Fluorogenic Probes of the Mycobacterial Membrane as Reporters of Antibiotic Action.

The genus Mycobacterium includes species such as Mycobacterium tuberculosis, which can cause deadly human diseases. These bacteria have a protective cell envelope that can be remodeled to facilitate their survival in challenging conditions. Understanding how such conditions affect membrane remodeling can facilitate antibiotic discovery and treatment. To this end, we describe an optimized fluorogenic probe, N-QTF, that reports on mycolyltransferase activity, which is vital for cell division and remodeling. N-QTF is a glycolipid probe that can reveal dynamic changes in the mycobacterial cell envelope in both fast- and slow-growing mycobacterial species. Using this probe to monitor the consequences of antibiotic treatment uncovered distinct cellular phenotypes. Even antibiotics that do not directly inhibit cell envelope biosynthesis cause conspicuous phenotypes. For instance, mycobacteria exposed to the RNA polymerase inhibitor rifampicin release fluorescent extracellular vesicles (EVs). While all mycobacteria release EVs, fluorescent EVs were detected only in the presence of RIF, indicating that exposure to the drug alters EV content. Macrophages exposed to the EVs derived from RIF-treated cells released lower levels of cytokines, suggesting the EVs moderate immune responses. These data suggest that antibiotics can alter EV content to impact immunity. Our ability to see such changes in EV constituents directly results from exploiting these chemical probes.

'. . . and then no more kisses!' Exploring patients' experiences on multidrug-resistant bacterial microorganisms and hygiene measures in end-of-life care A mixed-methods study.

BACKGROUND: In end-of-life care hygiene, measures concerning multidrug-resistant bacterial microorganisms may contradict the palliative care approach of social inclusion and be burdensome for patients. OBJECTIVES: To integrate patients' perspectives on handling multidrug-resistant bacterial microorganisms at their end of life, their quality of life, the impact of positive multidrug-resistant bacterial microorganisms' diagnosis, protection and isolation measures on their well-being and patients' wishes and needs regarding their care. DESIGN: A mixed-methods convergent parallel design embedded quantitative data on the patients' multidrug-resistant bacterial microorganisms' trajectory and quality of life assessed by the Schedule for the Evaluation of Individual Quality of Life in qualitative data collection via interviews and focus groups. Data analysis was performed according to Grounded Theory and qualitative and quantitative results were interrelated. SETTING/PARTICIPANTS: Between March 2014 and September 2015 at two hospitals adult patients diagnosed with multidrug-resistant bacterial microorganisms and treated in a palliative care department or a geriatric ward were included in the sample group. RESULTS: Patients in end-of-life and geriatric care reported emotional and social impact through multidrug-resistant bacterial microorganisms' diagnosis itself, hygiene measures and lack of information. This impact affects aspects relevant to the patients' quality of life. Patients' wishes for comprehensive communication/information and reduction of social strain were identified from the focus group discussion. CONCLUSION: Patients would benefit from comprehensible information on multidrug-resistant bacterial microorganisms. Strategies minimizing social exclusion and emotional impact of multidrug-resistant bacterial microorganisms' diagnosis in end-of-life care are needed as well as adaption or supplementation of standard multidrug-resistant bacterial microorganisms' policies of hospitals.

Disilane Cleavage with Selected Alkali and Alkaline Earth Metal Salts.

The industry-scale production of methylchloromonosilanes in the Müller-Rochow Direct Process is accompanied by the formation of a residue, the direct process residue (DPR), comprised of disilanes Men Si2 Cl6-n (n=1-6). Great research efforts have been devoted to the recycling of these disilanes into monosilanes to allow reintroduction into the siloxane production chain. In this work, disilane cleavage by using alkali and alkaline earth metal salts is reported. The reaction with metal hydrides, in particular lithium hydride (LiH), leads to efficient reduction of chlorine containing disilanes but also induces disproportionation into mono- and oligosilanes. Alkali and alkaline earth chlorides, formed in the course of the reduction, specifically induce disproportionation of highly chlorinated disilanes, whereas highly methylated disilanes (n>3) remain unreacted. Nearly quantitative DPR conversion into monosilanes was achieved by using concentrated HCl/ether solutions in the presence of lithium chloride.

Synthesis of Functional Monosilanes by Disilane Cleavage with Phosphonium Chlorides.

The Müller-Rochow direct process (DP) for the large-scale production of methylchlorosilanes Men SiCl4-n (n=1-3) generates a disilane residue (Men Si2 Cl6-n , n=1-6, DPR) in thousands of tons annually. This report is on methylchlorodisilane cleavage reactions with use of phosphonium chlorides as the cleavage catalysts and reaction partners to preferably obtain bifunctional monosilanes Mex SiHy Clz (x=2, y=z=1; x,y=1, z=2; x=z=1, y=2). Product formation is controlled by the reaction temperature, the amount of phosphonium chloride employed, the choice of substituents at the phosphorus atom, and optionally by the presence of hydrogen chloride, dissolved in ethers, in the reaction mixture. Replacement of chloro by hydrido substituents at the disilane backbone strongly increases the overall efficiency of disilane cleavage, which allows nearly quantitative silane monomer formation under comparably moderate conditions. This efficient workup of the DPR thus not only increases the economic value of the DP, but also minimizes environmental pollution.

