Recent trends in the antibiotic resistance of Helicobacter pylori in patient with dyspepsia.

The aim of this study was to determine the resistance status and to identify the point mutations conferring resistance to clarithromycin and fluoroquinolones among dyspeptic patients in Manisa, Turkey. The study included a sample of 140 patients with an indication for upper gastrointestinal endoscopy randomly selected from 2100 dyspeptic patients attending to the Gastroenterology and Endoscopy Unit at Manisa Celal Bayar University Hafsa Sultan Hospital between April 2016 and May 2018. A commercially available GenoType Helico DR test was used to detect the presence of Helicobacter pylori and mutations associated with resistance to clarithromycin and fluoroquinolones in biopsy specimens. In total, 116 (82.9%) of 140 biopsies obtained from the same number of dyspeptic patients were positive for H pylori and 82 (approximately 71%) of them harbored resistance mutations in 23SrRNA and/or gyrA. Resistance to clarithromycin, levofloxacin, or both were detected in 43.1% (50/116), 27.6% (32/116), and 16/116 (13.8%) of tested biopsies, respectively. The most common mutation conferring resistance to clarithromycin was A2147G (96%, 48/50). Resistance to fluoroquinolones was frequently due to mutation in codon 91 and the most common mutation detected was D91G (34.4%). Heteroresistance patterns were observed in 48.0% (24/50) of clarithromycin-resistant samples and 28.1% (9/32) of levofloxacin-resistant samples. The resistance rates and detected mutations in this study are in line with the country data. However, to achieve better H pylori eradication and to prevent the spread of multidrug-resistant strains in Turkey, the molecular-based susceptibility tests should be considered routinely. Further studies are needed to determine the various mutations among resistant strains.

Seroprevalence of West Nile virus, Crimean-Congo hemorrhagic fever virus, Francisella tularensis and Borrelia burgdorferi in rural population of Manisa, western Turkey.

BACKGROUND & OBJECTIVES: Zoonotic diseases are well recognised threat to public health globally. The information of regional prevalence and associated risk factors allow the national programmes to determine and frame better strategies for their control, as they also provide the actual status of zoonosis in the region. The aim of this study was to determine the seroprevalence of West Nile virus (WNV), Crimean-Congo hemorrhagic fever virus (CCHFV), Francisella tularensis and Borrelia burgdorferi among the rural residents of Manisa region, Turkey and to identify the associated risk factors. METHODS: Cross sectional study was conducted in rural parts of Manisa, Aegean region of western Turkey in 2012. Blood samples from 324 randomly selected subjects were screened for the presence of IgG antibodies to WNV, CCHFV, F. tularensis and B. burgdorferi with commercially available kits. The demographic structure of the rural residents and risk factors related to lifestyle such as outdoor agriculture activities, animal husbandry, hunting and history of tick bite were questioned and their relationships with positive results were analyzed statistically. RESULTS: It was observed that 49 subjects (15%) had IgG antibodies to at least one of the zoonotic agents studied. The seroprevalence of F. tularensis was highest with a percentage of 7.1% (n = 23). Distribution of the positive results for WNV, CCHFV and B. burgdorferi were 4.3% (n = 14), 3.7% (n = 12) and 0.9% (n = 3), respectively. Older age and uncompleted secondary education were the statistically significant risk factors for seropositivity to at least one zoonotic agent investigated. Logistic regression analyses confirmed that older age (over 50) increased the risk of WNV and CCHFV seropositivity. INTERPRETATION & CONCLUSION: Seropositivity rates were not found to be higher than the expected rates. Further, studies are needed to evaluate the threat of vector borne zoonoses and associated risk factors in the study area.

Clarithromycin resistance and 23S rRNA gene point mutations of Helicobacter pylori infection in children.

