[The Importance of Gram-stained Smears in the Diagnosis of Nocardia Infections]. / Nocardia Enfeksiyonlarinin Tanisinda Gram Boyanmis Yaymalarin Önemi.

Nocardia species are low virulence bacteria found in nature. They can be an infectious agent, especially in patients with risk factors such as underlying immunosuppression, chronic lung disease, and malignancy. They can be easily overlooked because they are not seen frequently and has no pathognomonic symptoms. With this study, it was aimed to draw attention to the importance of microscopic examination of Gram-stained smears in the diagnosis of Nocardia infections in routine microbiology laboratories. Cases in which Nocardia spp. were detected in their clinical samples between November 2014-December 2015 in Hacettepe University Medical Faculty Hospital were included in the study. In the direct microscopic examination of Gram-stained smears of the samples arriving to the laboratory, the incubation periods of the cultures of the samples compatible with Nocardia spp. were extended. Then relevant colonies were identified by conventional microbiological methods and also by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS, bioMerieux, France) automated system. Species-level identification of Nocardia isolates was performed by 16S rRNA gene sequence analysis. To demonstrate the genetic relationship between Nocardia isolates, pulsed-field gel electrophoresis (PFGE) was performed. In vitro susceptibility of the isolates against amoxicillin-clavulanate (AMC), linezolid, moxifloxacin, trimethoprim-sulfamethoxazole (TMP-SXT), amikacin, imipenem, clarithromycin, cefepime, cefotaxime, ceftriaxone, and ciprofloxacin was determined using the gradient strip method (E-test). A total of 19 Nocardia spp. strains were isolated from eight patients. Four cases exhibited repeated growth of Nocardia spp. up to a period of nine months. The most frequently isolated species was N.cyriacigeorgica, which was identified in four cases. Other species isolated from patients were N.asteroides, N.transvalensis, N.farcinicia, and N.asiatica/arthritidis. When the results obtained with DNA sequence analysis and MALDI-TOF MS were compared, 16 (84.2%) of 19 isolates were correctly identified to the genus level and 9 (47.4%) to the species level with MALDI-TOF MS, while three (15.8%) isolates could not be identified, and seven (36.8%) isolates were misidentified. According to the PFGE results, it was determined that the strains isolated from the same patient were genetically identical. All isolates were susceptible to amikacin, cefepime, cefotaxime, ceftriaxone, imipenem, linezolid, and except one isolate to TMP-SXT. Among the study isolates, the most common resistance was against ciprofloxacin (62.5%), followed by clarithromycin (37.5%). N.cyriacigeorgica was determined as the most frequently detected and the most resistant species to antibiotics in the study population. Direct microscopic examination of clinical specimens is one of the most valuable methods for the identification of Nocardia-type bacteria, which is difficult to isolate in microbiology laboratories. With this study, the importance of examining Gram-stained clinical samples was emphasized in the identification of Nocardia species, which can emerge with a wide variety of clinical forms and can be easily overlooked. In addition, antibiotic susceptibility profiles of the isolated bacteria were determinedto contribute to species-specific susceptibility profiles. Accurate identification of Nocardia species will contribute to clinical and epidemiological studies.

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

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

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.

Whole-Genome Sequence Analysis of Carbapenem-Heteroresistant Klebsiella pneumoniae and Escherichia coli Isolates.

Carbapenem-heteroresistant isolates can be misclassified as susceptible by in vitro susceptibility tests, leading to treatment failure. The underlying mechanisms of heteroresistance, where the bacterial isolate harbors both resistant and susceptible subpopulations, are poorly understood. The aim of the current study was to clarify molecular mechanisms responsible for carbapenem heteroresistance. Whole-genome shotgun sequencing was performed for both resistant and susceptible subpopulations of three Klebsiella pneumoniae and one Escherichia coli blood isolates, which were identified as carbapenem-heteroresistant by the population analysis profile method. The software from the Center for Genomic Epidemiology was used to identify genomic similarities, antibiotic resistance genes, Multilocus Sequence Typing (MLST), and core-genome MLST(cgMLST). Both susceptible and resistant subpopulations of the E. coli strain had the same MLST profiles. MLST1/2 and cgMLST for E. coli were 46/736 and 119473, respectively. The susceptible and resistant subpopulations of each K. pneumoniae strain exhibited identical MLST profiles. The genetic background for antimicrobial resistance in three K. pneumoniae strains was almost similar between the colonies inside and outside the inhibition zone of each strain, however, there were remarkable differences between the three strains. The blaKPC-2 and blaOXA-48 genes were responsible for carbapenem resistance for E. coli and K. pneumoniae strains, respectively. This is the first study, which has demonstrated similar genotypic and resistant gene profiles in the resistant and susceptible subpopulations of each strain. Additional metabolic and transcriptomic investigations are needed to understand the mechanisms responsible for carbapenem heteroresistance.

