Mikrobiyoloji bülteni (MIKROBIYOL BUL )

Publisher: Ankara Mikrobiyoloji Derneği


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    Mikrobiyoloji bülteni, Bulletin of microbiology
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Publications in this journal

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    ABSTRACT: Stenotrophomonas maltophilia, which is a non-fermentative gram-negative bacillus, has an increasing importance in nosocomial and opportunistic infections. Since it exhibits resistance to numerous broad-spectrum antibiotics such as aminoglycosides, beta-lactams and tetracyclines, it may considerably limit empirical treatment options. Trimethoprim-sulfamethoxazole (SXT) is recommended as the first-line therapy in the treatment of S.maltophilia infections thanks to its high potency and usefulness in a range of patients. In recent years, however, studies in different geographical regions have started to report resistance to SXT. In this study, we aimed to investigate the genes sul1, sul2, dfrA9, dfrA10, dfrA20 and class I, class II integron gene cassettes which are known to play role in SXT resistance among SXT-resistant S.maltophilia strains. A total of 618 S.maltophilia strains isolated from various clinical samples of 339 patients between January 2006 and October 2011 at the laboratory of Medical Microbiology Department, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey, were included in the study. The isolates were identified by both conventional methods and the Phoenix automated identification system (Becton Dickinson, USA). SXT resistance was determined in the isolates of 32 patients (32/339, 9.4%) by both the automated system and agar dilution method of them 29 (90.6%) were hospital-acquired, and 3 (9.4%) were community-acquired. The genes which are known as SXT resistance determining genes including sul1, sul2, dfr genes, and class I and class II integron gene cassettes were analyzed by using specific primers with polymerase chain reaction in the 32 SXT-resistant isolates. Subsequently, nucleotide sequence analysis of the amplified materials was performed. As a result of this assay, the presence of class I integron gene cassette and sul1 gene were detected in one isolate. Nucleotide sequence analysis of the gene cassette revealed oxacilinase (oxa2) type of beta-lactamase, an aminoglycoside 6'-N-acetyltransferase [aac(6')-IIc], leading to resistance of aminoglycosides, and a quaternary ammonium compounds resistance gene (qacF), respectively. In conclusion, to best of our knowledge the sequences of class I integron gene cassette including oxa2, aac(6')-IIc, qacF genes were identified in S.maltophilia for the first time. It should be kept in mind that the co-presence of a class I integron gene cassette and the sul1 gene in S.maltophilia may lead to the development of multi-drug resistance and may act as a potential source for the dissemination of resistance.
    Mikrobiyoloji bülteni 04/2014; 48(2):201-12.
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    ABSTRACT: Writing a thesis is mandatory for getting a postgraduate medical degree in Turkey. Publication of the results of the thesis in an indexed journal makes the results available to researchers, however publication rate is usually low. The aim of this retrospective observational study was to investigate the publication rate of Turkish Infectious Diseases and Clinical Microbiology, Medical Microbiology specialty theses and Microbiology doctorate theses in international peer-review journals. On August 17th 2007, the thesis database of the Council of Higher Education of the Republic of Turkey (YOK) where all specialization and doctorate theses are recorded obligatorily, was searched for Infectious Diseases and Clinical Microbiology and Medical Microbiology specialty and Microbiology doctorate theses. Assuming that publication of a thesis would last at least six months, theses dated to February 2007 and after were excluded. The publication rate of those theses was found out by searching Science Citation Index-Expanded database for thesis author and supervisor between August 17-September 12, 2007. Chi-square test was used for statistical analysis. Our search yielded a total of 834 theses dated from 1997 to 2007, however 10 of them were excluded, since they were dated to February 2007 or after. It was found that the overall publication rate was 11.4% (94/824). The publication rates for Microbiology doctorate, Medical Microbiology and Infectious Diseases and Clinical Microbiology specialty theses were 13.7% (34/249), 10.7% (33/309) and 10.2% (27/266), respectively, with no statistical significance (p> 0.05). It was determined that nine (9.6%) of the 94 published theses belonged to 1997-2001 period, whereas 85 (80.4%) were in 2002-2007 period (p< 0.05). The probable reason for this increase was thought to be related with the updated criteria of YOK carried out in 2000 for academic promotions, nevertheless the publication rate of the investigated theses in international peer-review journals was still low. Thesis is an important part of specialty and doctorate education and necessitates intense work. The created knowledge usually contains important data about the country and the world. Publication of the theses supplies dissemination of new knowledge and completes the process of a scientific study. Solutions must be generated to promote the publication of specialty and doctorate theses.
    Mikrobiyoloji bülteni 04/2014; 48(2):341-5.
