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Öğe Assessment of the Genetic Diversity of Mycobacterium tuberculosis esxA, esxH, and fbpB Genes among Clinical Isolates and Its Implication for the Future Immunization by New Tuberculosis Subunit Vaccines Ag85B-ESAT-6 and Ag85B-TB10.4(Hindawi Ltd, 2010) Davila, Jose; Zhang, Lixin; Marrs, Carl F.; Durmaz, Riza; Yang, ZhenhuaThe effort to develop a tuberculosis (TB) vaccine more effective than the widely used Bacille Calmette-Guerin (BCG) has led to the development of two novel fusion protein subunit vaccines: Ag85B-ESAT-6 and Ag85B-TB10.4. Studies of these vaccines in animal models have revealed their ability to generate protective immune responses. Yet, previous work on TB fusion subunit vaccine candidate, Mtb72f, has suggested that genetic diversity among M. tuberculosis strains may compromise vaccine efficacy. In this study, we sequenced the esxA, esxH, and fbpB genes of M. tuberculosis encoding ESAT-6, TB10.4, and Ag85B proteins, respectively, in a sample of 88 clinical isolates representing 57 strains from Ark, USA, and 31 strains from Turkey, to assess the genetic diversity of the two vaccine candidates. We found no DNA polymorphism in esxA and esxH genes in the study sample and only one synonymous single nucleotide change (C to A) in fbpB gene among 39 (44.3%) of the 88 strains sequenced. These data suggest that it is unlikely that the efficacy of Ag85B-ESAT-6 and Ag85B-TB10.4 vaccines will be affected by the genetic diversity of M. tuberculosis population. Future studies should include a broader pool of M. tuberculosis strains to validate the current conclusion.Öğe Beijing/w and major spoligotype families of Mycobacterium tuberculosis strains isolated from tuberculosis patients in Eastern Turkey(Edizioni Int Srl, 2009) Otlu, Baris; Durmaz, Riza; Gunal, Selami; Sola, Christophe; Zozio, Thierry; Rastogi, NalinThe aim of this study was to determine the Beijing/W family and major phylogenetic clades of Mycobacterium tuberculosis strains Of tuberculosis patients in a city with a tuberculosis incidence higher than the country average. A total of 220 M. tuberculosis strains isolated over a period of more than four years were typed by spoligotyping. Spoligotyping resulted in 64 different patterns, 38 (17.3%) of which were unique, and 26 were clusters including 182 (82.7%) strains. The major shared types were ST 53 (n=55, 25%), ST 41 (LAM7-TUR; n=19, 8.6%), and ST 284 (n=15, 6.8%). The major clades observed ranked in the following order: ill-defined T superfamily (n=112, 50.9%); Latino-American-Mediterranean (LAM; n=33, 15%); Haarlem (n=24, 10.9%); and the S family (n=9, 4.1%). Three strains were in the Beijing family. A high number of strains (33 strains) showed patterns that did not fall within any of the major clades described. M. tuberculosis strains in Malatya have both STs showing a widespread distribution over the world and those restricted to this city, confirming the highly diverse nature of tuberculosis. Our results Suggest that the Beijing clade, which is more prevalent among the strains with MDR and isoniazid resistance, is currently not a problem in Eastern Turkey.Öğe The characteristics of nasopharyngeal Streptococcus pneumoniae in children attending a daycare unit(Edizioni Int Srl, 2008) Abut, Latife Iseri; Apan, Teoman; Otlu, Baris; Caliskan, Ahmet; Durmaz, RizaS. pneumoniae is a component of normal nasopharyngeal flora in children. Nasopharyngeal colonization in children attending daycare units has an important effect on the spread of S. pneumoniae. In this study, we aimed to investigate colonization status, antimicrobial susceptibility, and clonal relatedness of the S. pneumoniae strains in children attending a daycare unit. One hundred and six nasopharyngeal swabs were collected from 25 children attending a daycare unit in an 8-month period. S. pneumoniae was identified by a conventional method. Antibacterial sensitivities of the strains were tested by disc diffusion method. Pulsed field gel electrophoresis (PFGE) was used to analyze the clonal relationship of the strains. A total of 25 (23.5 %) S. pneumoniae strains were identified from 106 nasopharyngeal swaps. S. pneumoniae growth was detected in at least one culture of the 19 