A twenty years' results of the antimicrobial resistance profile and multidrug resistance trend of invasive Streptococcus pneumoniae isolates recovered from adult patients in Turkey: A literature review.

PURPOSE: The aim of this study is to analyze antimicrobial resistance and multidrug (MDR)/extensively (XDR) resistance trend among Streptococcus pneumoniae isolates causing invasive disease in adult patients. METHODS: We analyzed antimicrobial resistance and multidrug resistance trend among invasive S.pneumoniae isolates recovered from adult patients (≥18-years) in a tertiary University Hospital, Turkey between 1996 and 2018. The antibiotic susceptibility pattern was determined by using gradient-test for penicillin and cefotaxime and disk-diffusion method for other antibiotics. RESULTS: A total of 272 isolates (74.3% from the bloodstream) of S. pneumoniae were collected during the study period. The highest non-susceptibility rate was obtained for tetracycline (63.5%), followed by trimethoprim/sulfamethoxazole (48%), penicillin-oral (30.4%), erythromycin (21.7%), clindamycin (15.8%), ciprofloxacin/levofloxacin (5.9%), penicillin-parenteral (5.5%), cefotaxime (2.2%), and rifampisin (1.8%), respectively. No resistance was observed against vancomycin during the years studied. Over the study period, a significant increase in the rate of antimicrobial resistance among invasive pneumococcal isolates was detected with a peak at period 2014-2018. Although there was an increase in the rates of non-susceptibility to penicillin oral, parenteral penicillin, cefotaxime, erythromycin and clindamycin in adult patients, the results were not statistically significant except erythromycin. Prevalence of MDR and XDR S. pneumoniae were 29% and 9.2% respectively. When the serotypes of MDR isolates were examined, it was noted that serotype 19F (35%) and 14 (12.5%) were the most common. CONCLUSIONS: Our study showed an overall increase in non-susceptibility rates of penicillin and erythromycin in invasive S.pneumoniae isolates recovered from Turkish adult patients. Although the prevalence of MDR showed fluctuation between years, the incidence of MDR remained stable. These data indicate the necessity for continuous monitoring and assessment of serotypes and antimicrobial resistance trends in S.pneumoniae in different age groups at both the national and the regional levels as it can be affected by the serotypes dominant in that region, rational use of antibiotics and the vaccination programs.

[The Use of Resapolymyxin NP Test in Determining the Sensitivity of Colistin in Escherichia coli, and Klebsiella pneumoniae Isolates]. / Escherichia coli ve Klebsiella pneumoniae Izolatlarinda Kolistin Duyarliliginin Belirlenmesinde ResaPolymyxin NP Testinin Kullanimi.

Colistin is used as the last choice of drug in multidrug resistant gram-negative bacilli infections; therefore, accurate detection of colistin susceptibility has gained critical importance. Unfortunately, many of the widely used and practical methods in the clinical laboratory have various limitations for the determination of colistin susceptibility. This situation has led researchers to search for new methods to determine colistin susceptibility. In this study, the performance of the ResaPolymyxin NP test, which was developed for the rapid detection of colistin susceptibility of Pseudomonas aeruginosa and Acinetobacter baumannii isolates, was evaluated for various Gram-negative bacteria for the determination of colistin susceptibility. For this purpose, the colistin MIC values of 105 Escherichia coli, and 196 Klebsiella pneumoniae isolates were determined by broth microdilution (BMD) using cation-adjusted Mueller-Hinton broth and then ResaPolymyxin NP test was applied for each isolate. While 242 (%80.4) of the isolates included in the study were found to be susceptible to colistin with BMD, 214 (71.1%) of the isolates were found as sensitive to colistin with the ResaPolymyxin NP test. The categorical agreement rate for the ResaPolymyxin NP test was 85.7% for E.coli isolates, and 92.3% for K.pneumoniae isolates. The major error rate was 14.7% for E.coli, 10.8% for K.pneumoniae, whereas the very major error rate was 1.8% for K.pneumoniae. For ResaPolymyxin NP test, sensitivity, specificity, positive and negative predictive values were %98,3; %88.0; %66.7; and %99.5. In contrast to the available data about the ResaPolymyxin NP test, both the categorical agreement rate with BMD, and the very major and major error rates varied according to the isolate type, and it was concluded that the test performed relatively better in E.coli and K.pneumoniae isolates. Since the data obtained in this study are quite different from the previously published data, more comprehensive and multicenter studies are needed to evaluate the test effectiveness in order to recommend the use of the ResaPolymyxin NP test in clinical microbiology laboratories.

