Evaluation of probiotics' efficiency on cariogenic bacteria: randomized controlled clinical study.

BACKGROUND: Probiotics are live beneficial bacteria to human health and their efficiency on oral health is still being investigated. The purpose of this study was to evaluate the level of Streptococcus mutans and Lactobacillus species with and without the use of probiotics for six-months after the treatment of all dental caries under general anesthesia. METHODS: Fifty-eight pediatric patients without any systemic diseases, whose dental treatments were completed under general anesthesia (GA), were included in the study. The patients were recruited in two-groups; Group A: Patients started using probiotics after GA and Group B: Patients did not use probiotics after GA. Saliva samples were taken from all patients on the day before GA (T0), at one-month (T1), three-month (T2) and six-month (T3) follow-up after GA. The counts of cariogenic bacteria were determined by the analysis of saliva samples using real-time polymerase chain reaction. Statistical significance level was accepted as p < 0.05. RESULTS: There was statistically significant difference between Group A and B for T0, T1, T2 and T3 regarding S. mutans (p = 0.001, p = 0.04, p = 0.04, p = 0.03; p < 0.05). However, there was no statistically significant difference between groups regarding Lactobacillus species (p ≥ 0.05). CONCLUSIONS: Probiotic use and treatment of all caries significantly reduced the level of S. mutans but not Lactobacillus species. Furthermore, S. mutans decreased after cessation of probiotics, but it was not statistically significant. TRIAL REGISTRATION: Study was registered as "Effects of Probiotics on Streptococcus mutans and Lactobacillus species" with the registration number of NCT05859646 (16/05/2023) at https://www. CLINICALTRIALS: gov Protocol Registration and Results System.

In vitro activity of cefiderocol against carbapenem-resistant Acinetobacter baumannii carrying various ß-lactamase encoding genes.

OBJECTIVES: This study aimed to determine the in vitro efficacy of cefiderocol in carbapenem-resistant Acinetobacter baumannii (CRAB) isolates and evaluate the disk-diffusion (DD) method as an alternative method to broth-microdilution (BMD). METHODS: Totally 89 CRAB isolates were included. Cluster analysis was determined by Pulsed-Field Gel Electrophoresis (PFGE). Resistance genes; blaOXA-51, blaOXA-23, blaOXA-24, blaOXA-58,blaPER-1, blaNDM, blaIMP and mcr-1 were screened. Cefiderocol susceptibility testing was performed by both DD and BMD. Interpretation was made according to EUCAST and CLSI. Categorical agreement (CA), minor errors (mEs), major errors (MEs), and very major errors (VMEs) were determined. RESULTS: PFGE revealed 5 distinct pulsotypes; 86 of the isolates were extensively drug-resistant (XDR). All the isolates were negative for blaNDM, blaIMP, mcr-1, while positive for blaOXA-58 and blaOXA51. blaPER-1 was positive for 33.7%; blaOXA-23 for 74.2%; blaOXA-24 for 12.3%. According to CLSI, the MEs rate was 1.85%, mEs was 7.86% and there were no VMEs. According to EUCAST, MEs rate was 3.70%, there were no mEs and VMEs. CA was 91% for CLSI and 97.8% for EUCAST. MICs of cefiderocol against A. baumannii isolates ranged from 0.06 to > 128 mg/L, with MIC50 and MIC90 values of 0.5 and > 128 mg/L, respectively. CONCLUSIONS: Cefiderocol susceptibility was 60.7% in CRAB isolates. MIC50, MIC90 of blaPER-1 positive and blaPER-1 negative groups were > 128/>128 and 0.25/>128 mg/L. A correlation between the presence of blaPER-1 and cefiderocol resistance was observed (p < 0.0001). Among colistin-resistant isolates, the presence of blaPER-1 was 47.1% and 75% of them were resistant to cefiderocol respectively.

Biological and genomic characteristics of three novel bacteriophages and a phage-plasmid of Klebsiella pneumoniae.

Bacteriophages have emerged as promising candidates for the treatment of difficult-to-treat bacterial infections. The aim of this study is to isolate and characterize phages infecting carbapenem-resistant and extended-spectrum beta-lactamase producer Klebsiella pneumoniae isolates. Water samples were taken for the isolation of bacteriophages. One-step growth curve, the optimal multiplicity of infection (MOI), thermal and pH stabilities, transmission electron microscopy and whole-genome sequencing of phages were studied. Four phages were isolated and named Klebsiella phage Kpn02, Kpn17, Kpn74, and Kpn13. The optimal MOI and latent periods of phage Kpn02, Kpn17, Kpn74, and Kpn13 were 10, 1, 0.001, and 100 PFU/CFU and 20, 10, 20, and 30 min, respectively. Burst sizes ranged from 811 to 2363. No known antibiotic resistance and virulence genes were identified. No tRNAs were detected except Klebsiella phage Kpn02 which encodes 24 tRNAs. Interestingly, Klebsiella phage Kpn74 was predicted to be a lysogenic phage whose prophage is a linear plasmid molecule with covalently closed ends. Of the Klebsiella-infecting phages presented in current study, virulent phages suggest that they may represent candidate therapeutic agents against MDR K. pneumoniae, based on short latent period, high burst sizes and no known antibiotic resistance and virulence genes in their genomes.

