Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes.

Genotype-fitness maps of evolution have been well characterized for biological components, such as RNA and proteins, but remain less clear for systems-level properties, such as those of metabolic and transcriptional regulatory networks. Here, we take multi-omics measurements of 6 different E. coli strains throughout adaptive laboratory evolution (ALE) to maximal growth fitness. The results show the following: (i) convergence in most overall phenotypic measures across all strains, with the notable exception of divergence in NADPH production mechanisms; (ii) conserved transcriptomic adaptations, describing increased expression of growth promoting genes but decreased expression of stress response and structural components; (iii) four groups of regulatory trade-offs underlying the adjustment of transcriptome composition; and (iv) correlates that link causal mutations to systems-level adaptations, including mutation-pathway flux correlates and mutation-transcriptome composition correlates. We thus show that fitness landscapes for ALE can be described with two layers of causation: one based on system-level properties (continuous variables) and the other based on mutations (discrete variables). IMPORTANCE Understanding the mechanisms of microbial adaptation will help combat the evolution of drug-resistant microbes and enable predictive genome design. Although experimental evolution allows us to identify the causal mutations underlying microbial adaptation, it remains unclear how causal mutations enable increased fitness and is often explained in terms of individual components (i.e., enzyme rate) as opposed to biological systems (i.e., pathways). Here, we find that causal mutations in E. coli are linked to systems-level changes in NADPH balance and expression of stress response genes. These systems-level adaptation patterns are conserved across diverse E. coli strains and thus identify cofactor balance and proteome reallocation as dominant constraints governing microbial adaptation.

Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli.

Previously, Escherichia coli was engineered to produce isobutyl acetate (IBA). Titers greater than the toxicity threshold (3 g/L) were achieved by using layer-assisted production. To avoid this costly and complex method, adaptive laboratory evolution (ALE) was applied to E. coli for improved IBA tolerance. Over 37 rounds of selective pressure, 22 IBA-tolerant mutants were isolated. Remarkably, these mutants not only tolerate high IBA concentrations, they also produce higher IBA titers. Using whole-genome sequencing followed by CRISPR/Cas9 mediated genome editing, the mutations (SNPs in metH, rho and deletion of arcA) that confer improved tolerance and higher titers were elucidated. The improved IBA titers in the evolved mutants were a result of an increased supply of acetyl-CoA and altered transcriptional machinery. Without the use of phase separation, a strain capable of 3.2-fold greater IBA production than the parent strain was constructed by combing select beneficial mutations. These results highlight the impact improved tolerance has on the production capability of a biosynthetic system.

A biochemically-interpretable machine learning classifier for microbial GWAS.

Current machine learning classifiers have successfully been applied to whole-genome sequencing data to identify genetic determinants of antimicrobial resistance (AMR), but they lack causal interpretation. Here we present a metabolic model-based machine learning classifier, named Metabolic Allele Classifier (MAC), that uses flux balance analysis to estimate the biochemical effects of alleles. We apply the MAC to a dataset of 1595 drug-tested Mycobacterium tuberculosis strains and show that MACs predict AMR phenotypes with accuracy on par with mechanism-agnostic machine learning models (isoniazid AUC = 0.93) while enabling a biochemical interpretation of the genotype-phenotype map. Interpretation of MACs for three antibiotics (pyrazinamide, para-aminosalicylic acid, and isoniazid) recapitulates known AMR mechanisms and suggest a biochemical basis for how the identified alleles cause AMR. Extending flux balance analysis to identify accurate sequence classifiers thus contributes mechanistic insights to GWAS, a field thus far dominated by mechanism-agnostic results.

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens.

The evolution of antimicrobial resistance (AMR) poses a persistent threat to global public health. Sequencing efforts have already yielded genome sequences for thousands of resistant microbial isolates and require robust computational tools to systematically elucidate the genetic basis for AMR. Here, we present a generalizable machine learning workflow for identifying genetic features driving AMR based on constructing reference strain-agnostic pan-genomes and training random subspace ensembles (RSEs). This workflow was applied to the resistance profiles of 14 antimicrobials across three urgent threat pathogens encompassing 288 Staphylococcus aureus, 456 Pseudomonas aeruginosa, and 1588 Escherichia coli genomes. We find that feature selection by RSE detects known AMR associations more reliably than common statistical tests and previous ensemble approaches, identifying a total of 45 known AMR-conferring genes and alleles across the three organisms, as well as 25 candidate associations backed by domain-level annotations. Furthermore, we find that results from the RSE approach are consistent with existing understanding of fluoroquinolone (FQ) resistance due to mutations in the main drug targets, gyrA and parC, in all three organisms, and suggest the mutational landscape of those genes with respect to FQ resistance is simple. As larger datasets become available, we expect this approach to more reliably predict AMR determinants for a wider range of microbial pathogens.

