The emergence of Klebsiella pneumoniae sequence type 395 non-susceptible to carbapenems and colistin from Turkey.

PURPOSE: OXA-48 producing Klebsiella pneumoniae is an emerging threat and outbreaks due to specific sequence types have been commonly reported. Here, we report an outbreak due to multidrug-resistant ST395 K. pneumoniae ST395. To the best of our knowledge, this is the first outbreak of K. pneumoniae ST395 harbouring blaOXA-48 genes in our country. METHODS: The strains were characterized by antimicrobial susceptibility, extended-spectrum ß-lactamase (ESBL) and carbapenemase production, plasmid-mediated colistin, high-level aminoglycoside, and quinolone resistance. Also multidrug efflux pumps and porin coding genes were investigated. Pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), wzi typing and plasmid analysis were used for the epidemiological relationships. RESULTS: All strains were positive for blaOXA-48 with at least one of the ß-lactamase genes (blaCTX-M, blaTEM, blaSHV) and harboured IncL plasmids. 16 of 20 (80%) isolates carried qnrA. All isolates were positive for aac(6')-1b, acrAB-tolC, ompK35, and ompK36 genes but none of them harboured 16s rRNA methyltransferase, mcr-1-5, qepA, oqxAB, and mdtK genes. All strains had the same PFGE pattern, that is, wzi type K2 and found to be ST395 with MLST. CONCLUSION: The association of ST395 with OXA-48-producers could be an emerging threat for Turkey and continuous monitoring is crucial to prevent the spread of these powerful strains.

[Investigation of Virulence Factors, Phylogenetic Group Features, and the Presence of ST131 Clone in Escherichia coli Isolates, a Urinary Tract Infection Agent in Children]. / Çocuklarda Üriner Sistem Enfeksiyonu Etkeni Olan Escherichia coli Izolatlarinda Virülans Faktörleri, Filogenetik Grup Özellikleri ve ST131 Klonu Varliginin Arastirilmasi.

Urinary tract infection (UTI) caused by Escherichia coli is a significant health issue in children. Today especially E.coli O25b/ST131, defined as a pandemic clone, is a serious public health problem due to its high virulence and antimicrobial resistance rates. In this study, a total of 200 (100 first and 100 recurrent UTI-causing) E.coli isolates from urine samples sent to the Ankara University School of Medicine Cebeci Training and Research Hospital Central Laboratory between January and September 2021 with the preliminary diagnosis of UTI in pediatric patients aged three to 18 years were analyzed for antimicrobial resistance rates, phylogenetic group distributions, virulence factor frequencies and whether they belong to the O25b/ST131 clone. It is aimed in this study that, the obtained data will shed light on new studies for diagnosis, treatment and prophylaxis options that can be developed for more effective UTI management by contributing to the surveillance studies in our country. Antimicrobial susceptibility of E.coli isolates identified by conventional methods was evaluated by Kirby-Bauer disc diffusion method and extended spectrum beta-lactamase (ESBL) production was evaluated by double disc synergy test. Polymerase chain reaction (PCR) was used for the investigation of phylogenetic grouping, the O25b/ST131 clone, virulence genes and the molecular level classification of the isolates detected as uropathogenic E.coli (UPEC). Pulsed-field gel electrophoresis (PFGE) was performed with the isolates collected at different times from the same patient. The highest antimicrobial resistance rates observed were against ampicillin (n= 100, 50%), cefazolin (n= 99, 49.5%), trimethoprim-sulfamethoxazole (n= 55, 27.5%), amoxicillin-clavulanic acid (n= 43, 21.5%) and cefotaxime (n= 43, 21.5%). In recurrent UTI agents, resistance rates were higher for cefotaxime (n= 29, 29%), trimethoprim-sulfamethoxazole (n= 35, 35%) and cefepime (n= 25, 25%) and in O25b/ST131 isolates (n= 67) the rates were higher for amikacin (n= 3, 4.5%), gentamicin (n= 10, 14.9%) and ciprofloxacin (n= 17, 25.4%) when compared to the first UTI agents and non-O25b/ ST131 isolates (p< 0.05). It was found that 29% (n = 58) of the isolates were multidrug resistant (MDR) and 19% (n = 38) produced ESBL.The rate of recurrent UTI agents was found to be higher among ESBL producing isolates and/or MDR isolates (n= 36, 62% and n= 27, 71%, respectively, p< 0.05). It was found that 45.5% (n= 91) of the isolates were in D, 37.5% (n= 75) in B2, 12.5% (n= 25) in A, and 4.5% (n= 9) in B1 phylogenetic groups and isolates belonging to B2 and D phylogenetic groups had higher antibiotic resistance rates and carried more virulence genes (p< 0.05). Of the isolates, 33.5% (n= 67) were found to belong to the O25b/ST131 clone, no significant difference was found between the O25b/ST131 rates among the first and recurrent UTI agents (p> 0.05). It was determined that the isolates most frequently carry virulence genes for adhesion [fimH 97% (n= 194), papA 57% (n= 114), yfcV 49.5% (n= 99)] and iron uptake systems [fyuA 85.5% (n= 171), chuA 78% (n= 156), iutA 73% (n= 146)]. All virulence factors were detected more frequently in isolates belonging to the O25b/ST131 clone (p< 0.05). Of the isolates, 97% (n= 65) belonging to the O25b/ST131 clone and 27.1% (n= 36) not belonging to this clone were defined as UPEC with molecular analysis (p< 0.0001). Thirty-three isolates belonging to 15 patients were evaluated with PFGE, and it was observed that the latter isolate and the first isolate of eight patients (53%) had the same band profile. Focusing on surveillance, diagnostic testing, treatment algorithms, and preventive measures for E.coli and especially for ST131 clone, which is frequently observed as causative agent in childhood UTIs, will help to manage challenging E.coli infections.