children (colonization rate; 76%). Seven of the 25 strains (28%) showed resistance to penicillin, 5 (20%) were resistant to trimethoprim-sulfomethoxsazole. The other tested antibiotics were almost effective. The clonal relationship among strains was found as 54.5%. The highest rate of strain entry was in the winter months with strains of opaque colonies, which are known to be more pathogenic. However, the spreading rate among the children was the highest in the summer months and the strains detected in these months had transparent colonies with more transmitting characteristics. Therefore, to prevent S. pneumoniae infection in closed crowded areas, the summer months should not be overlooked.Öğe Clinical, microbiologic, and epidemiologic characteristics of Pseudomonas aeruginosa infections in a University Hospital, Malatya, Turkey(Mosby-Elsevier, 2006) Yetkin, Gulay; Otlu, Baris; Cicek, Aysegul; Kuzucu, Cigdem; Durmaz, RizaBackground: Pseudomonas aeruginosa strains are generally resistant to many antibiotics, and nosocomial infections because of this species are one of the major problems in many hospitals. Molecular typing provides very useful information about origin and transmission of the strains. The aims of the present study were to investigate clinical and microbiologic characteristics of the nosocomial infections caused by P aeruginosa strains in a medical center and to bring up the cross-transmission level of this opportunistic pathogen in a university hospital by analyzing the clonal relationship among the isolates. Methods: A total of 105 P aeruginosa strains had been identified among the 80 inpatients in a 1-year period from August 2003 to August 2004. Demographic, clinical, and epidemiologic data of the patients were prospectively recorded. The standardized disk-diffusion method was used to determine resistance of the strains to imipenem, ceftazidime, aztreonam, amikacin, gentamicin, mezlocillin, cefepime, tobramycin, meropenem, ceftriaxone, and ciprofloxacin. Clonal relatedness of the strains was investigated by pulsed-field gel electrophoresis (PFGE). Results: Of the 105 P aeruginosa strains identified, 45 (43%) were isolated from the patients hospitalized in intensive care units. Thirteen patients had repeated pseudomonas infection (total 38 infections/13 patients); 26 of these repeated infections in 9 patients showed the same localization. Half of the patients had at least 1 underlying disease such as burn (48%), chronic illness (32%), and malignancy (20%). Fifty-seven patients (71%) had urinary and/or other catheterization. Urinary tract infection (35 %) was the most frequent infection encountered, followed by respiratory tract infection (34%) and sepsis (13%). Resistance to the antibiotics tested was in the 12% to 88% range; amikacin was the most effective and ceftriaxone was the least effective antibiotic, The PFGE typing method showed that 28 of the 80 patients' isolates were clonally related, including 23 indistinguishable or closely related strains (29%), and 5 possibly related strains (6%). Epidemiologic data of the 16 patients (20% of the patients) confirmed a clonal relationship among the strains. Of the 26 isolates of the 9 patients having repeated infection in the same location, 18 (69%) were in the clonally related groups, whereas 11 of the 12 strains isolated from repeated infections on different body sites were clonally different. Conclusion: Our results indicated that P aeruginosa infections in our hospital mainly affected the patients hospitalized in intensive care units and those having catheterization, burn, and/or chronic illness. Amikacin was the best antibiotic as far as bacterial resistance was considered. Although lack of major PFGE type confirmed no P aeruginosa outbreak, typing results showed that cross transmission and treatment failure are the 2 main problems, which should be consider together to prevent this bacterial infection in medical centers.