[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.

[Salmonella serovars isolated in Turkey up to the end of year 2011]. / Türkiye'de 2011 yili sonuna kadar izolasyonu bildirilen Salmonella serovarlari

Bacteria in Salmonella genus are separated into more than 2600 serovars. It is important that the isolated serovars and their sources are known in a certain country. This will help the identification of new Salmonella serovars that will be isolated later on. Since there is no Salmonella reference center in Turkey, Salmonella serovars isolated in Turkey were mainly reported by the articles of Aksoycan's manuscripts in various years, and in the list of Töreci and Ang in 1991. The aim of this meta-analysis was to detect and prepare a list for all the Salmonella serovars isolated from human and non-human samples in Turkey up to the end of 2011. In creating this serovar list, libraries, personal and institutional archives, theses, publication lists, books published after scientific meetings and congresses, and international and local periodicals have been explored, and members of Turkish Microbiology Society are communicated via the web site of the society and personal e-mail addresses, and their publications regarding Salmonella serovars were requested. The list also includes the modifications on the names and antigenic formulae of the serovars that were carried out in recent years. The number of serovars isolated in Turkey up to the end of 2011 is 129. Fifty three of them were isolated from humans, 38 from humans and non-human samples, and 38 from non-human samples. The total number of serovars isolated from humans is 91. Twenty seven serovars from serogrup 0:4 (B); 23 serovars from serogrup 0:7 (C1); 25 serovars from serogrup 0:8 (C2-C3); 16 serovars from serogrup 0:9 (D1); 8 serovars from serogrup 0:3,10 (E1) and 5 serovars from serogrup 0:28 (M) have been reported. Only two of the more than 2600 serovars known were isolated firstly in Turkey: S. Istanbul (8:z10: e,n,x) in 1969 and S. Adana (43:z10:1,5) in 1977. Previously, serovars containing 1 and 25 O antigen of S. Boecker ([1],6,14,[25]) were isolated in 1967 and 1971 for the first time in Turkey. In 1967, a serovar containing T1 antigen that appears during S-R alteration in Salmonella, with (T1: b: e,n,x) antigen formula has been isolated from non-human samples and was reported to be a probable S-R alteration of Salmonella Benfica. Furthermore, non-motile isolates of Salmonella enterica subsp enterica serogrup 0:7 (C1) and serogrup 0:9 (D) were reported as well. While reporting a new Salmonella isolation in a country one should not be content with only giving the name of the serovar, but also emphasize the antigenic structure and the identification method clearly.

[Characterization of Shigella strains isolated in ankara, Turkey by antimicrobial resistance models, plasmid profile analysis and pulsed-field gel electrophoresis]. / Ankara'da Izole Edilen Shigella Kökenlerinin Antibiyotik Direnç Modelleri, Plazmid Profil Analizi ve Degisken Alanli Jel Elektroforezi ile Incelenmesi.

Shigella is one of the most important causative agents of diarrhea especially in childhood. Since man is the main reservoir of Shigella and human to human transmission is possible, Shigella can easily spread in public and cause outbreaks. In this study, a total of 60 Shigella strains isolated in Ankara, Turkey by years 2001, 2008 and 2009 were investigated by their antimicrobial susceptibility profiles, plasmid profile analysis (PPA) and pulsed-field gel electrophoresis (PFGE). For epidemiological investigation, the results obtained by antibiotic resistance typing (ART) which was the phenotyping method, was compared to the results of the genotyping methods which were PPA and PFGE. Of the isolates 49 (81.6%) were S.sonnei, 10 (16.6%) were S.flexneri and one was (1.6%) S.dysenteriae. Antimicrobial susceptibilities were evaluated by disc diffusion method and the highest resistance rates were found against trimethoprim/sulfamethoxazole (91.6%), followed by tetracycline (68.3%) and ampicillin (26.6%). Resistance against ampicillin, chloramphenicol and amoxycillin/clavulanic acid were found higher in S.flexneri isolates than S.sonnei (p< 0.001). All isolates were found to be susceptible to ciprofloxacin, gentamicin and ceftazidime. S.sonnei demonstrated 12 and S.flexneri demonstrated 4 antibiotic resistance models. All isolates were carrying plasmids with varying sizes and varying numbers between 1 to 7. S.sonnei isolates demonstrated 27 and S.flexneri isolates demonstrated 8 plasmid profiles. S.sonnei isolates were clustered in 4 patterns and S.flexneri were clustered in 5 patterns by PFGE. This method demonstrated obvious clonal similarity among S.sonnei strains isolated in Ankara and discriminative power (DP) was calculated as 0.26. PPA and ART demonstrated higher DP among S.sonnei strains (0.97 and 0.75, respectively). In this study gain or loss of instable genetic mobile elements were thought to be responsible for higher discriminative powers of PPA and ART methods. These typing methods were found to be appropriate for the epidemiological investigation of strains collected in a short time period. PFGE was found to be convenient for the evaluation of clonal relatedness of the strains, however, in such geographical areas where the same clone was in circulation, use of ART and/or PPA together with PFGE would be useful for precise discrimination of Shigella strains.