This study aims to evaluate Helicobacter pylori with clarithromycin resistant genotypes in Manisa region, Turkey. Two hundred patients, who received diagnosis of Helicobacter pylori infection histopathologically, were included. The sex, age and endoscopy indications of the patients were recorded. Polymerase chain reaction method was applied to determine the clarithromycin resistance rate and resistance genotypes at the histologic sections prepared from gastric biopsies that had been embedded in paraffin after fixation by formalin. Helicobacter pylori resistance to clarithromycin was found in 19/200 (9.5%) patients. 10/19 (52.6%) of these clarithromycin-resistant patients had A2143G mutation and 9/19 (47.4%) had A2142G mutation. A2142C mutation on 23S rRNA gene was not detected for any of the patients. Clarithromycin can be used as a first step treatment in the eradication of Helicobacter pylori for the children in our region; if the treatment fails for some patients, clarithromycin resistance, especially A2143G and A2142G mutations should be considered.

[Investigation of bacterial etiology with conventional and multiplex PCR methods in adult patients with community-acquired pneumonia]. / Toplum Kökenli Pnömonisi Olan Eriskin Hastalarda Konvansiyonel ve Multipleks PCR Yöntemleriyle Bakteriyel Etiyolojinin Arastirilmasi

Community-acquired pneumonia (CAP) is still a serious life-threatening disease, in which the etiologic agent cannot be identified in more than 50% of patients despite advanced diagnostic methods. The most commonly used methods in the determination of CAP etiology are culture and serological tests. Since early and accurate therapy reduces the mortality in CAP cases, rapid and reliable diagnostic methods are needed. The aim of this study was to determine the bacterial etiology in adult patients with CAP by implementing multiplex polymerase chain reaction/reverse line blot hybridization (M-PCR/RLBH) assay combined with conventional methods. A total of 128 cases (94 were male; age range: 19-81 years, mean age: 58) who were admitted to our hospital and clinically diagnosed as CAP between November 2008 - November 2010, were included in the study. Respiratory samples (sputum and/or bronchoalveolar lavage) obtained from patients were searched by M-PCR/RLBH method (Gen ID®, Autoimmun Diagnostika GmbH, Germany) in terms of the presence of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Mycoplasma pneumoniae, Chlamydia pneumoniae and Legionella pneumophila nucleic acids. The samples were simultaneously inoculated onto 5% sheep blood agar, chocolate agar, haemophilus isolation agar, buffered charcoal yeast extract-selective agar and EMB agar media for cultivation. Serum samples obtained from the cases were tested for IgM and IgG antibodies against C.pneumoniae by microimmunofluorescence (Focus Diagnostic, USA) and against L.pneumophila and M.pneumoniae by indirect immunofluorescence (Euroimmun, Germany) methods. The bacterial etiology was identified in 59 (46.1%) of 128 patients with CAP and a total of 73 pathogens were detected. The leading organism was S.pneumoniae (n= 32, 25%), followed by H.influenzae and M.pneumoniae (n= 9, 7%), gram-negative bacilli (n= 10, 7.8%), M.catarrhalis (n= 6, 4.7%), C.pneumoniae (n= 4, 3.2%), L.pneumophila (n= 2, 1.6%) and Staphylococcus aureus (n= 1, 1.4%). Infection with atypical pathogens were detected in 15 (11.7%), and mixed infections in 14 (10.9%) patients. The detection rate of microorganisms (S.pneumoniae, H.influenzae, M.catarrhalis, C.pneumoniae, L.pneumophilia, M.pneumoniae) searched by M-PCR/RLBH method was 41.4% (53/128), while those microorganisms were detected in 23.4% (30/128) of the patients by conventional methods, representing a significant difference (p< 0.05). It was concluded that M-PCR/RLBH method supplemented the determination of bacterial etiology in CAP cases by increasing the rate of detection from 23.4% to 41.4%. The results indicated that empirical treatment of CAP should primarily include antibiotics against S.pneumoniae, M.pneumoniae and H.influenzae in our region.

Evaluation of real-time PCR method for rapid diagnosis of brucellosis with different clinical manifestations.

