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Introduction: The assessment of the clonal spread of methicillin resistant Staphylococcus aureus (MRSA) in nosocomial and communityacquired infections through characterization of the isolates is critical for tracking the evolution of the epidemics, implementing effective control measures, and preventing future outbreaks of MRSA. In this context, it is aimed with this study to determine the clonal relationships between the S. aureus isolates obtained from the patients receiving treatment in the intensive-care units of a state hospital in Turkey. Methodology: A total of 80 MRSA isolates obtained from the patients receiving treatment in three different intensive-care units were analyzed for their antibiotic susceptibilities, pulsed-field gel electrophoresis profiles, and multilocus sequence types. Results: The dendrogram of the pulsed-field gel electrophoresis profiles revealed two major pulsed-field gel electrophoresis pulsotypes: A and B, which were further divided into two (A1 and A2) and four (B1-B4) subgroups, respectively. Multilocus sequence typeanalysis indicated that all isolates belonged to a single MRSA clone, sequence type 239. No significant difference was found between the antibiotic sensitivity profiles of strains isolated from different intensive-care units. All of the strains were sensitive to linezolid and vancomycin. Conclusions: It was concluded that the MRSA strains isolated from the patients receiving treatment at the intensive-care units of the hospital constituted two major pulse-field types and belonged to the ST239 lineage, one of the most extensively distributed MRSA lineages throughout the world. [ABSTRACT FROM AUTHOR]

Salmonella spp. is the most frequently isolated foodborne pathogens causing human and animal diseases. The aim of this study was to investigate antimicrobial susceptibility profiles and the molecular typing of 200 Salmonella Enteritidis strains isolated from the patients' stools between 2016 and 2019 in Turkey. The isolates were examined for antibiotic susceptibility patterns (21 antimicrobial agents) by Kirby-Bauer disc diffusion method or molecular typing by Pulsed-field gel electrophoresis (PFGE) and plasmid profiling. Although all isolates were susceptible to four antibiotics (suphamethoxazole/trimethoprim, chloramphenicol, streptomycin and trimethoprim), all were resistant to 15 different antibiotics. In the PFGE study performed with XbaI enzyme, all isolates were found to be related to each other according to similarity rates of 85% and above. There were two major clones, clone A and B. Clone A was divided into 6 pulsotypes (A1-A2-A3-A4-A5-A6) and clone B was divided into 3 pulsotypes (B1-B2-B3). Clone A had 87% similarity and Clone B had 90% similarity. The clustering rate was 86% (172/200). All isolates harboured 1-4 plasmid ranging in size from 2.5 to 57 kb and showed 6 plasmid profiles (P1-P6). All isolates carried the 57 kb plasmid individually or in combination with other plasmids. Most of the isolates 136 (68%) had P2 profile. Our findings indicate that the majority of all isolates were clonally related and had cross contamination problems. In this study, the importance of molecular typing methods in order to take more effective protection and control measures against Salmonella has been demonstrated and proposed to use such methods. [ABSTRACT FROM AUTHOR]

The purpose of this study was to determine the phenotypic antibiotic susceptibility patterns, extended-spectrum β- lactamase (ESBL) genes and genotypic profiles of ESBL-positive Escherichia coli strains isolated from urine samples obtained from outpatients with urinary tract infection in Turkey. A total of 120 E. coli strains during 2017, 2018, and 2019 (40 patients per year) were examined for antibiotic susceptibility patterns by disc diffusion method, for ESBL genes using PCR and sequencing and for molecular typing by pulsed-field gel electrophoresis (PFGE) method. The isolates were evaluated for their sensitivity to 21 different antibiotics. Four different antimicrobial resistance patterns were determined according to antibiotic susceptibility status of the isolates. The β- lactamase genes detected in the isolates were CTX-M-15 + OXA-1 (n= 14), CTX-M-15 (n= 24), TEM-1 + CTX-M-15 (n= 52), TEM- 1 + SHV-12 (n=6), SHV-12 1 (n= 6), TEM-1 + CTX-M-1 (n= 6), TEM-1 + CTX-M-16 (n= 6) and TEM-1 + CTX-M-9 (n= 6). The CTX-M-15 was the most prevalent ESBL enzyme in the isolates. As a result of PFGE analysis performed by XbaI enzyme restriction process, one major PFGE profile and three main groups (Group I-II-III) were observed. While antibiotic resistance profiles of the strains showed four groups (RI-RII-RIII-RIV), PFGE band profiles showed a major group (90% similarity ratio). High ESBL production and decreased susceptibility to broad-spectrum cephalosporins were observed in E. coli strains. In addition, PFGE analysis showed high clonal similarity among E. coli isolates. [ABSTRACT FROM AUTHOR]

The 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 μg/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. [ABSTRACT FROM AUTHOR]

