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Aims: Campylobacter sp. are important causes of reproductive disease in ruminants worldwide. Although healthy bulls are well-known carriers for infection of cows, the role of rams as a potential source for infecting ewes is unclear. This study aimed to determine prevalence, species distribution, genetic diversity and antimicrobial susceptibility profiles of Campylobacter sp. isolated from the preputial cavity of healthy rams. Methods and Results: The material of this prospective study comprised 191 swab samples taken from the preputial cavity of healthy rams. Enrichment and membrane filtration were employed for the isolation of Campylobacter. Presumptive isolates were confirmed as Campylobacter by phenotypic and molecular tests. 16S rRNA gene sequence analysis was used for the definitive identification of the isolates at species level, and genotyping was performed using pulsed-field gel electrophoresis (PFGE). The susceptibility of the Campylobacter sp. isolates to various antibiotics was determined by the disk diffusion test. In all, 27 of the 191 (14•13%) swab samples were found to be positive for Campylobacter sp. (28 isolates were recovered in total). Per phenotypic and genotypic analyses, one isolate was identified as Campylobacter mucosalis and the remaining 27 isolates were identified as Campylobacter sputorum bv. faecalis. The PFGE analysis of the C. sputorum biovar faecalis isolates produced 17 clusters and 24 different pulsotypes, indicating high genetic heterogeneity. All 28 isolates were found to be susceptible to all of the antibiotics tested. Conclusions: Healthy rams may be an important reservoir of different Campylobacter species in the preputium. Significance and Impact of the Study: This study demonstrated for the first time that healthy rams can carry different Campylobacter sp. including genetically diverse C. sputorum bv. faecalis and C. mucosalis in the preputial cavity. Further investigation on the potential implication of this finding on sheep reproductive health (e.g. infectious infertility, and abortion) and overall epidemiology of Campylobacter may be warranted. [ABSTRACT FROM AUTHOR]

