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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. Current machine learning classifiers have been applied to whole-genome sequencing data to identify determinants of antimicrobial resistance, but they lack interpretability. Here the authors present a metabolic machine learning classifier that uses flux balance analysis to estimate the biochemical effects of alleles. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Some physical (density, coefficient of filtration, particle-size composition, etc.) and chemical (contents of carbonates, organic carbon, nitrogen, etc.) properties of an alluvial calcareous soil were studied in Central Anatolia (Konya province, Çumra region). These heavy-textured (medium clay) soils with a low content of organic carbon (less than 1%) have favorable agrophysical properties due to the stable structure of the pore space. The studies of the water regime of soils under drop irrigation confirm the favorable hydrological properties of these soils. The use of the known agrophysical estimates (after Medvedev, the index of the optimal water regime, etc.) has revealed the high dispersal of the data related to the low humus content in these heavy-textured soils. The favorable structure of the pore space is suggested to be stipulated by the active activity of the numerous and diverse representatives of soil biota. Four phyla predominate in the microbio-logical composition of the soils studied; among them, Actinobacteria is the dominant. The composition of this phylum is dominated by the elevated number of both higher ( Streptomyces) and lower (three species of Rhodococcus) actinobacteria. The high biodiversity of bacteria against the background of their great total number and the developed trophic interactions in the microbial community promote the well-balanced production of specific metabolites, including gaseous ones (CO, H). This circumstance allows this clayey soil to function rather actively while protecting the pore space against compaction and maintaining the optimal density, porosity, and hydrological properties. [ABSTRACT FROM AUTHOR]

Corrosion and scaling of metal surfaces are the major problems caused by geothermal fluids when metallic structures are used. This article describes a study of corrosion and scaling problems in the Afyonkarahisar Geothermal Heating System (AFJET) in Afyonkarahisar, Turkey. Water analysis, XRD, SEM, EDX, IC, ICP-OES analyses, and electrochemical methods were used in this study. Pentasodium triphosphate (NaPO), maleic anhydride (CHO), and 1,3-benzendisulfonic acid disodium salt (CHNaOS) were used as corrosion inhibitors. Tests were carried out using geothermal water from AF11 well. The experimental temperatures were chosen as 298, 333, and 358 K. Inhibitor concentrations were chosen as 1 × 10, 1 × 10, 1 × 10, and 1 × 10 mol/dm. Moreover, mixed inhibitor solutions were prepared using the inhibitor concentrations that showed the best inhibition. The first mixed inhibitor solution showed 96% inhibition. The second mixed inhibitor solution showed 90% inhibition. The tested inhibitors act as anodic inhibitors. XRD analysis shows that there is CaCO aragonite scaling in the system. Increasing TDS, alkalinity, and hardness all promote scale formation. The photomicrographs from SEM-EDX and the metallographic microscope show that the tested inhibitors form a protective film on the surface. IC and ICP-OES analyses show that the concentration of Ca is very high, which supports scale formation. [ABSTRACT FROM AUTHOR]

In this retrospective study, 132 cases of anthrax observed in a Turkish hospital over a 14-year period (October 1986 to October 2000) were evaluated with respect to clinical features, therapy, and outcome. The results show that anthrax is a disease of significance in the Eastern Anatolian region of Turkey. Preventive measures such as education of the population and vaccination of animals against anthrax would reduce the incidence of the disease. [ABSTRACT FROM AUTHOR]

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. Mycobacterium tuberculosis exhibits complex evolution of antimicrobial resistance (AMR). Here, the authors perform machine learning and structural analysis to identify signatures of AMR evolution to 13 antibiotics. [ABSTRACT FROM AUTHOR]

Presents a letter to the editor on penicillin therapy for anthrax, published in the previous issue of the "European Journal of Clinical Microbiology & Infectious Diseases."