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    ABSTRACT: Although Salmonella enterica serotype Paratyphi B is the less frequently isolated serotype worldwide and in Turkey, it is the most common serotype in our hospital, with a marked increase in 2007. The purpose of this study was to investigate the antibiotic susceptibility and the extended spectrum beta-lactamase (ESBL) profile, and molecular epidemiology of S. Paratyphi B isolates detected in our hospital microbiology laboratory. Seventy isolates identified as S. Paratyphi B from 109 Salmonella isolates obtained from clinical specimens from different patients between October 2005 and December 2012, were included in the study. In addition to conventional methods, isolates were identified using the Phoenix automated microbiology system (Becton Dickinson, USA). Serotyping of the isolates was performed on the basis of slide agglutination and the Kauffmann-White scheme. The antibiotic susceptibility of the isolates was determined using the BD Phoenix' automated system and disk diffusion test. ESBL enzymes were investigated using the combined disk test, isoelectric focusing, polymerase chain reaction (PCR) and sequence analysis. The molecular epidemiology of the 51 isolates obtained between October 2005 and August 2008 was examined with pulsed-field gel electrophoresis (PFGE) using the XbaI enzyme. S. Paratyphi B isolates were obtained from 70 specimens (46 blood, 16 fecal, 4 bone marrow, 2 urine and 2 wound) each from different patients. Resistance to nalidixic acid was determined in 18.6%, resistance to ampicillin, cefotaxime and cefepime in 2.9% and to ceftazidime and co-trimoxazole in 1.4% of the isolates. ESBL production was detected only in two isolates; in one TEM-1 was accompanied by CTX-M-15 and in the other isolate CTX-M-3 was found. Forty-six of the 51 isolates (90%) were found to be genetically related by PFGE and were placed in cluster A. The distribution of the isolates in cluster A revealed six subtypes as A1 (n= 7), A2 (n= 11), A3 (n= 7), A4 (n= 18), A5 (n= 2) and A6 (n= 1). Three different patterns not related to the cluster A were determined in the remaining five isolates (two were B, one of each was C, D and E). In conclusion, although the rate of antibiotic resistance was low in the S. Paratyphi B isolates in our hospital, rare types of ESBLs such as CTX-M-3 and CTX-M-15 were detected in Salmonellae. As far as the current literature is considered, this is the first report in Turkey of blaCTX-M-15 in Salmonella spp. and blaCTX-M-3 genes in S. Paratyphi B. The results may indicate a possible future threat to the treatment of Salmonella infections. Since most of the isolates were genetically related, this might suggest an epidemic in our region.
    Mikrobiyoloji bülteni 04/2014; 48(2):191-200.
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    ABSTRACT: The host immune response is closely related to the prognosis of disease and viral persistence in hepatitis B (HBV) and hepatitis C virus (HCV) infections. Althought it is well known that cytokines and genetic factors play important roles in the pathogenesis of chronic HBV and HCV infections, the underlying mechanisms are not fully understood. This study was conducted to determine the role of interleukin (IL)-1β, IL-1 receptor antagonist (IL-1RA) and IL-8 gene polymorphisms in chronic hepatitis B and C infections. A total of 361 subjects, 171 with chronic hepatitis B (62 female, 109 male; age range: 18-74 yrs) and 104 with chronic hepatitis C (63 female, 41 male; age range: 25-79 yrs), and a control group of 86 healthy subjects (41 female, 45 male; age range: 18-72 yrs) were included in the study. Following the DNA extractions from peripheral blood leukocytes of the study groups, single nucleotide polymorphisms of IL-1β -31, -511, +3954; IL-1RA and IL-8 -251, -353, -738, -845 gene regions were investigated by using specific primers with real-time PCR method. It was found that the genotype frequency of IL-8 -251 AT (OR: 7.895, p= 0.003) and IL-8 -738 TA (OR: 6.317, p= 0.007) in patients with chronic hepatitis B and the genotype frequency of IL-1β-31 CT (OR: 6.757, p= 0.001), IL-1β -511 CT (OR: 4.060, p= 0.004), IL-8 -251 AT, (OR: 13.622, p= 0.001), IL-8 -738 TA (OR: 14.058, p= 0.001), and IL-8 -845 TC (OR: 2.539, p= 0.004) in patients with chronic hepatitis C was significantly higher than the control group. When the allelic frequency was compared between chronic hepatitis B patients and the control group, it was determined that IL-1β +3954 T allel increased the disease risk 1.5 times (p< 0.05), however, no statistically significant difference was detected for the other allels. It was also determined that IL-8 -845 C allel increased the disease risk 0.6 times in chronic hepatitis C (p< 0.05) and no statistically significant difference was detected for the other allels (p> 0.05). In conclusion, IL-1β -31, -511 and IL-8 -251, -738, -845 gene polymorphisms may play a role in the chronicity of hepatitis B and C infection. In order to determine the importance of this cytokine polymorphisms in hepatitis B and hepatitis C virus infections, large-scale studies with different patient groups such as carriers, chronic hepatitis, cirrhosis, and hepatocellular carcinoma should be conducted to elucidate the molecular mechanisms underlying the disease process.
    Mikrobiyoloji bülteni 04/2014; 48(2):271-82.