In this study, we tested the advantages of TaqMan real time PCR technique and compare it to conventional methods using serum samples from patients with different clinical forms of brucellosis. A total of 50 patients were included in the study. Blood culture using BACTEC 9240 system, Standard Wright's tube agglutination, and real time PCR methods were used. Control blood samples from 30 people with no history of brucellosis or exposure to Brucella spp. were examined too. Serological assay was positive for 49 patients (98%). Forty-four (88%) of the 50 patients had a positive PCR result, whereas Brucella spp were isolated from blood cultures of 18 patients (36%). STA test was all positive for focal brucellosis. Real time PCR test was positive in 9 patients with focal disease (90%), whereas blood culture was positive only in 4 patients (40%). The sensitivity, specificity, positive and negative predictive values of the real time PCR method were calculated as 88%, 100%, 100%, and 83%, respectively. Our results suggest that the high sensitivity and specificity of real time PCR method make it a useful tool for diagnosis of brucellosis with different clinical manifestations.

[The rate of inducible clindamycin resistance and susceptibilities to other antimicrobial agents in staphylococci]. / Stafilokokoklarda indüklenebilir klindamisin direnci ve diger antibiyotiklere duyarlilik oranlari.

Staphylococci are one of the most common pathogens isolated from nosocomial and community acquired infections. Antibiotics used by oral route such as erythromycin, clindamycin, trimethoprim-sulphamethoxazole (TMP-SMX) and quinolones are of value especially in the treatment of community acquired infections and resistance to those antibiotics may lead to therapeutic failure. Therefore in this study, susceptibility of staphylococci to TMP-SMX, rifampin, tetracycline, gentamicin, ciprofloxacin and vancomycin and the presence of inducible clindamycin resistance were investigated in two distinct university hospitals in Turkey. A total of 286 staphylococcus strains [184 Staphylococcus aureus, 102 coagulase negative staphylococci (CoNS)] were studied. Of the 90 hospital-acquired S. aureus, 44.6% were methicillin-resistant while all of the community acquired strains were methicillin-susceptible. All of the CoNS strains were isolated from nosocomial infections and 71.6% of them were resistant to methicillin. Inducible clindamycin resistance rate of CoNS strains (34.3%) was higher than that of S. aureus strains (7.1%) and the difference was statistically significant (p= 0.00001). Positive D-test among CoNS were significantly higher in S. hominis strains (p= 0.00001). Susceptibilities of S. aureus strains to tetracycline, rifampin, ciprofloxacin, gentamicin and TMP-SMX were 56%, 59%, 56%, 56% and 99%, respectively. Susceptibilities of CoNS strains to tetracycline, rifampin, ciprofloxacin, gentamicin and TMP-SMX were 73%, 72%, 39%, 40% and 46%, respectively. None of these strains were vancomycin resistant. Differences between tetracycline, rifampin, ciprofloxacin and gentamicin resistance rates among D-test positive and negative S. aureus strains were found statistically significant. Although among CoNS isolates, no statistically significant difference was found between the resistance rates, D-test positive strains were determined to be more resistant. Differences between tetracycline, rifampin, ciprofloxacin and gentamicin resistance rates among D-test positive S. aureus and CoNS strains were found statistically significant. It can be concluded that inducible clindamycin resistance should be tested for staphylococci during routine antibiotic susceptibility testing. According to the presented data, clindamycin still can be used empirically in methicillin-susceptible S. aureus infections in our region, however, the routine use of rapid, easy, reproducible and economic D-test for the determination of inducible clindamycin resistance in erythromycin resistant strains should be considered in clinical microbiology laboratories. Inducible clindamycin resistance must be anticipated carefully while considering therapeutic options especially for CoNS infections.

Early renal parenchymal histological changes in an experimental model of vesico-ureteral reflux and the role of apoptosis.

