate of invasive mold infection was 1.2% (n= 145). The most common hematological disease for which antifungal treatment initiated was acute myeloid leukemia (AML) with a rate of 50% (n= 206/412). Of patients, 73% received induction chemotherapy (42%, first induction, 31% reinduction), 13.4% received consolidation therapy. Invasive mold infection was diagnosed as 40% possible, 59% probable, 1% proven. While patients had similar characteristics such as age, gender, hematological disease, chemotherapy regimens and antifungal prophylaxis prior and after transportation, the rate of development of invasive mold infection was 2.1%, 2.06 / 1000 patient days, before transportation, 1.37% (p= 0.009), 1.15/1000 patient days (p<0.001) after transportation, and it was statistically significantly lower after transportation. The median value of galactomannan antigen was detected as 0.17 (0.02-5.9). Blood cultures revealed 10.3% fungal growth and the most common growth was Candida albicans with 54.8% and Mucor spp. as mold with 3.2%. Large-scale construction works such as renovation, extension and demolition works in old hospital buildings are a permanent condition in different units. Clinicians should be aware of that infections due to opportunistic fungi can be seen in immunosuppressive patients close to such construction sites, and even cause epidemics. It should be kept in mind that these infections, which can progress with serious morbidity and mortality are difficult to treat but can be prevented by infection control measures.

Frequency of azole resistance in clinical and environmental strains of Aspergillus fumigatus in Turkey: a multicentre study.

OBJECTIVES: Aspergillus fumigatus causes several diseases in humans and azole resistance in A. fumigatus strains is an important issue. The aim of this multicentre epidemiological study was to investigate the prevalence of azole resistance in clinical and environmental A. fumigatus isolates in Turkey. METHODS: Twenty-one centres participated in this study from 1 May 2018 to 1 October 2019. One participant from each centre was asked to collect environmental and clinical A. fumigatus isolates. Azole resistance was screened for using EUCAST agar screening methodology (EUCAST E.DEF 10.1) and was confirmed by the EUCAST E.DEF 9.3 reference microdilution method. Isolates with a phenotypic resistance pattern were sequenced for the cyp51A gene and microsatellite genotyping was used to determine the genetic relationships between the resistant strains. RESULTS: In total, resistance was found in 1.3% of the strains that were isolated from environmental samples and 3.3% of the strains that were isolated from clinical samples. Mutations in the cyp51A gene were detected in 9 (47.4%) of the 19 azole-resistant isolates, all of which were found to be TR34/L98H mutations. Microsatellite genotyping clearly differentiated the strains with the TR34/L98H mutation in the cyp51A gene from the strains with no mutation in this gene. CONCLUSIONS: The rate of observed azole resistance of A. fumigatus isolates was low in this study, but the fact that more than half of the examined strains had the wild-type cyp51A gene supports the idea that other mechanisms of resistance are gradually increasing.

Bloodstream infections due to Trichosporon species in paediatric patients: Results from the first national study from Turkey.

BACKGROUND: Invasive Trichosporon infections are rarely seen opportunistic fungal infections in children and mainly affect immunocompromised patients. This multicenter retrospective study has rewieved the characteristics, risk factors, treatment modalities and outcomes of bloodstream infections caused by Trichosporon species in children diagnosed over the past ten years in Turkey. METHODS: The study was performed with the participation of 12 of 55 hospitals invited from Turkey. In each center, the patients with bloodstream infections caused by Trichosporon spp. between January 2010 and December 2020 were retrospectively ascertained and the results were reported to the study coordinator by means of a simple case report. Data were collected on patient demographics, underlying condition(s), treatment of.infections caused by Trichosporon spp, and 7 and 30- day mortality rates. RESULTS: A total of 28 cases with fungemia caused by Trichosporon spp. were included in the study. The most common underlying disease was paediatric cancers (39.3%). T. asahii infections were detected in 78.5 % (n=22) of patients. A various spectrum of antifungal treatment regimens were used including intravenous amphotericin B monotherapy in 35.7%, intravenous amphotericin B and voriconazole combination in 32.1% and intravenous voriconazole monotherapy in 28.6% of the patients. The overall mortality rate was 28.5 %. The mortality rates were 12.5% in the voricanozole, 30% in the amphotericin B and 33.3% in combined voriconazole -amphotericin B arms CONCLUSIONS: Invasive Trichosporon infections with an important impact of patients quality of life are almost related to underlying diseases with an overall mortality rate of 28.5%. Voriconazole was found to be associated with lower mortality rates when compared with other treatment regimens.

Prevalence of Fosfomycin Resistance Among Enterobacterales Isolates in A Tertiary Care Hospital from Turkey.