It was aimed to determine the prevalence of Helicobacter in some reptilian and amphibian species in Türkiye and to describe the bacteria. For this purpose, 73 cloacal swab samples were used as material. The description of the isolates was performed by detailed phenotypic tests, whole genome analyses, and MALDI-TOF MS. As a result of the phenotypic analysis, two helical, curved Gram-negative, motile isolates were recovered. It was determined through the analysis of 16S rRNA gene sequences that two isolates belonged to the genus Helicobacter. These isolates were found to be in a distinct group from other Helicobacter species. However, the 16S rRNA sequence did not match any identified species, with the closest match being Helicobacter mustelae strain R85-13-6 T , which had an identity level of 96.2 %. Additionally, it was found that strains faydin-H75 T and faydin-H76 had a 99.3 % identity level for their 16S rRNA genes. After conducting dDDH and ANI analyses, it was found that strains faydin-H75 T and their close neighbors H.anseris ATCC BAA-1299 T shared 13.5 % and 68.8 % similarity, respectively. The genome size of the strains was 1.7 Mb while G + C contents were 33.5 %. Metagenomic analyses using IMNGS and Protologger tools revealed the presence of faydin-H75 T in various lizard species with high similarity, confirming its broad distribution and host specificity. The results indicated that these two strains represent a novel species, for which we propose the name Helicobacter cappadocius with faydin-H75 T (=NCTC014972 = LMG 33382 = DSM117062) as the respective type strain. The current novel species is the first Helicobacter species to exhibit a psychrotrophic feature., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Helicobacter pylori is a pathogen associated with gastroduodenal diseases. This study aimed; (i) to investigate H. pylori presence by invasive tests in adult dyspeptic patients, (ii) to determine antibiotic susceptibility and genotypic characteristics of the H. pylori isolates, and (iii) to investigate the relationship between the H. pylori genotypes and the histopathological findings. In this cross-sectional study, gastric biopsy samples from 208 adult dyspeptic patients were used for culture, tissue Polymerase Chain Reaction (PCR), and histopathological analysis. Antibiotic susceptibility of the H. pylori isolates was analyzed by gradient method. Analysis of the virulence genes was performed by monoplex PCR. Genetic profiles (from A to H) were created based on the virulence genes presence. Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR) was used for the genotyping of the H. pylori isolates. The mean age of the patients was 46 (± 15) years and 128 (61.5%) of them were female. H. pylori positivity was detected by culture, tissue PCR and histopathological examination in 59 (28.4%), 114 (54.8%) and 81 (38.9%) patients, respectively. The overall prevalence of H. pylori was found to be 63% (131/208). All H. pylori isolates were susceptible to tetracycline and amoxicillin. The resistance rates for metronidazole, clarithromycin, levofloxacin, and rifampicin were 67.2%, 27.9%, 34.4% and 13.11%, respectively. Multi drug resistance (MDR) was detected at the rate of 45.9% (28/61). While the most common virulence gene was cagA (93.44%), the least common was vacAm1 (23%). The predominant genetic profile was profile A (47.5%). ERIC-PCR results revealed a total of 26 different patterns. A high prevalence of H. pylori was detected in adult dyspeptic patients as in developing countries. It was observed significant genotypic heterogeneity and virulence gene diversity within the isolates. A considerable resistance rate detected against antibiotics such as clarithromycin, metronidazole, and levofloxacin, which are frequently used in the eradication of H. pylori, should be taken into consideration when creating regional empirical treatment regimens., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Brucellosis is a chronic disease caused by Brucella species with a wide range of hosts, from marine mammals to terrestrial species, but with strict host preferences. With the zoonotic character, the prevalence of human brucellosis cases is a reflection of animal infections. This study aimed to identify 192 Brucella isolates obtained from various sources by Bruce-ladder PCR and to determine their antibiotic susceptibilities by gradient diffusion method (E-test). As a result of the PCR, all human isolates (n = 57) were identified as B. melitensis. While 58 (82.9%) of the cattle isolates were identified as B. abortus, 59 (90.8%) of the sheep isolates were identified as B. melitensis. In addition, 12 (17.1%) of the cattle isolates and 6 (9.2%) of the sheep isolates were determined as B. melitensis and B. abortus, respectively. The primary host change behavior of B. melitensis was 1.9 times higher than that of B. abortus. While gentamicin and ciprofloxacin susceptibilities of Brucella isolates were 100%, tetracycline, doxycycline, streptomycin, trimethoprim/sulfamethoxazole and rifampicin susceptibilities were 99%, 99%, 97.4%, 91.7% and 83.9%, respectively. The lowest sensitivity of the isolates was determined against to cefoperazone as 26%. A triple-drug resistance was detected in 1 B. abortus isolate that included simultaneous resistance to cefoperazone, rifampicin, and trimethoprim/sulfamethoxazole. The high susceptibility profiles we found against to antibiotics such as tetracycline, doxycycline gentamicin and ciprofloxacin, used widely in treatment, are encouraging. However, the change in the canonical Brucella species-primary host preference suggests the need to reconsider eradication program, including updating vaccine formulations., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

This study was conducted to determine the overall genetic diversity, as well as prevalence and mechanisms of resistance to quinolone antibiotics of 178 Campylobacter jejuni isolated from humans, cattle, dogs, and chickens in Turkey. Multilocus sequence typing (MLST) and E-test were performed for genotyping and antimicrobial susceptibility testing, respectively. Mismatch Amplification Mutation Assay, Polymerase Chain Reaction (MAMA-PCR) was used to detect point mutations associated with quinolone resistance. Of the 178 isolates tested, 151 were included in 21 clonal complexes (CCs); the remaining 27 isolates did not belong to any existing CCs. CC21, CC353, CC206, and CC257 were the predominant clones, representing 38 % of all C. jejuni isolates tested. The isolates were assigned to 78 different sequence types (STs), three of which were novel (ST 8082, ST 8083, and ST 8084). Resistance to quinolones was found in 73 (41 %) of the isolates (42.85 %, 2.85 %, 20.58 %, and 43.75 % in human, cattle, dog, and chicken isolates, respectively). All of the resistant isolates had Thr-86-Ile mutation in the gyrA gene. The highest Sorensen coefficient index was detected for human/chicken meat and human/dog C. jejuni isolates (Ss = 0.71), suggesting a strong link between the isolates from respective sources. The Simpson diversity index of C. jejuni isolates analyzed was detected between 0.92 and 0.98. The study provides detailed information on the quinolone resistance and MLST-based genetic relatedness of C. jejuni isolates from humans, cattle, dog, and broiler meat in Turkey for the first time, enabling a better understanding of the transmission pathways of C. jejuni in this country. Our results suggest that broiler meat and dogs may be the most important sources of human campylobacteriosis in Turkey., Competing Interests: Conflict of interest The authors declare that there is no conflict of interest., (Copyright © 2023 Elsevier B.V. All rights reserved.)