Evaluation of the Lytic Activity of Various Phage Cocktails Against, ESBL-Producer, Non-Producer and Carbapenem-Resistant Escherichia coli Isolates.

Bacteriophages have been proposed as an alternative therapy for the treatment of bacterial infections. This research aims to determine the lytic activity of bacteriophage-cocktails (BC) against carbapenem-resistant (CR-EC), ESBL-producer (EP-EC), and non-producer (NP-EC) E. coli isolates. Related resistance genes in 87 E. coli isolates were screened by PCR. The efficacies of BCs were determined by spot test and lytic zones were evaluated from fully-confluent to opaque. MOIs of the BCs were compared for fully-confluent and opaque lytic zones. BCs were also evaluated in terms of their biophysical characteristics including latency, burst size, pH and temperature stabilities. Among EP-EC, 96.9% of the isolates carry blaCTX-M, 25% of them blaSHV and 15.6% of them carry blaTEM. All CR-EC isolates carried blaOXA-48, but not blaKPC and blaNDM. CR-EC isolates were the least susceptible for the each of four BCs. MOIs for ENKO, SES and INTESTI-phage forming fully-confluent zone in E. coli isolates EC3 (NP-EC), EC8 (EP-EC) and EC27 (NP-EC), respectively were 10, 100 and 1, respectively. MOIs for ENKO, SES and INTESTI opaque zone in EC19 (EP-EC), EC10 (EP-EC), EC1(NP-EC), respectively were 0.01, 0.01, 0.1 PFU/CFU, respectively. The MOI for PYO-phage forming a semi-confluent zone in EC6 (NP-EC) isolate was 1 PFU/CFU. The phages were thermally stable and tolerant to a wide pH range. Comparison of MOIs according to lysis zone characteristics demonstrated that the activities of phages in phage cocktails vary depending on the characteristics of each bacterial host. Supplementary Information: The online version contains supplementary material available at 10.1007/s12088-023-01074-9.

Comparative in vitro activities of omadacycline, eravacycline and tigecycline against non-ESBL-producing, ESBL-producing and carbapenem-resistant isolates of K. pneumoniae.

Introduction. Extended-spectrum ß-lactamase (ESBL)-producing Enterobacteriaceae and carbapenem-resistant Enterobacteriaceae are characterized by the World Health Organization as pathogens for which new antibiotics are urgently needed. Omadacycline and eravacycline are two novel antibacterials within the tetracycline class.Gap Statement. There are limited data regarding the comparison of the activities of omadacycline, eravacycline and tigecycline against K. pneumoniae isolates with different antimicrobial susceptibility profiles.Aim. Our objective was to compare the in vitro activities of omadacycline, eravacycline and tigecycline against a collection of K. pneumoniae isolates, including non-ESBL-producing, ESBL-producing and carbapenem-resistant strains.Methodology. Ninety-four K. pneumoniae isolates, including 30 non-ESBL-producing, 30 ESBL-producing and 34 carbapenem-resistant (22 carrying bla OXA-48, 12 carrying bla NDM) strains were included in the study. ESBL and carbapenemase genes were detected by conventional PCR. Omadacycline, eravacycline and tigecycline MICs were determined by the gradient diffusion method and interpreted using US Food and Drug Administration (FDA)-defined breakpoints.Results. Overall, the percentage of tigecycline-susceptible strains (97.9 %) was higher than the percentage of omadacyline-susceptible (75.5 %) and eravacycline-susceptible (72.3 %) strains. The omadacycline and eravacycline susceptibility rates were 83.3 % among non-ESBL-producing isolates and 66.7 % among ESBL-producing isolates. The most common ESBL gene detected was blaCTX -M (90 %), followed by bla TEM (50 %) and bla SHV (50 %). The omadacycline and eravacycline susceptibility rate among isolates carrying bla TEM was 33.3 %, whereas it was 100 % among isolates that do not carry bla TEM. The omadacycline and eravacycline susceptibility rates among carbapenem-resistant isolates were 76.5 and 67.6 %, respectively. The omadacycline susceptibility rates among bla OXA-48-positive and bla NDM-positive isolates were 77.3 and 75.0 %, respectively. The eravacycline susceptibility rates among bla OXA-48-positive and bla NDM-positive isolates were 68.2 and 66.7 %, respectively. One carbapenem-resistant isolate was intermediate and one ESBL-producing isolate was resistant to tigecycline.Conclusion. Overall, tigecycline was the most active tetracycline against isolates. Omadacycline and eravacycline showed excellent activity against ESBL-producing K. pneumoniae isolates that do not carry bla TEM. Omadacycline showed reasonable activity against carbapenem-resistant K. pneumoniae isolates carrying bla OXA-48 or bla NDM.

