An investigation into respiratory tract viruses in children with acute lower respiratory tract infection or wheezing.

BACKGROUND: This study aimed to determine the frequencies of respiratory tract viruses in patient (acute lower respiratory tract infection [LRTI] or wheezing) and control (history of asthma without symptoms) groups. METHODS: Using multiplex-polymerase chain reaction (PCR), respiratory tract viruses were investigated in the respiratory tract specimens from patient and control groups followed in the Pediatric Clinic. RESULTS: The viruses detected in the patient and control groups (P=0.013) were as follows, respectively: rhinoviruses A, B, C (25.6% and 36.7%), influenza virus A (21.1% and 0.0%), parainfluenza virus type 1 (7.8% and 1.7%), parainfluenza virus type 4 (5.6% and 0.0%), adenoviruses A, B, C, D, E (4.4% and 1.7%), parainfluenza virus type 3 (4.4% and 1.7%), coronaviruses 229E and NL63 (4.4% and 1.7%), coronavirus OC43 (3.3% and 0.0%), respiratory syncytial virus A (3.3% and 0.0%), parainfluenza virus type 2 (2.2% and 0.0%), influenza virus B (2.2% and 0.0%), and respiratory syncytial virus B (1.1% and 1.7%). No bocavirus, metapneumovirus or enterovirus was found in any specimen. Statistically significant differences in the detection of influenza virus A (P=0.000), the total detection of parainfluenza viruses (P=0.008) and coinfection (P=0.004) were observed between the patient and control groups. CONCLUSIONS: The advantage of our study compared with other studies is the inclusion of not only wheezing patients but also children with asthma without symptom. The higher detection of rhinoviruses both in patient and control groups give rise to thought that these viruses may be responsible for asthma exacerbations and may be related with long duration of virus shedding.

In vitro susceptibility of Candida species to four antifungal agents assessed by the reference broth microdilution method.

This study was performed to determine the distribution of Candida species isolated from the blood cultures of the patients hospitalized in our hospital and to investigate their antifungal susceptibility. Candida strains were identified at species level by using classical methods and API ID 32C (bioMerieux, France) identification kits. The susceptibility of the strains to amphotericin B, fluconazole, voriconazole, and caspofungin was evaluated by using the reference broth microdilution method in document M27-A3 of the Clinical and Laboratory Standards Institute. Of the 111 Candida strains isolated, 47.7% were identified as C. albicans and 52.3% as non-albicans Candida strains. The MIC ranges were 0.03-1 µg/mL for amphotericin B, 0.125-≥64 µg/mL for fluconazole, 0.03-16 µg/mL for voriconazole, and 0.015-0.25 µg/mL for caspofungin. All Candida strains were susceptible to amphotericin B and caspofungin. 10.8% isolates were resistant to fluconazole and 8.1% isolates were dose-dependent susceptible. While 0.9% isolate was resistant to voriconazole, 0.9% isolate was dose-dependent susceptible. In our study, C. albicans and C. parapsilosis were the most frequently encountered agents of candidemia and it was detected that voriconazole with a low resistance rate might also be used with confidence in the treatment of infections occurring with these agents, primarily besides amphotericin B and caspofungin.

The prevalence of Chlamydia trachomatis and Neisseria gonorrhoeae in the endocervical swab specimens of symptomatic, asymptomatic and infertile women in Turkey.

PURPOSE: To investigate C. trachomatis and N. gonorrhoeae prevalence in three different female populations in Turkey. METHODS: A total of 370 women, 170 symptomatic, 100 asymptomatic, and 100 infertile, were included. Of the endocervical specimens collected from all women using a Dacron swab, the first one was taken to Stuart's transport medium to culture, while the second one was transferred onto slides to perform direct fluorescent antibody test (DFA) and Gram staining, and the third specimen was used for Becton Dickinson BDProbeTec ET system (BDPT). RESULTS: C. trachomatis was detected in 5.16% of symptomatic, 1.11% of asymptomatic, and 2.15% of infertile women with BDPT. Sensitivity and specificity of the DFA test were 72.73 and 97.85%, respectively. N. gonorrhoeae was detected in 2.42% of symptomatic and in 1.02% of infertile women. N. gonorrhoeae was not detected in any asymptomatic women. In N. gonorrhoeae-positive patients, sensitivity and specificity of culture were 60 and 100%, respectively, while they were 80 and 100% for BDPT. CONCLUSIONS: Prevalence of N. gonorrhoeae and C. trachomatis was detected to be low in Turkish women, and the difference between the groups was not significant. Both agents were more prevalent in subjects over 25 years of age.