Investigation of the presence of Capnophilic bacteria in routine urine cultures.

Capnophilic Escherichia coli (CEC) strains are rarely isolated from urinary tract infections (UTIs). The purpose of this research was to look into the incidence and traits of the CEC strains that cause UTIs. Nine (0.11%) epidemiologically unrelated CEC isolates with varying antibiotic susceptibility patterns were identified from patients with various co-morbidities after the evaluation of 8500 urine samples. Three of these strains belonged to the O25b-ST131 clone, and none of them possessed the yadF gene. Due to adverse incubation conditions, CEC isolation is difficult. Although rare, capnophilic incubation of urine cultures may be considered particularly for patients with underlying predisposing conditions.

Medically important Candida spp. identification: an era beyond traditional methods.

BACKGROUND: Candida infections are gaining more attention for the last few decades so diagnostic tools are very important for early diagnosis. Conventional identification of yeasts is time-consuming, molecular methods are more complicated and relatively expensive gold-standard methods. Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) was put into the market due to its speed and high accuracy. The aim of this study was to evaluate the performance of corn meal tween-80 agar (CMTA), CHROMagar Candida medium, and MALDI-TOF MS and to compare the obtained results with DNA sequencing. METHODS: The CHROMagar Candida medium, CMTA, and MALDI-TOF MS Biotyper System were used to test 416 isolates. The isolates with discrepant results by at least one of the three methods were subjected to sequence analysis. RESULTS: The identification results of the 351 (%84.4) were compatible with all three methods. When compared to the sequencing results, the most accurate results were obtained by the MALDI-TOF MS, especially for rare Candida species. DISCUSSION: MALDI-TOF MS is found to be the most accurate identification tool for clinically important Candida strains. CMTA alone should not be used for the final identification of Candida species and the chromogenic medium should always be considered presumptive.

[Investigation of Biofilm Formation Properties of Coagulase Negative Staphylococci Isolated from Catheter-Related Bloodstream Infections]. / Kateter Iliskili Kan Dolasimi Enfeksiyonlarindan Izole Edilen Koagülaz Negatif Stafilokoklarin Biyofilm Olusturma Özelliklerinin Arastirilmasi.

In view of the significant negative impact of biofilm-mediated infection on patient health and the necessity of a reliable phenotypic method to detect biofilm producers, this study aimed to demonstrate phenotypic and molecular biofilm formation in coagulase-negative staphylococci (CoNS) isolated from catheter related infections and to compare the methods used with each other. The study was also aimed to determine the biofilm eradication effect of vancomycin in order to guide for the treatment. For the detection of biofilm formation, a total of 154 CoNS clinical isolates of which 30 being causative agents of catheter related bloodstream infection (CRBSI) (isolated from both the catheter tip and blood cultures of 15 patients), 89 being isolated from peripheral blood cultures of patients without a central venous catheter (CVC) (13 of them were bloodstream infection agents, 76 of them were contaminant), and 35 being isolated as catheter colonizer, were screened by tissue culture plate (TCP), Congo red agar (CRA) method and polymerase chain reaction (icaA, icaD and IS256). Vancomycin minimum inhibitory concentration (MIC) and minimum biofilm eradicating concentration (MBEC) values were determined. The pulsed field gel electrophoresis (PFGE) method was used to show the clonal relationship between CoNS isolated from the catheter tips and peripheral blood of patients with CRBSI. Of the 154 CoNS isolates included in the study, 38.9% were Staphylococcus epidermidis (n= 60), 34.4% were Staphylococcus haemolyticus (n= 53), 20.7% were Staphylococcus hominis (n= 32), and 3.8% were detected as Staphylococcus capitis (n= 6). In our study, biofilm formation was shown in 31.8% with the CRA method and in 68.1% with the TCP method. By TCP method, 22% (n= 34) were determined as weak, 31.2% (n= 48) medium and 14.9% (n= 23) strong biofilm producers. While the sensitivity of the CRA method was found to be low for isolates that were determined as weak positive in the microplate method, the high sensitivity of the CRA method for isolates with medium and strong positivity was found remarkable. The positivity rates of icaA, icaD and IS256 genes in a total of 154 CoNS isolates were found to be 40 (25.9%), 57 (37%) and 77 (50%), respectively. In total, at least one gene positivity was detected in 107 (69.5%) isolates. Single gene positivity was detected in 55 (35.7%), two gene positivity in 35 (22.7%) and three gene positivity was detected in 17 (11%) of the included CoNS. Biofilm formation (four weak, four medium, two strong) was detected by microplate method in 10 of 47 CoNS isolates (five S.epidermidis, three S.hominis, one S.haemolyticus and one S.capitis) in which no genes were detected. Vancomycin MBEC/ MIC values were found to be high and it was observed that as the biofilm forming power of the isolates increased, the MBEC/MIC ratio also increased. The CoNS isolated from the catheter samples and blood of patients diagnosed with CRBSI had a 100% similar profile with PFGE except for one unevaluable isolate. The tissue culture plate (TCP) method was found to be most sensitive, accurate and reproducible screening method for detection of biofilm formation by staphylococci and has the advantage of being a quantitative model to study the adherence of staphylococci. The presence of the icaAD and IS256 gene is not always associated with in vitro biofilm formation. For this reason, it is more appropriate to use more than one method together for the evaluation of biofilm formation. It was thought that the use of reliable methods to specifically detect biofilms could be helpful in diseases that are difficult to treat. Considering the high rates of biofilm and antimicrobial resistance of biofilm-forming isolates in biomedical device associated infections, it was determined that it would not be sufficient to evaluate only the MIC results for susceptibility results.