In this study, it was aimed to determine the phylogroups of Escherichia coli isolates from horse, cat, dog, sheep, cattle, and chicken feces samples and to investigate some important virulence genes of the isolates. For this purpose, a total of 600 feces samples, 100 from each animal species, were used as material. For the isolation of E.coli, feces samples were directly inoculated on MacConkey agar. The identification of the isolates was performed via phenotypic tests and species-specific multiplex Polymerase Chain Reaction (mPCR) method. PCR methods were used to phylotype E.coli isolates and to investigate virulence genes (bfpA, eaeA, LT, ST, Stx1, and Stx2). Of the total 600 E.coli isolates recovered in this study, 120 (20%), 269 (44.8%), 58 (9.7%), 19 (3.2%), 35 (5.8%), 56 (9.3%), 31 (5.2%), and 12 (2%) were identified as phylogroup A, B1, B2, C, D, E, F, and Escherichia clade I, respectively. While the virulence gene was detected in 149 (24.8%) E.coli isolates, no virulence gene was detected in 451 (75.2%) isolates. According to the analysis results, the most determined virulence gene was Stx1, while the least determined virulence gene was LT. In conclusion, in this study, when both the animal species and the number of E.coli isolates examined are considered, the data obtained are of great importance in epidemiological terms. However, the detection of virulence genes in 13.5% among phylogroup A, B1, and C isolates with commensal characteristics suggest that these isolates may show pathogenic characteristics with the virulence genes they contain., (© 2022. The Author(s), under exclusive licence to Springer Nature B.V.)

A total of 26 Gram-negative, motile, gently curved, and rod-shaped isolates were recovered, during a study to determine the faeco-prevalence of Helicobacter spp. in urban wild birds. Pairwise comparisons of the 16S rRNA gene sequences indicated that these isolates belonged to the genus Helicobacter and phylogenetic analysis based on the 16S rRNA gene sequences showed that the isolates were separated into two divergent groups. The first group consisted of 20 urease-positive isolates sharing the highest 16S rRNA gene sequence identity levels of 98.5-98.6% to H. mustelae ATCC 43772 T , while the second group contained six urease-negative isolates with the sequence identity level of 98.5% to the type strain of H. pametensis ATCC 51478 T . Five isolates were chosen and subjected to comparative whole-genome analysis. The phylogenetic analysis of the 16S rRNA, gyrA and atpA gene sequences showed that Helicobacter isolates formed two separate phylogenetic clades, differentiating the isolates from the other Helicobacter species. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains faydin-H8 T , faydin-H23 T and their close neighbors H. anseris MIT 04-9362 T and H. pametensis ATCC 51478 T , respectively, confirmed that both strains represent novel species in the genus Helicobacter. The DNA G+C contents of the strains faydin-H8 T and faydin-H23 T are 32.0% and 37.6%, respectively. The results obtained for the characterization of the wild bird isolates indicate that they represent two novel species, for which the names Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., are proposed, with faydin-H8 T (=LMG 32237 T  = DSM 112312 T ) and faydin-H23 T (=LMG 32236 T  = CECT 30508 T ) as respective type strains., (Copyright © 2022 Elsevier GmbH. All rights reserved.)

Eleven Gram-negative, curved and S-shaped, oxidase activity positive, catalase activity negative bacterial isolates recovered from faeces of Anatolian ground squirrel ( Spermophilus xanthoprymnus ) in the city of Kayseri, Turkey, were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR revealed that these isolates belonged to the genus Helicobacter . The 16S rRNA gene sequence analysis revealed that the 11 isolates had over 99 % sequence identity with each other and were most closely related to Helicobacter ganmani CMRI H02 T with 97.0-97.1 % identity levels and they formed a novel phylogenetic line within the genus Helicobacter . Faydin-H64 and Faydin-H70 T strains were subjected to gyr A and atp A gene and whole genome sequence analyses. These two Helicobacter strains formed separate phylogenetic clades, divergent from other known Helicobacter species. The DNA G+C content and genome size of the strain Faydin-H70 T were 35.3 mol% and 1.7 Mb, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain Faydin-H70 T and its close phylogenetic neighbour H. winghamensis ATCC BAA-430 T were determined as 81.7 and 34.9 %, respectively. Pairwise sequence comparison showed that it was closely related to H. ganmani CMRI H02 T however it shared the highest ANI and dDDH values with H. winghamensis ATCC BAA-430 T . The data obtained from the polyphasic taxonomy approach, including phenotypic characterization and whole-genome sequences, revealed that these strains represent a novel species within the genus Helicobacter , for which the name Helicobacter turcicus sp. nov., is proposed with Faydin-H70 T as the type strain (=DSM 112556 T =LMG 32335 T ).