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    ABSTRACT: Viruses are the most frequently detected etiologic agents of gastroenteritis seen in small children. In addition to classical gastroenteritis viruses namely rotavirus, norovirus, adenovirus type 40/41, astrovirus and sapovirus, some novel picornaviruses (Aichi virus, parechovirus, enterovirus) that have been identified in parallel to the developments in molecular diagnostic methods, thought to be associated with diarrhea in humans. However, the data are not enough to prove their actual roles in the pathogenesis of gastroenteritis. The aim of this study was to investigate the presence of rotavirus, norovirus, sapovirus, astrovirus, Aichi virus, parechovirus and enterovirus in the stool samples of children with diarrhoea by reverse-transcriptase polymerase chain reaction (RT-PCR). A total of 50 samples from children admitted to our hospital with diarrhoea between June-December 2012 were included in the study. All the patients were under 5 years of age. Routine bacteriological and parasitological examinations of the patients' stool samples were negative. Total RNAs were extracted from each of the samples and cDNAs were obtained by reverse transcription. All cDNAs were investigated first with the internal control (IC) using PCR. Thirty-one of the 50 cDNAs (62%) were found IC positive. Those 31 samples were further investigated in terms of rotavirus group A and C, norovirus (NoV) genogroup GI and GII, sapovirus, astrovirus, Aichi virus, parechovirus and enterovirus by PCR using specific primer pairs. The predicted sized PCR products obtained were cloned into the pBSK cloning vector and were sequenced. Sequences obtained were subjected to a BLAST search with registered sequences in the GenBank database for the confirmation of the PCR product. Out of 31 RNA positive stool specimens, 12 (38.7%) were found positive for five types of the target viruses. NoV GII (6/31, 19.3%) were detected as the most prevalent virus, followed by NoV GI (2/31, 6.5%), rotavirus group A (2/31, 6.5%), astrovirus (1/31, 3.2%) and sapovirus (1/31, 3.2%). The results of this study revealed that the most frequently detected agents were noroviruses (8/50, 16%) followed by rotavirus (2/50, 4%), astrovirus (1/50, 2%) and sapovirus (1/50, 2%). It was concluded that RT-PCR performed with the primers used in this study could be applied effectively for the molecular epidemiological analysis of RNA viruses leading to gastroenteritis. Larger scale studies conducted in different areas for longer time periods and with a larger population size will provide data for the epidemiological properties of agents of viral gastroenteritis.
    Mikrobiyoloji bülteni 04/2014; 48(2):233-41.
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    ABSTRACT: Saccharomyces cerevisiae, known as baker's yeast, is also used as a probiotic agent to treat gastroenteritis by modulating the endogenous flora and immune system. However, since there have been increasing reports of fungemia due to S.cerevisiae and its subspecies S.boulardii, it is recommended that probiotics should be cautiously used in immunosuppressed patients, people with underlying diseases and low-birth weight babies. To emphasize this phenomenon, in this report, a case of S.cerevisiae fungemia developed in a patient given probiotic treatment for antibiotic-associated diarrhea, was presented. An 88-year-old female patient was admitted to our hospital with left hip pain, hypotension, and confusion. Her medical history included hypertension, chronic renal failure, left knee replacement surgery, and recurrent urinary tract infections due to neurogenic bladder. She was transferred to the intensive care unit with the diagnosis of urosepsis. After obtaining blood and urine samples for culture, empirical meropenem (2 x 500 mg) and linezolid (1 x 600 mg) treatment were administered. A central venous catheter (CVC) was inserted and after one day of inotropic support, her hemodynamic parameters were stabilized. The urine culture obtained on admission yielded extended-spectrum beta-lactamase-producing Klebsiella pneumoniae and Escherichia coli. Urine culture was repeated after three days and no bacteria were isolated. On the 4th day of admission she developed diarrhea. Toxin A/B tests for Clostridium difficile were negative. To releive diarrhea, S.boulardii (Reflor 250 mg capsules, Sanofi Aventis, Turkey) was administered twice a day, without opening capsules. Two days later, her C-reactive protein (CRP) level increased from 23.2 mg/L to 100 mg/L without fever. Her blood culture taken from the CVC yielded S.cerevisiae. Linezolid and meropenem therapies were stopped on the 13th and 14th days, respectively, while prophylactic fluconazole therapy was replaced with caspofungin 1 x 50 mg on the fifth day. After seven days of therapy CRP and serum creatinine levels decreased to 9.1 mg/L and 1.2 mg/dl, respectively; and she was discharged from the hospital with improvement. The probiotic capsules were used unopen, thus, it was proposed that S.cerevisiae fungemia originated from translocation from the intestinal mucosa. Since it was not possible to investigate the molecular genetics of the strain isolated from the blood culture and the strain present in the probiotic, a definite conclusion about the origin of the strain could not be reached. It was thought that old age and underlying disease of the patient were the related predisposing factors for S.cerevisiae fungemia. This case emphasized that clinicians should be cautious in case of probiotic application eventhough in encapsulated form, even in immunocompetent patients with a history of long-term hospital stay and use of broad-spectrum antimicrobials since there may be a risk of S.cerevisiae fungemia development.
    Mikrobiyoloji bülteni 04/2014; 48(2):351-5.
  • Mikrobiyoloji bülteni 04/2014; 48(2):356-61.