Objective: Urinary tract infections are one of the most common causes of morbidity around the world. Fosfomycin is a specific broad-spectrum antibiotic used to treat these infections. However, in recent years, many studies have reported increased fosfomycin resistance in Enterobacterales isolates. Therefore, this study aimed to evaluate the distribution of pathogens isolated from urine samples and find the fosfomycin resistance rates over nine years (2012-2020). Materials and Methods: A total of 18,884 uropathogenic Enterobacterales isolates were included in the study between 2012 and 2020. The isolates were identified by VITEK® 2 Compact (bioMérieux, Marcy l'Etoile, France), and the antimicrobial susceptibilities of the isolates were also evaluated using the VITEK® MS automated system (bioMérieux, Marcy l'Etoile, France). Results: Escherichia coli (64.04%) was the most common bacteria among Enterobacterales. Fosfomycin resistance rates were 1.98%, 21.64%, and 10.36% in E. coli, Klebsiella pneumoniae, and all bacteria, respectively. The 34.97% of isolates were extended-spectrum ß-lactamase (ESBL)-producing Enterobacterales, and the fosfomycin resistance rate was 13.08% in these isolates. In addition, fosfomycin resistance rates were found as 3.06% and 23.84% in ESBL-producing E. coli and ESBL-producing K. pneumoniae, respectively. Conclusion: Fosfomycin seems a good option for effectively treating UTIs caused by E. coli. On the other hand, we found that fosfomycin resistance tends to increase over the years. Therefore, we recommend further studies to evaluate fosfomycin resistance.

Investigation of NDM, VIM, KPC and OXA-48 genes, blue-carba and CIM in carbapenem resistant Enterobacterales isolates.

INTRODUCTION: Carbapenem resistance is an emerging problem in Enterobactarales. We aimed to investigate the presence of carbapenemase genes blaNDM, blaKPC, blaVIM and blaOXA-48 and evaluate the phenotypic blue-carba method and carbapenem inactivation method (CIM) in Enterobacterales isolates. METHODOLOGY: Total of 153 Enterobacterales isolates were tested in the study. Presence of blaNDM, blaKPC, blaVIM and blaOXA-48 genes was investigated by polymerase chain reaction (PCR) method. Carbapenemase production of the isolates was also tested by blue-carba method and CIM. RESULTS: The presence of blaOXA-48 gene was detected in 110 (71.4%) and blaNDM gene was detected in 2 (1.3%) of the Enterobacterales isolates by PCR method. None of the isolates were positive for blaKPC and blaVIM genes. The 121 (78.54%) of the isolates were found to be positive by blue-carba method and CIM. And 105 (68.18%) of the isolates were determined as positive by both PCR, blue-carba and CIM. CONCLUSIONS: In our study, 112 (72.7%) of the Enterobacterales isolates were found to be positive for carbapenemase genes (blaoxa-48 and blaNDM), and 121 (78.57%) of different isolates were found to be positive for blue-carba and CIM. However, 105 (68.18%) of the carbapenem resistance isolates found to be positive for all three methods.

Evaluation of three different methods for susceptibility testing of gentamicin in carbapenem resistant Enterobacterales.

Carbapenem-resistant Enterobacterales (CRE) have become a growing problem worldwide in recent years. Options for the treatment of CRE are limited and one of these options is gentamicin. For this reason, gentamicin susceptibility should be properly determined. In a recently reported study, it is recommended to review the results of automated systems for assessing gentamicin susceptibility in carbapenem-resistant isolates. In this study, we aimed to determine gentamicin susceptibility using three different methods and compare the methods. The study included 107 CRE isolates from different samples. Gentamicin susceptibility was determined using Vitek 2 Compact (bioMérieux, France), Microscan Walkaway Plus (Beckman Coulter, USA) automatic systems, and disk diffusion (DD) method. The broth microdilution method (BMD) was used as reference method. Minor, major, and very major errors and categorical agreement rates were determined for each method. Aminoglycoside-modifying enzymes (aac(6')Ib and aph(2″)Ia) were assayed in discrepant isolates. According to BMD results, 90.7%, 1,8 %, and 7.5 % of the isolates were determined as susceptible, intermediate, and resistant to gentamicin, respectively. Compared to the results of the BMD for detecting gentamicin susceptibility, disk diffusion method showed the highest categorical agreement (98.1%), and Vitek 2 Compact showed the lowest categorical agreement (90.6%). The very major error rates were determined 7.5%, 0.9%, and 0.9% for Vitek 2 Compact, Microscan Walkaway Plus, and DD method, respectively. In addition, aac(6')Ib and aph(2″)Ia genes were detected in 8 discrepant isolates. For gentamicin susceptibility, the DD showed the most compatible results. The DD can be used as a reliable method for determining gentamicin susceptibility. Compatibility of automated systems with BMD was acceptable, although lower than DD. The discrepancies detected in the Vitek 2 Compact results could be due to the presence of aac(6')Ib and/or aph(2″)Ia aminoglycoside-modifying enzymes.