Sensitivity Affected by Disease Severity and Serum Sampling Time: a Performance Evaluation of Six SARS-CoV-2 Antibody Immunoassays.

Comparative validation and clinical performance data are essential for the reliable interpretation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antibody test results. This study aimed to assess the performance of six SARS-CoV-2 IgG immunoassays in the context of different disease severities. Four automated chemiluminescence immunoassays (Access [Beckman Coulter], Architect [Abbott], Atellica-IM [Siemens], and Elecsys [Roche]) as well as two ELISA assays (SARS-CoV-2 IgG-S1-based and NCP IgG [Euroimmun]) were evaluated using samples from 143 patients as well as 50 pre-pandemic control serum samples. Accuracy and precision tests were performed for validation purposes. Overall sensitivity ranged between 73.38-88.65% and was higher in spike protein-based assays, while the specificity was ≥98% in all immunoassays. The clinical performance of the immunoassays differed depending on disease severity and target antigen. For instance, the IgG response was lower for samples taken <20 days post-symptom onset (87.30%) compared with those taken ≥20 days post-symptom onset (94.80%). Moreover, moderate disease levels led to the highest levels of IgG. Higher levels of antibodies were detected in the clinically moderate disease group. In asymptomatic and mild groups, more antibody positivity was detected with spike protein-based assays. All the assays tested could be used to detect SARS-CoV-2 IgG. However, spike-based assays revealed relatively higher sensitivity rates than nucleoprotein-based assays, particularly in cases of asymptomatic and mild disease.

A retrospective observational cohort study of the clinical epidemiology of bloodstream infections due to carbapenem-resistant Klebsiella pneumoniae in an OXA-48 endemic setting.

This study aimed to characterize the epidemiology and clinical outcomes of patients with bloodstream infections (BSIs) due to carbapenem-resistant Klebsiella pneumoniae (CRKP) in an OXA-48-predominant environment. This was a retrospective single-centre cohort study including all consecutive patients with CRKP BSIs treated between 1 January 2014 and 31 December 2018. Multivariate analysis, subgroup analysis and propensity-score-matched analysis were employed to analyse 30-day mortality as the primary outcome. Clinical cure at day 14 was also analysed for the whole cohort. In total, 124 patients with unique isolates met all the inclusion criteria. OXA-48 was the most common type of carbapenemase (85.5%). Inappropriate therapy was significantly associated with 30-day mortality [70.6% vs 39.7%, adjusted odds ratio (aOR) 4.65, 95% confidence interval (CI) 1.50-14.40, P=0.008] and 14-day clinical failure (78.5% vs 56.2%, aOR 3.14, 95% CI 1.09-9.02, P=0.033) in multivariate analyses. Among those treated appropriately, the 30-day mortality rates were similar in monotherapy and combination therapy arms (OR 2.85, 95% CI 0.68-11.95, P=0.15). INCREMENT CPE mortality score (aOR 1.16, 95% CI 1.01-1.33, P=0.029), sepsis at BSI onset (aOR 2.90, 95% CI 1.02-8.27, P=0.046), and inappropriate therapy (aOR 4.65, 95% CI 1.50-14.40, P=0.008) were identified as independent risk factors for 30-day mortality. Colistin resistance in CRKP had no significant impact on 30-day mortality. These results were also confirmed in all propensity-score-matched analyses and sensitivity analyses. Appropriate regimens were associated with better clinical outcomes than inappropriate therapies for BSIs with CRKP predominantly possessing OXA-48.