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    ABSTRACT: Acinetobacter spp. are opportunistic bacterial pathogens primarily associated with hospital-acquired infections and the spread of multidrug resistant Acinetobacter strains is a growing problem in terms of infection control. The aim of this study was to determine the clonal relationship between strains of nosocomial Acinetobacter baumannii by using rep-PCR method. A total of 75 Acinetobacter strains isolated from various clinical samples of the hospitalized patients between October 2011-May 2012 were included in the study. Antibiotic susceptibilities of Acinetobacter isolates were investigated by Kirby-Bauer disk diffusion method according to CLSI guidelines. According to disk diffusion test, the resistance rates for piperacillin, piperacillin-tazobactam, cefepime, ceftazidime, imipenem, meropenem, gentamicin, amikacin, tetracycline, levofloxacin, ciprofloxacin and trimetoprim-sulfamethoxazole were 96%, 96%, 97.3%, 89.3%, 96%, 94.6%, 66.7%, 85.3%, 68%, 82.7%, 97.3% and 89.3% respectively. In this study, 73 (97%) strains were found resistant to three or more than three antibiotics (multidrug resistant). Rep-PCR analysis have shown the presence of eight clones, including two major clones [A (7subtypes), B (3 subtypes)] and six unique clones (C-H). Clone A was found to be the dominant type. Fifty-four (72%) of the 75 Acinetobacter strains belonged to clone A, 13 (17.3%) to clone B, two strains to clone C, D, and one of each to the other clones (E, F, G, H). Clone A was isolated from 71% (20/28), 70% (7/10) and 100% (6/6) of the samples sent from reanimation intensive care unit, surgery ward and internal diseases intensive care units, respectively. The time interval between the first and last strain was eight months. The results of this study indicated an increase in the resistance rates of Acinetobacter strains in our hospital and this increase was attributed to the clonal dissemination of the strains. Strains of the clone A were found to be dominant at the intensive care and other clinics of our hospital. It is contemplated that Acinetobacter strains were scattered as a result of cross transmission and patient transfer among clinics. The rep-PCR method which was used in this study was evaluated as a rapid, easily applicable and successful procedure for epidemiological studies. Clonal distribution of resistant strains in the hospital environment emphasizes the significance of infection control measures.
    Mikrobiyoloji bülteni 04/2014; 48(2):316-24.
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    ABSTRACT: Cryptococcus neofomans is an encapsulated yeast-like fungus that causes life-threatening infections, especially in immunosuppresive patients. C.neoformans infection is believed to be acquired via inhalation of aerosolized particles from the environment. Avian guano, decaying tree hollows and soil are the related known environmental niches. Brown pigmented yeast growth from the precursors in growth media is an important step for the identification and isolation of C.neoformans. Seeds of plants in nature are preferred owing to easy accessibility and low costs for the preperation of such media. Guizotia abysinicca (Niger seed) as Staib agar, Helianthus annus (Sunflower) as Pal's medium, Brassica nigra (Mustard) agar, tobacco agar, Mucuna pruriens (Velvet bean) seed agar, Perilla frutescens (Beefsteak plant) seed agar, Rubus fruticosus (Blackberry) agar and ground red hot pepper agar are pigment-based selective media for the differantiation of C.neoformans. The aim of this study was to observe the pigment production of C.neoformans in a new medium based on eggplant (Solanum melongena) and also to compare its performance with the simplified Staib, Pal's and tobacco agar for isolation from the environment. Three different eggplant-based medium (S.melongena Melanzaza viserba, S.melongena Pinstripe F1 and S.ovigerum Ivory F1) were included in the study. Pigment-forming eggplant medium, simplified Staib agar, Pal's agar and tobacco agar were used for the cultivation of the environmental swabbed samples from 19 Eucalyptus camaldulensis trunk hollows in continuous colonization region. While pigment formation were observed with S.melongena Melanzaza viserba and S.melongena Pinstripe F1 containing media, S.ovigerum Ivory F1 medium was found to be non-reactive. In colonization area (Gökova-Akyaka, Turkey), 11 (57.9%) out of 19 E.camaldulensis samples were positive with simplified Staib agar, Pal's agar and eggplant agar while 10 (52.6%) of them are positive with tobacco agar. C.neoformans colony forming unit (cfu) per plate were found as 51, 57 and 48 (median values) on simplified Staib agar, Pal's agar and eggplant agar, respectively, while tobacco agar has lower performance with 33 cfu/petri. No statistically significant difference were found between simplified Staib agar, Pal's agar and eggplant agar's performances for C.neoformans isolations from the nature (p=0.71). In conclusion, easily prepared eggplant agar is as functional as widely used media such as simplified Staib agar and Pal's agar for the isolation of C.neoformans from the natural environment.
    Mikrobiyoloji bülteni 04/2014; 48(2):292-9.