Wohlfahrtiimonas chitiniclastica-related soft-tissue infection and osteomyelitis: A rare case report.

Wohlfahrtiimonas chitiniclastica is a rare pathogen that was first isolated from Wohlfahrtia magnifica, a parasitic fly. It is an uncommon, but an emerging human pathogen reported only in Europe and South America. Until today, it has been reported to be a zoonotic pathogen originating from different geographic locations. The present case, a patient suffering from osteomyelitis in Turkey, represents the first report of this pathogen in this country and so far no reports of related osteomyelitis associated with W. chitiniclastica is available. Clin-ical awareness of these emerging human pathogens is crucial for controlling infectious diseases.

Viral nucleic acid analysis with PCR in lacrimal tissue and nasal swab samples of primary acquired nasolacrimal duct obstruction cases.

PURPOSE: To evaluate the role of viral infections in the pathogenesis of primary acquired nasolacrimal duct obstruction. METHODS: The study included 48 patients diagnosed with primary acquired nasolacrimal duct obstruction undergoing dacryocystorhinostomy surgery. Prior to dacryocystorhinostomy surgery, nasal swab sample was taken from the inferior meatus at the same side. During dacryocystorhinostomy, tissue biopsy sample (2 × 2 mm) was taken from the junction area of the lacrimal sac and nasolacrimal duct. Following nucleic acid extraction, polymerase chain reaction was performed. RESULTS: The patients consisted of 9 (18.8%) men and 39 (81.2%) women with a mean age of 51.0 ± 14.3 years. Qualitative polymerase chain reaction showed viral genome in the nasal swabs of 10 (20.8%) patients, including coronavirus 229E (three cases), coronavirus HKU1 (two cases), respiratory syncytial virus (two cases), coronavirus OC43 (one case), coronavirus NL63 (one case), and adenovirus (one case). In the dacryocystorhinostomy samples, viral genomes were detected in four (8.3%) cases, including respiratory syncytial virus (two cases), coronavirus HKU1 (one case), and adenovirus (one case). There was a statistically significant agreement between nasal mucosal swab and dacryocystorhinostomy biopsy samples in terms of respiratory syncytial virus positivity (kappa = 1.000, p = 0.001). CONCLUSION: Although the viral genome was detected in the samples, a direct relationship between viruses and pathogenesis of primary acquired nasolacrimal duct obstruction could not be revealed because of the low number of positive results. However, considering the profibrotic characteristics of specific viruses such as respiratory syncytial virus and adenovirus, viral infections may be one of the many predisposing factors of primary acquired nasolacrimal duct obstruction.

Detection of sasX Gene and Distribution of SCCmec Types in Invasive and Non-invasive Coagulase-negative Staphylococci