Factors Associated with Gram-Negative Bacteremia and Mortality in Neutropenic Patients with Hematologic Malignancies in a High-Resistance Setting.

Objective: Patients with hematological malignancies (HMs) have a substantial incidence of febrile neutropenic episodes. Gram-negative bacteremia (GNB) is still the major cause of these episodes. We evaluated the factors associated with GNB and mortality of bacteremic patients with HMs in a high-resistance setting. Materials and Methods: We conducted a prospective cohort study from March 2018 to June 2019 with 66 bacteremic and 132 non-bacteremic patients. Regression analyses were used to identify factors associated with GNB and 30-day mortality. Results: The mean age was 53.83±15.21 years, and 129 (65.2%) of the patients were male. In multivariable analysis, factors independently associated with GNB were male gender, duration of hospitalization and neutropenia before the febrile neutropenic episode, leukemias and allogeneic transplant recipients, radiotherapy, receiving glucocorticosteroids, colonization with resistant microorganisms. All-cause mortality and 30-day mortality were 47.0% and 30.3% in cases of GNB, compared to non-bacteremic controls 25.0% and 10.6%, respectively. Sepsis, duration of hospitalization before the febrile neutropenic episode, carbapenem-resistant GNB, and inappropriate empirical antibiotic treatment was found as factors associated with 30-day mortality. Prior antibiotic exposure particularly beta-lactamase inhibitor combinations and carbapenems during the past 30 days was more frequent in the bacteremic group. An increasing trend was observed in multidrug-resistant (MDR) bacteria (p=0.03) and carbapenem-resistant Enterobacterales (p=0.02) over the years. Conclusion: By considering the risk factors associated with GNB and 30-day mortality that we detected in our study among neutropenic patients, a personalized approach for the management of febrile neutropenic patients can be designed by means of an effective antimicrobial stewardship program including the appropriate use of broad-spectrum antibiotics.

Evaluation of a Commercial Broth Microdilution Panel for Colistin Susceptibility Testing of Clinical Isolates of Escherichia coli and Klebsiella pneumoniae.

BACKGROUND: Colistin is among the last resort antibiotics for the treatment of infections caused by multidrug-resistant Gram-negative pathogens. Antimicrobial susceptibility testing of colistin is challenging due to its physicochemical properties. Broth microdilution (BMD) is the recommended method for colistin susceptibility testing. However BMD is not practical for clinical microbiology laboratories as manual preparation of BMD plates is time-consuming and labor intensive. Recently, some more user-friendly BMD products with commercial panels have become available. Our objective was to evaluate the performance of a commercial broth microdilution (BMD) product [Sensititre (Thermo Fisher Scientific)] for colistin MIC determination by comparison with reference BMD method using a collection of E. coli and K. pneumoniae isolates. METHODS: A total of 323 unique patient isolates (102 E. coli, 221 K. pneumoniae) were included in the study. Isolates were stored at -70°C and subcultured twice on sheep blood agar before testing. Colistin MICs of the isolates were determined using Sensititre (a premade BMD product with dried antibiotics) and an 'in-house prepared BMD panel prepared in accordance with CLSI guidelines' (reference method). MIC determination with Sensititre was performed according to manufacturer's instructions. The reference method was performed using untreated 96-well sterile polystyrene plates. Colistin MIC results were interpreted according to EUCAST breakpoints (susceptible, ≤ 2 mg/L; resistant, > 2 mg/L). RESULTS: Overall susceptibility rate of isolates to colistin by reference BMD was 75.9%. Overall categorical agreement (CA), essential agreement (EA), very major error (VME), and major error (ME) rates for Sensititre were 98.5%, 72.5%, 3.8%, and 0.8%, respectively. The CA and EA between Sensititre and reference BMD for the isolates with reference colistin MICs close to the susceptibility breakpoint (2 - 8 mg/L) was 94.2% and 48.1%, respectively. Sensititre yielded a VME rate of 15% and ME rate of 0%, respectively, for this subset of isolates. CONCLUSIONS: In conclusion, Sensititre showed high CA but low EA with reference BMD for entire collection of isolates. The VME rate was just slightly above 3% and ME rate was acceptable. The rates of CA and EA were decreased and the rate of VME was increased when a subset consisting of more challenging isolates was used.