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    ABSTRACT: Myiasis is defined as a parasitic infestation of tissues and organs in living vertebrates with dipterous larvae. Infestation with dipterous larvae can occur when flies deposit their eggs or first stage larvae on the host's tissues. Myiasis is seen more frequently in tropical and subtropical countries, especially in rural regions where people are in close contact with animals. Diagnosis of myiasis depends on the demonstration of larvae on the host's tissues or organs. Correct identification of the larvae is important for the initiation of appropriate treatment and establishment of preventive measures. In this report, a case of diabetic wound ulcer complicated with myiasis was presented. A 68 years old male patient with a diabetic wound was admitted to the Hacettepe University Department of Infectious Diseases and Clinical Microbiology, Ankara in July 2013. The patient had a history of insulin-dependent diabetes mellitus over 10 years and hypertension, coronary artery disease and chronic renal failure for several years. His left leg under the knee and his right toe were amputated because of diabetic foot. The infection on his right heel had started as a single, painless ulcer 5 months ago. He had medical advice from a health care provider and used ampicilin-sulbactam for 3 months. However, the wound progressed in spite of the treatment and upon admission to our hospital, he was hospitalized with the diagnosis of diabetic foot ulcer. The C-reactive protein, sedimentation rate, white blood cell count and HbA1c values were found to be high. Piperacillin-tazobactam therapy was started and debridement of necrotic tissue was planned. During the debridement prosedure larvae were observed under the necrotic tissue. Two larvae were collected and delivered to the parasitology laboratory. After morphological examination the larvae washed in distilled water and killed in 70% alcohol and they were taken to the Ankara University Veterinary Faculty, Department of Parasitology for identification. The morphological characteristics of cephalopharyngeal skeleton, anterior spiracles and slits of the posterior spiracles were examined and the larvae were identified as third stage of Sarcophaga spp. Diabetes, coronary artery disease and low socio-economic level as well as the presence of an open, neglected wound were attributed as the most important predisposing factors that led to the development of myiasis in this patient. It should be kept in mind that the diabetic patients with open wounds may develop myiasis especially in the summer months and larvae can cause progressive wound infection.
    Mikrobiyoloji bülteni 04/2014; 48(2):356-61.
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    ABSTRACT: Pneumococci are one of the most common causes of bacterial meningitis in children. It's also responsible for the other invasive pneumococcal diseases (IPD) including bacteremia and pneumonia worldwide. Unvaccinated children are more prone to IPD. Although IPD tend to have a higher prevalence under 2 years of age and in children with primary/secondary immunodeficiencies, and various predisposing factors, older age groups with no underlying diseases also experience IPD. In this report, a pediatric case diagnosed with meningitis due to Streptococcus pneumoniae serotype 35F with no underlying condition and no history of pneumococcal vaccination was presented. An 11-year-old male patient was admitted to the hospital with the complaints of high (39.4°C) fever, headache, vomiting and sleepiness. On the basis of findings from physical examination and laboratory results, the patient was prediagnosed as bacterial meningitis and empirical ceftriaxone and vancomycin therapy was initiated. The cerebrospinal fluid culture of the patient yielded penicillin-susceptible pneumococci and the isolate was identified as serotype 35F by quellung reaction. Vancomycin treatment discontinued depending on the culture result, and the patient fully recovered with 14-days of ceftriaxone therapy without any complications during his follow-ups. Although effective antibiotics are available for IPD, vaccination is indispensable considering the high mortality rates. Seven serotypes (1, 5, 6A, 6B, 14, 19F, 23F) which are currently included in the vaccine, were the most common serotypes related to IPD globally. After mass infant vaccination has been introduced, invasive pneumococcal diseases due to the vaccine serotypes have tended to decrease in both vaccinated young children and non-vaccinated age groups due to herd immunity. Nevertheless, non-vaccine serotypes (NVTs) have emerged as the agents of IPD as a result of serotype replacement. 13-valent pneumococcal conjugate vaccine (PCV13) was introduced in April, 2011 nationwide in our country. This case report was about a patient who had developed meningitis after the introduction of PCV13. There has been no data evaluating the pneumococcal serotype distribution after PCV13 in our country yet. On February, 2013, the Advisory Committee on Immunization Practices (ACIP) recommended routine use of PCV13 for children aged 6-18 years with underlying disease conditions. However, there is no recommendation for children with no underlying diseases in this age group. Vaccination can be extended for otherwise healthy children older than 6 years of age because of increasing trends in incidence of IPD both with vaccine and NVTs like serotype 35F. Recent studies have indicated the emergence of serotype 35F as a cause of IPD in children over 6 years of age and there have been also reports of IPD cases with 35F after the introduction of PCV13. Although serotype 35F is not yet a well-known serotype causing IPD, it might probably gain importance owing to its increasing frequency and virulence and might attract attention to be considered for inclusion in the future pneumococcal vaccines.
    Mikrobiyoloji bülteni 04/2014; 48(2):346-50.