Retrospective evaluation of viral respiratory tract infections in a university hospital in Ankara, Turkey (2016-2019).

INTRODUCTION: Viruses are responsible for two-thirds of all acute respiratory tract infections. This study aims to retrospectively detect respiratory tract viruses in patients from all age groups who visited the hospital. METHODOLOGY: A total of 1592 samples from 1416 patients with respiratory tract symptoms were sent from several clinics to the Molecular Microbiology Laboratory at Gazi University Hospital from February 2016 to January 2019. Nucleic acid extraction from nasopharyngeal swabs, throat swabs or bronchoalveolar lavage (BAL) samples sent to our laboratory was done using a commercial automated system. Extracted nucleic acids were amplified by a commercial multiplex-real time Polymerase Chain Reaction (PCR) method, which can detect 18 viral respiratory pathogens. RESULTS: Among 1592 samples, 914 (57.4%) were positive for respiratory viruses. The most prevalent were rhinovirus (25.2%) and influenza A virus (12.1%), the least prevalent was the bocavirus (2.6%). Rhinovirus was the most detected as a single agent (21.2%, 194/914) among all positive cases, followed by coronavirus (9.3%, 85/914). The detection rates of coronavirus, human adenovirus, respiratory syncytial virus A/B, human parainfluenza viruses, human metapneumovirus-A/B, human parechovirus, enterovirus and influenza B virus were 9.9%, 8%, 7.7%, 5%, 3.4%, 3.1%, 3%, and 2.8%, respectively. CONCLUSIONS: The most detected viral agents in our study were influenza A virus and rhinovirus. Laboratory diagnosis of respiratory viruses is helpful to prevent unnecessary antibiotic use and is essential in routine diagnostics for antiviral treatment. Multiplex Real-time PCR method is fast and useful for the diagnosis of viral respiratory infections.

Molecular Epidemiological Analysis of Bacillus Pseudo-Outbreak due to Contaminated Culture Tubes Containing Stuart Medium.

BACKGROUND: It is challenging to determine whether Bacillus species other than Bacillus anthracis cause infections. Pseudo and true outbreaks of Bacillus spp. have been noted. Here, we present a molecular analysis of a Bacillus spp. pseudo-outbreak caused by contaminated culture tubes containing Stuart medium. METHODS: Between January and March 2015, a high percentage of Bacillus spp. was isolated from the wound samples of inpatients at the Karabuk University Hospital, and an outbreak was suspected. Environmental and staff nasal samples were cultured aerobically, and Bacillus spp. were isolated from some of them. However, the isolation of Bacillus spp. in throat cultures of outpatients suggested contamination caused by culture tubes containing Stuart medium. We examined two lots of culture tubes used in the hospital. Although the culture tubes' expiry date and storage conditions were suitable, Bacillus spp. grew in one of these lots. A total of 47 Bacillus spp. isolated during this period were identified, and the clonal relationship among the isolates was investigated by arbitrarily primed polymerase chain reaction. RESULTS: Twenty-seven strains were identified as Bacillus megaterium and 20 as Bacillus firmus. Of the four strains isolated from the Stuart medium, two were identified as B. firmus and the other two were B. megaterium. Two B. firmus strains isolated from the Stuart medium and two B. firmus strains obtained from the coronary intensive care environmental samples were matched and clustered within the same genotype. We recalled all culture tubes containing Stuart medium. After another brand's culture tubes were distributed, no growth was observed. It was then understood that the pseudo-outbreak source was contaminated culture tubes containing Stuart medium. CONCLUSIONS: Microbiological controls of medical materials and equipment should be regularly checked to prevent outbreaks (true or pseudo).

Comparison of in vitro activities of plazomicin and other aminoglycosides against clinical isolates of Klebsiella pneumoniae and Escherichia coli.

OBJECTIVES: To compare the in vitro activity of plazomicin and two older aminoglycosides (gentamicin and amikacin) against 180 isolates of Escherichia coli and Klebsiella pneumoniae, including subsets of 60 non-ESBL-producing, 60 ESBL-producing and 60 carbapenem-resistant (46 carrying blaOXA-48, 11 carrying blaNDM and 3 carrying blaOXA-48 and blaNDM) strains. METHODS: MICs of plazomicin, gentamicin and amikacin were determined by a gradient diffusion method. Gentamicin and amikacin MICs were interpreted according to CLSI criteria and EUCAST breakpoint tables. Plazomicin MICs were interpreted using FDA-defined breakpoints. RESULTS: All non-ESBL-producing and ESBL-producing isolates were susceptible to plazomicin. The plazomicin susceptibility rate (71.7%) in carbapenem-resistant isolates was significantly higher than those observed for gentamicin (45%) and amikacin (56.7% and 51.7% according to CLSI and EUCAST breakpoints, respectively). Gentamicin, amikacin and plazomicin susceptibility rates (35.6% for gentamicin; 44.4% and 37.8% for amikacin according to CLSI and EUCAST breakpoints, respectively; 64.4% for plazomicin) in carbapenem-resistant K. pneumoniae were significantly lower than those observed for carbapenem-resistant E. coli isolates (73.3% for gentamicin; 93.3% for amikacin and plazomicin). Gentamicin, amikacin and plazomicin susceptibility rates for blaNDM-positive isolates were lower than those observed for blaOXA-48-positive isolates, but differences were not statistically significant. Among the isolates that were non-susceptible to both gentamicin and amikacin, the plazomicin susceptibility rate was less than 30%. CONCLUSIONS: Although plazomicin showed excellent in vitro activity against carbapenem-susceptible isolates, the plazomicin resistance rate increased to 35.6% among carbapenem-resistant K. pneumoniae and further increased to 45.5% among blaNDM-positive isolates.