[Comparison of disc diffusion, E-test, and broth microdilution methods for the determination of resistance to colistin, polymyxin B, and tigecycline in multi-resistant Acinetobacter baumannii isolates]. / Cogul dirençli Acinetobacter baumannii izolatlarinda kolistin, polimiksin B ve tigesiklin direncinin saptanmasinda disk difüzyon, E-test ve buyyon mikrodilüsyon yöntemlerinin karslastirilmasi.

The increased rate of antimicrobial resistance in Acinetobacter baumannii made it necessary to reconsider old antibiotics such as polymyxins and develop new drugs such as tigecycline. The aim of this study was to investigate the susceptibility rates of multi-drug resistant A. baumannii clinical isolates to colistin, polymyxin B, and tigecycline by three different methods in microbiology laboratory of Gaziantep University Research Hospital, between September 2006 and April 2008. A total of 200 A. boumannii strains isolated from various clinical samples (tracheal aspirate, blood, sputum, surgical wound, catheter, pleural fluid, urine, and others) were included to the study. Identification of bacteria was performed by conventional microbiological methods and by an automatized identification system (Vitek 2, bioMerieux, France). Antimicrobial susceptibility pattern of A. baumannii isolates was determined by disc diffusion method and 95 multiple resistant A. baumannii isolates were identified. Susceptibilities of these multiple resistant bacteria to colistin, polymyxin B, and tigecycline were tested with disc diffusion, E-test, and broth microdilution methods. All of the isolates (100%) were sensitive to colistin with all three methods. Ninety-two (96.8%) of them were sensitive to polymyxin B with both disc diffusion and broth microdilution methods, and 90 (94.7%) of them were sensitive to polymyxin B with E-test. Eighty-three (87.4%) of them were sensitive to tigecycline by disc diffusion method, 78 (82.1%) by E-test, and 90 (94.7%) by broth microdilution method. No statistically significant difference was detected for the three methods in terms of susceptibility testing for polymyxin B (p > 0.05). However, while no significant difference wa detected for tigecycline susceptibility testing by disk diffusion and broth microdilution (p > 0.05), statistically significant difference was determined for broth microdilution and E-test methods (p = 0.000). In conclusion, comparison of disc diffusion, E-test, and broth microdilution methods yielded that all three methods were concordant to each other in terms of susceptibility testing of polymyxins. Susceptibility rate to tigecycline was found lower by E-test method than that obtained by other methods. These results emphasized that antimicrobial activities of colistin, polymyxin B and tigecycline against A. baumannii isolates obtained in our hospital were high, however, for tigecycline susceptibility testing against A. boumannii, disk diffusion or broth microdilution methods would rather be preferred.

[Investigation of the frequency of extended spectrum beta-lactamases and antibiotic resistance in clinical isolates of Escherichia coli and Klebsiella sp]. / Escherichia coli ve klebsiella sp. klinik izolatlarinda genislemis spektrumlu beta-laktamaz sikliginin ve antibiyotik direncinin arastirilmasi.