Background: Coagulase-negative staphylococci, which belong to the normal microbiota of the skin and mucous membranes, are opportunistic pathogens. sasX, a newly described protein, is thought to play an important role in nasal colonization and methicillin-resistant Staphylococcus aureus virulence, and it may be acquired from coagulase-negative staphylococci by horizontal gene transfer. It has been considered that understanding the function of sasX gene may help clarify the relevance of the different adhesion mechanisms in the pathogenesis of infections associated with biofilm. Aims: To investigate the sasX gene presence, staphylococcal cassette chromosome mec types, and antimicrobial resistance patterns of invasive and noninvasive coagulase-negative staphylococci isolates. Study Design: Cross-sectional study. Methods: The study included a total of 180 coagulase-negative staphylococci strains. Non-invasive isolates (n=91) were obtained from the hands of healthy volunteers who do not work at the hospital (n=30), the nasal vestibule of healthy volunteer hospital workers (n=26), and central venous catheter (n=35). Invasive isolates (n=89) were isolated from peripheral blood cultures of inpatients who do not have catheters. All isolates were identified by conventional microbiological methods, automated systems, and, if needed, with matrix-assisted laser desorption/ionization-time of flight. Staphylococcal cassette chromosome mec typing, sasX and mec gene detection, antibiotic susceptibility, and sasX gene sequence analysis were performed. Results: Peripheral blood, central venous catheter colonization, and nasal vestibule isolates were positive for the sasX gene, whereas hand isolates were negative. sasX gene was present in 17 isolates, and no statistical significance was found between invasive and noninvasive isolates (p=0.173). Sequence analysis of the sasX genes showed high homology to related proteins of Staphylococcus phage SPbeta-like and Staphylococcus epidermidis RP62A. staphylococcal cassette chromosome mec type V was the most prevalent regardless of species. staphylococcal cassette chromosome mec type II was more frequent in invasive isolates and found to be statistically important for invasive and noninvasive S. epidermidis isolates (p=0.029). Staphylococcus haemolyticus isolates had the overall highest resistance rates. Resistance to ciprofloxacin, trimethoprim-sulfamethoxazole, and erythromycin was found to be higher in isolates from catheter and blood culture. Staphylococcus hominis isolates had the highest rate for inducible clindamycin resistance. None of the isolates were resistant to vancomycin, teicoplanin, and linezolid. Conclusion: The sasX gene is detected in 9.44% of the isolates. There is no statistical difference between the sasX-positive and -negative isolates in terms of antibacterial resistance and the presence of sasX and SCCmec types. Further studies about the role of sasX at virulence in coagulase-negative staphylococci, especially from clinical samples such as tracheal aspirate and abscess isolates, and distribution of staphylococcal cassette chromosome mec types are needed.

Evaluation of the Presence and Characterization of Vancomycin-Intermediate and Heterogeneous Vancomycin-Intermediate Level Resistance Among Bloodstream Isolates of Methicillin-Resistant Staphylococcus aureus.

Aims: Heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) could be misinterpreted as "susceptible" with routine susceptibility testing procedures, and the subpopulations with reduced susceptibility to glycopeptides can lead to therapeutic failure. The aim of this study was to evaluate the presence of VISA and hVISA strains among stocked bloodstream methicillin-resistant S. aureus (MRSA) isolates of 14 years. Materials and Methods: A total of 127 nonduplicate MRSA strains isolated from blood cultures between 2001 and 2014 were investigated. Glycopeptide minimum inhibitory concentration values were detected by microbroth dilution method. Susceptibilities to other antimicrobials were determined by the disk diffusion method and interpreted according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. Macrogradient test (MGT) and modified population analysis profile-area under the curve (modified PAP-AUC) methods were used to detect VISA and hVISA. Staphylococcal Cassette Chromosome mec (SCCmec), agr, and toxin gene typing were done by polymerase chain reaction. Genetic relatedness of the strains were evaluated by pulsed-field gel electrophoresis (PFGE). Results: All isolates were susceptible to glycopeptides, linezolid, and quinupristin-dalfopristin. All were resistant to tetracycline, 96% were resistant to aminoglycosides, fluoroquinolones, and rifampin. Only 58.3% of the isolates were susceptible to ceftaroline. Six isolates were suspected as hVISA by the MGT, but none could be confirmed by the modified PAP-AUC analysis. All isolates carried type-III SCCmec, sea was the most prevalent (96.9%) enterotoxin gene and agr group I locus was predominant (93.7%). PFGE analysis revealed four main and four unique patterns. Conclusion: No hVISA or VISA were detected. The resistance rate to ceftaroline seems remarkable due to its recent entry into the market in Turkey.

Characterization of Klebsiella pneumoniae Coproducing KPC and NDM-1 Carbapenemases from Turkey.

Aims: The emergence of multidrug-resistant and carbapenem-resistant Klebsiella pneumoniae has became a major public health threat. In this study, we describe the characteristics of isolates coproducing KPC and NDM-1 carbapenemases from patients hospitalized at an emergency unit in Ankara, Turkey, between January and August 2018. The isolates were characterized by antibiogram susceptibility, carbapenemase and extended-spectrum beta-lactamase production, plasmid-mediated colistin (COL) resistance, and high-level aminoglycoside resistance. Pulsed field gel electrophoresis (PFGE), sequencing, wzi typing, multilocus sequence typing, and plasmid analysis were used to investigate the epidemiological relationship between the isolates. Results: All isolates were found to be resistant to amoxicillin-clavulanic acid, piperacillin-tazobactam, cefotaxime, cefoxitin, cefuroxime, ceftazidime, cefepime, imipenem, meropenem, ertapenem, amikacin, gentamicin, ciprofloxacin, levofloxacin, and trimethoprim-sulfamethoxazole. The minimum inhibitory concentration values for imipenem, meropenem, and ertapenem were >32 µg/mL, and >256 µg/mL for amikacin and gentamicin, and two isolates were found to be susceptible to both tigecycline and COL. All strains were positive for SHV, CTX-M, and rmtC, and negative for mcr-1 genes. A/C and FIIAS plasmids were found in all isolates. All isolates had the same PFGE pattern: wzi type 93 and ST15. Conclusion: Here, we have documented the characteristics of KPC- and NDM-1-coproducing isolates that harbored SHV, CTX-M, and rmtC and were typed as wzi 93 and ST15. We conclude that continuous monitoring of carbapenemases for unusual carbapenemase production is crucial to prevent the spread of these powerful isolates.