Antibacterial Resistance in Lower Respiratory Tract Bacterial Pathogens: A Multicenter Analysis from Turkey.

INTRODUCTION: This study aimed to evaluate the etiology of lower respiratory tract infections (LRTIs) and their antibiotic resistance. METHODOLOGY: Bacterial culture results of LRT samples from 17 hospitals between 2016-2019 were included in the study. All isolates were identified and AST were performed by automated microbiology systems. AST was performed according to EUCAST. RESULTS: Non-duplicate 30,051 (26,890 HA and 3156 CA) isolates detected as causative pathogen. LRTIs are caused by 85.1% Gram-negative bacterial pathogens and 14.9% Gram-positive. The most common isolates among HA pathogens were Acinetobacter spp. (27.4%), P.aeruginosa (22.2%), K.pneumoniae (17.9%); among CA pathogen S.pneumoniae (19.9%), P. aeruginosa (18.9%), H.influenzae (14.6%). ESBL rate was 62.5% in K.penumoniae; 53.1% in E.coli; 19.1% in Klebsiella spp; 13.9% in Enterobacter spp.; 8.6% in Proteus spp.; 6.3% in Citrobacter spp.; and 4.3% in Serratia spp. Resistance rates to carbapenems and colistin were 92.8% and 12.8% in A baumannii, 39.8% and 7.5% in P.aeruginosa, 47.3% and 18.5% in K.penumoniae. Among staphylococci, 27.3% of S. aureus and 82.4% of CoNS were methicillin resistant. 7.6% of E.faecium and 0.9% of E.faecalis were vancomycin resistant.  Linezolid resistant S. aureus, CoNS, E.faecalis and E.faecium rates were 0.3%, 2.9%, 0.0% and 4.6%. Inducible clindamycin resistant rate was 17.2% in S. aureus 38.2% in CoNS. Non-susceptible S.pneumoniae isolate rate to penicillin was 37.0%. 6.5% of S.maltophilia and 4.4% of B.cepacia isolates were resistant to trimethoprim/sulfamethoxazole. CONCLUSIONS: Antibiotic resistance was mainly observed among A.baumannii and K.pneumoniae and continuous surveillance of antimicrobial resistance patterns in the management of LRTIs is important.

[Determination of Biofilm Formation Properties of Methicillin Sensitive and Resistant Staphylococcus aureus Isolates by Conventional and Molecular Methods]. / Metisiline Duyarli ve Dirençli Staphylococcus aureus Izolatlarinin Biyofilm Olusturma Özelliklerinin Konvansiyonel ve Moleküler Yöntemlerle Belirlenmesi.

Biofilm-related infections are considered as among the foremost causes of treatment failure nowadays. One of the most common causes of biofilm-related infections is Staphylococcus aureus. It becomes extremely difficult to determine the appropriate treatment protocol while biofilm-related infections are coexisting with bacterial methicillin resistance. The aim of this study was to observe the potential of biofilm formation of methicillin-sensitive and -resistant S.aureus strains isolated from different clinical specimens and to determine reliable and effective methods for biofilm detection. A total of 200 S.aureus strains (100 methicillin-resistant and 100 methicillin-susceptible) isolated from 107 wound, 93 blood and catheter specimens, which were accepted as causative agents, included in the study. In order to determine the methicillin sensitivity, oxacillin minimal inhibitory concentration value obtained by an automated system and cefoxitin disc diffusion method were evaluated together. Biofilm formation was investigated by modified Christensen (MC), MTT, BioTimer and Congo Red Agar (CRA) methods, and the presence of ica operon responsible for biofilm formation was also observed by polymerase chain reaction. It has been shown that methicillin-resistant isolates produce biofilms in a shorter time and higher rate, and their biofilm structure is denser than methicillin-sensitive isolates in all MC, MTT and BioTimer methods. There was no difference between blood and wound isolates in biofilm formation. The most sensitive and specific conventional methods were MTT and BioTimer methods respectively. There was no significant difference between the isolates containing a gene region of icaADBC operon and the biofilm forming isolates according to MC, MTT, BioTimer and CCA methods. There was a high correlation between the presence of biofilm and ica positivity, and the tendency to form biofilm augmented as the number of ica genes increased. It has been emphasized that more virulent strains such as methicillin-resistant S.aureus have a higher tendency to form biofilm, and these two resistance mechanisms have been shown to support each other as cascade. ica detection may be an important reagent in itself for the detection of virulent strains, thus detection of the ica presence may be an early marker of treatment decisions, determination of protection strategies, and struggle with biofilm-related infections. In cases where molecular methods are not available, the existence of quick, easy-to-apply and reliable conventional methods to detect biofilm formation is extremely important. All conventional methods used in this study seem to be sufficient in this respect. MC and MTT methods stand out in terms of biofilm quantitation. BioTimer method is a very new and remarkable test used to detect biofilm formation. In conclusion, determining the potential of biofilm formation of colonizing or causative agents and taking essential precautions before interventional procedures will decrease biofilm related infections and related morbidity and mortality.