Purpose: Bacterial virulence factors play a major role in the pathogenesis of Helicobacter pylori infection. The aims of this study were to evaluate virulence genes in H. pylori isolates and to compare the presence of these genes and associated clinical pathologies., Methods: A total of 148 H. pylori isolates, recovered from adult dyspeptic patients, were used. The patients, from whom the isolates were obtained, were assigned to two groups by their endoscopic findings, which manifested as chronic gastritis or peptic ulcer. The presence of gastric atrophy and intestinal metaplasia was recorded for each patient, based on histopathological examination. Analyses of the virulence genes were performed by the polymerase chain reaction technique., Results: The patients had a mean age of 47 ​± ​15 years and 86 (58%) of them were female. Based on endoscopic examination, 103 (69.6%) patients were diagnosed with chronic gastritis and 45 (30.4%) with peptic ulcer. Histopathological examination revealed intestinal metaplasia in 30 (20%) patients and gastric atrophy in 12 (8%) patients. The prevalence rates of cagA, cagE, iceA1, iceA2, and babA2 were determined to be 87%, 74%, 58%, 26%, and 95%, respectively. The most prevalent vacA alleles were s1/s1a (82%/97%) and the least prevalent allele was s2 (20%). A new vacA genotype (s1as1bs1c) was detected, for the first time, in 18 (12%) isolates. No significant difference was found between the patient groups with chronic gastritis and peptic ulcer for the prevalences of the virulence genes (p ​> ​0.05). Furthermore, intestinal metaplasia and gastric atrophy showed no significant correlation with the virulence genes (p ​> ​0.05)., Conclusions: It is thoughted that H. pylori isolates with predominant cagA, cagE, VacA (s1, s1a), and babA2 virulence genes are associated with gastroduodenal diseases. However, there is no correlation between gastric premalignant lesions and virulence genes., Competing Interests: Declaration of competing interest The manuscript has not been published previously elsewhere. There is no specific funding has been received to report this submission. All of the authors declare that they have all participated in the design, execution, and analysis of the paper, and that they have approved the final version. All authors are in agreement with the content of the manuscript. The authors have no conflict of interest to disclose., (Copyright © 2022 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Seventy-four Gram-negative, motile, slightly curved rod-shaped, microaerophilic, oxidase-positive and catalase-negative isolates, recovered from fecal samples of the Anatolian ground squirrel (Spermophilus xanthoprymnus) in Kayseri, Turkey, were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR indicated that all isolates belonged to the genus Campylobacter. 16S rRNA gene sequence analyses revealed the closest match as Campylobacter curvus DSM 6644 T with identity levels of 96.41-96.70%. Based on the 16S rRNA gene phylogeny of the 74 isolates, six isolates (faydin-G24, faydin-G52, faydin-G105, faydin-G114, faydin-G129 and faydin-G140 T ) were chosen as representatives for further characterization. The overall genome relatedness indices for the strain faydin-G140 T , compared to the most closely related type strain C. curvus ATCC 35224 T , were calculated as 15.2%, 72.5%, and 83.7% for digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANIb and ANIm), respectively. The G+C content and genome size of the strains ranged between 35.2-35.4 mol% and 1.7-1.8 Mb, respectively. Based on data obtained from the polyphasic taxonomy approach, including phenotypic characterization as well as genomic and chemotaxonomic analyses, these strains are concluded to represent a novel species, for which the name Campylobacter anatolicus sp. nov. is proposed with faydin-G140 T as the type strain (=DSM 112311 T  = LMG 32238 T )., (Copyright © 2021 Elsevier GmbH. All rights reserved.)