The aim of this study was to detect the presence of extended spectrum beta-lactamase (ESBL) in clinical isolates of Escherichia coil and Klebsiella sp. and to determine in vitro antibiotic resistance of these strains. A total of 78 E. coli and 40 Klebsiella sp. strains isolated from urine, blood, bronchoalveolar lavage, tracheal aspirate, abscess, cerebrospinal fluid and throat swab samples, and identified by conventional methods were included in the study. ESBL activity was screened with double disk synergy test. Antibiotic susceptibilities of the clinical isolates were determined by disc diffusion method using CLSI (Clinical and Laboratory Standards Institute) guidelines. ESBL production was found positive in 25 (32.1%) E. coli and 18 (45%) Klebsiella isolates. The resistance rates of ESBL producing E. coli and Klebsiella strains were as 76% and 5.6% for ciprofloxacin, 68% and 55.6% for trimethoprim/sulfamethoxazole, 64% and 77.8% for gentamicin, 28% and 50% for piperacillin/tazobactam, 0% and 5.6% for cefoxitin, respectively. In ESBL negative isolates of E. coli and Klebsiella sp. these rates were found as follows; 58.5% and 63.6% for amoxicillin/clavulanate, 54.7% and 40.9% for trimethoprim/sulfamethoxazole, 41.5% and 54.5% for piperacillin/tazobactam, 35.8% and 4.5% for ciprofloxacin, 18.9% and 45.5% for gentamicin, 15.1% and 50% for cefotaxime, 13.2% and 36.4% for ceftazidime, 13.2% and 54.5% for aztreonam, 11.3% and 50% for ceftriaxone, 7.5% and 4.5% for cefoxitin, respectively. While all isolates were susceptible to meropenem, cefoxitin was the second most effective antibiotic. It was concluded that ESBL determination should be added to routine antibiotic suspectibility testing in members of Enterobacteriaceae isolates in order to prevent the selection of resistant bacteria and treatment failure.

[Enterococcus spp. colonized in the gastrointestinal tract of patients in hemato-oncology and intensive care units and their resistance profiles to vancomycin]. / Yogun bakim ve onkoloji-hematoloji hastalarinda gastrointestinal sistemde kolonize olan enterokok türleri ve vankomisine direnç profilleri.

The aim of this study was to identify the Enterococcus spp. and to determine their vancomycin-resistance profiles, in the samples collected from the patients who were described as risky groups for vancomycin-resistant enterococcal (VRE) colonization, in scope of a survey study carried out in our hospital for the first time. Rectal swab samples were taken once in a month from a total of 180 patients who were hospitalized in the Surgery and Intensive Care Units, adult Oncology-Hematology and Pediatric Oncology Units between March-December 2006. The samples were cultivated onto bile-esculine agar media, and Miniapi system (bioMerieux, France) was used for the identification at species-level (Rapid ID 32 Strep kit, bioMerieux, France) and for the detection of antimicrobial susceptibilities (ATB Enterococcus kit, bioMerieux, France). MIC levels have been determined by the use of vancomycin E-test (AB Biodisk, Sweden) strips in brain-heart infusion agar (Merck, France). According to the culture results, 126 of the patients (70%) have been found to be colonized with Enterococcus spp. The most frequently isolated species were as follows respectively; E. faecium (42%), E. faecalis (31%), E. avium (12%), E. gallinarum (8%) and E. casseliflavus, (5.6%). Four of the E. faecium strains (3.2%) were found resistant to vancomycin by both automated antibiotic susceptibility test system and E-test (MIC >256 mg/ml). Vancomycin-resistant strains have been identified as being VanA genotypes by polymerase chain reaction. Beta-lactamase production has not been detected in any one of the strains with the use of nitrocephin (Remel, U.S.A.) disk. As a result the colonization rates of enterococcal species and VRE were found as 70% and 3.2%, respectively in our patients. Infections with VRE have not been detected in colonized patients during the follow-up period. In conclusion, in order to detect and prevent the spread of VRE, surveillance cultures should be regularly performed from hospitalized patients, in collaboration with educational studies for hospital personel, controlling the use of vancomycin and cephalosporins and cooperation between microbiology laboratories and inpatient clinics.

Real-time polymerase chain reaction assay for detection of Streptococcus pneumoniae in sputum samples from patients with community-acquired pneumonia.

BACKGROUND AND PURPOSE: A quantitative real-time polymerase chain reaction (PCR) method targeting the pneumolysin gene of Streptococcus pneumoniae in sputum specimens from patients with community-acquired pneumonia (CAP) was evaluated for the identification of pneumococci. METHODS: The applicability of the assay to clinical samples was evaluated by studying 140 sputum specimens from patients with CAP. Of the specimens, 96 (68.6%) were found to be positive by real-time PCR. The results were compared to culture findings. RESULTS: The sensitivity and specificity of the real-time PCR assay developed in this study as compared to those of the culture method were 97.2% and 60.9%, respectively. CONCLUSION: Real-time PCR assay was found to be a rapid and sensitive method for the detection of pneumococci.