Objective: Enterococci are the second most common cause of nosocomial urinary tract and wound infections, also third most common cause of nosocomial bacteremia. Currently, especially vancomycin-resistant enterococci (VRE) are one of the significant pathogens that cause nosocomial infections and increase mortality, morbidity, and healthcare costs. Therefore prevention and control of the nosocomial VRE outbreaks and epidemiological analysis of the infection are important. Pulsed-Field Gel Electrophoresis (PFGE) is accepted as a "gold standard" method in the molecular epidemiological analysis of enterococcal infections. The aims of this study are to determine the clonal relationship among the nosocomial enterococcal isolates and the rate of cross-contamination between them. Method: Thirty-six Enterococcus strains isolated from hospitalized patients with nosocomial infection in different clinics of Dicle University Hospital between November 2010 and June 2012 were included in this study. A total of 36 isolates were obtained from various clinical samples including urine (n=18), blood (n=6), bronchoalveolar lavage (BAL) fluid (n=5), wound biopsy sample (n=5), vaginal smear (n=1) and catheter tip (n=1). Nine of the thirty-six isolates were VRE. Isolation and identification of the isolates were conducted in the bacteriology laboratories of Dicle University Medical Faculty, Department of Medical Microbiology. The conventional methods and BD PhoenixTM 100 (Becton Dickinson, MD, USA) fully automated microbiology system were used for the identification. Antimicrobial susceptibilities of enterococcal strains were determined by a fully automated microbiology system according to the Clinical and Laboratory Standards Institute (CLSI). In addition, vancomycin susceptibilities of the isolates were performed by E-test method. Staphylococcus aureus ATCC 25923 strain was used for quality control. PFGE was studied for determining of rate of cross-contamination. PFGE was performed in National Molecular Microbiology Referance Laboratory, Public Health Institution of Turkey (PHIT). DNA restriction fragments were obtained by cutting bacterial DNA with the SmaI enzyme. DNA restriction fragments were used by CHEF DR II (Bio-Rad Laboratories, Nazareth, Belgium) system. PFGE results were evaluated by Bionumerics software system (version 6.01; Applied Maths, Sint-Martens-Latem, Belgium). Results: DNA patterns of the isolates were obtained by PFGE, and dendrogram of DNA patterns were made. Comparison of DNA patterns obtained by PFGE showed that 26 E. faecium strains were divided into four different clusters and one major group, 10 E. faecalis strains were three clusters and one major group. Twenty-six Enterococcus faecium isolates were involved in a joint cluster (97% similarity). The cluster rate was found to be 77% (20/26), number of E. faecium strains in each cluster ranged from 2 to 14 strains. Conclusion: In this study, cross-contamination was highlighted among enterococcal strains causing nosocomial infections in Dicle University Hospital between November 2010 and June 2012. Our data revealed that more effective infection control programs should be implemented to prevent cross-transmission. [ABSTRACT FROM AUTHOR]

Objective: For the detection of outbreaks caused by Proteus mirabilis, strains clonal relations are determined methods as "pulsed-field gel electrophoresis (PFGE)". The aim of this study was optimization of a pulsed-field gel electrophoresis for molecular typing of P. mirabilis. Methods: In this study, PFGE' protocol is optimized for use in molecular typing of P. mirabilis. Phylogenetic analyzes of strains were evaluated with Bionumerics software system (version 6.01; Applied Maths, Sint-Martens- Latem, Belgium). Results: This protocol compared with Gram-negative bacteria PFGE protocols, NotI enzyme is suitable for this bacterium. Electrophoresis conditions should be revealed as; - block 1: initial pulse duration 1 sec, ending pulse duration 30 sec, striking angle 120°, the current 6 V/cm2, temperature 14°C, time 8 hours; - block 2: initial pulse duration 30 sec, ending pulse duration 70 sec, striking angle 120°, the current 6 V/cm2, temperature 14°C, time 16 hours; - TBE, pH=8.4. Conclusion: P. mirabilis strains were typed by PFGE and Bionumerics analysis program were determined clonal relationships. The procedure was simple, reproducible and suitable for these bacteria. Also it was evaluated, because of reducing time, the solution volumes and enzymes can be economically. Outbreaks of nosocomial infections due to bacteria studied assessment and the potential to provide useful information about the degree of prevalence. This optimized protocol is allowed different centers' PFGE results to compare with other laboratories results. [ABSTRACT FROM AUTHOR]