Öğe Demographic and microbial characteristics of extrapulmonary tuberculosis cases diagnosed in Malatya, Turkey, 2001-2007(Biomed Central Ltd, 2011) Gunal, Selami; Yang, Zhenhua; Agarwal, Mansi; Koroglu, Mehmet; Arici, Zeynep Kazgan; Durmaz, RizaBackground: Extrapulmonary tuberculosis (EPTB) has an increasing rate in Turkey. The reason remains largely unknown. A better understanding of the demographic and microbial characteristics of EPTB in the Turkish population would extend the knowledgebase of EPTB and allow us to develop better strategies to control tuberculosis (TB). Methods: We retrospectively evaluated clinical and laboratory data of 397 bacteriologically-confirmed TB cases diagnosed during an eight year-period using by chi-square analysis and multivariate logistic regression model. Results: Of the 397 study patients, 103 (25.9%) had EPTB and 294 (74.1%) had pulmonary tuberculosis (PTB). The most commonly seen two types of EPTB were genitourinary TB (27.2%) and meningeal TB (19.4%). TB in bone/joints, pleural cavity, lymph nodes, skin, and peritoneal cavity occurred at a frequency ranging from 9.7% to 10.7%. The age distribution was significantly different (P < 0.01) between PTB and EPTB, with patients older than 45 years tending to have an increased risk of EPTB. Furthermore, the distribution of different types of EPTB differed significantly among age groups (P = 0.03). Meningeal and bone and/or joint TB were more commonly observed among the male patients, while lymphatic, genitourinary, and peritoneal TB cases were more frequently seen among females. Unique strain infection was statistically significantly associated with EPTB (OR: 2.82, 95% CI [1.59, 5.00]). Conclusions: EPTB accounted for a significant proportion of TB cases in Malatya, Turkey between 2001 and 2007. The current study has provided an insight into the dynamics of EPTB in Malatya, Turkey. However, the risk factors for having EPTB in Malatya, Turkey remain to be assessed in future studies using population-based or randomly selected sample.Öğe Distribution of Spoligotyping Defined Genotypic Lineages among Drug-Resistant Mycobacterium tuberculosis Complex Clinical Isolates in Ankara, Turkey(Public Library Science, 2012) Kisa, Ozgul; Tarhan, Gulnur; Gunal, Selami; Albay, Ali; Durmaz, Riza; Saribas, Zeynep; Zozio, ThierryBackground: Investigation of genetic heterogeneity and spoligotype-defined lineages of drug-resistant Mycobacterium tuberculosis clinical isolates collected during a three-year period in two university hospitals and National Tuberculosis Reference and Research Laboratory in Ankara, Turkey. Methods and Findings: A total of 95 drug-resistant M. tuberculosis isolates collected from three different centers were included in this study. Susceptibility testing of the isolates to four major antituberculous drugs was performed using proportion method on Lowenstein-Jensen medium and BACTEC 460-TB system. All clinical isolates were typed by using spoligotyping and IS6110-restriction fragment length polymorphism (RFLP) methods. Seventy-three of the 95 (76.8%) drug resistant M. tuberculosis isolates were isoniazid-resistant, 45 (47.4%) were rifampicin-resistant, 32 (33.7%) were streptomycin-resistant and 31 (32.6%) were ethambutol-resistant. The proportion of multidrug-resistant isolates (MDR) was 42.1%. By using spoligotyping, 35 distinct patterns were observed; 75 clinical isolates were grouped in 15 clusters (clustering rate of 79%) and 20 isolates displayed unique patterns. Five of these 20 unique patterns corresponded to orphan patterns in the SITVIT2 database, while 4 shared types containing 8 isolates were newly created. The most prevalent M. tuberculosis lineages were: Haarlem (23/95, 24.2%), ill-defined T superfamily (22/95, 23.2%), the Turkey family (19/95, 20%; previously designated as LAM7-TUR), Beijing (6/95, 6.3%), and Latin-America & Mediterranean (LAM, 5/95 or 5.3%), followed by Manu (3/95, 3.2%) and S (1/95, 1%) lineages. Four of the six Beijing family isolates (66.7%) were MDR. A combination of IS6110-RFLP and spoligotyping reduced the clustering rate from 79% to 11.5% among the drug resistant isolates. Conclusions: The results obtained showed that ill-defined T, Haarlem, the Turkey family (previously designated as LAM7-TUR family with high phylogeographical specifity for Turkey), Beijing and LAM were predominant lineages observed in almost 80% of the drug-Resistant M. tuberculosis complex clinical isolates in Ankara, Turkey.