In vitro activity of ceftolozane-tazobactam and ceftazidime-avibactam against clinical isolates of meropenem-non-susceptible Pseudomonas aeruginosa: A two-centre study.

OBJECTIVES: This study aimed to compare the activity of ceftazidime-avibactam (C/A), ceftolozane-tazobactam (C/T) and three anti-pseudomonal ß-lactams (piperacillin-tazobactam, ceftazidime and cefepime) against a collection of meropenem-non-susceptible Pseudomonas aeruginosa (P. aeruginosa) clinical isolates recovered from two centres in Turkey. METHODS: A total of 102 unique patient isolates of meropenem-non-susceptible P. aeruginosa were included in the study. MICs of antimicrobials were determined by the gradient diffusion method. RESULTS: Overall susceptibility rates for C/A and C/T were 83.3% and 82.4%, respectively. Both C/A and C/T had better activity than any one of the three anti-pseudomonal ß-lactams. According to the MIC50 values, C/T was the most potent agent against isolates. Although the susceptibility rates of isolates to C/T and C/A were similar, C/T (MIC50, 1 µg/mL) was four-fold more potent than C/A (MIC50, 4 µg/mL). The MIC50 values of C/A and C/T for the isolates that were non-susceptible to three ß-lactams were significantly higher than those for isolates that were non-susceptible to zero, one or two ß-lactams. Also, the C/A MIC50 value for the isolates that were non-susceptible to two ß-lactams was higher than that for isolates which were non-susceptible to one ß-lactam. CONCLUSIONS: C/A and C/T showed good activity against meropenem-non-susceptible P. aeruginosa isolates. However, resistance to these agents was not uncommon among these isolates. The overall ß-lactam susceptibility profile of isolates seems to have an effect on the probability of susceptibility to C/A and C/T. Antimicrobial susceptibility testing should be performed for C/A and C/T if these agents are considered for treatment of infections caused by meropenem-non-susceptible P. aeruginosa.

[Evaluation of blood culture practices: Use of system (Epicenter) data]. / Kan kültürü uygulamalarinin degerlendirilmesi: Isletim sistemi (Epicenter) verilerinin kullanimi.

Sepsis is a serious clinical problem and estimated to be responsible for 18 million annual deaths worldwide. Therefore, the use and the rapid processing of blood cultures are important for the transition from empiric therapy to directed therapy. The aim of this study was to assess the best blood culture practices in Turkey. We have examined the collection practices and techniques at four different hospitals, and a total of 165.443 blood culture bottles were evaluated (2013-2015). At the preanalytical phase most of the data which were important and which could support hospital quality systems/practices were not entered into the HIS and EpiCenter system. At the analytical phase loading of the bottles and removal of positive bottles primarily occurred between 6:00 and 9:00 AM but the positivity rate of the bottles showed a homogeneous distribution throughout the day. In other words, there were significant delays at processing positive blood culture bottles related to laboratory workers. The effect of education regarding best practices, transition from single bottle to two bottle cultures was successful in all hospitals. Single bottle usage decreased below 10% in all hospitals. Significantly more positive cultures were detected at multiple cultures when compared with the single bottle collection practice. In retrospective patient records, it was seen that all the laboratories reported the results of Gram staining to the clinics. However, these data were not recorded to the EpiCenter. The contamination rates of Ankara Numune Hospital and Akdeniz University Faculty of Medicine Hospital are 6.2% and 5.4% respectively, contamination rates were not reported in other hospitals. The most common isolates detected in blood cultures were Escherichia coli, Klebsiella pneumoniae, Enterococcus faecium, Staphylococcus aureus, and Acinetobacter baumannii. The mean time for the detection of these organisms were less than 20 hours in the aerobic bottle and anaerobic bottles. A total of 79.6% of facultative anaerobic isolates were detected in both bottles; 9.8% were detected only in the aerobic bottles; 10.6% of the isolates were detected only in the anaerobic bottles. As a result, the educational efforts in Turkey have met with success for transition from collecting single bottle blood culture sets to two bottle blood cultures. However, further efforts are needed to increase the number of blood culture sets collected during a 24 hours' period. In addition, errors at the preanalytical, analytical and postanalytical periods (taking samples, loading bottles into the system and processing positive blood cultures) should be eliminated.