Prospective Analysis of Hemorrhagic Cystitis and BK Viremia in Allogeneic Hematopoietic Stem Cell Transplantation

Objective: BK virus (BKV) infection has been shown to be related to hemorrhagic cystitis (HC) in allogeneic hematopoietic stem cell transplantation (allo-HSCT). There are conflicting data regarding the association between BKV titers in plasma and clinical disease as well as the risk factors for BKV-related HC. Our aim is to study the risk factors and relationship with plasma BK viral load for development of HC in a prospective analysis. Materials and Methods: We prospectively evaluated 59 patients who received allo-HSCT between 2014 and 2016 by quantitative BK virus polymerase chain reaction (PCR) (Altona Diagnostics, Germany) from blood samples at days 0, 30, 60, and 90 after allo-HSCT. The patients were monitored for signs and symptoms of HC. Results: HC was diagnosed in 22 patients (37%) at a mean of 100 days (range: 0-367 days). In multivariate analysis, the usage of cyclophosphamide (sub-distribution hazard ratio [sdHR]: 7.82, confidence interval [CI]: 1.375-39.645, p=0.02), reactivated CMV (sdHR: 6.105, CI: 1.614-23.094, p=0.008), and positive BKV viremia (sdHR: 2.15, CI: 1.456-22.065, p=0.01) significantly increased the risk of developing HC. Patients with higher viral loads at day 30 and day 60 were diagnosed with more severe HC (p<0.001). Median BK viral loads of >101.5 copies/mL at day 0 (sensitivity 0.727, specificity 0.875), >98.5 copies/mL at day 30 (sensitivity 0.909, specificity 0.875), and >90.0 copies/mL at day 60 (sensitivity 0.909, specificity 0.875) were indicative of HC. Conclusion: Our study showed that administration of cyclophosphamide, CMV reactivation, and BK virus positivity were associated with HC. Plasma BK virus PCR titers at days 0, 30, and 60 after transplant were sensitive tools for predicting clinically proven HC.

[Investigation of carbapenemase genes and molecular epidemiology of Enterobacteriaceae strains isolated between 2010-2014 in a university hospitals]. / Bir üniversite hastanesinde 2010-2014 yillari arasinda izole edilen Enterobacteriaceae türlerinin karbapenemaz genlerinin arastirilmasi ve moleküler epidemiyolojisinin belirlenmesi.

The worldwide spread of carbapenemase producing Enterobacteriaceae isolates has become a major threat of public health. This worrisome situation leads the development of new methods for carbapenemase screening, detection, prevention of spread and epidemiological data collection as mandatory. In this study, it was aimed to investigate existence and distribution of carbapenemase-encoding genes (CEGs) among carbapenem-resistant Enterobacteriaceae isolated from various clinical samples in Ankara University Faculty of Medicine, Ibni Sina Hospital, Central Microbiology Laboratory between June 2010-May 2014 and detect their clonal relationship. A total of 112 non-repetitive Enterobacteriaceae isolates which were intermediate or resistant to ertapenem were identified by using Phoenix (BD Diagnostic Systems, Sparks, USA) automated microbiology system. After DNA extraction from the isolates, 11 carbapenemase-encoding genes (CEGs) (blaIMP, blaVIM, blaSPM, blaKPC, blaNDM, blaOXA-48, blaGIM, blaSIM, blaAIM, blaDIM ve blaBIC) were detected with PCR. The clonal relationship among the isolates was determined by PFGE method following digestion with Xbal DNA macrorestriction endonuclease. Among 112 isolates Klebsiella pneumoniae was the most frequent (n= 79, 70.5%) bacteria followed by Escherichia coli (n= 15, 13.4%), Enterobacter cloacae (n= 10, 8.9%), Enterobacter aerogenes (n= 4, 3.6%) and Klebsiella oxytoca (n= 4, 3.6%) respectively. blaOXA-48 was the most frequent gene detected. Among 83 (74.1%) isolates blaOXA-48 was detected alone and in 7 (6.3%) of the isolates it was identified with blaVIM gene coexistence. blaVIM gene was identified as the second most frequent CEG among the isolates. blaVIM gene was detected positive in 9 (8%) isolates. blaNDM gene was identified in 2 (1.8%) isolates. Ten of the K.pneumoniae isolates with identical PFGE pattern were named as pulsotype B. These isolates were found to be similar in terms of isolate location, isolation dates, antibiotic resistance patterns and the carbapenemase genes they carry, and are considered to be potential outbreak isolates originated from intensive care units. On the other hand CEGs were found in the clinical samples obtained from five out-patients suggesting that community-acquired infections may also arise due to carbapenemase producing Enterobacteriaceae in our country where blaOXA-48 producers are endemic. According to this study, blaOXA-48 producing gram negative bacteria were frequent in our hospital. The prevalance of blaVIM gene among metallo-beta-lactamases and coexistence with blaOXA-48 gene was remarkable. The frequency of blaNDM producing isolates in our hospital was not detected as high yet. In this study, the identification of carbapenemase producing bacteria as outbreak strains in our hospital indicated that cross-sectional surveillance for carbapenemase-producing bacteria from each patient was valuable in terms of early diagnosis of outbreaks.