Öğe DNA polymorphisms in the pepA and PPE18 genes among clinical strains of Mycobacterium tuberculosis(Amer Soc Microbiology, 2007) Hebert, Andrea M.; Talarico, Sarah; Yang, Dong; Durmaz, Riza; Marrs, Carl F.; Zhang, Lixin; Foxman, BetsyTuberculosis continues to be a leading cause of death worldwide. Development of an effective vaccine against Mycobacterium tuberculosis is necessary to reduce the global burden of this disease. Mtb72F, consisting of the protein products of the pepA and PPE18 genes, is the first subunit tuberculosis vaccine to undergo phase I clinical trials. To obtain insight into the ability of Mtb72F to induce an immune response capable of recognizing different strains of M. tuberculosis, we investigated the genomic diversity of the pepA and PPE18 genes among 225 clinical strains of M. tuberculosis from two different geographical locations, Arkansas and Turkey, representing a broad range of genotypes of M. tuberculosis. A combination of single nucleotide polymorphisms (SNPs) and insertion/deletions resulting in amino acid changes in the PPE18 protein occurred in 47 (20.9%) of the 225 study strains, whereas SNPs resulted in amino acid changes in the PepA protein in 14 (6.2%) of the 225 study strains. Of the 122 Arkansas study strains and the 103 Turkey study strains, 32 (26.2%) and 15 (14.6%), respectively, had at least one genetic change leading to an alteration of the amino acid sequence of the PPE18 protein, and many of the changes occurred in regions previously reported to be potential T-cell epitopes. Thus, immunity induced by Mtb72F may not recognize a proportion of M. tuberculosis clinical strains.Öğe Epidemiologic characterization of nosocomial Acinetobacter baumannii infections in a Turkish university hospital by pulsed-field gel electrophoresis(Mosby-Elsevier, 2009) Cetin, Emel Sesli; Durmaz, Riza; Tetik, Tulay; Otlu, Baris; Kaya, Selcuk; Caliskan, AhmetBackground: Although members of the Acinetobacter genus are not commonly part of the human flora, their relatively high prevalence in hospital environment frequently results in colonization of the skin and respiratory tract. Objectives: The present investigation was carried out to elucidate epidemiologic characteristics of nosocomial Acinetobacter baumannii infections in a teaching hospital. Methods: Epidemiologic, clinical, and demographic features of the 66 patients with A baumannii infection during a 14-month period were recorded. Antibiotic susceptibilities of the isolates were determined by the standardized disk-diffusion method, and the clonal relationship of the isolates was analyzed by pulsed-field gel electrophoresis (PFGE). Results: The incidence of A baumannii infection was especially high in January, April, May and June 2006. The isolates were most frequently obtained from blood and tracheal aspirates sent from the intensive care unit and neurosurgery ward. Although the most frequently identified predisposing factors were cerebrovascular disease and surgical operation, the main risk factors identified in these patients were catheterization and mechanical ventilation. Genotype analysis of the 66 A baumannii strains by PFGE revealed the circulation of 36 different PFGE types. of which type A (12) and K (17) accounted for 44% of the isolates. We found high clonal relationship (80.3%) among the typed strains. Thirteen antibiotypes were observed. Most of the isolates were multidrug resistant. Resistance to imipenem, meropenem, gentamicin, amikacin, tobramycin, netilmicin, ampicillin-sulbactam, trimethoprim-sulfamethoxazole, piperacillin-tazobactam, cefoperazone-sulbactam, ciprofloxacin, and levofloxacin were found in 44%, 47%, 47%, 84.8%, 21.2%, 3%, 62.1%, 57.6%, 94%, 62.1%, 95.5%, and 95.5% of the isolates, respectively. Conclusion: The epidemiologic data obtained suggested that the increase in the number of A baumannii infections in our hospital was caused by the interhospital spread of especially 2 epidemic clones. We determined that clonally related strains can survive for a long time in our hospital and cause nosocomial infections in the predisposed patients. (Am J Infect Control 2009;37:56-64.)