A comprehensive study of Helicobacter pylori infection: molecular analysis, antibacterial susceptibility, and histopathological examination.

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.

The canonical Brucella species-host dependency is changing, however, the antibiotic susceptibility profiles remain unchanged.

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.

MLST genotypes and quinolone resistance profiles of Campylobacter jejuni isolates from various sources in Turkey.

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.

Escherichia coli in different animal feces: phylotypes and virulence genes.

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.

Description of the two novel species of the genus Helicobacter: Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., isolated from feces of urban wild birds.

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 43772T, 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 51478T. 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-H8T, faydin-H23T and their close neighbors H. anseris MIT 04-9362T and H. pametensis ATCC 51478T, respectively, confirmed that both strains represent novel species in the genus Helicobacter. The DNA G+C contents of the strains faydin-H8T and faydin-H23T 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-H8T(=LMG 32237T = DSM 112312T) and faydin-H23T(=LMG 32236T = CECT 30508T) as respective type strains.

Helicobacter turcicus sp. nov., a catalase-negative new member of the Helicobacter genus, isolated from Anatolian Ground Squirrel (Spermophilus xanthoprymnus) in Turkey.

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 H02T with 97.0-97.1 % identity levels and they formed a novel phylogenetic line within the genus Helicobacter. Faydin-H64 and Faydin-H70T strains were subjected to gyrA and atpA 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-H70T were 35.3 mol% and 1.7 Mb, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain Faydin-H70T and its close phylogenetic neighbour H. winghamensis ATCC BAA-430T were determined as 81.7 and 34.9 %, respectively. Pairwise sequence comparison showed that it was closely related to H. ganmani CMRI H02T however it shared the highest ANI and dDDH values with H. winghamensis ATCC BAA-430T. 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-H70T as the type strain (=DSM 112556T=LMG 32335T).

Clinical relevance of virulence genes in Helicobacter pylori isolates recovered from adult dyspeptic patients in Turkey.

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 â€‹± â€‹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 â€‹> â€‹0.05). Furthermore, intestinal metaplasia and gastric atrophy showed no significant correlation with the virulence genes (p â€‹> â€‹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.

Campylobacter anatolicus sp. nov., a novel member of the genus Campylobacter isolated from feces of Anatolian Ground Squirrel (Spermophilus xanthoprymnus) in Turkey.

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 6644T 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-G140T) were chosen as representatives for further characterization. The overall genome relatedness indices for the strain faydin-G140T, compared to the most closely related type strain C. curvus ATCC 35224T, 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-G140T as the type strain (=DSM 112311T = LMG 32238T).

Detection of Helicobacter pylori by invasive tests in adult dyspeptic patients and antibacterial resistance to six antibiotics, including rifampicin in Turkey. Is clarithromycin resistance rate decreasing?

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 18­90), 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.

Prevalence of Protective Measles Virus Antibody Levels in Umbilical Cord Blood Samples and Sera of Mothers and Transplacental Transport Ratio in Turkey.

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.

Antibiotic resistance of Campylobacter jejuni isolates recovered from humans with diarrhoea in Turkey.

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.

[Investigation of the frequency and distribution of beta-lactamase genes in the clinical isolates of Acinetobacter baumannii collected from different regions of Turkey: a multicenter study]. / Türkiye'nin farkli bölgelerinden toplanan klinik Acinetobacter baumannii izolatlarinda beta-laktamaz gen sikligi ve dagiliminin arastirilmasi: Çok merkezli bir çalisma.