Molecular characteristics of Staphylococcus aureus strains isolated from nasal samples of sixth year medical students during their pediatric services practices.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) strains are prevalent in healthcare services. Medical students are at risk for MRSA carriage, subsequent infection and potential transmission of nosocomial infection.Few studies have examined MRSA carriage among medical students. METHODS: In this prospective cohort study, between July 2016 and June 2017, two nasal swab samples were taken per student 4 weeks apart during their pediatric internship. MRSA typing was performed by staphylococcal cassette chromosome mec (SCCmec) types, Panton Valentine leukocidin (PVL) encoding genes. RESULTS: A total of 239 sixth year medical students, 164 (68.6%) male (M/F:2.1),with median age 25 years (min-max; 23-65 years) were included in this prospective cohort study. Among 239 students, 17 students (7.1%) were found to be colonized with methicillin-sensitive S. aureus (MSSA) at the beginning of pediatric internship. After 4 weeks, at the end of pediatric internship totally 52 students were found to be S. aureus colonized (21.8%). Three of 52 S. aureus isolates were MRSA (1.3%) and the rest was MSSA (20.5%), all were PVL gen negative. Two of three MRSA isolates were characterized as SCCmec type IV, one isolate was untypeable SCCmec. Nasal carriage of S. aureus increased from 7.1% to 21.5% (p < 0.001). Nasal S. aures colonization ratio was higher in students working in pediatric infectious disease service (p = 0.046). Smoking was found to be associated with a 2.37-fold [95% CI (1.12-5.00); p = 0.023] and number of patients in pediatric services was 2.66-fold [95% CI (1.13-6.27); p = 0.024] increase the risk of nasal S. aureus colonization. Gender was not found to increase risk of MRSA carriage. CONCLUSION: MSSA nasal carriage increased at the end of pediatric internship and significantly high in students working in pediatric infectious diseases services. Smoking and high number of patients in pediatric services significantly increase S.aureus colonization.

Comparison of Conventional Methods, Automated Systems, and DNA Sequence Analysis Methods in the Identification of Corynebacterium afermentans and Corynebacterium mucifaciens Bacteria Isolated from Blood and Catheter Culture Samples.

The aim of this study is to compare different methods due to the difficulties in identifying coryneform bacteria to species level and to determine antibiotic resistance profiles. Isolates identified as Turicella otitidis (n:45) by VITEK 2 Compact and Corynebacterium mucifaciens (n:1) by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), isolated from blood and catheter cultures between 2015 and 2017 were included in the study. For identification of the isolates, conventional tests and 16S rDNA sequence analysis were performed. Antibiotic susceptibilities of the isolates were determined by Etest. The isolates identified as T. otitidis with VITEK 2 Compact could not be identified by MALDI-TOF MS and described as C. mucifaciens/Corynebacterium afermentans spp. by 16S rDNA sequence analysis. One isolate identified as C. mucifaciens by MALDI-TOF MS could not be identified with VITEK 2 Compact and described as C. mucifaciens by 16S rDNA sequence analysis and conventional methods. All isolates (n:45) described as C. mucifaciens/C. afermentans spp. by 16S rDNA sequence analysis were identified as C. afermentans subsp. afermentans with conventional methods. All 45 isolates identified as C. afermentans subsp. afermentans were resistant to penicillin, erythromycin, and clindamycin and were susceptible to vancomycin and daptomycin, whereas 31 (69%) were resistant to trimethoprim-sulfamethoxazole (TMP-SXT). The isolate identified as C. mucifaciens was susceptible to penicillin, vancomycin, daptomycin, and TMP-SXT; it was resistant to erythromycin and clindamycin. In this study, we reported 45 C. afermentans isolates misidentified as T. otitidis in routine laboratory processes. To our knowledge, this is the first study to include the highest number of C. afermentans blood isolates.

Prevalence of O25b-ST131 clone and fosfomycin resistance in urinary Escherichia coli isolates and their relation to CTX-M determinant.

