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Stenotrophomonas maltophilia is one of the most frequently isolated multidrug-resistant nosocomial opportunistic pathogens. It contributes to disease progression in cystic fibrosis (CF) patients and is frequently isolated from wounds, infected tissues, and catheter surfaces. On these diverse surfaces S. maltophilia lives in single-species or multispecies biofilms. Since very little is known about common processes in biofilms of different S. maltophilia isolates, we analyzed the biofilm profiles of 300 clinical and environmental isolates from Europe of the recently identified main lineages Sgn3, Sgn4, and Sm2 to Sm18. The analysis of the biofilm architecture of 40 clinical isolates revealed the presence of multicellular structures and high phenotypic variability at a strain-specific level. Further, transcriptome analyses of biofilm cells of seven clinical isolates identified a set of 106 shared strongly expressed genes and 33 strain-specifically expressed genes. Surprisingly, the transcriptome profiles of biofilm versus planktonic cells revealed that just 9.43% ± 1.36% of all genes were differentially regulated. This implies that just a small set of shared and commonly regulated genes is involved in the biofilm lifestyle. Strikingly, iron uptake appears to be a key factor involved in this metabolic shift. Further, metabolic analyses implied that S. maltophilia employs a mostly fermentative growth mode under biofilm conditions. The transcriptome data of this study together with the phenotypic and metabolic analyses represent so far the largest data set on S. maltophilia biofilm versus planktonic cells. This study will lay the foundation for the identification of strategies for fighting S. maltophilia biofilms in clinical and industrial settings.IMPORTANCE Microorganisms living in a biofilm are much more tolerant to antibiotics and antimicrobial substances than planktonic cells are. Thus, the treatment of infections caused by microorganisms living in biofilms is extremely difficult. Nosocomial infections (among others) caused by S. maltophilia, particularly lung infection among CF patients, have increased in prevalence in recent years. The intrinsic multidrug resistance of S. maltophilia and the increased tolerance to antimicrobial agents of its biofilm cells make the treatment of S. maltophilia infection difficult. The significance of our research is based on understanding the common mechanisms involved in biofilm formation of different S. maltophilia isolates, understanding the diversity of biofilm architectures among strains of this species, and identifying the differently regulated processes in biofilm versus planktonic cells. These results will lay the foundation for the treatment of S. maltophilia biofilms.

The quantification of fluid flow in rough fractures is of high interest for reservoir engineering, especially for deep geothermal applications. Herein, rough self-affine fractures are stochastically generated with incremental shear displacement and geometrically described by two aperture definitions, the vertical aperture avert and the effective aperture aeff. In order to compare their effect on fracture flow, such as anisotropy and channelling, Local Cubic Law (LCL) model-based 2D fluid flow is simulated. The particularity of this approach is the combination of a stochastic generation of self-affine fractures with a statistical analysis (560 individual realizations) of the impact of the LCL’s aperture constraint on fracture flow. The results show that aperture definition affects the quantitative interpretation of flow anisotropy and channeling as well as the aperture distribution of the fractures with shearing. Higher values of mean aperture for a given fracture are found using avert, whereas the aperture standard deviation is larger with aeff. In addition, flow anisotropy is significantly sensitive to aperture definition for small shear displacements and shows a relative higher dispersion with aeff. Thus, LCL prediction models based on avert are expected to lead to higher dispersion of anisotropy results with a higher uncertainty (factor ~ 2). Realizations based on avert lead to an enhanced clustering of high flow rates for higher shearing displacements. This channeling development results in higher total flow rates for these simulations. These findings support the direct calibration of pre-existing LCL anisotropy simulations based on avert towards more representative results using aeff.

The contemporary crustal stress state is primarily driven by gravitational volume forces and plate tectonics. However, there are various smaller-scale sources such as geological structures and stiffness contrast that perturb stresses and deviate them from the regional pattern. For example, borehole stress analysis in numerous cases has revealed abrupt rotations of horizontal stress orientation of up to 90° when faults are crossed. Herein, we investigate the rotation of principal stress axes at a fault by means of a 2D generic numerical model. We focus on the near field of the fault and the damage zone with a fault parameterized as a rock stiffness contrast. A substantial influence of the far-field stress field in terms of the differential stress and in terms of the stress ratio RS=S1/S_3 is shown. Furthermore, the contrast in material properties is the basis for any stress rotation, and in particular the stiffness is demonstrated to have a significant influence. Eventually, the impact of the angle between the fault strike and the orientation of SHmax is demonstrated. Our results show that the stress rotation is negatively correlated with the ratio of principal far-field stresses. A small angle between the far-field stress orientation and the fault facilitates stress rotation. A high contrast in rock stiffness further increases the stress rotation angle. Faults striking perpendicular to the maximum principal stress orientation experience no rotation at all. However, faults oriented parallel to the maximum principal stress orientation experience either no rotation or a 90° rotation, dependent on the ratio of principal stresses and the rock stiffness contrast. A comparison with observations from various boreholes worldwide shows that in general the findings are in agreement, even though the dip angle proves to have an influence on the stress rotation, in particular for shallow-dipping faults. [ABSTRACT FROM AUTHOR]

BackgroundThe World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear.MethodsWe obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance.ResultsA total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted.ConclusionsGenotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.).

Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) ( https://github.com/CPTR-ReSeqTB/UVP ) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9% agreement with the variants identified using Sanger sequencing and was 100% concordant with conventional methods of assigning lineage. We analyzed 4636 publicly available MTBC isolates in the ReSeqTB platform representing all seven major MTBC lineages. The variants detected have an above 94% accuracy of predicting drug based on the accompanying DST results in the platform. The aggregation of variants over time in the platform will establish confidence-graded mutations statistically associated with phenotypic drug resistance. These tools serve as critical reference standards for future molecular diagnostic assay developers, researchers, public health agencies and clinicians working towards the control of drug-resistant tuberculosis.

Damage distribution and evolution have a significant effect on borehole stress concentrations. To model the complex fracturing process and inelastic deformation in the development of the borehole breakout, we implement a continuum damage mechanics (CDM) concept that takes tensile and compressive failure mechanisms into account. The proposed approach explicitly models the dissipative behavior of the material due to cracking and its evolution, which leads to an inhomogeneous redistribution of material properties and stresses in the vicinity of the borehole wall. We apply a constitutive plastic model for Berea sandstone and compare our numerical results to laboratory experiments performed on Tablerock sandstone. We are able to reproduce several characteristics of the failure process during the breakout development as observed in experimental tests, e.g. localized crack distribution in the vicinity of the borehole wall, damage evolution, which exhibits a widening process in the beginning followed by subsequent growth in depth, and shear fracturing-dominated breakout growth in sandstone. A comparison of our results with laboratory experiments performed on a range of stress conditions shows a good agreement of the size of borehole breakouts. The importance of the constitutive damage law in defining the failure mechanisms of the damaging processes is discussed. We show that the depth and the width of breakouts are not independent of each other and no single linear relation can be found between the size of breakouts and the magnitude of the applied stress. Consequently, only one far field principal stress component can be estimated from breakout geometry, if the other two principal stresses are known and sufficient data on the plastic parameters are available.