Leg motion classification with artificial neural networks using wavelet-based features of gyroscope signals.

We extract the informative features of gyroscope signals using the discrete wavelet transform (DWT) decomposition and provide them as input to multi-layer feed-forward artificial neural networks (ANNs) for leg motion classification. Since the DWT is based on correlating the analyzed signal with a prototype wavelet function, selection of the wavelet type can influence the performance of wavelet-based applications significantly. We also investigate the effect of selecting different wavelet families on classification accuracy and ANN complexity and provide a comparison between them. The maximum classification accuracy of 97.7% is achieved with the Daubechies wavelet of order 16 and the reverse bi-orthogonal (RBO) wavelet of order 3.1, both with similar ANN complexity. However, the RBO 3.1 wavelet is preferable because of its lower computational complexity in the DWT decomposition and reconstruction.

[Investigation of Salmonella serotype Enteritidis isolates by plasmid profile analysis and pulsed field gel electrophoresis]. / Salmonella Serotip Enteritidis Izolatlarinin Plazmid Profil Analizi ve "Pulsed Field" Jel Elektroforezi ile Incelenmesi.

In this study a total of 122 Salmonella serotype Enteritidis stock strains selected from the culture collection of Enterobacteriaceae Laboratory of Ankara University Faculty of Medicine, Department of Medical Microbiology, were investigated by plasmid profile analysis with the method defined by Kado and Liu and pulsed field gel electrophoresis (PFGE) according to World Health Organization protocols using SpeI and XbaI macrorestriction enzymes, for better understanding of the molecular epidemiology of S. Enteritidis. The study strains were selected from a collection of previously isolated epidemic (n= 13) and sporadic (n= 109) strains (103 stool, 16 blood and one each bile, urine and cerebrospinal fluid) obtained from 10 different cities after the year 2000. PFGE patterns were analyzed with Gene Directory software (Syngene, UK) and a similarity index was determined by using Dice coefficient and the unweighted pair group method with mathematical averaging (UPGMA). Plasmid-carrying 110 (90%) strains that harbored 1-4 plasmids with sizes ranging from 2.0 to 100 kb were separated into patterns more than 14 (p1-p14). A total of 85 (69.7%) isolates harbored the 57 kb plasmid solely or in combination with other plasmids. By PFGE, 11 distinct patterns were shown with each enzyme SpeI and XbaI. S. Enteritidis strains after digestion with macrorestriction enzyme SpeI generated 11 different PFGE patterns (A to K), whereas XbaI generated also 11 different PFGE patterns (a to k). PFGE pattern A consisted of 93 strains (76.2%) after digestion with macrorestriction enzyme SpeI, while PFGE pattern a consisted 53 (43.4%) and PFGE pattern b 42 strains (34.4%) after digestion with macrorestriction enzyme XbaI. Using two macrorestriction enzymes two PFGE cluster profiles Aa (50 strains, 40.9%) and Ab (42 strains, 34.4%) were found to be predominating among 17 different PFGE clusters. Our results confirmed the clonal nature of S. Enteritidis strains in Turkey. The use of two enzymes in PFGE analysis appeared to increase the discriminatory power of PFGE, leading to greater diversity among strains. PFGE analysis performed by SpeI and XbaI enzymes combined with plasmid profiling could be established as a useful tool for detection of genetic relationship between isolates.

Molecular investigation of salmonella choleraesuis and salmonella hadar strains isolated from humans in Turkey.