Assessment of novel biomarkers: sTREM-1, pentraxin-3 and pro-adrenomedullin in the early diagnosis of neonatal early onset sepsis.

BACKGROUND: Early onset bacterial sepsis in neonates (EOS) is recognized as an important health condition. Early diagnosis is crucial. However, blood culture results are released in 48-72 hours. Many biomarkers have been investigated but none have been accepted as the gold standard. This study aimed to investigate the diagnostic value of the molecules: soluble form of triggering receptor expressed on myeloid cells-1 (sTREM-1), pentraxin-3 (PTX-3) and pro adrenomedullin (pro-ADM) in EOS and compare with currently used biomarkers. METHODS: In this multicenter prospective study, patients were enrolled from different NICUs around the Turkey. Patient data were collected via web-based registry system from attending centers. Neonates, hospitalized with a suspicion of EOS were enrolled. Blood culture and routine blood tests were collected and a serum sample was obtained and kept in - 80°C for studying the molecules. According to laboratory results, patients were divided into three groups as; proven sepsis, clinical sepsis and control group. Groups were compared in terms of demographic, clinical and laboratory findings. The primary outcome of the study was to assess any difference between groups in terms of the diagnostic value of the markers aforementioned. RESULTS: A total of 130 patients were enrolled; proven sepsis (n = 36), clinical sepsis (n = 53) and control (n = 41) groups. Groups were similar in terms of demographic findings; mean WBC (P = 0.445), procalcitonin (PCT) (P = 0.083) and IL-6 (P = 0.814) levels. Mean C-reactive protein (CRP) level was significantly higher in clinical sepsis and proven sepsis groups compared to control group (P < 0.001). Mean PTX-3 (P = 0.547), pro-ADM (P = 0.766) and sTREM-1 (P = 0.838) levels were similar between groups. CONCLUSION: These promising molecules failed to help in early diagnosis of EOS. Their relation to correlation with disease progression may make more sense as they seem to be expressed in higher amounts with the progression of the disease in previous studies. CRP was the most frequently used biomarker for detecting the sepsis in our study population.

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance.

Mycobacterium tuberculosis is a serious human pathogen threat exhibiting complex evolution of antimicrobial resistance (AMR). Accordingly, the many publicly available datasets describing its AMR characteristics demand disparate data-type analyses. Here, we develop a reference strain-agnostic computational platform that uses machine learning approaches, complemented by both genetic interaction analysis and 3D structural mutation-mapping, to identify signatures of AMR evolution to 13 antibiotics. This platform is applied to 1595 sequenced strains to yield four key results. First, a pan-genome analysis shows that M. tuberculosis is highly conserved with sequenced variation concentrated in PE/PPE/PGRS genes. Second, the platform corroborates 33 genes known to confer resistance and identifies 24 new genetic signatures of AMR. Third, 97 epistatic interactions across 10 resistance classes are revealed. Fourth, detailed structural analysis of these genes yields mechanistic bases for their selection. The platform can be used to study other human pathogens.

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions.