Upper respiratory viral infections in patients with haematological malignancies after allogeneic haematopoietic stem cell transplantation: a retrospective study.

BACKGROUND: Community respiratory viruses (CRVs) are associated with upper respiratory viral infections (URI), pneumonia or life-threatening respiratory disease in patients with allogeneic haematopoietic stem cell transplantation (allo-HSCT). Our aim is to demonstrate our URI experience related to CRVs after allo-HSCT. METHODS: From January 2013 to November 2015, 39 post allo-HSCT patients with acute URI symptoms were included in the study. We evaluated CRVs by multiplex PCR from nasopharyngeal wash and throat swabs. RESULTS: The median age of the patients was 39 (range 20-67 years). A total of 25 patients (64%) had viral panel positivity at a median 140 days post-transplant (range 3-617 days). The most common agents detected were respiratory syncytial virus (32%) and parainfluenza (32%). The patients with viral panel positivity had significantly lower lymphocyte count (1.05×109/l versus 3.09×109/l; P=0.013). During follow-up, 20 patients (80%) were diagnosed with pneumonia. Patients with concurrent bacterial or fungal infections were more likely to have pneumonia (100% versus 68%; P=0.023). 10 patients (40%) died due to pneumonia and related complications. Lower lymphocyte counts and higher C-reactive protein levels at the time of viral panel positivity were risk factors for mortality (1.5×109/l versus 0.39×109/l, P=0.007; 74.2 versus 199.7, P=0.006). CONCLUSIONS: The viral panel was positive in 64% of patients with acute URI symptoms. Lower lymphocyte count was detected in CRV-positive patients. The onset of concomitant bacterial or fungal infections increased the risk of lower respiratory infection disease. Indeed, prospective studies should be designed for risks and outcomes of CRVs in allo-HSCT recipients.

[In vitro effect of vancomycin and daptomycin on biofilm formation of coagulase-negative staphylococci strains]. / Vankomisin ve daptomisinin koagülaz-negatif stafilokok izolatlarinin olusturdugu biyofilm üzerine in vitro etkisi.

Coagulase-negative staphylococci (CNS) are one of the primer agents of blood stream infections (BSI) and catheter-related bloodstream infections (CR-BSI) which are associated mostly with the usage of central venous catheters and, important causes of morbidity and mortality despite the usage of antibacterial and supportive treatment. It is important to determine the properties of these causative microorganisms in order to make appropriate treatment of such infections. The aims of our study were to evaluate the biofilm formation of coagulase negative staphylococci (CNS) which were causative agents of bloodstream (BSI) and catheter related bloodstream infections (CR-BSI), to determine the minimum inhibitory concentration (MIC) of planktonic forms and minimal biofilm eradication concentration (MBEC) of sessile forms for vancomycin and daptomycin and to evaluate the efficacy of these antibiotics in infections with biofilm-forming isolates in vitro. A total of 65 CoNS (n= 26 catheter colonizers, n= 28 CR-BSI, n= 11 BSI agents) were identified by conventional methods and also with BD Phoenix (Becton Dickinson, USA) and Bruker Microflex MS (Bruker Daltonics, Germany) systems. Methicillin resistance was determined by the presence of mecA gene with PCR. MIC values of vancomycin and daptomycin were investigated by broth microdilution, for daptomycin medium containing 25 and 50 µg/ml Ca++ were used. Assessment of biofilm formation and detection of MBEC were determined by microplate method. The clonal relationship was investigated by the PFGE method. A total of 65 isolates; 26 catheter colonizers, 28 CR-BSI agents and 11 BSI agents were evaluated and identified as Staphylococcus epidermidis (n= 33), Staphylococcus haemolyticus (n= 16), Staphylococcus hominis (n= 15), and Staphylococcus capitis (n= 1). 81.5% of the isolates were found to be methicillin resistant and all of them were found to be sensitive to vancomycin (MIC= 0.125-4 µg/ml) and daptomycin (MIC= 0.062-0.25 µg/ml in 25 µg/ml Ca++ and MIC= 0.031-0.50 µg/ml in 50 µg/ml Ca++ containing medium). MIC values were lower in medium containing 50 µg/ml Ca++ for daptomycin. As it is known that the efficacy of daptomycin depends on the physiological levels of Ca++, which causes conformational changes in the structure of these antibacterials. Our findings also suggested that high levels of Ca++ are needed to ensure the efficacy of daptomycin. All of the isolates produced biofilm at different strengths of positivity (n= 12/18.5% weak, n= 35/%53.8 moderate, n= 18/%27.7 strong). MBEC and MBEC/MIC values for vancomycin were found to be higher than daptomycin (p< 0.001). Strong biofilm producers had higher MBEC and MBEC/MIC, MBEC50/MIC50 ve MBEC90/MIC90 values (p< 0.05). Especially in infections with biofilm forming isolates, the detection of only MIC values are not always sufficient in the treatment of biofilm-related infections as they reflect the sensitivity of planktonic bacteria. The inconsistency between the MIC and MBEC values and the high rates of MBEC/MIC found in our study supported this prediction.The lower detection of MBEC and MBEC/MIC values of daptomycin compared to the same values of vancomycin suggested that daptomycin might be effective at lower doses than vancomycin in the treatment of biofilm infections.