Escherichia coli ST131 clone and H30-R/H30-Rx subclones are the most common multidrug-resistant high-risk clones in UTIs. Antimicrobial susceptibility of fosfomycin was compared to five other agents in consecutively collected 299 urinary isolates using the agar dilution method. Prevalence of the ST131 clone and the occurrence of blaCTX-M were also investigated. Overall resistance to fosfomycin, cefuroxime, and ceftriaxone were 2.7%, 35.4%, and 30.1% respectively. fosA, fosA3, and fosC2 genes were not detected. In isolates resistant to ciprofloxacin (34.7%), the prevalence of ST131 clone was 31.7%, of which 81.8% belonged to H30-R and 66.7% to H30-Rx subclones. None of the isolates of the ST131 clone were resistant to fosfomycin. However, blaCTX-M occurred in 57.6% of the isolates among this clone, 62.9% in H30-R and 68.2% in H30-Rx subclones. The results of this study suggest that fosfomycin resistance is not prevalent in urinary isolates, however, blaCTX-Mpositive ST131 clone is quite common.

Low prevalence of hypervirulent Klebsiella pneumoniae in Anatolia, screened via phenotypic and genotypic testing.

Hypervirulent Klebsiella pneumoniae (hvKP) strains are associated with vigorous clinical presentation and relapses. Initially reported from Asia, these variants have spread globally and become an emerging agent of significant health threat. This study was carried out to identify hvKP strains in a previously uninvestigated region and to evaluate the impact of commonly-employed phenotypic and genotypic markers as diagnostic assays. A total of 111 blood culture isolates, collected at a tertiary care center was investigated. The hvKP strains were sought by a string test and the amplification of partial magA, rmpA, iucA and peg344. All products were characterized via sequencing. Evidence for hvKP was observed in 10.8% via iucA amplification (7.2%), string test (2.7%) and magA amplification (0.9%). Specific products were not produced by assays targeting rmpA and peg344 genes. Antibiotic susceptibility patterns compatible with possible extensive or pan-antimicrobial resistance was noted in 66.7% of the hvKP candidate strains. Capsule type in the magA positive strain was characterized as K5. We have detected hvKP in low prevalence at a region with no prior documentation. Targetting the aerobactin gene via iucA amplification provided the most accurate detection in this setting. The epidemiology of hvKP in Anatolia requires elucidation for effective control and management.

Bacteriemia por Stenotrophomonas maltophilia en niños: análisis de 10 años / Stenotrophomonas maltophilia bacteremia in children - A 10-year analysis

Stenotrophomonas maltophilia es un microorganismo gramnegativo, multirresistente. La información sobre la bacteriemia por S. maltophilia en niños es limitada. Se revisaron los datos de 10 años de un hospital de niños de alta complejidad. Se incluyó a niños de 0 a 18 años con hemocultivos o cultivos del catéter positivos. Se identificaron 20 cepas de S. maltophilia en 12 niños con infección confirmada, cuya mediana de edad fue 28 meses (intervalo: 3,1-187,3). El índice de antibioticoterapia previa fue 83 %, con una mediana de tres antibióticos (intervalo: 0­7) en los 30 días previos a la bacteriemia por S. maltophilia. La infección relacionada con el catéter fue la principal fuente de infección (8/12). La mortalidad fue de 4/12; y en dos casos, estuvo asociada con neumonía. S. maltophilia puede considerarse un agente muy invasivo productor de bacteriemia en niños con enfermedad preexistente expuestos a antibióticos durante una hospitalización prolongada.

Stenotrophomonas maltophilia is a multidrug-resistant, Gram-negative, and biofilm-forming pathogen. Information is limited concerning S. maltophilia bacteremia in children. Clinical data and microbiological test results collected in a tertiary children's hospital over a ten-year period were reviewed. Children 0­18 years old who had positive clinical specimen, blood and/or catheter cultures were included. We identified 20 S. maltophiliaisolates from 12 pediatric patients with confirmed infections. The median age was 28 months (range: 3.1-187.3). The rate of previous use of antimicrobial therapy was 83 %. The median antibiotic number was 3 (range: 0­7) within 30 days prior to onset of S. maltophilia bacteremia. Catheter related infection was the main infectious source (66.6 %). The mortality rate was 33.3 %. The death of two non-survivors was associated with pneumonia. S. maltophilia should be considered a breakthrough agent for bacteremia in children with underlying disease exposed to broad-spectrum antibiotics during long-term hospitalization

Epidemiologic and Molecular Characteristics of Staphylococcus aureus Strains Isolated From Hospitalized Pediatric Patients.