BACKGROUND: The efficacy of antibiotics against M. tuberculosis has been shown to be influenced by experimental media conditions. Investigations of M. tuberculosis growth in physiological conditions have described an environment that is different from common in vitro media. Thus, elucidating the interplay between available nutrient sources and antibiotic efficacy has clear medical relevance. While genome-scale reconstructions of M. tuberculosis have enabled the ability to interrogate media differences for the past 10 years, recent reconstructions have diverged from each other without standardization. A unified reconstruction of M. tuberculosis H37Rv would elucidate the impact of different nutrient conditions on antibiotic efficacy and provide new insights for therapeutic intervention. RESULTS: We present a new genome-scale model of M. tuberculosis H37Rv, named iEK1011, that unifies and updates previous M. tuberculosis H37Rv genome-scale reconstructions. We functionally assess iEK1011 against previous models and show that the model increases correct gene essentiality predictions on two different experimental datasets by 6% (53% to 60%) and 18% (60% to 71%), respectively. We compared simulations between in vitro and approximated in vivo media conditions to examine the predictive capabilities of iEK1011. The simulated differences recapitulated literature defined characteristics in the rewiring of TCA metabolism including succinate secretion, gluconeogenesis, and activation of both the glyoxylate shunt and the methylcitrate cycle. To assist efforts to elucidate mechanisms of antibiotic resistance development, we curated 16 metabolic genes related to antimicrobial resistance and approximated evolutionary drivers of resistance. Comparing simulations of these antibiotic resistance features between in vivo and in vitro media highlighted condition-dependent differences that may influence the efficacy of antibiotics. CONCLUSIONS: iEK1011 provides a computational knowledge base for exploring the impact of different environmental conditions on the metabolic state of M. tuberculosis H37Rv. As more experimental data and knowledge of M. tuberculosis H37Rv become available, a unified and standardized M. tuberculosis model will prove to be a valuable resource to the research community studying the systems biology of M. tuberculosis.

Tetanus in adults: results of the multicenter ID-IRI study.

Tetanus is an acute, severe infection caused by a neurotoxin secreting bacterium. Various prognostic factors affecting mortality in tetanus patients have been described in the literature. In this study, we aimed to analyze the factors affecting mortality in hospitalized tetanus patients in a large case series. This retrospective multicenter study pooled data of tetanus patients from 25 medical centers. The hospitals participating in this study were the collaborating centers of the Infectious Diseases International Research Initiative (ID-IRI). Only adult patients over the age of 15 years with tetanus were included. The diagnosis of tetanus was made by the clinicians at the participant centers. Izmir Bozyaka Education and Research Hospital's Review Board approved the study. Prognostic factors were analyzed by using the multivariate regression analysis method. In this study, 117 adult patients with tetanus were included. Of these, 79 (67.5%) patients survived and 38 (32.5%) patients died. Most of the deaths were observed in patients >60 years of age (60.5%). Generalized type of tetanus, presence of pain at the wound area, presence of generalized spasms, leukocytosis, high alanine aminotransferase (ALT) and C-reactive protein (CRP) values on admission, and the use of equine immunoglobulins in the treatment were found to be statistically associated with mortality (p < 0.05 for all). Here, we describe the prognostic factors for mortality in tetanus. Immunization seems to be the most critical point, considering the advanced age of our patients. A combination of laboratory and clinical parameters indicates mortality. Moreover, human immunoglobulins should be preferred over equine sera to increase survival.

Are serum leptin levels a prognostic factor in advanced lung cancer?

AIM: The aim of the present study was to evaluate pre-treatment concentrations of leptin in patients with advanced lung cancer and to investigate possible associations between their levels and clinicopathological variables, response to therapy and overall survival. MATERIAL AND METHODS: There are 71 previously untreated patients with cytological or histological evidence of primary lung cancer who were admitted to the oncology department between November 2013 and August 2014. Forty-five healthy individuals with age, sex and BMI matching the lung cancer patients, were recruited to take part in the study as a control group. Leptin levels were measured quantitatively by using a microELISA kit. RESULTS: The serum leptin levels at diagnosis were significantly lower in lung cancer patients than those in control subjects (4.75±4.91 ng/ml, 9.67±8.02 ng/ml; p<0.001). We did not find any significant difference in leptin values related to clinicopathological parameters such as ECOG PS, weight loss, histological type, disease stage and TNM classification. Nevertheless, we demonstrated a significant correlation between serum leptin levels and BMI in lung cancer patients (correlation coefficient: 0.303; p>0.010). The analysis of serum leptin values did not show any association with the overall survival of the patients. CONCLUSION: Our results showed that the serum leptin level has no prognostic indications in advanced lung cancer patients. Leptin is decreased in lung cancer, and there is lack of correlation with tumour­related factors including prognosis. Therefore, leptin is not a useful clinical marker in lung cancer (Tab. 2, Fig. 2, Ref. 22).