Objective: In this study, "Pulsed-Field Gel Electrophoresis" (PFGE) protocol was optimized for use Providencia stuartii's typing in Molecular Microbiology Research and Application Laboratory, Public Health Agency of Turkey. Methods: This protocol compared with Gram-negative bacteria PFGE protocols, SpeI enzyme is suitable for this bacterium. Electrophoresis conditions should be revealed as 1. block: initial pulse duration 5 sec, ending pulse duration 40 sec, striking angle 120°, the current 6 V/cm2, temperature 14°C, time 19 hours; 2. block: initial pulse duration 35 sec, ending pulse duration 45 sec, striking angle 120°, the current 6 V/cm2, temperature 14°C, time 5 hours; TBE buffer pH=8.4. Phylogenetic analyzes were evaluated with Bionumerics software system (version 6.01; Applied Maths, Sint-Martens-Latem, Belgium). Results and conclusion: This procedure is simple, reproducible and suitable for P. stuartii. It has the potential evaluating the outbreaks due to bacteria performed, and providing useful information about the prevalence of nosocomial infections. This optimized protocol is allowed different centers' PFGE results to compare with other laboratories results. [ABSTRACT FROM AUTHOR]

Bacillus cereus is an aerobic and facultatively anaerobic, spore-forming bacterium, and it is found naturally in soil and poses a risk factor for the contamination of food and foodstuffs including cereals, vegetables, spices, ready-to-eat (RTE) foods, meats, milk, and dairy products. This study determined the prevalence of B. cereus in raw poultry meat, raw cow's milk, cheese, spices, and RTE foods in Hatay province. The study also analysed the psychrotrophic properties, toxigenic characteristics, and pulsed-field gel electrophoresis (PFGE) profiles of the isolates. The levels of contamination with B. cereus determined for cheese, raw milk, RTE foods, spices, and raw poultry meat were 16.6%, 34.2%, 42.8%, 49%, and 55.5%, respectively. B. cereus was isolated from 84 (42%) of the 200 samples analysed and the 84 isolates were verified by PCR analysis targeting the haemolysin gene specific for B. cereus. Of the total isolates, 64 (76.1%) were psychrotrophic. The toxin gene profiling of B. cereus isolates was determined by amplifying the four genes nhe, hbl, cytK, and ces. The nhe and cytK genes were most frequently detected in the isolates, while the hbl and ces genes were not found. In addition, a high genetic relationship between the isolates was detected at a 92% similarity level by PFGE analysis. In conclusion, the occurrence of both psychrotrophic and toxigenic B. cereus strains in this study indicated a potential risk for food spoilage and food poisoning. [ABSTRACT FROM AUTHOR]

Background: With this study, the detection of the resistance rates of A.baumannii strains isolated from the patients in the intensive care units to the antibiotics and the demonstration of the clonal relationship of the isolates with multi-drug resistant of the factor of nosocomial infection were aimed by using the method of pulsed-field gel electrophoresis (PFGE). Materials and Methods: At the Medical Faculty Hospital of Yüzüncü Yıl University, 69 patients followed between January 2010-October 2011 at the Intensive Care Unit of Anesthesiology and Reanimation (ICUAR), Intensive Care Unit of Chest Diseases and Pediatric Intensive Care Unit and July-November 2012 at ICUAR and the same number of isolates formed with A.baumanii, Ventilator Associated Pneumonia (VAP) and diagnosis of Primary Bloodstream Infection (PBI) were enrolled to the study. Results: Of the 69 patients included in the study, 35 were men (50.7%) and 34 (49.3%) were women. The ages of the patients ranged from 1 to 86 years (mean age 54). 63 (91%) of the patients were diagnosed with VAP and 6 (9%) of them with PBI. At least two invasive interference had been performed to the all patients during the staying at the ICU. Urinary catheterization (100%), mechanical ventilation (94.2%) and peripheral venous catheterization (91.3%) were the most frequently performed invasive interferences. Antibiotic susceptibilities to imipenem, colistin and tigecycline were studied with the E-test and to the other antibiotics with the disk diffusion. Colistin was the most effective antibiotic for all of the strains (98.6%). Then, tigecycline (97.1%) and levofloxacin (69.6%) were in the second place. All of the strains were resistant to ceftriaxone, piperacillin/tazobactam, meropenem and imipenem. With the PFGE analysis of A.baumannii isolates performed to the genomic DNA cut with ApaI, it was found that 62 of the 69 A.baumannii strains (89.9%) were within the cluster. These strains were located within 16 clusters. 7 of the strains (10.1%) showed the profiles of specific PFGE and 23 pulsotip were detected among the strains. Conclusion: Being high of clustering rate of multidrug-resistant A. baumannii isolates and isolating the isolates in similar genotypes from the patients in different units is the indicator of these bacteria to be endemic situation in the ICUs of our hospital. If precautions are not taken, A. baumannii has been able to remain in the hospitals for many years and can be easily transmitted among the patients. Especially for the prevention of cross-contamination, the necessity and importance of infection control programs have once again emphasized. [ABSTRACT FROM AUTHOR]