BACKGROUND: We aimed to determine molecular characteristics of Staphylococcus aureus isolates cultured from hospitalized pediatric patients. METHODS: All accessible S. aureus isolates cultured from hospitalized pediatric patients were analyzed for staphylococcal cassette chromosome mec (SCCmec) types, Panton-Valentine Leukocidin (PVL) encoding genes and antibiotic resistance patterns. RESULTS: A total of 132 S. aureus isolates, 102 methicillin-susceptible S. aureus (MSSA) (81.8%), 30 methicillin-resistant S. aureus (MRSA) (18.2%) were included in the study. Sixty of 132 (45.5%) S. aureus isolates were cultured from skin and soft tissue infections (SSTIs), 50 (37.9%) from bloodstream infections, 11 (8.3%) from bone infections and 11 (8.3%) from other sterile sites. Fifty-three of 102 (52%) MSSA isolates were cultured from SSTI, 35 (34.3%) from bloodstream infections, 7 (6.9%) from bone infections and 7 (6.9%) from other sterile sites (P = 0.083). Fifteen MRSA isolates (50%) were cultured from blood culture, 7 from (23.3%) SSTI, 4 (13.3%) from bone infections and 4 from (13.3%) other sterile sites. Nine PVL gene harboring S. aureus isolates were isolated from SSTI (75%), 2 from blood culture (16.7%) and 1 from other sterile site (8.3%). Three MRSA (6.7%) isolates were found to be positive for SCCmec type III and 16 MRSA isolates (53.3%) were found to be positive for SCCmec type IV. Three MRSA isolates harboring SCCmec type III was isolated from blood culture, 11 of 16 MRSA isolates harboring SCCmec type IV was isolated from blood culture, 3 isolates were isolated from bone infections and 2 isolates were isolated from SSTI (P < 0.001). Five of 72 (6.9%) hospital-acquired S. aureus isolates and 7 of 60 (11.7%) community-acquired S. aureus isolates were PVL gene positive. Twenty-two of 72 (30.6%) hospital-acquired S. aureus infections and 8 of 60 (13.3%) community-acquired S. aureus isolates were MRSA (P = 0.015). All of the 3 SCCmec III harboring MRSA isolates and 11 of 16 SCCmec IV carrying MRSA isolates were hospital acquired. Hospitalization in the past 1 year was found to increase MRSA infections 3.95 times (P = 0.038, 95% confidence interval: 1.078-14.48). CONCLUSIONS: As distribution of virulence genes differs among S. aureus isolates from different regions, it is necessary to monitor the emergence of genes encoding PVL, SCCmec in both MRSA and MSSA throughout the world. Our results show a high prevalence of PVL in community-onset S. aureus infections in children. SCCmec type IV was more commonly isolated in hospital-acquired MRSA isolates, and PVL gene was more commonly isolated in community-acquired S. aureus infections.

Stenotrophomonas maltophilia bacteremia in children - A 10-year analysis. / Bacteriemia por Stenotrophomonas maltophilia en niños: análisis de 10 años.

Stenotrophomonas maltophilia is a multidrug-resistant, Gramnegative, and biofilm-forming pathogen. Information is limited concerning S. maltophilia bacteremia in children. Clinical data and microbiological test results collected in a tertiary children's hospital over a ten-year period were reviewed. Children 0-18 years old who had positive clinical specimen, blood and/or catheter cultures were included. We identified 20 S. maltophilia isolates from 12 pediatric patients with confirmed infections. The median age was 28 months (range: 3.1-187.3). The rate of previous use of antimicrobial therapy was 83 %. The median antibiotic number was 3 (range: 0-7) within 30 days prior to onset of S. maltophilia bacteremia. Catheter related infection was the main infectious source (66.6 %). The mortality rate was 33.3 %. The death of two non-survivors was associated with pneumonia. S. maltophilia should be considered a breakthrough agent for bacteremia in children with underlying disease exposed to broad-spectrum antibiotics during long-term hospitalization.