Assessment of Palliative Care in Lung Cancer in Turkey.

OBJECTIVE: To investigate the symptoms of lung cancer in Turkey and to evaluate approaches to alleviate these symptoms. SUBJECTS AND METHODS: This study included 1,245 lung cancer patients from 26 centers in Turkey. Demographic characteristics as well as information regarding the disease and treatments were obtained from medical records and patient interviews. Symptoms were evaluated using the Edmonton Symptom Assessment Scale (ESAS) and were graded on a scale between 0 and 10 points. Data were compared using the χ2, Student t, and Mann-Whitney U tests. Potential predictors of symptoms were analyzed using logistic regression analysis. RESULTS: The most common symptom was tiredness (n = 1,002; 82.1%), followed by dyspnea (n = 845; 69.3%), appetite loss (n = 801; 65.7%), pain (n = 798; 65.4%), drowsiness (n = 742; 60.8%), anxiety (n = 704; 57.7%), depression (n = 623; 51.1%), and nausea (n = 557; 45.5%). Of the 1,245 patients, 590 (48.4%) had difficulty in initiating or maintaining sleep. The symptoms were more severe in stages III and IV. Logistic regression analysis indicated a clear association between demographic characteristics and symptom distress, as well as between symptom distress (except nausea) and well-being. Overall, 804 (65.4%) patients used analgesics, 630 (51.5%) received treatment for dyspnea, 242 (19.8%) used enteral/parenteral nutrition, 132 (10.8%) used appetite stimulants, and 129 (10.6%) used anxiolytics/antidepressants. Of the 799 patients who received analgesics, 173 (21.7%) reported that their symptoms were under control, and also those on other various treatment modalities (dyspnea: 78/627 [12.4%], appetite stimulant: 25/132 [18.9%], and anxiolytics/antidepressants: 25/129 [19.4%]) reported that their symptoms were controlled. CONCLUSION: In this study, the symptoms progressed and became more severe in the advanced stages of lung cancer, and palliative treatment was insufficient in most of the patients in Turkey.

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

BACKGROUND: The mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question. RESULTS: In this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations. CONCLUSIONS: Overall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches.

AN UNUSUAL PRESENTATION OF JOUBERT SYNDROME AND RELATED DISORDERS IN A NEWBORN: PANHYPOPITUITARISM.

The Joubert syndrome is characterized by hypotonia, ataxia, facial dysmorphism, abnormal eye movement, irregular breathing pattern and cognitive impairment. The molar tooth sign is the pathognomonic midbrain-hindbrain malformation for Joubert syndrome. Joubert syndrome and related disorders (JSRD), are the clinically and genetically heterogen disorders in which the obligatory hallmark is the molar tooth sign (MTS). In this report, it was described the association of the molar tooth sign, absence of pituitary gland and corpus callosum agenesis on an infant with JSRD. To the best of our knowledge, this is the first case diagnosed as JSRD and panhypopituitarism without features of OFD VI.

The clinical features, diagnosis, treatment, and prognosis of neuroinvasive listeriosis: a multinational study.

The aim of this study was to determine the independent risk factors, morbidity, and mortality of central nervous system (CNS) infections caused by Listeria monocytogenes. We retrospectively evaluated 100 episodes of neuroinvasive listeriosis in a multinational study in 21 tertiary care hospitals of Turkey, France, and Italy from 1990 to 2014. The mean age of the patients was 57 years (range, 19-92 years), and 64% were males. The all-cause immunosuppression rate was 54 % (54/100). Forty-nine (49 %) patients were referred to a hospital because of the classical triad of symptoms (fever, nuchal rigidity, and altered level of consciousness). Rhombencephalitis was detected radiologically in 9 (9 %) cases. Twenty-seven (64 %) of the patients who had cranial magnetic resonance imaging (MRI) performed had findings of meningeal and parenchymal involvement. The mean delay in the initiation of specific treatment was 6.8 ± 7 days. Empiric treatment was appropriate in 52 (52 %) patients. The mortality rate was 25 %, while neurologic sequelae occurred in 13 % of the patients. In the multivariate analysis, delay in treatment [odds ratio (OR), 1.07 [95 % confidence interval (CI), 1.01-1.16]] and seizures (OR, 3.41 [95 % CI, 1.05-11.09]) were significantly associated with mortality. Independent risk factors for neurologic sequelae were delay in treatment (OR, 1.07 [95 % CI, 1.006-1.367]) and presence of bacteremia (OR, 45.2 [95 % CI, 2.73-748.1]). Delay in the initiation of treatment of neuroinvasive listeriosis was a poor risk factor for unfavorable outcomes. Bacteremia was one of the independent risk factors for morbidity, while the presence of seizures predicted worse prognosis. Moreover, the addition of aminoglycosides to ampicillin monotherapy did not improve patients' prognosis.