The diversity and distribution of TEM, SHV and CTX-M type of extended-spectrum beta-lactamases (ESBLs) are important for the treatment and control of infections. Determination of ESBL genes in clinical isolates by polymerase chain reaction (PCR) and DNA sequencing can obtain useful data for their molecular epidemiology and risk. The aim of this study was to investigate the frequency of beta-lactamase genes in Acinetobacter baumannii strains isolated from different regions of Turkey. A total of 519 A.baumannii strains collected from hospitals located at 12 different provinces of Turkey (Bolu (n= 67), Tokat (n= 47), Trabzon (n= 25), Ordu (n= 27), Diyarbakir (n= 47), Nigde (n=31), Kayseri (n= 36), Ankara (n= 41), Kirikkale (n= 26), Kahramanmaras (n= 25), Mersin (n= 40), Istanbul (n= 107)] between 2011-2012 period were included in the study. Identification of the isolates were performed by both conventional methods and automated systems, VITEK2 Compact (BioMerieux, France) and API 32GN (BioMerieux, France). Disc diffusion method was used for the detection of antibiotic susceptibilities of the isolates and the results were evaluated according to CLSI (Clinical and Laboratory Standards Institute) criteria. Tigecycline and colistin sensitivities of the isolates were evaluated according to BSAC (British Society for Antimicrobial Chemotherapy) criteria. The presence of beta-lactamase genes, namely blaoxa-51, blaTEM, blaSHV, blaCTX-M1, blaCTX-M2, blaGES and blaVIM were detected by PCR. In our study, the resistance rates against colistin, tigecycline, ampicillin-sulbactam, amoxicillin-clavulanic acid, cefoperazone/sulbactam, tobramycin, ceftriaxone, piperacillin-tazobactam, gentamicin, ampicillin, tetracycline, cefepime, piperacillin, amikacin, trimethoprim-sulfamethoxazole, meropenem, levofloxacin, ciprofloxacin, imipenem and ceftazidime were detected as; 0.6%, 2.7%, 11.9%, 15.2%, 21%, 22.9%, 23.9%, 48.6%, 59.5%, 61.8%, 66.3%, 67.8%, 69.2%, 71.1%, 77.5%, 78.6%, 81.1%, 82.9%, 87.5% and 89.4%, respectively. All of the isolates (100%) were OXA-51 positive, while 443 (85.4%) out of 519 strains harbored other beta-lactamase genes searched in the study. When the distribution of the genes were evaluated, blaTEM-1 was found as the predominant one with a frequency rate of 55.7% (n=289/519), followed by blaCTX-M2 (63/519, 12.1%), blaCTX-M1 (42/519, 8.1%), blaSHV (40/519, 7.7%), blaGES (8/519, 1.5%) and blaVIM (1/519, 0.2%). Cooccurence of ESBL genes was detected in 16.3% (72/443) of the strains, being mostly TEM+CTX-M2 (20/72, 27.8%), TEM+SHV (11/72, 15.3%) and TEM+CTX-M1 (10/72, 13.9%). In addition, it was noted that the distribution of ESBL genes between isolates showed differences according to the provinces. Accordingly, none of the strains isolated from four provinces (Bolu, Nigde, Mersin, Kahramanmaras) and from three provinces (Bolu, Kahramanmaras, Diyarbakir) harbored blaCTX-M1/M2 and blaSHV genes, respectively. The blaTEM gene was detected in isolates collected from all of the provinces, with a highest frequency in Nigde (28/31, 90.3%) and lowest in Trabzon (1/25, 4%). The presence of GES-11 type ESBLs was found only in the isolates sent from Nigde province (8/31; 25.8%). Screening of metallo-beta-lactamase VIM gene also yielded a single positive result amongst only Nigde isolates (1/31; 3.2%), and this gene was identified as VIM-5 type by DNA sequencing. This study which is the first comprehensive national research to characterize ESBLs in A.baumannii isolates by molecular methods, showed that the most prevalent ESBL type is TEM (289/519, 55.7%) amongst A.baumannii strains isolated from different regions of our country. The data of our study is parallel to the results of previous studies carried out from Turkey.

Characterization of HCV genotype 4d infections in Kayseri, Turkey.

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.

Genetic diversity and antibiotic resistance profiles of Campylobacter jejuni isolates from poultry and humans in Turkey.

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.

[Epidemiology, clinical and microbiological characteristics of invasive streptococcal infections in Turkey, 2010-2011]. / Türkiye'de invazif streptokok enfeksiyonlarinin epidemiyolojisi, klinik ve mikrobiyolojik özellikleri, 2010-2011.

A one-year active surveillance study was conducted to investigate the epidemiological and microbiological characteristics of invasive group A streptococci (GAS) infections in Turkey and to provide data for the establishment of national preventive strategies related to invasive GAS infections. A total of 46 clinical microbiology laboratories from 12 different regions of Turkey (Istanbul; Eastern and Western Marmara; Eastern and Western Blacksea; Aegean; Mediterranean; Western, Central, Northeastern, Middle-eastern and Southeastern Anatolia) participated in the study. Accordingly, GAS strains isolated from sterile body sites (blood, cerebrospinal, synovial, pleural, peritoneal, pericardial fluids) in the study centers between June 2010-June 2011, were sent to Maltepe University Hospital Clinical Microbiology Laboratory for microbiological confirmation and further analysis. The isolates were identified by conventional methods, and for serotyping, opacity factor (OF) and T protein types were investigated. For genotyping GAS lysate preparation, emm gene amplification and sequencing were performed by using the protocols recommended by Centers for Disease Control and Prevention. A total of 65 invasive GAS strains were isolated in 15 of the participant centers, during the study period. The rate of invasive GAS isolation exhibited regional variation, with the highest rates in the Eastern Blacksea (Trabzon, n= 19), followed by Istanbul (n= 17) and Western Anatolia (Ankara, Konya, n= 14). Of the patients with invasive GAS infection 33 were female, 32 were male, with the age range of 0-89 years. GAS strains were most commonly isolated from soft tissue specimens (n= 18), followed by abscess material (n= 10), sterile body fluids (n= 8) and blood (n= 7) samples. Serotyping revealed that 55% (36/65) of the strains were OF positive, and the majority of T protein was polygroup T (n= 20), followed by U (n= 14), B (n= 5), X (n= 3) and Y (n= 2). T protein was not detected in 22 isolates. The strains were found to have 17 different emm types;emm1 (n= 13), emm4 (n= 6), emm6 (n= 6), emm12 (n= 6), emm24 (n= 4), emm14 (n= 3) and emm28 (n= 3). Nine of the strains could not be typed by sequencing. The correlation between emm typing and serotyping was detected as 58%. It was observed that 26-valent vaccines included 70.5% of the invasive GAS strains included in this study. Our study provided initial data concerning the epidemiological properties of invasive GAS infections and characterization of GAS strains in Turkey. The incidence of invasive GAS infections is low in our country. Although immunization programme by 26-valent GAS vaccine is not currently an urgent public health issue for our country, the results of this study indicated that emm types 4 and 24 should better be included in such a vaccine to be used in Turkey. Additionally, since epidemiological features of GAS infections and the microbiological characteristics of the strains can vary by time, for the diagnosis of invasive streptococcal infections and to take the necessary preventive measures, epidemiological studies should be conducted repeatedly.

Phylogenetic analysis of HCV-4d in Turkey: the curious case of Kayseri province.

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).

Two bacteremia cases associated with Rothia mucilaginosa.

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.