The effects of Helicobacter pylori genotypes on clinical prognosis in the Cukurova region of Turkey were investigated by PCR. The prevalence of type I strains carrying the s1c allele, unlike in neighboring regions and countries, was found to be significantly higher in patients with gastritis and/or gastric ulcers (P ‫؍‬ 0.001), and that of type I strains carrying the s1a allele was found to be significantly higher in patients with duodenal ulcers (P < 0.001). The cagA gene was strongly associated with the more virulent vacA genotypes (P < 0.001).

Helicobacter pylori was examined in 110 patients (82 (74.5) with gastritis, 18 (16.4) with duodenitis, six (5.5) with duodenal ulcer and gastroesophageal reflux, and four (3.6 %) with normal) with gastrointestinal problems living in rural area, no history of macrolide use, and detected by culture (71.8) or direct detection from gastric biopsies by PCR (82.7 %). Also, cagA gene was identified using PCR and was found positive in 68/91 (74.7 %) strains. The prevalence of clarithromycin-resistant H. pylori was investigated by two methods including PCR-RFLP (7.7 (A2142G 1.1 and A2143G 6.6 %)) and twofold agar dilution (8.9 %) to detect phenotypic and genotypic status simultaneously. Among all the H. pylori positive patients, eight (8.8 %) isolates were found to be resistant to clarithromycin by at least one of the AD and/or PCR-RFLP methods. H. pylori positive rates were significantly correlated with patients' sex, age, and endoscopic findings (p = 0.040, <0.001 and <0.001, respectively). There were no differences in gender or endoscopic findings related to cagA (+) and cagA (-) patients. The gene of cagA was not significantly helpful in predicting the clinical outcome of H. pylori infection alone. In conclusion, we revealed that there was a low prevalence of primer clarithromycin resistance in patients living in rural area with no history of macrolide use. The prevalence of mutant strains among the macrolide-resistant H. pylori varies even geographically between close provinces.

BackgroundThe resistance of aminoglycosides in strains that produce beta-lactamase can be developed through the multidrug resistant encoding genes carried by common plasmids. Recently, the association between 16S rRNA methyltransferase resistance and beta-lactamase enzymes carried by the same plasmids has drawn increased attention from researchers, particularly the association in aminoglycoside-resistant strains with a minimum inhibitory concentration (MIC) of ≥ 256 µg/mL.ObjectivesWe aimed to investigate the co-existence of 16S rRNA methyltransferase and beta-lactamase genes in multidrug resistant (MDR) Klebsiella pneumoniae strains isolated from clinical samples.MethodsWe determined the molecular mechanisms of aminoglycoside resistance and its relationship with resistance to carbapenem and beta-lactam group antibiotics in 40 extended-spectrum beta-lactamase (ESBL)-positive carbapenem- and aminoglycoside-resistant K. pneumoniae strains. Multidrug resistant K. pneumoniae was isolated from various clinical samples in the faculty of medicine of Cukurova University, Turkey. First, the resistance of aminoglycoside and beta-lactam antibiotics was phenotypically investigated using the Kirby-Bauer disk diffusion test, double disk synergy test, and modified Hodge test. The MIC values of aminoglycoside were determined using the agar dilution method. Polymerase chain reaction was performed to detect the carbapenemases, ESBL, and 16S rRNA methyltransferase genes. The results were confirmed by a sequence analysis.ResultsTwenty K. pneumoniae strains showed resistance to amikacin, and 40 were resistant to gentamicin. The MIC value was found to be > 512 µg/mL in five amikacin-resistant strains and > 128 µg/mL in 10 gentamicin-resistant isolates. The rmtC gene, a type of 16S rRNA methyltransferase, was amplified in four isolates (MIC amikacin: > 512 µg/mL, gentamicin: > 128 µg/mL). Of these four isolates, three had the blaNDM-1 gene and all contained at least one ESBL gene.ConclusionsThis study demonstrated the co-existence of rmtC and blaNDM-1 genes for the first time in Turkey. The spread of this resistant type should be monitored and limited through molecular surveillance.