Öğe Expression of Cell Proliferation Markers in Benign, Premalignant and Malignant Lesions and Human Papillomavirus Isolation(Deri Zuhrevi Hastaliklar Dernegi, 2007) Serarslan, Gamze; Atik, Esin; Otlu, Baris; Bakaris, Sevgi; Durmaz, RizaBackground and Design: This study was designed to investigate the role of proliferation markers in various benign, premalig- nant and malignant skin lesions and also aimed to detect HPV positivity in these lesions. Material and Method: A total of 62 paraffin blocks [12 seborrheic keratoses (SK), 10 keratoacantoma (KA), 8 actinic keratoses (AK), 22 basal cell carcinoma (BCC), and 10 squamous cell carcinoma (SCC)] were included in the study. Specimens were stud- ied immunohistochemically for the expression of Ki-67, p21 and bcl-2. PCR was performed to detect HPV DNA. Results: HPV positivity was detected in two tissues of BCC (HPV type-16). In the lesions, the Ki-67, p21 and bcl-2 expressions were found to be increased respectively: KAÖğe Genetic diversity and major spoligotype families of drug-resistant Mycobacterium tuberculosis clinical isolates from different regions of Turkey (vol 7, pg 513, 2007)(Elsevier, 2008) Durmaz, Riza; Zozio, Thierry; Gunal, Selami; Yaman, Akgun; Cavusoglu, Cengiz; Guney, Cengiz; Sola, Christophe[Abstract Not Available]Öğe HPV-DNA testing and Ki-67 immunocytochemistry in liquid based cervical cytology in prostitute women(De Gruyter Open Ltd, 2006) Atik, Esin; Otlu, Baris; Cetin, Meryem; Tok, Devrim; Durmaz, RizaHPV causes several changes in the function of host genes, and these interactions cause deregulation of the cell cycle manifested by abnormal expression of cell cycle associated proteins, such as Ki-67. The detection of Ki-67 can play a role in screening and diagnosis of HPV infection with risk of progression towards dysplasia and carcinoma. To show this relation in prostitute women, cervical cells were collected in the PapSpin Collection Fluid. A starting volume of 1000 mu l for each sample, and a 200 mu l cell suspension were used to prepare each sample for thin layer liquid based cytology and then they were stained by Papanicolaou method. The cytological results were classified according to the Bethesda 2001 system. From the remaining cell suspension of 800 mu l, a 400 mu l sample was used for HPV-DNA detection by PCR, a 50 mu l alliquot was used to make thin layer preparations for immunocytochemistry. Single antigen staining was performed with Ki-67 protein. Cells were considered immunopositive if the nuclei were stained. All cells in one high power field (x400) were counted, and the fraction of immunopositive cells on the slide was calculated. This fraction was expressed as the number of positive cells per 1000 cells to facilitate comparisons of differential cell counts. HPV types 6 and 32 in the study, and HPV types 6 and 51 in the control group were detected. The mean Ki-67 values were 2.7 +/- 1.2 and 3.6 +/- 4.1 in HPV positive and negative cases respectively. There was a positive correlation only with nuclear changes and HPV positivity (x(2) = 28.8, p < 0.001). There was not any significant correlation between HPV or Ki-67 and leukocytosis. An association with HPV and contraception, smoking, and concurrent genital infection was not found. The prevalence of HPV types in different geographical locations and races may indicate different etiologies of cervical cancer. Our results suggest that Ki-67 immunocytochemistry is not useful as a surrogate marker for HPV types of 6, 32 and 51.Öğe Hpv-dna testing and ki-67 immunocytochemistry in liquid based cervical cytology: in prostitute women(Springer, 2007) Atik, Esin; Otlu, Baris; Cetin, Meryem; Tok, Devrim; Durmaz, Riza[Abstract Not Available]Öğe Integration of Mycobacterium tuberculosis Drug Susceptibility Testing and Genotyping with Epidemiological Data Analysis To Gain Insight into the Epidemiology of Drug-Resistant Tuberculosis in Malatya, Turkey(Amer Soc Microbiology, 2010) Agarwal, Mansi; Gunal, Selami; Durmaz, Riza; Yang, ZhenhuaDrug-resistant tuberculosis (TB) presents a major challenge to global TB control. To gain a better understanding of drug-resistant TB epidemiology in Malatya, Turkey, we conducted the present study using 397 Mycobacterium tuberculosis clinical isolates collected from Malatya, Turkey, in recent years (2000-2007). Resistance to any anti-TB drug was found in 29% (114 of 397) of the study isolates, while the multidrug resistance (MDR) rate was similar to 4.5% (18 of 397). Resistances