Recent Increase in the Prevalence of Fluconazole-Non-susceptible Candida tropicalis Blood Isolates in Turkey: Clinical Implication of Azole-Non-susceptible and Fluconazole Tolerant Phenotypes and Genotyping.

Candida tropicalis is the fourth leading cause of candidemia in Turkey. Although C. tropicalis isolates from 1997 to 2017 were characterized as fully susceptible to antifungals, the increasing global prevalence of azole-non-susceptible (ANS) C. tropicalis and the association between high fluconazole tolerance (HFT) and fluconazole therapeutic failure (FTF) prompted us to re-evaluate azole susceptibility of C. tropicalis in Turkey. In this study, 161 C. tropicalis blood isolates from seven clinical centers were identified by ITS rDNA sequencing, genotyped by multilocus microsatellite typing, and tested for susceptibility to five azoles, two echinocandins, and amphotericin B (AMB); antifungal resistance mechanisms were assessed by sequencing of ERG11 and FKS1 genes. The results indicated that C. tropicalis isolates, which belonged to 125 genotypes grouped into 11 clusters, were fully susceptible to echinocandins and AMB; however, 18.6% of them had the ANS phenotype but only two carried the ANS-conferring mutation (Y132F). HFT was recorded in 52 isolates, 10 of which were also ANS. Large proportions of patients infected with ANS and HFT isolates (89 and 40.7%, respectively) showed FTF. Patients infected with azole-susceptible or ANS isolates did not differ in mortality, which, however, was significantly lower for those infected with HFT isolates (P = 0.007). There were significant differences in mortality (P = 0.02), ANS (P = 0.012), and HFT (P = 0.007) among genotype clusters. The alarming increase in the prevalence of C. tropicalis blood isolates with ANS and HFT in Turkey and the notable FTF rate should be a matter of public health concern.

Serotype distribution of Streptococcus pneumonia in children with invasive disease in Turkey: 2015-2018.

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.

First multicentre report of in vitro resistance rates in candidaemia isolates in Turkey.

OBJECTIVES: This study investigated the antifungal resistance rates of isolates from candidaemia patients in 12 tertiary-care centres in Turkey. METHODS: A total of 1991 Candida spp. isolates from 12 centres isolated from 1997-2017 were included in the study. Species/species complex (SC) identification was performed using conventional methods in all centres, occasionally accompanied by MALDI-TOF/MS. Antifungal susceptibility testing was performed for amphotericin B, fluconazole, itraconazole, posaconazole, voriconazole and micafungin (as echinocandin class representative) using the CLSI microdilution method. Resistance rates were determined according to CLSI clinical breakpoints (CBPs). For drugs and species with undetermined CBPs, epidemiological cut-off values were used for wild-type (WT)/non-WT categorisation. RESULTS: No or low rates of resistance were detected in general for tested Candida spp. isolates. Specifically, overall resistance to fluconazole in isolates of Candida parapsilosis SC and Candida glabrata SC were 7.7% and 0.9%, respectively. Resistance rates for C. parapsilosis SC varied extensively from one center to other (0-47.1%). Importantly, no echinocandin resistance was detected. Rates of non-WT isolates were also generally low: fluconazole against Candida lusitaniae, 4.3%; posaconazole against C. parapsilosis SC, 3.5%; posaconazole against Candida krusei, 1.9%; and voriconazole against C. glabrata SC, 0.5%. CONCLUSION: This is the first multicentre report of antifungal resistance rates among candidaemia isolates in Turkey, suggesting low resistance rates in general. Due to varying rates of fluconazole resistance in C. parapsilosis SC isolates that was detected at remarkably high levels in some centres, further studies are warranted to explore the source, clonal relatedness and resistance mechanisms of the isolates.

Health care-associated invasive Candida infections in children.

The aims of the study were to examine the distribution of Candida spp. isolated from sterile body sites, the antifungal susceptibility of the isolates to amphotericin B, and fluconazole, risk factors and clinical outcomes associated with invasive health care-associated Candida infections in neonates and children. Between January 2007 and January 2012, the patients with invasive candidiasis were detected from microbiology laboratary records and medical records were examined retrospectively. Candida spp. were isolated from sterile body sites in 94 patients. The most common underlying diseases were prematurity in neonates and surgery in children. Parenteral nutrition, stay in intensive care unit (ICU), and mechanical ventilation (MV) were major risk factors in neonates. Hospitalization before infection and immunosuppressant therapy were significantly more frequent in children. Of Candida infection episodes, 29.8% was due to C. albicans and 70.2% was due to non-albicans Candida spp. The most common isolated species was C. parapsilosis. Of the Candida species, 90.8% were sensitive, and 9.2% were resistant to fluconazole. The rate of amphotericin B resistant was 1.3%; 23.4% of the patients died in the first 30 days. The main variables associated with mortality were neonates, prematurity, stay in the ICU, parenteral nutrition, MV, length of stay, amphotericin B susceptibility, and high levels of C-reactive protein.