Background/aim: The prevalence of Helicobacter pylori is reported to be roughly 80% in Turkey, and only very few culture-based studies are available on antibacterial resistance in adult dyspeptic patients. This study was carried out in adult dyspeptic patients with an aim to: (i) detect H. pylori by invasive tests (culture, polymerase chain reaction, and histopathology) and (ii) determine the current resistance rates of H. pylori isolates to six antibiotics, including rifampicin., Materials and Methods: This study was conducted in 422 adult dyspeptic patients. The presence of H. pylori was demonstrated by culture, polymerase chain reaction, and the histopathology of gastric biopsy material. Antibacterial susceptibility was determined with the E-test., Results: The mean age of the patients was 50 ± 15 (range 18–90), and 265 (63%) of them were female. By culture, polymerase chain reaction, and histopathology, the presence of H. pylori was detected at rates of 35% (148/422), 67% (281/422), and 53% (224/422), respectively. The prevalence of H. pylori was determined as 75.6% (319/422). Metronidazole, levofloxacin, clarithromycin, and rifampicin resistance rates were 62%, 36%, 19%, and 12%, respectively. Monodrug, dual-drug, and multidrug resistance rates were ascertained as 36.9%, 29.4%, and 10.5%, respectively. All of the isolates were susceptible to amoxicillin and tetracycline., Conclusion: This study revealed the current prevalence of H. pylori in adult dyspeptic patients as 75.6%, and thereby, showed that infection with this pathogen remains highly prevalent. Although resistance to metronidazole and levofloxacin has increased over time, clarithromycin resistance rate has decreased. The high levels of resistance to metronidazole and levofloxacin limit the empirical use of these antibiotics in the eradication protocol. Owing to the low level of resistance determined for rifampicin, this antibiotic could be included in the eradication protocol, in the event of the need for rescue therapy in Turkey., Competing Interests: The authors have no conflict of interest to disclose., (This work is licensed under a Creative Commons Attribution 4.0 International License.)

In Turkey, the Measles Elimination Program has been implemented since 2002. The aim of this study was to evaluate the measles-specific antibody levels of mothers admitted to a hospital for birth and their infants, to determine the factors influencing the antibody levels of both, and to evaluate the transplacental transport ratio. We selected healthy women who came to the hospital for birth and their healthy newborns. We collected blood samples from 1,547 mothers and 1,529 infants. The protective prevalence of measles antibody levels of mothers was 80% (95% confidence interval [CI]: 78-82%) and that of newborns was 85% (95% CI: 83-86%). The antibody levels of mothers and newborns were positively linearly correlated (R: 0.922, p < 0.001) and were associated with parity (p < 0.001). The ratio of neonatal to maternal antibody levels increased with gestational age. The protective levels were 1.6 times higher (95% CI: 1.1-2.4) in mothers ≥ 32 years of age and 2.1 times higher (95% CI: 1.4-3.3) in naturally immune mothers. Two factors affecting the antibody levels of newborns were the mothers' antibody levels and their immunization status. The antibody level of mother was the most significant factor that influenced the infant's antibody level. Vaccination of women before pregnancy could enhance passive antibody protection by increasing the level of transplacental transmission.

Purpose: This study was aimed at investigating the occurrence and genetic mechanisms of resistance to ciprofloxacin, tetracycline and erythromycin in clinical isolates of Campylobacter jejuni recovered from human cases of acute gastroenteritis in Turkey., Methodology: MIC values of each antibiotic were determined with the epsilometer test (E-test). Resistance genes/mutations were first screened by PCR and analysed by subsequent DNA sequencing., Results: From a total of 152 C. jejuni isolates tested, 113 (74.3%), 38 (25%) and 9 (5.9%) were found to be resistant to ciprofloxacin, tetracycline and erythromycin, respectively. Sequence analysis of ciprofloxacin-resistant isolates showed that all resistant strains (n=113) carried Thr-86-Ile substition in the gyrA gene, which is the most frequently observed mutation in fluoroquinolone-resistant Campylobacter. All of the tetracycline-resistant isolates (n=38) carried the tetO gene. All of the erythromycin-resistant isolates (n=9) harboured the point mutation A2075G in the 23S rRNA gene, which is the most common mutation conferring macrolide resistance in C. jejuni., Conclusion: The phenotypic susceptibility testing results were found to agree well with those obtained by genetic detection methods for the C. jejuni isolates tested. The findings of this study showed a very high level of resistance to ciprofloxacin and to a lesser extent to tetracycline while resistance to erythromycin remained at a low level. Thus, erythromycin may be considered as the first choice for treatment of Campylobacter infections in this geographical region when indicated.