Eleven Salmonella Choleraesuis and seven Salmonella Hadar strains isolated from various clinical humand samples were investigated by plasmid profile analysis, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and pulsed-field gel electrophoresis (PFGE) in order to obtain information at a molecular level on the epidemiology of S. Choleraesuis and S. Hadar, which are significantly present in Turkey. Plasmid profile analysis showed that 10 (90.9%) of 11 S. Choleraesuis isolates harbored one to two plasmids with sizes of 2.0, 5.0 or 6.5 kb; and 5 (71.4%) of 7 S. Hadar isolates harbored one to three plasmids ranging from 2.5 to 70 kb. ERIC-PCR was performed using ERIC-2 primers; since isolates within each serotype showed similar band models, we concluded that ERIC-PCR is not suitable for differentiating isolates within the same serotype and for grouping into clusters. In PFGE using the AvrII enzyme, S. Choleraesuis isolates formed three clusters, and S. Hadar isolates formed three clusters; using the XbaI enzyme, S. Choleraesuis isolates formed two clusters, and S. Hadar isolates formed four clusters. These results showed that plasmid profile analysis and PFGE are reliable and discriminative methods that would complement antibiograms, and could contribute to the investigation of outbreak epidemiology. This is the first report on S. Choleraesuis and S. Hadar isolates from Turkey investigated by plasmid profile analysis, ERIC-PCR and PFGE methods.

[A novel Salmonella Typhimurium plasmid, pAnkS: an example for plasmid evolution in antibiotic resistance]. / Yeni bir Salmonella Typhimurium plazmidi, pAnkS: antibiyotik direnç gelisiminde plazmid evriminin bir örnegi.

In this study, a plasmid, carrying ampicillin resistance (ampR) gene, isolated from a clinical isolate of Salmonella enterica serotype Typhimurium presenting ACSSuT (ampicilin, chloramphenicol, streptomycin, sulphonamide, tetracycline) resistance phenotype, was defined. The length of complete sequence of this plasmid was 8271 base pairs (bp), and it was named as pAnkS owing to its isolation place (plasmid-Ankara- Salmonella). The plasmid was analyzed for potential reading frames and structural features indicative of transposons and transposon relics. The Xmnl enzyme restriction fragments of pAnkS were cloned into E. coli plasmid vectors (pBSK), sequenced and analyzed with the BLAST programs. Plasmid pAnkS has contained a previously defined enterohemorrhagic E. coli (EHEC) plasmid p4821 as a core region and also contained a complete Tn3-like transposon of 4950 bp consisting of the left terminal repeat, Tn3-related tnpR and tnpA genes for transposition functions, ampicillin resistance gene bla(TEM), and the right terminal repeats, pAnkS showed strong homology with another Salmonella plasmid, pNTP16, for sequences that belong to p4821 and partial Tn3 segments. It was found that pNTP16 also carries kanamycin resistance gene (kanR) in addition to ampR gene. Plasmid pAnkS is one of the few completely sequenced plasmids from Salmonella Typhimurium and is in the middle of the pathway of evolution of plasmid from p4821 to pNTP16. The identification of pAnkS might help better understanding of plasmid evolution.

Nalidixic acid resistance in Salmonella strains with decreased susceptibility to ciprofloxacin isolated from humans in Turkey.

The aim of this study was to evaluate the value of nalidixic acid resistance as an indicator of decreased susceptibility to ciprofloxacin (MIC = 0.125 - 1 mg/L) in Salmonella isolates from humans (n = 620) in Turkey. One isolate was found to be resistant, and the remaining isolates were susceptible to ciprofloxacin with the Clinical and Laboratory Standards Institute breakpoints; however, 75 isolates (12.1%) had decreased susceptibility. Resistance to nalidixic acid was observed in 76 (12.3%) isolates in the disk diffusion test. Seventy-four of these isolates had decreased susceptibility, one was fully resistant, and one isolate was susceptible to ciprofloxacin. One isolate with decreased susceptibility to ciprofloxacin was intermediate to nalidixic acid. Screening with 30-microg nalidixic acid disks had a sensitivity of 98.6% and a specificity of 99.8% for determination of decreased susceptibility to ciprofloxacin.

Plasmid profiles and randomly amplified polymorphic DNA analysis of Salmonella enterica serotype Enteritidis strains from outbreaks and sporadic cases in Turkey.