[The comparison of antibiotic susceptibilities of uropathogenic Escherichia coli isolates in transition from CLSI to EUCAST]. / CLSI'dan EUCAST'e geçiste üriner sistem enfeksiyonu etkeni Escherichia coli izolatlarinin antibiyotik duyarliliklarinin karsilastirilmasi.

Determination of treatment protocols for infections according to antimicrobial susceptibility test (AST) results is are important for controlling the problem of antibiotic resistance. Two standards are widely used in the world. One of them is Clinical Laboratory Standards Institute (CLSI) standards used in Turkey for many years and the other is the European Committee on Antimicrobial Susceptibility Testing (EUCAST) standards which is used in European Union member countries and came into use in 2015 in Turkey. Since the EUCAST standards had higher clinical sensitivity limits particularly for gram-negative bacilli compared to CLSI (2009) standards, there will be some changes in antibiotic resistance profiles of Turkey with the use of EUCAST. CLSI has changed zone diameters after 2009 versions and the differences between the two standards were brought to a minimum level. Knowledge of local epidemiological data is important to determine empirical therapy which will be used in urinary tract infections (UTI). The aim of this study was to determine the differences of antibiotic susceptibility zone diameters based on our local epidemiological data among uropathogenic Escherichia coli isolates according to EUCAST 2014 and CLSI 2014 standards. A total of 298 E.coli strains isolated from urine samples as the cause of uncomplicated acute UTI agents, were included in the study. Isolates were identified by conventional methods and with BBL Crystal E/NF ID System (Becton Dickinson, USA). AST was performed with Kirby Bauer disk diffusion method and results were evaluated and interpreted according to the CLSI 2014 and EUCAST 2014 standards. According to the results, susceptibility rates of isolates against amikacin (100%) and trimethoprim-sulfamethoxazole (63.09%) were identical in both standards. However, statistically significant differences were observed between CLSI and EUCAST standards in terms of susceptibilities against gentamicin (91.95% and 84.56%, respectively; p= 0.004), cefuroxime axetil (20.13% and 77.18%, respectively; p= 0.000) and levofloxacin (73.83% and 67.11%, respectively; p= 0.044). No statistically differences between two standards for ampicillin (32.89% and 36.24%, respectively; p= 0.219), ampicillin-sulbactam (65.77% and 69.13%, respectively; p= 0.216), ciprofloxacin (72.48% and 71.14%, respectively; p= 0.392) and imipenem (94.63% and 95.30%, respectively; p= 0.426) were determined. In this transitional period, continuity of cooperation between the clinician and microbiology laboratory should be kept forefront and the maintenance of local surveillance studies should be provided by taking into account the changes in antibiotic susceptibility results.

[Investigation of various virulence factors among the hospital and community-acquired Staphylococcus aureus isolates by real-time PCR method]. / Hastane ve Toplum Kaynakli Staphylococcus aureus Izolatlarinda Çesitli Virülans Faktörlerinin Gerçek Zamanli PCR Yöntemiyle Arastirilmasi

Staphylococcus aureus is the most common cause of skin and soft tissue infections in the community and the most important cause of nosocomial infections. In this research, it was aimed to detect the presence of staphylococcal enterotoxin A to D (SEA, SEB, SEC and SED, respectively), toxic shock syndrome toxin-1 (TSST-1), Panton-Valentine leukocidin (PVL) and SCCmec phenotype in methicillin-resistant S.aureus (MRSA) isolates and to demonstrate the genotypic association between hospital acquired and community acquired isolates. In the study the virulence factors of 147 S.aureus strains isolated from various clinical samples at Gulhane Military Medical Academy Hospital Microbiology Laboratory between 2007 and 2010 were investigated by real-time polymerase chain reaction. MLVA (multiple locus variable number of tandem repeat analysis) method was used to demonstrate the genotypic association between hospital-and community-acquired isolates. Seventy-two (%48.9) of 147 S.aureus isolates were determined as community acquired and 75 (%51.1) as hospital acquired. Ninety-three (63.2%) isolates possesed at least one toxin (77 strains harboured one, and 16 strains harboured more than one). Of the isolates in which toxin was detected 59.1% (55/93) were hospital acquired, 40.9% (38/93) were community acquired. SEA was determined in 59 (40.1%), SEB in 8 (5.4%), SEC in 12 (8.1%), SED in 8 (5.4%), TSST- 1 in 17 (11.5%) and PVL in 6 (4.0%) of the isolates. Methicillin resistance was determined in 61.1% (44/72) of the hospital acquired isolates and 6.7% of the (5/75) community acquired isolates. In our study, SCCmec type III was detected in 90.9% (40/44) of hospital acquired MRSA isolates and SCCmec type IV in 40.0% (2/5) of community acquired MRSA isolates. Most of the strains (40/47; 85.1%) carrying SEA were hospital acquired, and they were determined as methicillin-resistant. According to MLVA, hospital and community acquired groups' clustering rates, number of clones, number of unique profile were determined as; 73.6% and 57.3%; 34% and 47%; 19% and 32%, respectively. It was concluded that high prevalence of SEA toxin in hospital acquired MRSA isolates indicated that there was a possible association between the presence of toxin and antimicrobial resistance.