OBJECTIVES: To observe early renal parenchymal cellular changes in an experimental model of vesico-ureteral reflux (VUR) and to show whether the apoptotic pathway plays a role in these cellular changes. MATERIAL AND METHODS: Fourteen New Zealand breed rabbits were used and were divided into two equal groups (control and experimental groups). Urine samples were obtained in a sterile manner and cultured. In the study group, reflux was created in the right kidneys surgically. Renal scintigraphy and voiding cystourethrography (VCUG) were performed in both groups on Day 17. The kidneys were examined in terms of histology, apoptotic activity and caspase activity. RESULTS: No growth was observed in urine cultures in either group. VUR was manifested in only two rabbits in the experimental group on VCUG. On renal scintigraphy, no renal scarring was observed in either of the groups and renal uptake values were in the normal range. There was a greater increase in collagen in the right kidneys in the experimental group than in the control group and apoptotic activity was significantly increased in the study group: 0% in the control group, 10.8%+/-0.7% in the experimental group (p<0.001). Caspase-6 activity was strongly positive and caspase-8 and -9 activities were moderately positive in the right kidneys of the experimental group. Caspase-6 activity was moderately positive, and caspase-8 and -9 activities were weakly positive in the contralateral kidneys of the experimental group. Caspase activities in the control group were negative (p<0.001). CONCLUSIONS: In this experimental model of VUR, apoptotic activity was initiated via the caspase-8 and -9 pathway and collagen tissue increased in the renal parenchyma where reflux occurred. The balance of apoptotic activity may play a key role in the occurrence of reflux nephropathy.

[Investigation of glycopeptide resistance in methicillin resistant staphylococcal isolates]. / Metisiline dirençli stafilokok izolatlarinda glikopeptid direncinin arastirilmasi.

The emergence of Staphylococcus aureus strains with intermediate resistance (VISA) and heterogen resistance (hVISA) to vancomycin leads to the occurence of severe therapeutic problems. The aim of this study was to investigate the vancomycin resistance in methicillin resistant S. aureus (MRSA) and coagulase-negative staphylococci (MRCoNS) isolated from clinical samples in Bacteriology Laboratory of Microbiology and Clinical Microbiology Department of Celal Bayar University Faculty of Medicine, Manisa (located in western Anatolia, Turkey). A total of 120 staphyloccoccal strains (92 MRSA and 28 MRCoNS) isolated from different clinical specimens (tracheal aspirate, blood, abscess, wound swabs, sputum, catheter tips, etc) between the period of June 2005 to December 2006 were included to the study. Vancomycin resistance were determined by agar screening method using brain hearth infusion agar plates containing 6 microg/mL vancomycin. Standard E-test and macro E-test methods were performed for 17 (14%) staphylococcal strains (10 MRSA and 7 MRCoNS) which had grown in agar screening plates. Vancomycin and teicoplanin minimal inhibitory concentration (MIC) ranges of those strains were found as 1.5-4 microg/mL and 2-4 microg/mL, respectively, by standard E-test method. In our study, no VISA and hVISA isolates were detected when MIC value of > or =8 microg/mL for vancomycin and teicoplanin, or > or =12 microg/mL for teicoplanin only were accepted as the criteria for hVISA determination. Agar screening method which is preferably used in routine laboratories for practical and economical reasons, lower sensitivity and specificity than E-test. It can be concluded that, since agar screening method is not reliable for the detection of vancomycin resistance, further multi-center studies with the use of standard methods are needed in order to clarify the vancomycin resistance patterns of staphylococci in our country.

Use of DNA hybridization test for diagnosing bacterial vaginosis in women with symptoms suggestive of infection.

The purpose of this study was to evaluate a DNA hybridization test (Affirm VPIII) as an alternative to Gram stain for the rapid diagnosis of bacterial vaginosis in women with clinical signs of vaginal infection. Vaginal specimens were collected from 321 symptomatic women, and analyzed for bacterial vaginosis by both Gram stain using Nugent criteria and DNA hybridization test. Sensitivity, specificity, positive predictive value, and negative predictive value of the DNA hybridization test were determined using the Gram staining as the standard for diagnosis of bacterial vaginosis. Of the 321 patients, 115 (35.8%) were Gram positive for bacterial vaginosis and 126 (39.2%) were negative. 80 patients (25.0%) demonstrated intermediate Gram staining that was also considered negative. The Affirm system detected G. vaginalis in 107 (93.0%) of 115 vaginal specimens positive for bacterial vaginosis diagnosed by Gram stain. Compared to the Gram stain, DNA hybridization test had a sensitivity of 87.7% and a specificity of 96.0%. Positive and negative predictive values of the DNA hybridization test were 93.0% and 92.7%, respectively. In conclusion, Affirm VPIII hybridization test correlated well with Gram stain and may be used as a rapid diagnostic tool to exclude bacterial vaginosis in women with genital complaints.