Stenotrophomonas maltophilia es un microorganismo gramnegativo, multirresistente. La información sobre la bacteriemia por S. maltophilia en niños es limitada. Se revisaron los datos de 10 años de un hospital de niños de alta complejidad. Se incluyó a niños de 0 a 18 años con hemocultivos o cultivos del catéter positivos. Se identificaron 20 cepas de S. maltophilia en 12 niños con infección confirmada, cuya mediana de edad fue 28 meses (intervalo: 3,1-187,3). El índice de antibioticoterapia previa fue 83 %, con una mediana de tres antibióticos (intervalo: 0­7) en los 30 días previos a la bacteriemia por S. maltophilia. La infección relacionada con el catéter fue la principal fuente de infección (8/12). La mortalidad fue de 4/12; y en dos casos, estuvo asociada con neumonía. S. maltophilia puede considerarse un agente muy invasivo productor de bacteriemia en niños con enfermedad preexistente expuestos a antibióticos durante una hospitalización prolongada.

Resistance and heteroresistance to colistin among clinical isolates of Acinetobacter baumannii.

Colistin is one of the most effective alternatives for treating Acinetobacter baumannii infections. The aim of this study was to determine colistin resistance and heteroresistance rates in A. baumannii from clinical samples in Hacettepe University clinical microbiology laboratory between June 2016 and January 2017. A total of 200 isolates were included in the study. In vitro susceptibility to amikacin, gentamicin, ceftazidime, piperacillin/tazobactam, meropenem, ciprofloxacin, and tigecycline were determined by disk diffusion test. Most isolates were multiresistant as they exhibited resistance to aminoglycosides, ß-lactams, and fluoroquinolones. Colistin susceptibility was determined by broth microdilution (BMD) test (EUCAST standards) and was compared with E-test (bioMérieux, France) in 120 isolates. In 14 blood isolates that were susceptible to colistin (MIC ≤ 2 mg/L), heteroresistance was investigated with the population analysis profile (PAP) method. Overall resistance (n = 200) to colistin was 28% by BMD. Among the 120 isolates where the two tests were compared, resistance to colistin was 25.8% versus 4.2% with BMD and E-test, respectively. Three blood isolates (21.4%) were heteroresistant to colistin. With E-test, a majority of the resistant isolates are overlooked and in vitro susceptibility to colistin should be determined with broth dilution method. This is the first study in Turkey reporting heteroresistance in A. baumannii isolates by the PAP method and emphasizes the need to test for heteroresistance in relation to clinical outcome in serious infections due to A. baumannii.

Uropathogens and Gestational Outcomes of Urinary Tract Infections in Pregnancies that Necessitate Hospitalization.

BACKGROUND AND OBJECTIVES: Our aim is to identify uropathogens that cause urinary tract infections (UTIs) that necessitate hospitalization, and analyze outcomes of gestational UTIs. METHODS: This study consisted of 30 pregnant women who necessitate hospitalization because of UTI (7.8% of gestational UTIs during the same period of time). UTI that necessitates hospitalization is defined as clinical complaints, urination problems, urine analysis and culture positivity, fever and uterine discomfort. Patients with at least two positive cultures (≥ 100,000 cfu/ml) were included to this study. Antimicrobial susceptibility tests were obtained in all cases in order to determine antimicrobial resistance and to choose the ideal antibiotics for treatment. RESULTS: In our study, we have found that Escherichia coli is the most common microorganism (56.7%). Enterococcus faecalis (13.3%) and Klebsiella pneumonia (10%) were other frequently observed microorganisms. In this series, mean gestational week at birth was 35 weeks 5 days (range 23-40 weeks). Mean birthweight was 2,656 g (range 500-3,700 g). Twenty-three cases (76.7%) were hospitalized before 37th gestational week and preterm delivery rate was 56.3%. Maternal risk factors and coexisting diseases were detected in 11 (36.7%) patients as follows: diabetes mellitus in 4, thrombophilia in 3, thyroid disorders in 3 and hydroureteronephrosis in 1 case. Cesarean section rate was 65.2%. CONCLUSIONS: Knowing uropathogens of patient population is beneficial in the management of patients and better planning of future medical treatments. Preterm labor seems to be an important complication in pregnancies with UTIs going together with fever and urination problems.

A case of Raoultella ornithinolytica urinary tract infection in a pediatric patient.

Raoultella ornithinolytica is a Gram-negative, non-motile, encapsulated, biofilm producing, facultative aerobic bacillus and is found in natural environment. Human infections with R.ornithinolytica is rare in children with only five cases having been reported previously. The present case report describes an urinary tract infection caused by R. ornithinolytica that was identified by MALDI-TOF MS and successfully treated with antibiotic therapy in a 6.5-year-old female child.