[Resistance rates to major anti-tuberculosis drugs in Mycobacterium tuberculosis strains isolated from seven different regions of Turkey in 2003-2006 period]. / Ulkemizin yedi farkli bölgesinden 2003-2006 yillari arasinda izole edilen mycobacterium tuberculosis suslarinin majör antitüberkoloz ilaçlara direnç oranlari.

Multi-drug resistance in Mycobacterium tuberculosis (MDR-TB) is a global problem and has increased especially in areas where tuberculosis control programmes are inefficient. The aim of this study was to detect the resistance rates against isoniazide (INH), rifampisin (RMP), ethambutol (EMB) and streptomycin (SM) in M. tuberculosis strains collected from 7 different regions including 62 cities and sent to Refik Saydam Hygiene Center National Tuberculosis Reference and Research Laboratory. Of the patients included, 7.61% were children, 92.39% were adults; 76.16% were male and 23.84% were female. These strains were isolated from sputum (n = 885, 81.11%), gastric lavage (n = 49, 4.49%), pleural fluid (n = 43, 3.94%), urine (n = 30, 2.74%), bronchoalveolar lavage (n = 22, 2.01%), and other clinical samples (n = 62, 8.46%) such as cerebrospinal fluid, lymph node, abscess material, lung tissue. The susceptibilities of the 1091 M. tuberculosis strains against the major anti-tuberculosis drugs were determined by the proportion method in Lowenstein-Jensen medium. Three hundred ninety two of the isolates were from Central Anatolia, 146 from Black Sea, 419 from Aegean, 28 from Mediterranean, 20 from Marmara, 64 from Eastern Anatolia and 21 from South Eastern Anatolia regions of Turkey. The distribution of the strains according to years were as follows: 88 in 2003, 114 in 2004, 341 in 2005 and 548 in 2006. Resistance to at least one of the drugs tested was found in 264 (14.20%) strains. Overall drug resistance rates to INH, RMP, EMB and SM were 12.3%, 10.1%, 6% and 15.8%, respectively. MDR-TB rate was 10% for this 4 years study period. MDR-TB rate was detected as 13.2%, 9.7%, 10.1% and 9.6% in children, adult, male and female patients, respectively. MDR-TB rate did not exhibit a statistically significant difference in terms of sex, age and study years (p > 0.05). However, this rate showed statistically significant difference in terms of geographical regions (p < 0.05). This study emphasized that regular surveillance of M. tuberculosis resistance to the major anti-tuberculosis drugs will provide valuable data for the effective national control and treatment of tuberculosis.

[An outbreak of vanA genotype Enterococcus faecium in pediatric clinic of a training hospital]. / Bir egitim hastanesinin çocuk kliniginde vanA genotip Enterococcus faecium salgini.

Vancomycin-resistant enterococci (VRE) have been increasingly reported from most countries around the world following initial isolation from patients in United States and European countries. A vancomycin-resistant Enterococcus faecium (VREF) outbreak was determined by hospital infection control committee in the pediatric unit of Gulhane Military Medical Academy, Ankara, Turkey in the first week of March 2008. While one of the 4 VREF strains was isolated from urine culture of a patient with neuroblastoma, the remaining strains were isolated from cultures of urine and rectal swab samples of a patient with nephrotic syndrome and from the hospital room doorknob of this patient. Aims of this study were to determine antibiotic susceptibilities by E-test, to investigate the presence of vanA, vanB and vanC-2 resistance genes by polymerase chain reaction (PCR), and to genotype the 4 strains by pulsed field gel electrophoresis (PFGE) and repetitive PCR (rep-PCR) (DiversiLab, bioMérieux, France). All isolates conferred high level [minimum inhibitor concentration (MIC) > 256 mg/L] vancomycin and teicoplanin resistance by E-test method. The isolates were also found resistant to gentamicin, streptomycin, ampicillin, erythromycin, penicillin and were susceptible to tetracycline and linezolid. The vanA gene was detected in all strains by PCR. It was demonstrated that the 4 VRE strains belonged to a single clone as shown by both PFGE and rep-PCR methods. Prompt and accurate detection of VRE and determination of the genotypes is of crucial importance to prevent horizontal transfer of the strains in the hospital. When compared with PFGE, the DiversiLab commercial rep-PCR seems to be a reliable and more rapid method to detect the genetic relationship between strains leading to an outbreak.

[Genotypic characteristics of Neisseria meningitidis serogroup W-135 strains isolated as the agent of fatal meningitis in a military hospital]. / Bir askeri hastanede fatal menenjit etkeni olarak izole edilen Neisseria meningitidis serogrup W-135 suslarinin genotipik özellikleri.