Influence of oral intake of Saccharomyces boulardii on Escherichia coli in enteric flora.

Enteric flora constitutes 95% of the cells in the human body. It has been shown that the bacterial content of this flora is affected by diet and changes in nutrition. Considering that urinary tract infections (UTI) are mostly due to ascending infections from the gut flora, the importance of the elements of this flora and their characteristics becomes more evident. The aim of this study was to evaluate the influence of oral Saccharomyces boulardii (S. boulardii) intake on the number of Escherichia coli (E. coli) colonies in the colon. This study was carried out with 14 boys and 10 girls (total of 24 children) aged between 36 and 192 months (mean: 104.3+/-45.1 months). A commercial capsule or powder containing 5 billion colony-forming units (cfu) of S. boulardii was administered once a day for 5 days. The number of E. coli and yeast colonies was measured in the stool samples of the study group before and after the use of this drug. Before treatment, the mean number of E. coli colonies in g/ml stool was 384,625+/-445,744. This number decreased significantly to 6,283+/-20,283 after treatment (p=0.00). S. boulardii was not detected in stool before treatment and the number of colonies increased to 11,047+/-26,754 in g/ml stool. S. boulardii may be effective in reducing the number of E. coli colonies in stool. The influence of this finding on clinical practice such as prevention of UTI needs to be clarified by further studies.

Drug-resistant pulmonary tuberculosis in western Turkey: prevalence, clinical characteristics and treatment outcome.

BACKGROUND: Although high antituberculosis (anti-TB) drug resistance rates have been reported in Turkey, the clinical characteristics and implications for the outcome of anti-TB treatment have not been fully investigated. We determined the prevalence of anti-TB drug resistance and examined demographic data, clinical characteristics and treatment outcome in relation to patterns of resistance. METHODS: From the TB case registry of a university hospital and the two largest dispensaries in Manisa city, we identified all pulmonary TB cases with a culture-proven definitive diagnosis and antimicrobial susceptibility results for a 7-year period. We collected and analyzed demographic and clinical data and information on treatment outcome for those cases in relationship to anti-TB drug resistance. RESULTS: Of 355 M. tuberculosis strains, 71.5% were susceptible to streptomycin, isoniazid, rifampicin and ethambutol. Any drug resistance and multi-drug resistance (MDR) rates were 21.1% and 7.3% and were higher in males (53% and 9%, respectively) than in females (22% and 1%, respectively). Drug resistance was significantly higher in old cases (acquired drug resistance) vs new cases (primary drug resistance), and was associated with treatmentfailure (P<0.001). The prevalence of MDR was significantly higher in the old cases (22.4%) than in the new cases (4.4%) (P<0.001). Symptoms, radiographic findings, associated diseases, and sputum smear positivity were unrelated to the development of resistance. The prevalence of any drug resistance and MDR was significantly higher in those with treatment failure than in patients with treatment success. CONCLUSION: High resistance rates, particularly for acquired MDR, indicate a need for improvement in the TB control programme in our region.

Increasing antimicrobial resistance in Escherichia coli isolates from community-acquired urinary tract infections during 1998-2003 in Manisa, Turkey.

Urinary tract infections are among the most common infections with an increasing resistance to antimicrobials. The aim of this study was to determine the change in antimicrobial susceptibility of Escherichia coli isolates from patients with community-acquired urinary tract infection (UTI) for the years 1998 through 2003 and to suggest that the current empirical antibiotic therapy used for these patients is inappropriate. During the study period, 7,335 community urine samples of which 1,203 (16.4%) grew bacterial isolates were analyzed. Among the total of 1,203 isolates, 880 (73.2%) were E. coli. The range of resistance of E. coli to ampicillin was 47.8 to 64.6% and that to trimethoprim-sulfamethoxazole was 37.1 to 44.6% during the study period. The susceptibility pattern of E. coli to nitrofurantoin and cefuroxime did not vary significantly over the 6-year period. There was a significant increase in the susceptibility of E. coli to ciprofloxacin (11.3 - 26.7%), amoxicillin-clavulanate (18.4 - 29.2%) and gentamicin (7.0 - 25.6%) (P < 0.05). Empirical initial treatment with ampicillin and trimethoprim-sulfamethoxazole was thus inadequate in approximately half of UTI cases in our region.