Background/aim: The frequency of genotype 4 hepatitis C virus (HCV) infections is significantly higher in Kayseri compared to other provinces in Turkey. We aimed to characterize genotype 4 infections in Kayseri by analyzing the demographic and laboratory data of218 HCV RNA-positive, treatment-naive patients admitted to the Kayseri Training and Research Hospital in 2010 and 2011., Materials and Methods: The distributions of sex, age, and viral loads of these patients with respect to HCV genotypes were analyzed. We also characterized the type 4 sequences at the subtype level. Randomly selected sera from 32 of the 72 genotype 4 patients from this cohort were subjected to PCR amplification in the NS5B region and further characterized by sequencing and phylogenetic and molecular clock analysis., Results: Distribution rates of HCV genotypes 1, 4, and 2 in the 218 patients were 62.4%, 33.0%, and 4.6%, respectively. Most of the patients infected with types 1 and 4 were over the age of 40 and female. The NS5B sequences of 32 Kayseri genotype 4 isolates were closely related with type 4d sequences but formed a separate cluster., Conclusion: The introduction of type 4d HCV into the Kayseri region probably took place 30-75 years ago, as predicted by molecular clock analysis.

In this study, the investigation of clonal relations between human and poultry Campylobacter jejuni isolates and the determination of susceptibilities of isolates to various antibiotics were aimed. A total of 200 C. jejuni isolates concurrently obtained from 100 chicken carcasses and 100 humans were genotyped by the Pulsed-Field Gel Electrophoresis (PFGE) and automated Repetitive Extragenic Palindromic PCR (Rep-PCR, DiversiLab system) methods and were tested for their susceptibility to six antibiotics with disk diffusion method. The minimum inhibitory concentration (MIC) values of ciprofloxacin (CI), enrofloxacin (EF) and erythromycin (EM) were evaluated by E-test. By using PFGE 174 of (87.0%) the isolates were able to be typed. The clonally related strains were placed in 35 different clusters and 115 different genotypes were obtained. All of the two hundred isolates could be typed by using Rep-PCR and were divided into 133 different genotypes. One hundred and fourteen clonally related isolates (57.0%) were included in 47 clusters. In disk diffusion test, while the susceptibility rates of AMC and S to human and chicken derived C. jejuni isolates were 84.0%-96.0% and 96.0%-98.0%, respectively, all isolates were susceptible to gentamicin. The resistance rates of human isolates to AMP, NA and TE were detected as 44.0%, 84.0% and 38.0% of the resistances of chicken isolates to these antibiotics were 34.0%, 95.0% and 56.0%, respectively. The MIC values of human and chicken isolates to CI, EF and EM were detected as 81.0-93.0%, 85.0-88.0% and 6.0-7.0%, respectively. The clonal proximity rates were detected between human and poultry origin C. jejuni isolates. The discriminatory power of PFGE and Rep-PCR was similar, with Simpson's diversity indexes of 0.993 and 0.995, respectively. Concordance of the two methods as determined by Adjusted Rand coefficient was 0.198 which showed the low congruence between Rep-PCR and PFGE. High rates of quinolone resistance were detected in C. jejuni isolates. This study demonstrated that chicken meat played an important role for infections caused by C. jejuni in Turkey and erythromycin, amoxicillin clavulanic acid and gentamicin are recommended for the treatment of Campylobacteriosis in humans., (Copyright © 2014 Elsevier B.V. All rights reserved.)

In Turkey, genotype 1, especially type 1b virus, causes approximately 90% of these infections, while types 2, 3, and 4 exist, albeit in low prevalences and are due to relatively recent and limited introductions. Two recent reports from Kayseri, a relatively large city in Central Anatolia, indicated unusually high prevalence for type 4 infections in the province reaching a 35% among patients admitted to hospitals for treatment of chronic hepatitis C. In this study, the origin, the demographic history, and the dynamic of the epidemic of unusual HCV genotype 4d in Turkey by using Bayesian coalescent-based method were investigated. A gene flow migration approach was also used to describe the synchronous geographical dispersal and genetic diversification of this unusual genotype in Kayseri province. The Turkish clade had a tMRCA of 44 years corresponding to the year 1967 and seems to have a different origin being completely segregated from the European one. Gene flow migration analysis indicated that Kayseri province appeared to be the epicenter of HCV-4d epidemic, exporting the infections. The demographic history of HCV-4d showed that the epidemic started in 1970s year then following a slow exponential growth until 1980s. The Turkish monophyletic clade suggests a segregate circulation of the epidemic in this region mostly due to unsafe parenteral medical procedures (with drug addiction playing a relatively negligible role)., (© 2013 Wiley Periodicals, Inc.)