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    ABSTRACT: Health institutions use the accreditation process to achieve improvement across the organization and management of the health care system. An ISO 15189 quality and efficiency standard is the recommended standard for medical laboratories qualification. The "safety and accommodation conditions" of this standard covers the requirement to improve working conditions and maintain the necessary safety precautions. The most inevitable precaution for ensuring a safe environment is the creation of a clean and orderly environment to maintain a potentially safe surroundings. In this context, the 5S application which is a superior improvement tool that has been used by the industry, includes some advantages such as encouraging employees to participate in and to help increase the productivity. The main target of this study was to implement 5S methods in a clinical laboratory of a university hospital for evaluating its effect on employees' satisfaction, and correction of non-compliance in terms of the working environment. To start with, first, 5S education was given to management and employees. Secondly, a 5S team was formed and then the main steps of 5S (Seiri: Sort, Seiton: Set in order, Seiso: Shine, Seiketsu: Standardize, and Shitsuke: Systematize) were implemented for a duration of 3 months. A five-point likert scale questionnaire was used in order to determine and assess the impact of 5S on employees' satisfaction considering the areas such as facilitating the job, the job satisfaction, setting up a safe environment, and the effect of participation in management. Questionnaire form was given to 114 employees who actively worked during the 5S implementation period, and the data obtained from 63 (52.3%) participants (16 male, 47 female) were evaluated. The reliability of the questionnaire's Cronbach's alpha value was determined as 0.858 (p< 0.001). After the implementation of 5S it was observed and determined that facilitating the job and setting up a safe environment created a statistically significant effect on employees, and some sufficient satisfaction was observed. In addition, the non-conformity score, which was identified in the laboratory during the previous years, was significantly reduced at a rate of 69.7% after the implementation of 5S. 5S practices have successfully contributed to the establishment and to the sustainability of laboratory safety systems in the first public ISO 15189 accredited public clinical laboratory in Turkey. It is concluded that 5S methods can be used as an effective improvement tool in order to maintain a safe environment, to facilitate the job, and to encourage employees to participate in the management process.
    Mikrobiyoloji bülteni 04/2014; 48(2):300-10.
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    ABSTRACT: Early and accurate detection of tuberculosis (TB) is a global priority for TB control. In order to obtain results in a short period of time, nucleic acid amplification tests are increasingly used worldwide for the rapid diagnosis of tuberculosis. The Xpert MTB/RIF® (Cepheid, USA) is a commercially available, real-time PCR-based assay, which can detect both TB and resistance to rifampicin directly in clinical samples. The aim of this study was to evaluate the performance of Xpert MTB/RIF assay for M.tuberculosis detection in pulmonary and extrapulmonary clinical samples in routine laboratory practice in Turkey, an intermediate-prevalence setting. A total of 2639 clinical specimens, 1611 of which were pulmonary and 1028 were extrapulmonary, were included in the study. The results of Xpert MTB/RIF assay were evaluated by comparing the results with those obtained by culture [BACTEC MGIT 960 (Becton Dickinson, USA) and Löwenstein Jensen medium]. Overall sensitivity, specificity, positive and negative predictive values of Xpert MTB/RIF assay were determined as 73.9%, 98.6%, 79.6% and 98.1%, respectively. These values were calculated as 80.8%, 98.8%, 84.9% and 98.4% for pulmonary specimens, and 58.2%, 98.4%, 66.7% and 97.7% for extrapulmonary specimens. The sensitivity and specificity were 100% and 58.1%, respectively, for acid-fast bacilli (AFB) smear-positive specimens, 39.7% and 99.1%, respectively for smear-negative specimens. The sensitivity and specificity were 100% and 76.2% for smear-positive pulmonary specimens; 100% and 20% for smear-positive extrapulmonary specimens; 47.8% and 99.1% for smear-negative pulmonary specimens; and 28.2% and 99.2% for smear-negative extrapulmonary specimens, respectively. The sensitivity and specificity of microscopic examination were found to be 56.7% and 98.7% for all specimens; 63.2% and 98.6% for pulmonary specimens; and 41.8% and 99% for extrapulmonary specimens, respectively. Rifampicin resistance was detected by Xpert MTB/RIF assay in only two specimens, however, rifampicin resistance was failed to be detected by BACTEC MGIT 960 TB method in one of these samples. Xpert MTB/RIF assay appeared to be a reliable method for the diagnosis of TB for AFB smear-positive samples, but less sensitive for smear-negative samples, particularly for extrapulmonary samples which include low numbers of bacilli. However, we concluded that the MTB/RIF is a useful assay for rapid diagnosis of tuberculosis, considering that the results can be given in the same day of sample collection and the assay is superior in sensitivity than microscopic examination.
    Mikrobiyoloji bülteni 04/2014; 48(2):223-32.