to isoniazid (15.5%) and streptomycin (13.4%) were about twice as high as resistance to rifampin (RMP) (6.3%) and ethambutol (EMB) (6.0%). Importantly, 28% (7 of 25) of the RMP-resistant isolates were non-MDR isolates, as when a significant proportion of RMP-resistant isolates in a population are non-MDR, the predictive value of molecular detection of RMP resistance for MDR can be significantly reduced. Both identical and varied drug resistance patterns were seen in the same genotyping-defined clusters, suggesting that both primary and acquired resistance have contributed to the drug-resistant TB epidemic in Malatya, Turkey. In addition, drug-resistant cases were found to be more likely to be males (odds ratio [95% confidence interval], 1.82 [1.13, 2.94]), suggesting a potential role of gender in the epidemiology of drug-resistant TB in the study population. This study demonstrates that the integration of drug susceptibility testing with genotyping and epidemiological data analysis represents a useful approach to studying the epidemiology of drug-resistant TB.Öğe Investigation and analysis of a human orf outbreak among people living on the same farm(Edizioni Int Srl, 2011) Bayindir, Yasar; Bayraktar, Mehmet; Karadag, Nese; Ozcan, Hamdi; Kayabas, Uner; Otlu, Baris; Durmaz, RizaHuman orf is a viral zoonotic infection caused by Parapoxvirus. The skin lesions of human orf can be misdiagnosed as cutaneous anthrax leading to overtreatment and also fear This study was conducted to analyze an outbreak which led to deaths among kids and lambs in the same flock, and skin lesions in some persons who were living on the same farm that were initially diagnosed as cutaneous anthrax by a practitioner. Eight patients with skin lesions and eleven persons who had no skin lesion were considered as patients and control groups, respectively The cultures obtained from the lesions of all patients were negative for Bacillus anthracis. The diagnosis of skin lesions was done by clinical findings, histopathological examination and PCR as human if. To be under 20 years of age, direct contact with the animals, and contact with flayed skin of sick animals were the risk factors for human if (Odds Ratio 7.5; 95% Confidence Interval 1.02-54.54, OR 12.25; 95% CI:1.3-100.9, OR 16.67; 95% CI:1.65-148.20, respectively). Orf should be kept in mind in the differential diagnosis of skin lesions resembling anthrax. For control and prevention of orf, transmission routes should be known; good hand hygiene and other personal protective measures have to be implemented.Öğe INVESTIGATION OF AN OUTBREAK OF SALMONELLA TYPHI IN BATTALGAZI DISTRICT, MALATYA-TURKEY(Soc Brasileira Microbiologia, 2009) Iseri, Latife; Bayraktar, Mehmet Refik; Aktas, Elif; Durmaz, RizaSalmonella Typhi infections are important public health problems for the developing countries. In this study we investigated the molecular epidemiology of a suspected well-water borne S. Typhi outbreak occurred in a district of Malatya-Turkey. This outbreak affected 10 patients in two days. Arbitrary primed polymerase chain reaction (AP-PCR) based typing showed two clones, one had seven, and the other had three strains, supporting outbreak speculation. By adding chlorine to wells by local municipal authority, the outbreak ended within a very short time (about ten days).Öğe Investigation of human papillomavirus and Epstein-Barr virus DNAs in pterygium tissue(Sage Publications Ltd, 2009) Otlu, Baris; Emre, Sinan; Turkcuoglu, Peykan; Doganay, Selim; Durmaz, RizaPURPOSE. Recent studies postulated the presence of a probable relationship between pterygium and neoplasia. This study aimed to investigate the role of two oncogenic viruses, human papillomavirus (HPV) and Epstein-Barr virus (EBV), in the development of conjunctival pterygia. METHODS. Polymerase chain reaction was used to identify the presence of HPV and EBV in 30 primary and 10 recurrent pterygia samples. Twenty conjunctival samples obtained from patients undergoing cataract surgeries were used as the control group. Patient groups had similar sex, race, and age distribution to eliminate bias. For exploration of HPV in groups, two different PCR methods (in-house PCR with two different primer sets and one real-time PCR method) were