ÖZET Amaç: Helicobacter pylori (H.pylori)'nin in vitro şartlardaki üreme güçlüğü, bakteri izolasyonuna dayalı tanı yöntemlerinin duyarlılığını düşürmektedir. Buna karşılık, bakterinin glmM (eski ureC) genini hedef alan PCR yöntemi birçok çalışmada kültüre alternatif olarak gösterilmiştir. Çalışmamızda bu iki yöntemin karşılaştırılması, ayrıca H.pylori'nin gastrik lokalizasyonunun bu testlerin duyarlılık ve uygulanabilirliğine olan etkisinin belirlenmesi amaçlanmıştır. Gereç ve Yöntemler: Bu çalışmaya daha önce H.pylori için tedavi almamış olan toplam 231 hastadan (158'i gastrit ve/veya mide ülserli, 73'ü duodenal ülserli) alınan ikişer antrum ve ikişer korpus biyopsi örneği dahil edildi. Antrum ve korpus örneklerinden birer tanesi H.pylori izolasyonu için, %7 at kanı ve antibiyotik içeren modifiye Columbia Agar besiyerlerine ekildi. Kalan örnekler H.pylori glmM gen dizilerine özgül primerler kullanılarak PCR yöntemi ile incelendi. Bulgular: H.pylori, kültür yöntemi ile 231 antrum biyopsi örneğinden 163'ünde (%70.6) ve glmM-PCR yöntemi ile 201'inde (%87.0) tespit edildi (p< 0.001, χ2 testi). H.pylori-pozitif olan korpus örnek sayıları sırası ile 97 (%42.0) ve 154 (%66.7) olarak bulundu (p< 0.001, χ2 testi). H.pylori tanısında daha yüksek pozitiflik elde edilen glmM-PCR yöntemi tanı için altın standart olarak kabul edildiğinde, kültürün özgüllüğünün her iki örnek grubu için %100, duyarlılığının ise antrum örnekleri için %81.1 ve korpus örnekleri için %63.0 olduğu belirlendi. Sonuç: Bulgularımız, H.pylori ile ilişkili gastroduodenal hastalıkların tanısında kültür yönteminin daha az duyarlı olduğunu, özellikle korpus predominant gastrit ve/veya mide ülserli hastalardan alınan korpus biyopsi örneklerinde duyarlılığının %58.4'e düştüğünü göstermektedir.Anah tar Ke li me ler: Helicobacter pylori; kültür; polimeraz zincir tepkimesi; fosfoglukozamin mutaz; biyopsi ABS TRACT Objective: The difficulty of growing of Helicobacter Pylori (H.pylori) under in vitro conditions decreases sensitivity of diagnostic methods based on bacterial isolation. However, the PCR method targeting glmM (formerly ureC) gene of bacteria was shown as an alternative to culture in many studies. The aim of our study was to compare these two methods, as well as to determine the effect of gastric localization of H.pylori on sensitivity and applicability of these methods. Material and Methods: This study included two antral and two corpus biopsy samples obtained from 231 patients (158 with gastritis and/or gastric ulcer and 73 with duodenal ulcer) without prior treatment for H.pylori. One antral and one corpus sample were cultuvated in modified Columbia agar media containing horse blood (7%) and antibiotics for H.pylori isolation. The other samples were investigated by PCR assay using specific primers for H.pylori glmM gene sequences. Results: H.pylori was detected by culture method in 163 (70.6%) and by glmM-PCR method in 201 (87.0%) of 231 antral biopsy samples (p< 0.001, χ 2 test). The numbers of H.pylori-positive corpus samples were found as 97 (42...

Backgrounds. Diagnostic markers of extraintestinal infection in Escherichia coli (E. coli) remain unclear in the literature. Extraintestinal pathogenic E. coli (ExPEC) is differentiated from other E. coli isolates in terms of virulence factors, such as host cell adhesion, invasion, cytotoxic necrotizing factor (CNF (cnf1-cnf3)) and cytolethal distending toxin (CDT (cdt1-cdt4) that are responsible for cell death. We aimed to investigate the frequency of CNF-CDT and the relationship between the clinical diagnosis and genotypes in E. coli isolates with different clinical origins. Methods. A total of 646 E. coli isolates (obtained from 645 patients) isolated from different infection sites other than the intestine were evaluated in aspects of the CNF, CDT virulence genes, phylogenetic grouping, and phylogenetic relationship by using PCR and PFGE. Results. At least one virulence gene was present in 156 (24%) of the 646 ExPEC isolates. We detected cnf1, cnf2, and cnf3, in 78, 12, and 20 ExPEC isolates, respectively. Also, cdt1, cdt2, cdt3, and cdt4 genes were present in 20, 4, 4, and 4 isolates, respectively. Some isolates harbored more than one gene, being cnf1-cnf3 (n = 6), cnf1-cdt1 (n = 4), and cdt1-cdt4 (n = 4). These 156 isolates were distributed into 106 large clusters by PFGE. Virulent ExPEC is primarily related to groups B2 (60%) and D (32%). Conclusion. To our knowledge, this study demonstrated the presence of cnf2, cnf3, cdt1, cdt2, cdt3, and cdt4 genes for the first time in the literature for Turkey. The widespread presence of the CNF gene in E. coli helps distinguish ExPEC from commensal isolates.