Antimicrobial susceptibility of bacterial pathogens in the oropharynx of healthy school children in Turkey.

BACKGROUND & OBJECTIVES: Information on oropharyngeal carriage rates of Streptococcus pneumoniae, Haemophilus influenzae, Streptococcus pyogenes and Moraxella catarrhalis and their resistance pattern in healthy school children in Turkey is lacking. The present study was undertaken to determine the carriage rates and antimicrobial resistance of these bacterial pathogens in such children aged 6-14 yr in Manisa, Turkey. METHODS: A total of 1022 children were included from nine schools selected randomly from 32 schools. Throat swabs were cultured for bacteria which were identified using standard microbiological methods. Antimicrobial susceptibility was determined as per National Committee for Clinical Laboratory Standards guidelines. RESULTS: Of the 1022 children 240 (23.4%) harboured S. pneumoniae, 162 (15.8%) H. influenzae, 30 (2.9%) S. pyogenes and 82 (8%) M. catarrhalis in their oropharynx. For S. pneumoniae overall 17.9 per cent of the isolates were intermediately and 7 per cent were resistant to penicillin and resistance to erythromycin trimethoprim-sulphamethoxasole (TMP/SMX), and chloramphenicol was 13.7, 9.1 and 1.6 per cent, respectively. Ampicillin resistance observed in 20.9 per cent of H. influenzae isolates was associated with the presence of beta-lactamase, except two isolates interpreted as beta-lactamase-negative ampicillin resistant strains. Resistance of H. influenzae to TMP/SMX, chloramphenicol, azithromycin, cefaclor and amoxicillin/clavulanic acid was 14.2, 2.4, 1.8, 1.2 and 1.2 per cent, respectively. M.catarrhalis isolates produced beta-lactamase in 80.5 per cent of the cases and all were susceptible to macrolides and clavulanic acid/amoxicillin combination; the highest rate of resistance of 17 per cent was for TMP/SMX. One (3.3%) isolate of S. pyogenes was resistant to macrolides tested. INTERPRETATION & CONCLUSION: Our data shows that upper respiratory tract of about 50 per cent children was colonized with respiratory pathogens. There is a need for surveillance of nasopharyngeal carriage of resistant strains in healthy school children.

The effect of circumcision status on periurethral and glanular bacterial flora.

INTRODUCTION: Circumcision is a historical operation which is still performed for different purposes. The aim of this study is to investigate the changes in periurethral and glanular sulcus flora due to circumcision to determine the role of circumcision on urinary tract infections (UTIs). PATIENTS AND METHODS: Fifty patients who were circumcised for social-religious reasons between January 2000 and January 2001 were evaluated in this prospective study. Two swabs were taken from the periurethral and glanular sulcus regions both just before circumcision and 4 weeks after, and the bacteria cultured were recorded. RESULTS: We isolated pathogenic bacteria in the periurethral region of 32 (64%) patients (enterococci in 14 cases; Escherichia coli in 12 cases) before circumcision, and this number decreased to 5 (10%) after circumcision. Similarly, pathogenic bacteria were cultured from the glanular sulcus swabs of 33 (68%) patients (enterococci in 14 cases; E. coli in 10 cases), as well as coagulase-negative staphylococci in another 15 patients before circumcision. Following circumcision, we detected pathogenic bacteria in the glanular cultures of only 4 cases, whereas 40 children had non-pathogenic skin flora. Only 1 of 5 children with history of UTIs (n = 1) and retractable phimosis (n = 4) had periurethral pathogenic bacteria (Proteus spp.) in the post-circumcision period. The differences between pre- and post-circumcision values of the pathogenic bacterial colonizations were statistically significant in both groups sampled (p < 0.05). CONCLUSION: Non-circumcised patients have similar pathogenic bacterial colonizations in the periurethral and the inner preputial regions, although they have no phimosis. The origin of periurethral flora should be the deeper preputial regions. The flora greatly changed with skin commensals after circumcision. Circumcision might be beneficial from this point of view.