Local and systemic effects of low-dose transtympanic methotrexate: in vivo animal study.

OBJECTIVE: To evaluate the safety of low-dose transtympanic methotrexate in a rat model. DESIGN: Experimental animal study. SETTING: Tertiary training and research hospital. METHODS: Twenty-four rats were randomly divided into three study groups. Diluted methotrexate solution was administered transtympanically to fill the middle-ear cavity, twice a week in group one and three times a week in group two. Ringer lactate solution was administered transtympanically three times a week in the control group. MAIN OUTCOME MEASURES: Local and systemic effects of low-dose transtympanic methotrexate. RESULTS: In the methotrexate groups, middle-ear mucosal oedema was present in all animals. Auditory brainstem response thresholds indicated no inner-ear dysfunction in any group. Liver function and serum haemoglobin levels showed no statistically significant difference in any group. However, liver biopsies from groups one and two showed mild portal hyperaemia. CONCLUSION: These findings are encouraging, and support further investigation of the topical application of methotrexate in autoimmune hearing diseases, as an alternative or adjunct to transtympanic steroids.

Hopelessness and social comparison in Turkish adolescent with visual impairment.

The purpose of this study was to determine visually impaired adolescents' level of hopelessness and how they perceive of themselves socially compared to other individuals. Another purpose of this study was to look for relationships between hopelessness and social comparison in adolescents with visual impairment. The research population was comprised of 130 students at a secondary school for the visually impaired in Istanbul, Turkey. Our study demonstrated a weak relationship between social comparison and hopelessness (r=-0.46, P < 0.000). The mean hopelessness score for the adolescents with visual impairment was 4.59 ± 3.12 (girls: 4.23 ± 3.10; boys: 4.83 ± 3.11) and social comparison score was 87.50 ± 11.19 (girls: 88.67 ± 11.62; boys: 86.60 ± 10.85). Hopelessness and social comparison were not affected by being blind from birth compared to later or from being a full-time boarding student compared to being a day student. The hopeless (Beck Hopelessness Scale score ≥ 9) adolescents' social comparison scores were found lower than hopeful ones' scores (P < 000). Factors affecting hopelessness and social comparison were feelings about their father, teacher and school.

The comparison of pleural fluid TNF-alpha and IL-10 levels with ADA in tuberculous pleural effusion.

OBJECTIVES: Our aim was to evaluate the diagnostic value of pleural fluid TNF-alpha and IL-10 levels in tuberculous pleural effusion (TPE) and compare with that of ADA. MATERIAL AND METHODS: 70 patients were enrolled in the study. Fourteen patients had TPE, 19 patients malignant pleural effusion (MPE), 18 patients complicated parapneumonic effusion (PPE) and 19 patients had transudative pleural effusion. RESULTS: The pleural fluid TNF-alpha levels were significantly higher in TPE than MPE and transudates. There was no significant difference in pleural fluid IL-10 levels between groups. Among exudative effusions, TNF-alpha was significantly higher in tuberculous group, while there was no difference in IL-10 levels between tuberculous and nontuberculous group. The pleural fluid ADA levels were significantly higher in TPE than other groups. ROC analysis was performed and the optimal cut-off points of TNF-alpha and ADA were 13.3 pg/mL and 41.5 U/L, respectively. The sensitivity of TNF-alpha was 71% and specificity was 66% in the diagnosis of TPE. In contrast, the sensitivity and specificity of ADA was 78% and 86% respectively. CONCLUSION: TNF- alpha is a useful marker in the diagnosis of TPE and IL-10 has no diagnostic value. However, the sensitivity and specificity of TNF-alpha is lower than that of ADA.

The effect of calcium sulfate on hard-tissue healing after periradicular surgery.

