Phenotypic and molecular characterization of Rhizobium vitis strains from vineyards in Turkey

Crown gall-affected grapevine samples were collected during 2009–2010 from major vineyards, located in different Turkish provinces. One hundred and three bacterial strains were obtained from 88 vineyards and 18 grapevine varieties; they were tumorigenic when inoculated in tobacco, sunflower and Datura stramonium plants and were identified as Rhizobium vitis using biochemical and physiological tests as well as PCR and specific primers. Nineteen R. vitis strains presented a number of anomalous biochemical and physiological characters. PCR and opine-specific primers revealed the presence of octopine/cucumopine-type plasmid in 82 R. vitis strains, nopaline-type plasmids in 18 strains and vitopine-type plasmids in three strains. Clonal relationship of strains was determined using Pulsed Field Gel Electrophoresis following digestion of genomic DNA with the restriction endonuclease PmeI. The greatest genetic diversity was found for the strains from Denizli, Ankara and Nevşehir provinces. Nopaline and vitopine-types of Rhizobium vitis were detected for the first time in Turkey

Yeasts in sustainable bioethanol production: a review

Bioethanol has been identified as the mostly used biofuel worldwide since it significantly contributes to the reduction of crude oil consumption and environmental pollution. It can be produced from various types of feedstocks such as sucrose, starch, lignocellulosic and algal biomass through fermentation process by microorganisms. Compared to other types of microoganisms, yeasts especially Saccharomyces cerevisiae is the common microbes employed in ethanol production due to its high ethanol productivity, high ethanol tolerance and ability of fermenting wide range of sugars. However, there are some challenges in yeast fermentation which inhibit ethanol production such as high temperature, high ethanol concentration and the ability to ferment pentose sugars. Various types of yeast strains have been used in fermentation for ethanol production including hybrid, recombinant and wild-type yeasts. Yeasts can directly ferment simple sugars into ethanol while other type of feedstocks must be converted to fermentable sugars before it can be fermented to ethanol. The common processes involves in ethanol production are pretreatment, hydrolysis and fermentation. Production of bioethanol during fermentation depends on several factors such as temperature, sugar concentration, pH, fermentation time, agitation rate, and inoculum size. The efficiency and productivity of ethanol can be enhanced by immobilizing the yeast cells. This review highlights the different types of yeast strains, fermentation process, factors affecting bioethanol production and immobilization of yeasts for better bioethanol production

Characterization of Klebsiella isolates by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and determination of antimicrobial resistance with VITEK 2 advanced expert system (AES)

WOS: 000365510300024PubMed ID: 26775392Background/aim: The purpose of the study was to evaluate the performance of the VITEK mass spectrometry (MS) (bioMerieux, France) system for the identification of Klebsiella spp. isolated from different sources. Moreover, while assessing the ability of the VITEK 2 automated expert system (AES) to recognize antimicrobial resistance patterns, the researchers have extended the study to compare VITEK 2 with the routine antimicrobial susceptibility testing method. Materials and methods: This study tested 51 Klebsiella spp. isolates that were isolated from environmental examples and clinical examples. Results of conventional methods and the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS were compared. Then, any differing results were compared against a reference 16S rRNA gene sequence, and when indicated, a recA sequencing analysis was done. Results: VITEK MS correctly identified 100% of the Klebsiella spp. isolates. There were two K. oxytoca isolates incorrectly identified to the species level with conventional methods according to the 16S rRNA gene sequencing analysis. In addition, a VITEK 2 AST-N261 card was used for the detection of extended spectrum beta-lactamases (ESBL). Using the VITEK 2 AES, ESBL positivity was found at the rate of 16.3% whereas this rate was 4.08% using the disk diffusion method. Conclusion: MALDI-TOF MS is a rapid and accurate method for the identification of Klebsiella spp. Moreover, the bioMerieux AES provides a useful laboratory tool for the interpretation of susceptibility results

Nrg (Tm) Rf Powered Transseptal Needle: A Useful Technique For Transcatheter Atrial Septostomy And Fontan Fenestration: Report Of Three Cases

Transseptal puncture (TSP) is a frequently performed procedure for gaining access to the left atrium for catheter ablation, hemodynamic assessment of the left heart, left ventricular assist device implantation, percutaneous left atrial appendage closure or mitral valvuloplasty during childhood and adulthood. The standard technique for tsansseptal puncture applies mechanical pressure on the fossa ovalis with a Brockenbrough needle. However, this method is not feasible when the fossa ovalis is thick and aneurysmatic. In such patients, the radiofrequency ablation energy systems can be offered as a better alternative for TSP. Here, we aimed to demonstrate the outcome of transseptal puncture performed with an NRG (TM) RF powered transseptal needle in three patients.WoSScopu

First pediatric case of osteomyelitis caused by Robinsoniella peoriensis

Robinsoniella peoriensis is a gram-positive, spore-forming, anaerobic rod. In our study, we isolated It peoriensis from an open fracture of the left distal tibia of a three-year-old male patient. Tissue anaerobic culture was positive for R. peoriensis. It was identified with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry and confirmed via 16S rRNA gene sequencing. The patient responded to ampicillin-sulbactam and amikacin antibiotic therapy. Antimicrobial susceptibility testing should be performed to guide the choice of treatment. To the best of our knowledge, this is the first report of R. peoriensis osteomyelitis in a pediatric patient and first report from Turkey