studied. The presence of EBV was shown by real-time PCR method. RESULTS. HPV was identified in none of the pterygia and control group patients. However, EBV was detected in 3 out of 30 (10%) primary pterygia patients and in none of the recurrent pterygia and control patients. CONCLUSIONS. Up to now, HPV has been blamed as the major viral pathogen in the etiopathogenesis of pterygium. The current results suggest that EBV may also be involved in the pathogenesis of pterygium, but further larger studies with larger cohorts are required to confirm this hypothesis. (Eur J Ophthalmol 2009; 19: 175-9)Öğe Isolation and identification of Mycobacterium tuberculosis from the urine samples by conventional and molecular methods(Ankara Microbiology Soc, 2007) Aslan, Gonul; Doruk, Erdal; Emekdas, Gurol; Serin, M. Sami; Direkel, Sahin; Bayram, Gul; Durmaz, RizaGenitourinary tuberculosis presents a challenge in diagnosis and treatment due to variations in clinical and radiological signs, insufficient patient history and difficulty in the isolation of the bacilli. The aim of this study was to isolate and identify Mycobacterium tuberculosis from the urine samples obtained from patients with suspected urinary tuberculosis admitted to our hospital by using Ehrlich-Ziehl-Neelsen (EZN), culture and polymerase chain reaction-restriction analysis (PCR-RFLP) methods. A total of 1004 urine samples collected from 437 patients who were admitted to our hospital between January 2004- July 2006, were inoculated on Lowenstein-Jensen (LJ) and/or BACTEC 12B (Becton Dickinson, USA) after decontamination and, direct preparations stained with EZN method were evaluated microscopically. M.tuberculosis complex (MTC) and mycobacteria other than tuberculosis (MOTT) were differentiated by nitro-alpha-acetylamino-beta-hydroxypropiophenone (NAP) test and the susceptibility testing for the MTC strains to primary antituberculosis drugs were performed by BACTEC 460 TB (Becton Dickinson, USA) system. PCR-RFLP method was performed for the identification of Mycobacterium spp. Twenty-two (5%) patients have yielded positive results by at least one of the conventional methods (EZN, LJ and/or BACTEC). Fifteen samples were positive for acido-resistant bacilli (ARB) by EZN method, and 17 samples were positive for mycobacterial growth in the cultures. Ten of 22 patients were found positive by both of the methods, while seven were culture positive but ARB negative and five were culture negative but ARB positive. These five patients received BCG treatment because of the presence of bladder tumor. Twelve (70.5%) of 17 strains isolated from culture were identified as MTC, while five (29.4%) were identified as M.fortuitum. Of 12 MTC isolates, eight (66.7%) were found susceptible to all of the antituberculosis agents, while one was found resistant to isoniazide (INH) and ethambutole (ETB), one was resistant to INH and rifampicin (RIF), and two were resistant to only INK It is concluded that, in order to identify mycobacteria and to perform antituberculous susceptibility tests, cultivation of mycobacteria is a prerequisite.Öğe Molecular epidemiology of methicillin-resistant Staphylococcus aureus isolates from clinical specimens of patients with nosocomial infection(Edizioni Int Srl, 2007) Tekerekoglu, Mehmet Sait; Ay, Selma; Otlu, Baris; Cicek, Aysegul; Kayabas, Uener; Durmaz, RizaBacteriological and epidemiological studies were carried out on 90 isolates of methicillin-resistant Staphylococcus aureus (MRSA) at Turgut Ozal Medical Center of Inonu University, (Malatya/Turkey). MRSA isolates were obtained from patients with nosocomial infections. Staphylococcus aureus clinical isolates were collected between May 2004-May 2005. Isolates were tested for resistance to methicillin. Antimicrobial susceptibility testing and slime production evaluation was performed. Genotype studies were carried out by arbitrarily primed polymerase chain reaction (APPCR) and consequent cluster analysis. All of the isolates were mecA-positive in a PCR-based assay; all exhibited resistance to oxacillin, by agar dilution (MICs >= 4mg/L) and disc diffusion methods, and multiple antibiotics. Most MRSA isolates were collected in intensive care units. Of 90 samples, 53 were found to be unrelated to the others while the remaining 37 strains were either identical or closely related, Dendrogram analysis identified nine major clusters. These data support the opinion that MRSA are significant nosocomial pathogens in intensive care units and that resistant clones may be transmitted between patients. Molecular epidemiological tools are helpful for understanding transmission patterns and sources of infection, and are useful for measuring outcomes of intervention strategies implemented to reduce nosocomial MRSA.