[Investigation of biofilm formation properties of staphylococcus isolates]. / Stafilokok izolatlarinin biyofilm olusturma özelliklerinin arastirilmasi.

Biofilm production is an important virulence factor which allows staphylococci to adhere to medical devices. The principal component of biofilm is a "polysaccharide intercellular adhesin (PIA)" which is composed of a beta-1,6-N-acetylglucosamine polymer synthesized by an enzyme (N-acetylglucosamine transferase) encoded by the ica operon found on the bacterial chromosome. This operon is composed of four genes (A, B, C, and D), and a transposable element IS256. In this study, we aimed to determine the biofilm production characteristics of invasive/non-invasive staphylococcus isolates and different staphylococcus species. Biofilm production of 166 staphylococci was phenotypically investigated on Congo Red Agar (CRA); the presence of icaA, icaD and IS256 genes were investigated by polymerase chain reaction (PCR). 74 of the isolates (44.6%) were identified as methicillin resistant Staphylococcus aureus (MRSA), 25 (15.1%) as methicillin sensitive S.aureus (MSSA), 25 (37.3%) as Staphylococcus hominis, 20 (12%) as S.epidermidis, ten (15%) as Staphylococcus haemolyticus, nine (13.4%) as Staphylococcus capitis, two (3%) Staphylococcus saprophyticus and one (1.5%) as Staphylococcus warnerii. Of the MRSA strains, 52 were isolated from blood and 22 from nose; all MSSA strains were isolated from nose cultures. Coagulase-negative staphylococci (CoNS) strains were composed of invasive and non-invasive strains isolated from nose, catheter tip and blood cultures from patients with catheter. Production with CRA method was found to be statistically significant in invasive isolates (p< 0.001). It is concluded that; as the biofilm formation capacity of invasive isolates can cause refractory infections and the importance of carriage and hospital infections of these bacteria, it is important to prevent the spread of these isolates. A combination of phenotypic and genotypic tests is recommended for the investigation of biofilm formation in staphylococci. 40.3% of the CoNS isolates, and 85.8% of S.aureus isolates produced biofilm on CRA (p< 0.001) and with PCR method the ratio of carrying three genes was found to be statistically important in S.aureus when compared with CoNS. Carriage of three genes and biofilm formation capacity of invasive isolates can cause refractory infections and the importance of carriage and hospital infections of these bacteria, it is important to prevent the spread of these isolates. A combination of phenotypic and genotypic tests is recommended for the investigation of biofilm formation in staphylococci.

Wound and soft tissue infections of Serratia marcescens in patients receiving wound care: A health care-associated outbreak.

We described a health care-associated Serratia marcescens outbreak of wound and soft tissue infection lasting approximately 11 months at Ankara University Ibni Sina Hospital. After identification of S marcescens strains from the clinical and environmental samples, and their susceptibility testing to antimicrobial agents, pulsed-field gel electrophoresis (PFGE) was performed to detect molecular epidemiologic relationships among these isolates. The strains which were isolated from the saline bottles used for wound cleansing in the wound care unit were found to be 100% interrelated by PFGE to the strains from the samples of the outbreak patients. Reuse of the emptied bottles has no longer been allowed since the outbreak occurred. Besides, more efficient and frequent infection control training for hospital staff has been conducted.

Evaluation of antimicrobial susceptibilities and virulence factors of Staphylococcus aureus strains isolated from community-acquired and health-care associated pediatric infections.

Karbuz A, Karahan ZC, Aldemir-Kocabas B, Tekeli A, Özdemir H, Güriz H, Gökdemir R, Ince E, Çiftçi E. Evaluation of antimicrobial susceptibilities and virulence factors of Staphylococcus aureus strains isolated from community-acquired and health-care associated pediatric infections. Turk J Pediatr 2017; 59: 395-403. The aim of this study was to investigate the enterotoxins and Panton-Valentine leukocidin (PVL) gene as virulence factor, identification if antimicrobial sensitivity patterns, agr (accessory gene regulator) types and sequence types and in resistant cases to obtain SCCmec (staphylococcal cassette chromosome mec) gene types which will be helpful to decide empirical therapy and future health politics for S. aureus species. Total of 150 isolates of S. aureus were isolated from the cultures of the child patients in January 2011 and December 2012. In this study, the penicillin resistance was observed as 93.8%. PVL and mecA was detected positive in 8.7% and in 6% of all S. aureus strains, respectively. Two MRSA (methicillin resistant S.aureus) strains were detected as SCCmec type III and SCCmec type V and five MRSA strains were detected as SCCmec type IV. SET-I and SET-G were the most common detected enterotoxins. In both community-associated and healthcare-associated MRSA strains, agr type 1 was detected most commonly. The most common sequence types were ST737 in 13 patients than ST22 in eight patients and ST121 in six patients. This study highlights a necessity to review the cause of small changes in the structural genes in order to determine whether it is a cause or outcome; community-acquired and healthcare associated strains overlap.