Patterns of antimicrobial resistance in a surgical intensive care unit of a university hospital in Turkey.

BACKGROUND: Several studies have reported higher rates of antimicrobial resistance among isolates from intensive care units than among isolates from general patient-care areas. The aims of this study were to review the pathogens associated with nosocomial infections in a surgical intensive care unit of a university hospital in Turkey and to summarize rates of antimicrobial resistance in the most common pathogens. The survey was conducted over a period of twelve months in a tertiary-care teaching hospital located in the south-eastern part of Turkey, Gaziantep. A total of 871 clinical specimens from 615 adult patients were collected. From 871 clinical specimens 771 bacterial and fungal isolates were identified. RESULTS: Most commonly isolated microorganisms were: Pseudomonas aeruginosa (20.3%), Candida species (15%) and Staphylococcus aureus (12.9%). Among the Gram-negative microorganisms P. aeruginosa were mostly resistant to third-generation cephalosporins (71.3-98.1%), while Acinetobacter baumannii were resistant in all cases to piperacillin, ceftazidime and ceftriaxone. Isolates of S. aureus were mostly resistant to penicillin, ampicillin, and methicillin (82-95%), whereas coagulase-negative staphylococci were 98.6% resistant to methicillin and in all cases resistant to ampicillin and tetracycline. CONCLUSION: In order to reduce the emergence and spread of antimicrobial-resistant pathogens in ICUs, monitoring and optimization of antimicrobial use in hospitals are strictly recommended. Therefore local resistance surveillance programs are of most value in developing appropriate therapeutic guidelines for specific infections and patient types.

Automatized PCR evaluation of Mycobacterium tuberculosis complex in respiratory and nonrespiratory specimens.

In this study, Mycobacterium tuberculosis complex isolates recovered from respiratory and nonrespiratory specimens with culture were evaluated using an automatized PCR method. Specimens with suspected tuberculous disease were decontaminated and concentrated using the standard N-acetyl-L-cysteine NaOH method and were inoculated onto glycerol-supplemented Löwenstein-Jensen media and BACTEC B12 vials. Forty-one specimens with typical colonies on solid media and 127 specimens identified as M. tuberculosis complex in a BACTEC system were selected as the study group. As the control group, 46 specimens without growth on either culture media were selected. The PCR results were positive in 33 (80.5%) and 87 (68.5%) samples that were culture-positive on solid and liquid media, respectively. All (100%) culture-negative specimens within the control group were also negative in the COBAS AMPLICOR Mycobacterium tuberculosis (MTB) PCR method. In conclusion, although it is a fast method for identifying M. tuberculosis complex isolates from clinical specimens, the COBAS AMPLICOR MTB PCR method is found to be less sensitive than culture techniques, we propose therefore that it should only be used in combination with culture results in the clinical diagnosis of tuberculosis.

Evaluation of negative results of BacT/Alert 3D automated blood culture system.

Although automated continuous-monitoring blood culture systems are both rapid and sensitive, false-positive and false-negative results still occur. The objective of this study, then, was to evaluate negative results occurring with BacT/Alert 3D blood culture systems. A total of 1032 samples were cultured with the BacT/Alert 3D automated blood culture system, using both aerobic (FA) and anaerobic (FN) [corrected] media, and 128 of these samples yielded positive results. A total of 904 negative blood samples were then subcultured in 5% sheep blood agar, eosin methylene blue, chocolate agar, and sabouraud-dextrose agar. Organisms growing on these subcultures were subsequently identified using both Vitek32 (bioMerieux, Durham, NC) and conventional methods. Twenty four (2.6%) of the 904 subcultures grew on the subculture media. The majority (83.3%) of these were determined to be gram-positive microorganisms. Fourteen (58.3%) were coagulase-negative staphylococci, two (8.3%) were Bacillus spp., one (4.2%) was Staphylococcus aureus, and one (4.2%) was identified as Enterococcus faecium. Streptococcus pneumoniae and Neisseria spp. were isolated together in two (8.3%) vials. Gram-negative microorganisms comprised 12.5% of the subcultures, of which two (8.3%) were found to be Pseudomonas aeruginosa, and one (4.2%) was Pseudomonas fluorescens. The other isolate (4.2%) was identified as Candida albicans. We conclude that the subculture of negative results is valuable in the BacT/Alert 3D system, especially in situations in which only one set of blood cultures is taken.