The purpose of this study was to determine the effect of calcium sulfate (CS) on cementum deposition and osseous healing after periradicular surgery. The root canals of 24 mandibular premolars in four 2-yr-old beagle dogs were endodontically treated, followed 2 weeks later by periradicular surgery. Mineral trioxide aggregate (MTA) was used as root-end-filling material. The right or left side was assigned at random to receive CS alpha-hemihydrate or no material in the osteotomy sites before closure. The animals were killed after 4 months. Hard-tissue healing was analyzed histomorphometrically. All samples displayed evidence of cementum deposition adjacent to the root-end fillings and bone regeneration in the osteotomy sites. The data was analyzed using the Mann-Whitney U test, comparing the scores for cementum and osseous healing of the two groups at significance level of alpha = 0.05. The results indicated that placement of CS in osteotomy sites after periradicular surgery does not significantly affect periradicular healing.

Hard-tissue healing after application of fresh or set MTA as root-end-filling material.

The purpose of this study was to compare the effect of fresh mineral trioxide aggregate (MTA) with set MTA on hard-tissue healing after periradicular surgery. The root canals of 24 mandibular premolars in four 2-yr-old beagle dogs were filled with MTA. Two weeks later the root ends of half of the samples were surgically exposed and resected to the set MTA within the canals. After exposing and resecting the other 12 root ends, they were prepared with ultrasonic instrumentation and preparations were filled with fresh MTA. After 4 months, the animals were killed. Hard-tissue healing was analyzed histomorphometrically. The results indicated that although freshly placed MTA resulted in a significantly higher incidence of cementum formation (12 of 12 versus 8 of 12, p = 0.028), there is no significant difference in the quantity of cementum or osseous healing associated with freshly placed or set MTA when used as root-end-filling material.

Tuberculous meningitis in adults in Turkey: epidemiology, diagnosis, clinic and laboratory [corrected].

A retrospective study was performed to assess the epidemiology, diagnosis, clinic, and laboratory of the patients with tuberculous meningitis (TBM) in a multicentral study. The medical records of adult cases with TBM treated at 12 university hospitals throughout Turkey, between 1985 and 1998 were reviewed using a standardized protocol. The diagnosis of TMB was established with the clinical and laboratory findings and/or microbiological confirmation in cerebrospinal fluid (CSF). The non-microbiologically confirmed cases were diagnosed with five diagnostic sub-criteria which CSF findings, radiological findings, extra-neural tuberculosis, epidemiological findings and response to antituberculous therapy. A total of 469 patients were included in this study. Majority of the patients were from Southeast Anatolia (164 patients, 35.0%) and (108 patients, 23.0%) from East Anatolia regions. There was a close contact with a tuberculous patient in 88 of 341 patients (25.8%) and with a tuberculous family member in 53 of 288 patients (18.4%). BCG scar was positive in 161 of 392 patients (41.1%). Tuberculin skin test was done in 233 patients and was found to be negative in 75. Totally 115 patients died (24.5%) of whom 23 died in 24 hour after admittance. The diagnosis was confirmed with clinical findings and CSF culture and/or Ziehl-Nelson staining in 88 patients (18.8%). Besides clinical criteria, there were three or more diagnostic sub-criteria in 252 cases (53.7%), two diagnostic sub-criteria in 99 cases (21.1%), and any diagnostic sub-criteria in 30 patients (6.4%). Since TBM is a very critical disease, early diagnosis and treatment may reduce fatal outcome and morbidity.

Detection of Brucella melitensis by the BacT/Alert automated system and Brucella broth culture.

This study was conducted to evaluate the ability of the BacT/Alert automated blood culture system to detect Brucella spp. in comparison with traditional Brucella broth culture. Overall, 100 (50 bone marrow and 50 blood samples) paired cultures were obtained, and 59 were positive by at least one method. The Brucella broth culture method detected all 59 positive cultures (100%), and the BacT/Alert system detected 30 (50.8%) (P < 0.05). The mean detection times for B. melitensis were 4.5 days in the BacT/Alert system and 5 days in Brucella broth culture (P > 0.05). There is no significant difference between the two methods with respect to growth time of the microorganism, but Brucella broth culture is more sensitive than the BacT/Alert system.