Comparative studies of hydrochars and biochars produced from lignocellulosic biomass via hydrothermal carbonization, torrefaction and pyrolysis

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The First Molecular Detection and Genotyping of Encephalitozoon cuniculi in Rabbit's Eye in Turkey

WOS: 000440196100020Encephalitozoon cuniculi was first recognized as the disease agent in rabbits in 1922. The genotype of E. cuniculi isolated from laboratory rabbits with the neurologic disease was described as genotype I. In the eye, this parasite causes damage to the lens, causing phacoclastic uveitis and cataracts. Intraocular infection often occurs in cases of transplacental transmission. There has been no report on the molecular diagnosis of the parasite in Turkey. The current study is the first report on the detection of E. cuniculi spores using the molecular method in Turkey. In our previous study, a rabbit breeding facility was determined seropositive for E. cuniculi infection monitored for five years in terms of clinical symptoms. An autopsy was performed for a definite diagnosis of the infection. Samples were stained according to the hematoxylin-eosin (H&E) staining after tissue processing procedure and histopathologic analysis was performed. In addition to, the samples for DNA extraction were also taken during the autopsy. ECUNF and ECUNR species-specific primer pairs were used for amplification and genotyping of E. cuniculi. The animals were observed no clinical symptoms except ocular lesion (n=9). Therefore, one of these rabbits was used in the autopsy to definite diagnosis and determination of the damage to the eye. As histopathological, the lesions in the eye were found in the initial or middle stage of progressive infection. The DNA sequence showed that E. cuniculi examined in the present study were genotype I. Possible cause of the visible white mass in the rabbit's eye may be the parasite infection. Therefore, clinicians may consider E. cuniculi as one of the possible causes of ocular lesions in rabbits during daily inspection or ophthalmological examination

Extended-spectrum beta-lactamases among cloacal Escherichia coli isolates in healthy broilers in Turkey

WOS: 000394568600011The aim of this study was to determine the prevalence and clonal typing of extended-spectrum beta-lactamase (ESBL)producing Escherichia coli in healthy broilers in Turkey. Three hundred broiler cloacal samples were collected from various broiler slaughterhouses and inoculated on Levine agar plates supplemented with 2 mu g/mL cefotaxime. Suspected strains were identified using a BBL Crystal Enteric/Nonfermenter ID Kit (Becton Dickinson, USA) and ESBL production was confirmed using an ESBL phenotypic confirmatory test. ESBL types were analyzed using PCR and sequencing. Pulsed field gel electrophoresis (PFGE) was performed with XbaI for the clonal typing of ESBL-producing E. coli isolates. While 33 phenotypic ESBL-producing E. coli isolates were identified, eight of them had only the blaTEM-1. Twenty-five ESBL-producing isolates were detected. This research is the first on the investigation and detection of ESBL-producing E. coli isolates from broilers in Turkey. In this study, 8.3% ESBL-producing E. coli were isolated from the cloacal samples of broilers collected from slaughterhouses in Turkey. CTX-M-15 (80%) was the most frequently isolated ESBL type. Using PFGE analysis, it was determined that these isolates had clonal similarity.Kirikkale UniversityKirikkale University [2011/43]The authors thank Kirikkale University (project number: 2011/43) for supporting this research

Clonal distribution of vancomycin-resistantEnterococcus faeciumin Turkey and the new singleton ST733

Background The aim of this study was to provide information about the spread and characteristics of the vancomycin-resistantEnterococcus faeciumisolates (VREfm) in Turkey. Methods Seventy-one nonduplicate consecutive isolates of VREfm were obtained from various clinical specimens of inpatients treated at university or training hospitals in seven regions of Turkey. Further characteristics included antibiotic susceptibility testing, pulsed-field gel electrophoresis (PFGE) of SmaI-digested genomic DNA, and multilocus sequence typing (MLST) of selected isolates. The presence of vancomycin resistance and virulence genes (espandhyl) was investigated by polymerase chain reaction (PCR). Results All VREfm isolates had MICs to vancomycin of >= 32 mg/L and contained thevanA gene. The presence ofespgene was identified in 64 andhylin eight VREfm isolates. All VREfm showed the multiresistance phenotype, including ampicillin (99%), penicillin (99%), imipenem (99%), ciprofloxacin (87%), moxifloxacin (87%), erythromycin (97%), streptomycin (86%), gentamicin (82%), tetracycline (70%), and teicoplanin (99%). All were susceptible to tigecycline while quinupristin-dalfopristin (97%) and linezolid (93%) were the most active other agents. Analysis of the PFGE profiles showed that 53 (74.6%) VREfm isolates shared a similar electrophoretic profile, designed as type 1, and were closely related (>85%). The sequence type was identified by MLST in 44 VRE isolates with unrelated or closely related PFGE patterns. MLST revealed that nosocomial spread of VREfm resulted from dissemination of lineage C1E faeciumclones. Sequence types ST78, ST203, and ST117 were the most frequently isolated. This is the first report of ST733 around the world. Conclusions Lineage C1 clones are disseminated among clinical VREfm isolates in seven different regions in Turkey. Regarding VREfm isolates, the worldwide epidemic strains are in circulation in Turkey