The aim of the study was to investigate the characteristics of Salmonella serotype Enteritidis strains isolated from outbreaks and sporadic cases in Turkey by plasmid profiles and randomly amplified polymorphic DNA (RAPD) patterns. A total of 64 S. Enteritidis clinical strains were selected from the culture collection of the Enterobacteria Laboratory of Ankara University Medical School Department of Microbiology and Clinical Microbiology for molecular analysis using the plasmid profiles and RAPD method. Fifty-six isolates (88%) harbored one to four plasmids ranging in size from 2.5 to 100 kbp. 57 kbp plasmids were the most common plasmids, and forty-four strains (69%) carried 57 kbp plasmids alone or together with other plasmids. The outbreak strains carried the same plasmid profile: three plasmids sized 57, 40, 3.0 kbp. None of the strains analyzed displayed any RAPD bands with the primer OPB-17. By using primer p-1254, 42 strains (66%) were divided into fourteen RAPD patterns. Ten of the outbreak strains (77%) showed >80% similarity by cluster analysis program. Analysis of RAPD-PCR with primer p-1254 proved an easy, rapid and discriminative method complementing antibiogram and plasmid profiles in routine laboratories, and may contribute to the investigations of S. Enteritidis which still cause outbreaks in Turkey. This study presents the first report on S. Enteritidis isolates in Turkey investigated by plasmid profiles and RAPD methods.

A purulent pericarditis caused by Salmonella typhimurium.

A case of Salmonella typhimurium pericarditis is reported. The diagnosis was based on blood and pericardial effusion cultures.

[Salmonella enterica serotypes and Salmonella infections: a multicenter study covering ten provinces in Turkey]. / Salmonella enterica serotipleri ve Salmonella enfeksiyonlari: Türkiye'de on ili kapsayan çok merkezli bir çalisma.

In order to find the distinctive features of Salmonellae and Salmonella infections in Turkey, 620 Salmonellae strains, isolated from various clinical samples (481 stool, 108 blood, 12 urine, 3 bone marrow, 3 cerebrospinal fluid, 9 pus, and one from each of the bile, pleural fluid, wound, catheter samples) in 13 clinical microbiology laboratories of 10 provinces in Turkey (Ankara, Antalya, Bursa, Edirne, Eskisehir, Istanbul, Izmir, Kayseri, Konya and Trabzon) between July 1, 2000 and June 30, 2002, were serotyped. Among the patients 43% were female, 57% were male, 63.2% were from outpatient clinics and 36.8% were hospitalized patients. Seventy eight percent of the patients had gastroenteritis, 10.7% had septicemia/local infection, 9.8% had typhoid/paratyphoid fever and 1.5% were carriers. Incidence of gastroenteritis was higher in 0-5 years age group (p<0.001). Of the 620 Salmonella enterica isolates, 47.7% were S. Enteritidis, 34.7% S. Typhimurium, 6% S. Paratyphi B, 2.9% S. Typhi, 0.2% S. paratyphi A, 6.1% serogroup C1, and 2.4% serogroup C2. S. Enteritidis was the most common serotype in all provinces except for Kayseri, where S. Typhimurium was found to be the most common serotype (68.2%). Overall, the most frequently isolated serotype was S. Enteritidis, also being the most common serotype in stool and blood cultures. During the surveillance period two outbreaks have occurred, the first one by S. Enteritidis strains in Edirne, and the second one by S. Typhimurium strains in Kayseri. As a result, Salmonella infections are still a common health problem in Turkey, and active surveillance of Salmonella infections has vital importance.

Salmonella bacteraemia in Turkish children: 37 cases seen in a university hospital between 1993 and 2002.

The aim of the study was to evaluate the clinical pattern of Salmonella bacteraemia in Turkish children. From 1993 to 2002, all children with a blood culture positive for Salmonella were retrospectively evaluated in the Division of Paediatric Infectious Diseases in Ankara University School of Medicine. All Salmonella isolates were serotyped and investigated for antimicrobial susceptibility. During the 10-year study period, 40 patients with Salmonella bacteraemia were identified. Of 37 eligible children, eight had enteric fever and 29 had non-typhoidal salmonellosis. Salmonella typhimurium was the most common serotype in the group with non-typhoidal salmonellosis. No significant differences were found between the enteric fever and non-typhoidal salmonellosis groups with regard to clinical features, laboratory findings and outcome, except in mean platelet counts and mean serum alanine aminotransferase (ALT) levels. In vitro resistance rates of Salmonella strains were low. Outcome was excellent in all but one child with hydrocephalus and gross neurological sequelae owing to meningitis. Salmonella bacteraemia is relatively uncommon in Turkish children. Differentiating between enteric fever and non-typhoidal Salmonella bacteraemia on clinical grounds is difficult.