Molecular Characterization of Methicillin-Resistant Staphylococcus aureus Bloodstream Isolates in a Turkish University Hospital Between 2002 and 2012.

AIMS: Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most important pathogens in the hospital environment. Monitoring of this pathogen by molecular characterization and phenotypic methods is important for the development of suitable infection control measures and proper therapy design. In this study, our aim was to investigate the molecular epidemiological characteristics of MRSA bloodstream isolates obtained from patients hospitalized at Ankara University Ibn-i Sina Hospital in a 10-year period (2002-2012) and monitor the possible changes. A total of 134 isolates were characterized according to their antimicrobial susceptibility profiles, biofilm formation capabilities, accessory gene regulator (agr) locus types, presence of genes encoding Panton-Valentine leukocidin (PVL), staphylococcal enterotoxins A-J (SEs A-J), toxic shock syndrome toxin, sasX, and genes associated with biofilm formation (icaD, icaA, IS256) by polymerase chain reaction. The staphylococcal cassette chromosome mec (SCCmec) types of isolates were also defined and their clonal relationships were investigated by pulsed-field gel electrophoresis (PFGE) analysis and multilocus sequence typing was performed for representative isolates obtained by PFGE. RESULTS: The majority of the isolates were resistant to rifampin (100%), ciprofloxacin (97%), tetracycline (97.7%), and gentamicin (94.7%); 100% carried type-III SCCmec and 89.5% were agr type-1. All the isolates were negative for PVL, and sasX genes while all of them carried the icaD, icaA, and IS256 genes. The most common SE was enterotoxin A (97%). Four major PFGE patterns with the dominance of one pattern and seven unique patterns were obtained. All the representative PFGE isolates (n = 11) belonged to sequence type 239. CONCLUSION: We have documented the characteristics of the dominant MRSA clone in our hospital, which was a PVL (-), sasX (-) ST239 clone carrying sea (+) with type-III SCCmec, and type-1 agr locus.

[Molecular characterization of Salmonella enterica serovar Typhimurium strains isolated from humans in Turkey]. / Türkiye'de insanlardan izole edilen Salmonella enterica serovar Typhimurium suslarinin moleküler özellikleri.

Multidrug resistant (MDR) Salmonella infections, especially infections due to Salmonella Typhimurium DT104 phage type strains are an important public health issue in many parts of the world. S.Typhimurium is the most common serotype isolated from clinical samples in Turkey but we have limited data about the phage types of these isolates. The aims of this study were to find out whether these MDR S.Typhimurium isolates are DT104 phage type isolates and have class 1 integrons and to investigate the relationships of these characteristics between plasmid and pulsed field gel electrophoresis (PFGE) profiles. A total of 66 S.Typhimurium stock strains selected from Enterobacteria Laboratory culture collections of Ankara University School of Medicine, Department of Medical Microbiology were investigated by plasmid profile analysis (PPA) and PFGE with the use of XbaI and SpeI enzymes. The presence of class 1 integrons and the phage type 104 were investigated by polymerase chain reaction (PCR). The strains used in the study were sporadically isolated cases from seven provinces after year 2000 with ACSSuT (63), ACGSSuTT/S (1), ACSSuTT/S (1) and ASSuTT/S (1) resistance types [ampicillin (A), chloramphenicol (C), gentamicin (G), streptomycin (S), sulphonamide (Su), tetracycline (T), trimethoprim/sulfamethoxazole (T/S)]. Of the isolates 65 were found as DT104 phage type. Forty-three S.Typhimurium DT104 isolates that carry class 1 integrons had five different bands between 350-1600 base pairs (bp); all of the isolates harbored 1-4 plasmids with sizes ranging from 1.0-180 kbp and 62 isolates had 90 kbp plasmid which was serotype specific and virulence related. S.Typhimurium DT104 isolates were grouped into five (X1-X5) and seven (S1-S7) profiles with XbaI and SpeI enzymes, respectively. When the profiles of the two enzymes were evaluated, 58 of the 65 (89.2%) isolates showed similar (X1.S1) profile. The molecular characteristics of the most S.Typhimurium isolates were clustered in similar groups when class 1 integron, plasmid and PFGE types were analyzed together. In this study we showed that nearly all S.Typhimurium isolates with five drug resistance pattern (ACSSuT) were DT104 isolates. PFGE profiles of these sporadic isolates suggested that they were epidemiologically related.