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    ABSTRACT: Acinetobacter baumannii which is an opportunistic pathogen leading to nosocomial epidemics, exhibit high rates of antimicrobial resistance. Treatment of Acinetobacter infections is a challenge since most of the isolates are multiple antibiotic resistant. The aim of this study was to investigate minimum inhibitory concentrations (MICs) of sulbactam, imipenem, meropenem, and cefoperazone and in vitro synergistic activity of sulbactam in combination with imipenem, meropenem and cefoperazone against A.baumannii isolates of hospitalized patients. Forty A.baumannii strains isolated from various clinical specimens and found to be resistant to carbapenems by disc diffusion method, were included in the study. The isolates were identified by conventional methods and VITEK 2 (bioMerieux, France) automated identification system. MICs of sulbactam, imipenem, meropenem, and cefoperazone were determined by the broth microdilution method according to the standards of CLSI and in vitro synergy test was performed using the checkerboard microdilution method. Synergistic, partial synergistic, additive, indifferent and antagonistic effects of drug combinations were evaluated with the fractional inhibitory concentration index (FICI). Interpretation of the FICI was as follows: ≤ 0.5 synergy; > 0.5 to < 1 partial synergy; 1 additive; > 1 to < 4 indifference; and ≥ 4 antagonism. Forty A.baumannii isolates were resistant to imipenem and cefoperazone, but two were susceptible, seven were moderately susceptible and 31 were resistant to meropenem with the microdilution method. MIC values of the isolates for sulbactam were found to be 4 μg/ml in two, 8 μg/ml in five, 16 μg/ml in three, 32 μg/ml in 13, 64 μg/ml in three, 128 μg/ml in six and > 128 μg/ml in eight isolates. According to the FICI; imipenem/sulbactam combination exhibited synergy in 18 (45%), partial synergy in 4 (10%) and indifferent effect in 2 (5%) isolates, the combination of meropenem and sulbactam showed synergy in 19 (48%), partial synergy in 3 (7.5%), and indifferent effect in 3 (7.5%) isolates, the combination of cefoperazone/sulbactam demonstrated synergy in 18 (45%), partial synergy in 2 (5%), and indifferent effect in 2 (5%) isolates. There was no antagonistic effect with the tested combinations. In conclusion, MIC values of sulbactam were generally high in carbapenem-resistant A.baumannii strains. However, synergistic effect was detected in approximately half of the strains with the sulbactam/carbapenem combinations. The data obtained in this study should be supported by further advanced in vitro and clinical studies to predict the accurate clinical efficacy of sulbactam containing combinations on A.baumannii infections.
    Mikrobiyoloji bülteni 04/2014; 48(2):311-5.
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    ABSTRACT: Acute bronchiolitis, mostly seen in infants and younger children, is a lower respiratory tract infection frequently caused by viral agents. We aimed to determine the frequency of a broad panel of respiratory viruses including human bocavirus (HBoV) and to assess the clinical characteristics of acute bronchiolitis in a group of children under 24 months of age. A total of 62 children (45 male, 17 female; age range: 0-2 years) with the initial diagnosis of acute bronchiolitis and 33 healthy children (21 male, 12 female; age range: 0-2 years) as control group who were admitted to the Pediatrics Department of Mersin University Hospital, southern Turkey, from January to July 2010 were included in the study. Nasopharyngeal aspirates were collected from the study groups and the detection of respiratory viruses [respiratory syncytial virus (RSV) A & B; rhinovirus (RV); human metapneumovirus (hMPV) A & B; influenza virus type A [H1N1, H3N2, H1N1v], B & C; parainfluenza virus (PIV) type 1, 2, 3 & 4A/B; adenovirus (AdV); HBoV; coronavirus (CoV 229E); enterovirus (EV)], were performed by using a commercial system namely CLART®Pneumovir (Clinical Array Technology, Genomica, Spain) based on the principle of multiplex polymerase chain reaction (M-PCR) and DNA microarray. Demographic features, clinical and laboratory findings of the patients, treatment protocols and the relationship between the length of hospitalization and the viral agents determined were also evaluated. Of the 62 samples collected from bronchiolitis cases, at least one virus was detected in 52 (83.9%) and viral co-infections were detected in 31 (50%) of them. Including the co-infections, RSV was the most commonly identified virus (n= 21; 33.9%), followed by influenza A [H1N1] (n= 18; 29%), RV (n= 18; 29%), hMPV (n= 13; 21%), PIV (n= 10; 16.1%), AdV (n= 5; 8%), HBoV (n= 3; 4.8%) and EV (n= 1; 1.6%). Of the 33 samples from healthy children, at least one virus was detected in 21 (63.6%) and viral co-infections were detected in seven (21.2%) samples. Including the co-infections, the most commonly detected virus was RV (n= 10; 30.3%), followed by influenza A [H1N1] (n= 6; 18.1%), AdV (n= 6; 18.1%), RSV (n= 4; 12.1%) and PIV (n= 3; 9%), however HBoV and hMPV were not detected in the control group. The differences of demographic features (age, gender, history of atopy, exposure of smoking, length of breast-feeding, presence of school-age sibling) and frequency of virus detection (83.9% and 63.6%, respectively) between the patient and control groups were not statistically significant (p> 0.05). The most common complaints of patients on admission were cough (100%), runny nose (82.3%) and respiratory difficulty (71%), whereas fever was present in 21 (33.9%) patients. The most common findings on physical examination were prolonged expirium (98.4%), rhonchi (98.4%), rales (80.6%), tachypnea (71%) and tachycardia (67.7%). Pulmonary graphies revealed that diffuse air trappings were more common in virus-associated bronchiolitis (36/52; 69.2%) cases, on the other hand infiltrations were more common (6/10; 60%) in patients who were virus-negative (p< 0.05). The demographic features, clinical and laboratory findings, clinical severity scores, hospitalization rates and duration of hospitalizations in bronchiolitis cases did not show statistically significant differences between the viral agents (p> 0.05 for each parameter). However the rates of antibiotic and steroid use in hospitalized patients (24/34 and 5/34, respectively) were significantly higher than those of outpatients (7/28 and 0/28, respectively) (p= 0.001 and p= 0.03). Our data indicated a high rate (~84%) of respiratory viruses in children with bronchiolitis in the Mersin province and the detection of hMPV (21%) and HBoV (4.8%) only in the patient group encouraged their roles in the etiology of acute brochiolitis. It was concluded that viral etiology should be investigated in selected cases to prevent unnecessary antibiotic treatment and to initiate appropriate antiviral therapy when necessary.