Objective: To investigate the antibiotic resistance genes inserted into class 1 and class 2 integrons in Acinetobacter baumannii (A. baumannii) isolates obtained from nine different cities in Turkey., Methods: A collection of 281 A. baumannii clinical isolates were collected from nine diferent state hospitals in Turkey and were confirmed as A. baumannii by conventional biochemical, API testing and bla-OXA-51 specific PCR. The isolates were examined by PCR for existence of class 1 and 2 integron gene cassettes., Results: They were characterized by antimicrobial susceptibility testing and the highest resistance rates were determined for piperacillin (90.03%), ciprofloxacin (87.54%), cefepime and trimethoprim/sulfamethoxazole (81.13%). The lowest resistance rates was for cefotaxime (3.55%). class I integrons were detected in 6.4% (18/281) of A. baumannii strains and no class 2 integron was detected. The gene cassettes of class 1 integrons AacC1-AAC(3)I-aadA1, AacC1-aadA1, AAC(3)-I, AAC(3)-I -AAC(3)-I -aadA1, TEM-1, AAC(3)-I-aadA1 - AAC(3)-I -AAC(3)-I, AAC(3)-I -AAC(3)-I -AAC(3)-I -aadA1, AAC(3)-I - aadA1, AAC(3)-I-AAC(3)-I, AAC(3)-I-aadA1- AAC(3)-I-aadA1, AAC(3)-I- AAC(3)-I- aadA1-AAC(3)-I-aadA1 were detected in eighteen strains. The aac genes family were most frequently found integrated into the class 1 integrons and it was followed by aadA genes and TEM-1 genes., Conclusions: This is an extensive study on the distribution of class 1 integron among A. baumannii in Turkey. In addition to these, two new alleles were observed. Their percentage rates of similarity to other cassettes are 95% aadA1 ( TKA18) and 89% aadA1 (ANKA3).

We here report two cases of blood stream infection due to Rothia mucilaginosa. The isolates were identified as R. mucilaginosa using a VITEK 2 automated sytem and a MALDI-TOF MS system. Then, 16S rRNA gene sequencing was performed for the confirmation of the isolates. This is the first documented report of bacteremia due to this unusual agent in Turkey.

Background: Hepatitis C virus (HCV) is an important cause of chronic liver disease. There are six genotypes and more than 80 subtypes of HCV. The aim of this study was to investigate the distribution of HCV genotypes in Middle Anatolia in Turkey, and the association of HCV genotypes with pre-treatment HCV RNA viral load, serum transaminase levels, and histopathological grade of liver fibrosis., Methods: A total of 160 patients (103 female, 57 male) with chronic hepatitis C were retrospectively evaluated. HCV RNA level was determined by commercial real time PCR method. HCV RNA positive sera were genotyped by the Abbott Real Time HCV Genotype II assay and sequenced by the ABI Prism 310 Genetic Analyzer. Gender, age, serum ALT, AST, HCV RNA viral load, and fibrosis staging of liver were determined in all patients., Results: Genotype 1b was the most frequent (64.7%) followed by genotype 4d (28.3%), 2 (4.4%), and la (2.5%). The HCV genotype results were found consistent with both methods. The gender distribution of the 160 HCV infected patients was 57 male/103 female. Log HCVRNA was significantly higher in genotype 1b compared to genotype 4 and 1a. Stage of liver fibrosis, histology activity index, serum ALT and AST levels did not differ between groups depending on genotypes. Advanced liver fibrosis (Group 2) was found in 36 (76.6%) patients with genotype 1b and in 10 (21.3%) patients with genotype 4 and only in 1 patient (2.1%) with genotype 1a., Conclusions: HCV genotype 1b is the most frequent type (64.7%) in this region. Prevalence of genotype 4 in this region is higher than the national HCV genotype distribution. Serum transaminase levels and liver fibrosis scores are not associated with HCV genotypes.