The aim of this study was to describe the genetic characterization of a total of 6 Neisseria meningitidis serogroup W-135 strains isolated from patients with meningitis and carriers in a military hospital in 2007-2008. Suspected colonies on modified Thayer-Martin medium plates were screened for oxidase reactivity and Gram stain. If gram-negative diplococci were present, a biochemical profile by the API NH system was used for species confirmation. Pulse field gel electrophoresis typing of Nhel-digested DNA was performed by a previously described method. Multi-locus sequence typing (MLST) was performed using the standard primers as listed on the Neisseria MLST website. Three distinct sequence types (STs) were identified: ST-11, ST-2754, ST-3751. One of the clinical isolates was identified as the same sequence type with Hajj isolate (ST-11) and the isolate with ST-2754 was the same as the first Turkish clinical strain isolated in 2003. These data demonstrated that along with ST-11 which is a known Hajj isolate, the ST-2754 strain causing meningococcal disease in Turkey beginning from the year 2003, should be carefully monitored.

[Investigation of the presence and subgroups of adenoviruses in nasopharyngeal samples of military recruits with respiratory tract infections]. / Solunum yolu enfeksiyonu olan askerlerin nazofarengeal örneklerinde adenovirus varliginin ve alt gruplarinin arastirilmasi.

Adenoviruses (AdV) are important pathogens primarily associated to respiratory infections of children and military staff even though it is also associated to many clinical manifestations, such as cystitis, conjunctivitis, diarrhea, hepatitis, myocarditis, and encephalitis. The goals of this study were to detect and type acute respiratory disease associated AdV isolates among military trainees in a selected region without an evidence of an outbreak. Throat swab samples were obtained during February 2006-March 2006 period, from 180 military male trainees aged 20-29, who were presented with respiratory tract symptoms and an oral temperature of > or = 38.0 degrees C. All specimens were tested by HEp-2 cell culture and real-time TaqMan PCR with AdV specific primers and probes. Positive cell culture results, presented as AdV-specific cytopathic effects, were confirmed by real-time polymerase chain reaction (PCR). AdV subgroup differentiation were performed using conventional PCR assays with the primer set specific for subgroup B, C or E. Subgroup specific PCR products were restricted with Mspl enzyme in order to check whether they were specific or not. AdV positivity was detected in 8 (4.4%) samples by cell culture and in 9 (5.0%) by the real-time PCR. All culture positive samples were also positive by real-time PCR. Eight of the nine real-time PCR-positive specimens were found to be in the subgroup E (this group contains only AdV type 4) and the results were confirmed with restriction enzyme analysis. One isolate could not be typed with the available primers. These data indicated that both real-time TaqMan PCR and restriction enzyme analysis provide sensitive and specific tools for AdV detection and subgroup differentiation for throat swab specimens. It can be concluded that since the prevalence of AdV infections was low in the study group, AdV infections were not considered as a vaccine requiring health problem in Turkish armed forces, however, larger scale studies were needed to reach a more precise conclusion.

Acinetobacter septicus sp. nov. association with a nosocomial outbreak of bacteremia in a neonatal intensive care unit.

Acinetobacter species other than Acinetobacter baumannii have rarely been reported to be associated with nosocomial outbreaks of bloodstream infections. Within a period of 1 week, seven Acinetobacter-like isolates were recovered from peripheral blood and catheter specimens of five patients at a neonatal intensive care unit (NICU) in a tertiary hospital in Turkey. All five patients had placement of central venous catheters and had received total parenteral nutrition before the onset of bacteremia. Two of the five patients died. Medical devices, tap water, aerators, water samples, various surfaces, intravenous fluids, and the hands of health care workers in the NICU were sampled and were culture negative for the bacterium. All seven of the isolates had identical biochemical reactions, antimicrobial susceptibility results, and pulsed-field gel electrophoresis patterns, indicating a clonal nosocomial outbreak. A panel of standard biochemical reaction profiles and three phenotypic commercial identification systems failed to identify these isolates. Phenotypically, the isolate differed from Acinetobacter ursingii by its hemolysis on sheep blood agar and its negative citrate utilization. Sequences of the full 16S rRNA gene, which contained at least three different gene copies with polymorphic sequences between nucleotide positions 70 and 206, were determined from the first recovered isolate. The complete 1,529- to 1,531-bp 16S rRNA gene sequences and partial 801-bp rpoB gene sequences had similarities of 99.5% and 97.2%, respectively, to an A. ursingii isolate. The DNA-DNA similarities of the strain against the type strain of A. ursingii were 64.7 and 68.7%, which were lower than the recommended threshold value of 70% for the definition of bacterial species. These data indicate that a novel Acinetobacter organism caused the nosocomial outbreak of bacteremia in the NICU unit. We propose the designation of Acinetobacter septicus sp. nov. for these isolates, with isolate AK001 as the type strain.

First recurrent infection with vancomycin-resistant enterococcus from Turkey.

Here we describe a case of a neuroblastoma patient with recurrent vancomycin-resistant enterococcal infection successfully treated with ciprofloxacin. This is the first case of recurrent vancomycin-resistant enterococcal infection in our hospital and Turkey.