    Mikrobiyoloji bülteni 04/2014; 48(2):242-58.
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    ABSTRACT: Elimination of measles and rubella until the end of 2015 in parallel with the "World Health Organization (WHO) Europe Region's Measles Elimination" work-up has been targetted and "Measles Elimination Program'' has been carried out since 2002 in Turkey. Due to the routine vaccination programmes the number of the vaccinated children have increased and epidemic incidences have been falling. However, imported measles cases from Europe and other neighboring countries have been observed in Turkey in the recent two years. Patients who applied to Dr. Sami Ulus Maternity and Children's Training and Research Hospital with a pre-diagnosis of measles between December 2012 and April 2013 were screened in this study. Seventy-eight patients who match the clinical definition of the disease (> 38°C fever and maculopapular rash and cough or nasal discharge or conjunctivitis) were evaluated. Forty-four children (25 male, 19 female; age range: 4-191 months, mean age: 58.6 ± 59.5 months) with a positive measles IgM test result were taken into consideration and the epidemiological and clinical features of these children were evaluated. In addition to fever and rash, cough, nasal discharge and conjunctivitis were seen in 36 (82%), 24 (55%), and 18 (41%) patients, respectively. Thirty five (80%) patients were diagnosed in December, 6 (14%) in January, 2 (4%) in February, and 1 (2%) in March. All patients included in the study were unvaccinated or too young to be vaccinated according to the routine vaccination calendar. The index case was a three-year old unvaccinated girl who had a history of contact with the Syrian neighborhoods. During the study period; following contact with the index case, two doctors (born in 1986 with a history of single dose of vaccination at ninth month) and three children (without vaccination) were also diagnosed as measles. Eight (18%) patients were hospitalized because of complications. Four (50%) of them had pneumonia and the other four (50%) had lack of oral feeding and dehydration. Average duration of hospitalization for patients was 4 ± 1.7 (range: 2-6) days and all patients were discharged with full recovery. For molecular typing, viral RNAs were isolated from urine samples of two of the measles IgM positive patients, subjected to sequence analysis of 450 nucleotides comprising the most variable C-terminal region of the nucleoprotein (N) gene. Phylogenetic analysis revealed that those two strains belonged to genotype D8. This study represented the involvement of measles virus genotype D8 in an outbreak in Turkey for the first time. During a measles epidemic, following the index case; medical personnel should be informed about possible, probable, and definite case definitions and should apply for appropriate triage or fast-track (rapidly examination) if necessary, and routine announcements should be made precisely and accurately at proper times and unvaccinated medical personnel and any people in touch with the patient should be vaccinated. In order to reach the elimination goal declared by European WHO for 2015, susceptible populations should be identified and vaccinated in Turkey to obtain sufficient herd immunity for preventing outbreaks.
    Mikrobiyoloji bülteni 04/2014; 48(2):259-70.
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    ABSTRACT: Scedosporium apiospermum is a saprophytic fungus which is isolated worldwide in soil, fertilizers, polluted water, rotten vegetables, and other natural environments. It is the cause of mycetoma, a subcutaneous infection, characterized by granule formation. It may also cause severe local or diffuse infections in immunosuppressive patients. S.apiospermum-induced arthritis, endocarditis, keratitis, scleritis, endophthalmitis, meningitis, osteomyelitis, otomycosis, onychomycosis, chronic prostatitis, peritonitis, esophagitis, renal infection, and hepatosplenic abscess have been previously reported in the literature. Possible risk factors of fungal keratitis, one of the major causes of fungal ocular infection, include ocular injury, long-term therapy with topical or systemic steroids, immunosuppressive agents, and underlying diseases such as pre-existing corneal surface abnormality and diabetes mellitus, and wearing contact lenses. We paid great attention to the case report presented by Kalkan Akçay E et al. titled "Fungal keratitis caused by Scedosporium apiospermum: first report from Turkey", which was published in the October 2013 issue of Bulletin of Microbiology [Mikrobiyol Bul 2013; 47(4): 727-33]. Although it is deemed as the first case report of S.apiospermum-related fungal keratitis in Turkey, there were several previous case reports of ocular infections associated with this type of fungus in Turkey, including those of Yucel A titled "An eye mycosis caused by Scedosporium apiospermum (Monosporium apiospermum)" published in 1989, Kiratli et al. titled "Scedosporium apiospermum chorioretinitis" in 2001, Saracli et al. titled "Scedosporium apiospermum keratitis treated with itraconazole" in 2003 and Erdem et al. titled "Clinical follow up of a keratomycosis case with total corneal melting" in 2005. In conclusion, it should be highlighted that the report of Kalkan Akcay et al. is not the first case report of Scedosporium apiospermum-related fungal keratitis in Turkey. We believe, hence, that correction of this misinformation would be beneficial for further studies.
    Mikrobiyoloji bülteni 04/2014; 48(2):362-3.