The aims of this study were as follows: (i) to isolate Arcobacter spp. from the stool samples of patients with gastroenteritis; (ii) to identify them with molecular methods; (iii) to genotype them using enterobacterial repetitive intergenic consensus (ERIC)-PCR; and (iv) to determine their antibiotic susceptibilities. For the study, a total of 3287 diarrhoeal stool samples submitted to the Microbiology Laboratory of the Kayseri Training and Research Hospital, Kayseri, Turkey, between 2010 and 2011 were analysed. Campylobacter blood-free selective medium supplemented with cefoperazone, amphotericin B and teicoplanin was used for isolation. Medium inoculated with stool samples was incubated microaerobically at 37 °C for 72-96 h. Phenotypic tests, a genus-specific PCR and a multiplex PCR were used to identify the arcobacters, whilst ERIC-PCR was used for genotyping and the antibiotic susceptibilities of the isolates were detected by E-test. Arcobacter spp. were isolated from nine of the 3287 samples. These nine isolates were identified as Arcobacter butzleri and all showed different ERIC-PCR profiles. All nine isolates were resistant to ampicillin and susceptible to gentamicin, tetracycline, erythromycin and ciprofloxacin. As far as is known, this is the first study in which A. butzleri has been isolated from human acute gastrointestinal infections in Turkey. According to these results, it is recommended that, when investigating the aetiology of infections of the digestive system in humans, Arcobacter spp. be considered for inclusion. The results of this study should contribute to our knowledge related to A. butzleri infections in humans.

The objective of this study was to determine the antibiotic susceptibility of Arcobacter spp. isolated from various sources. Seventy Arcobacter spp. isolates were tested for their susceptibility to 13 antimicrobial agents. Antimicrobial susceptibility testing was performed by using the agar disc diffusion method on Mueller-Hinton agar supplemented with 5% defibrinated sheep blood. The antibiotics tested included enrofloxacin, erythromycin, streptomycin, gentamycin, rifampin, tetracycline, ampicillin, trimethoprim/sulfamethoxazole, nalidixic acid, danofloxacin, amoxycillin-clavulonic acid, cefuroxime-sodium, neomycine. Although all the arcobacters tested were susceptible to gentamycin, resistance to three or more antibacterial agents (especially, trimethoprim/sulfamethoxazole, cefuroxime-sodium and rifampin) was observed. A. butzleri isolates were found to be resistant to amoxycillin+clavulonic acid, nalidixic acid and ampicillin, at the rate of 20%, 44.28% and 78.57% respectively. In conclusion, gentamycin, streptomycin and tetracycline may be suitable antibiotics for the treatment or control of disease caused by Arcobacter spp. in veterinary and human medicine.

Background: Urine analysis is one of the most common tests for assessing urinary-tract infections, which are the most frequently occurring infectious diseases in community populations. Urine culture is still the 'gold standard' for the detection of urinary tract infection, however, it is time- and labor-intensive and and has a high number of unnecessary cultures. The aim of this study was to evaluate the analytical and diagnostic performance of a new urinalysis system LabUMat with UriSed (77 Elektronika, Budapest, Hungary) in comparison to urine culture as the reference method., Methods: By comparing the test results for 965 urine samples with quantitative urine cultures, we established cutoff criteria for the UriSed. The cut-off values by the receiver operating characteristic (ROC) curve technique, sensitivity, and specificity were calculated for bacteria (BACT) and white blood cells (WBCs)., Results: A bacterial cutoff value of 375/microL provided the best discrimination for community-acquired urinary tract infection, with a sensitivity of 96.5% and a specificity of 82.1% compared with 182 urine culture positive samples (AUC: 0.939). It was possible to forgo 62.6% of cultures with only 8 false-negative results. The best cut-off value for WBCs was 13/microL. When we used an algorithm in which the combination with the positivity for 85 BACT/microL and for 13 WBCs/microL count, the sensitivity and NPV improved to 99.8% and 100%, respectively, but the specificity declined from 78.8% to 52.0%., Conclusions: When screening with the UriSed for community-acquired urinary tract infection, a cut-off value of 85 bacteria/microL and 13 WBCs/microL should be adopted. Diagnostic performance of UriSed is satisfactory and use of this instrument is a reliable method for screening out a major part of the culture negative samples. It would improve the efficiency of microbiology laboratory, and unnecessary antibiotic prescriptions could be reduced.