A prospective epidemiologic survey on the prevalence of onychomycosis and dermatophytosis in male boarding school residents.

Dermatophyte infections and onychomycosis are not usually serious in term of mortality; however, they may have significant clinical consequences such as secondary bacterial infections, chronicity, therapeutic difficulties and esthetic disfigurement in addition to serving as a reservoir of infection. Our aim was to determine the prevalence of onychomycosis and dermatophytosis in a selected high risk group, consisting of male boarding school residents. A total of 410 males inhabiting two houses were evaluated by two dermatologists. In cases of clinical suspicion, appropriate samples were taken for direct microscopy and culture. The results showed that the prevalences of tinea pedis (athlete's foot) and pure pedal onychomycosis were 51.5% (n:211) and 4.4% (n:18), respectively. Thirty cases of those with tinea pedis were complicated by toenail onychomycosis. Tinea cruris was present only in five cases with tinea pedis. Interestingly 71.1% of those with tinea pedis and 45.8% of those with onychomycosis, associated with or without tinea pedis were unaware of their diseases. The most common fungal isolate was Trichophyton rubrum (76.6%) followed by Epidermophyton floccosum (11.6%), T. interdigitale (10.55%). Approximately one third of the cultures from nail specimens yielded pure growths of nondermatophyte moulds or Candida albicans. In conclusion, we found unexpectedly high prevalences of occult athlete's foot and toenail onychomycosis among the male residents of student houses. Our results indicate that health-care workers of such common boarding-houses should be more aware of clinical and subclinical dermatophyte infections and onychomycosis, and have more active approaches to educational measures and management strategies to prevent further infections. To our knowledge, this is the first epidemiologic study on the prevalences of dermatophytosis and onychomycosis in boarding-houses from Turkey.

Synergy tests by E test and checkerboard methods of antimicrobial combinations against Brucella melitensis.

Two different synergy testing methods, the checkerboard and the E test methods, were used to compare the in vitro efficacies of various antimicrobial combinations against 16 Brucella melitensis strains isolated from blood cultures. The rate of agreement of the E test and checkerboard methods was found to be 55%. The most concordant results were found for the streptomycin-doxycycline combination in 12 (75%) tests, in which four strains showed synergistic activity by E test and antagonistic activity by the checkerboard method and in which one strain showed antagonistic activity by both methods. Even though each of these methods uses different conditions and endpoints, the results of both methods frequently agreed.

Cutaneous hyalohyphomycosis and onychomycosis caused by Onychocola canadensis: report of the first case from Turkey.

We present the first Turkish case of skin and nail infection due to Onychocola canadensis in an otherwise healthy farmer who frequently worked barefoot on soil. Cutaneous involvement consisted of scaly and hyperkeratotic lesions resembling tinea pedis, erythematous plaques, and dermal papulonodules of various sizes simulating Majocchi's granuloma. Repeated cultures from nail plates, skin scrapings and needle aspiration materials from papules or nodules all yielded the same mold on Sabouroud dextrose media with and without cycloheximide, trichophyton agar, and potato dextrose agar at 26 degrees C. The causal isolate was identified as Onychocola canadensis Sigler gen. et sp. nov., a slow-growing arthroconidial hyphomycete, on the basis of its colonial and microscopic morphology. While skin lesions were responsive to daily itraconazole in a dose of 200 mg for three months, the onychomycosis was resistant to therapy. To our knowledge, this is the first presentation of O. canadensis as the cause of cutaneous hyalohyphomycosis to date.