Öğe Multiple-Locus Variable-Number Tandem-Repeat Analysis Genotyping of Human Brucella Isolates from Turkey(Amer Soc Microbiology, 2011) Kilic, Selcuk; Ivanov, Ivan N.; Durmaz, Riza; Bayraktar, Mehmet Refik; Ayaslioglu, Ergin; Uyanik, M. Hamidullah; Aliskan, HikmetA multiple-locus variable-number tandem-repeat analysis (MLVA) was applied to investigate the epidemiological relationship and genetic diversity among 162 human Brucella isolates collected from all geographic regions of Turkey in an 8-year period (2001 to 2008). The isolates were genotyped by using an MLVA assay developed in Orsay, France (MLVA-16(Orsay)) including eight minisatellite (panel 1) and eight microsatellite (panel 2, subdivided into 2A and 2B) markers. Panels 1 and 2A distinguish 14 genotypes; two of these represented 85% of the strains. Panel 2B displayed a very high discriminatory power. Three loci from panel 2B had diversity index values higher than 0.74. MLVA-16(Orsay) yielded 105 genotypes; 73 were represented by a unique isolate, and 32 included two to eight isolates. The isolates from different patients within the same outbreak or from the same patient before first-line therapy and after relapse showed identical genotypes. A number of MLVA genotypes appeared to be partially restricted to some geographic areas and displayed no annual variation, possibly reflecting persistence of genotypes in certain areas for a time span of at least a decade. This study, representing the first molecular typing results of human Brucella isolates from Turkey, indicated that Turkish human Brucella melitensis isolates were most closely related to the neighboring countries' isolates included in the East Mediterranean group.Öğe The Optimization of a Rapid Pulsed-Field Gel Electrophoresis Protocol for the Typing of Acinetobacter baumannii, Escherichia coli and Klebsiella spp.(Natl Inst Infectious Diseases, 2009) Durmaz, Riza; Otlu, Baris; Koksal, Fatih; Hosoglu, Salih; Ozturk, Recep; Ersoy, Yasemin; Aktas, ElifPulsed-field gel electrophoresis (PFGE) is the most common genotyping method used for the typing of a number of bacterial species. Generally, investigators use their own custom-developed protocol, but a standardized PFGE protocol would allow the comparison of typing results between laboratories and the tracing of strains around the country. In the present study, we optimized a PFGE protocol for subtyping of Acinetobacter baumannii, Escherichia coli and Klebsiella spp., which are commonly isolated from nosocomial infections in many hospitals. Reproducibility of our PFGE procedure was studied three times at 2- to 3-week intervals. Epidemiological concordance of the optimized PFGE procedure was tested on seven isolates of A. baumannii from a previous outbreak and seven A. baumannii isolates randomly selected among the clinical isolates. The optimized PFGE procedure was evaluated on a total of 174 clinical isolates including 62 A. baumannii, 50 E. coli and 62 Klebsiella spp. The inter-laboratory reproducibility of the optimized protocol was tested at four laboratories. The optimized procedure is completed in 28 h after culturing. It is likely to be cost-effective, due to the reduction in the time, reagent volume and enzyme concentration needed. The procedure showed high concordance with epidemiological data. There were no non-typeable isolates among the tested bacteria. It is reproducible and versatile. This protocol can be used to identify outbreaks and monitor the spreading rate of nosocomial infections caused by the tested bacterial isolates. Furthermore, due to its high intra- and inter-laboratory reproducibility, the protocol has the potential to be useful for comparing PFGE fingerprinting profiles of the isolates from different settings.