Making Use of the Direct Process Residue: Synthesis of Bifunctional Monosilanes.

The industrial production of monosilanes Men SiCl4-n (n=1-3) through the Müller-Rochow Direct Process generates disilanes Men Si2 Cl6-n (n=2-6) as unwanted byproducts ("Direct Process Residue", DPR) by the thousands of tons annually, large quantities of which are usually disposed of by incineration. Herein we report a surprisingly facile and highly effective protocol for conversion of the DPR: hydrogenation with complex metal hydrides followed by Si-Si bond cleavage with HCl/ether solutions gives (mostly bifunctional) monosilanes in excellent yields. Competing side reactions are efficiently suppressed by the appropriate choice of reaction conditions.

Perspectives on multidrug-resistant organisms at the end of life : A focus group study of staff members and institutional stakeholders.

BACKGROUND: There is a lack of research into how hospital staff and institutional stakeholders (i. e. institutional representatives from public health authorities, hospital hygiene, and the departments of microbiology, palliative care, and geriatrics) engage with patients who are carriers of multidrug-resistant organisms and receiving end-of-life care. Knowledge of their experiences, workload, and needs should be considered in dealing with hospitalized carriers of multidrug-resistant organisms as well as staff education. OBJECTIVE: This study explored and compared staff members' and stakeholders' perspectives on multidrug-resistant organisms and on provision of end-of-life care to carrier patients. METHODS: In this study four focus groups consisting of hospital staff members and institutional stakeholders were formed within a mixed-methods parent study in a palliative care unit at a university clinic and a geriatric ward of a Catholic and academic teaching hospital. Participants discussed results from staff and stakeholder interviews from a former study phase. Data were analyzed according to Grounded Theory and perspectives of staff members and institutional stakeholders were compared and contrasted. RESULTS: Key issues debated by staff members (N = 19) and institutional stakeholders (N = 10) were 1) the additional workload, 2) reasons for uncertainty about handling carrier patients, 3) the format of continuing education, and 4) the preferred management approach for dealing with multidrug-resistant organism carrier patients. Although similar barriers (e. g. colleagues' ambiguous opinions) were identified, both groups drew different conclusions concerning the management of these barriers. While institutional stakeholders recommended making decisions on hygiene measures under consideration of the specific patient situation, staff members preferred the use of standardized hygiene measures which should be applied uniformly to all patients. DISCUSSION: Staff members and institutional stakeholders perceived similar barriers to practice caused by multidrug-resistant organisms and similar needs for continuing education. The staff members' preferred management approach might originate from an uncertainty about the multidrug-resistant organism infection risk. Experiences and visions of both groups should be included in a specific recommendation for end-of-life care to ensure behavioral confidence.

Lewis Base Catalyzed Selective Chlorination of Monosilanes.

A preparatively facile, highly selective synthesis of bifunctional monosilanes R2 SiHCl, RSiHCl2 and RSiH2 Cl is reported. By chlorination of R2 SiH2 and RSiH3 with concentrated HCl/ether solutions, the stepwise introduction of Si-Cl bonds is readily controlled by temperature and reaction time for a broad range of substrates. In a combined experimental and computational study, we establish a new mode of Si-H bond activation assisted by Lewis bases such as ethers, amines, phosphines, and chloride ions. Elucidation of the underlying reaction mechanisms shows that alcohol assistance through hydrogen-bond networks is equally efficient and selective. Remarkably, formation of alkoxysilanes or siloxanes is not observed under moderate reaction conditions.

Multidrug-resistant bacterial microorganisms (MDRO) in end-of-life care: development of recommendations for hospitalized patients using a mixed-methods approach.

PURPOSE: Palliative care professionals are frequently confronted with patients colonized or infected with MDRO. One major challenge is how to balance necessary isolation measures and social inclusion as one of the main principles of palliative and end-of-life care. To date, MDRO-specific policies and protocols vary widely between institutions. AIM: provide empirical recommendations on how to deal with hospitalized MDRO patients in end-of-life care. METHODS: Recommendations were developed based on (i) initial results of face-to-face interviews and focus groups, (ii) impartial experts' comments and consensus on the draft via online survey and (iii) a face-to-face meeting with consortium members to finalize recommendations. Findings of 158 interviews and six focus groups (39 participants) with patients, family caregivers, staff members and institutional stakeholders contributed to the recommendations. The assessments of 17 experts were considered. RESULTS: In total, 21 recommendations were approved. The recommended strategy in dealing with MDRO at the end of life allows case-based application of protection and isolation measures. MDRO diagnostics and therapy involve screening at admission. The recommendations suggest consideration of required accommodation facilities, provided material as well as staff and time resources. The recommendations further highlight the importance of providing for strategies enabling the patient's social inclusion and provision of verbal and written information about MDRO for patients and family caregivers, transparent medical documentation, and staff member training. CONCLUSION: The recommendations summarize the perspectives of individuals and groups affected by MDRO at the end of life and provide practical guidance for clinical routine. Further dissemination and implementation requirements are discussed and should contain the evaluation of the knowledge, views, worries, and anxieties of the target groups.

Staff members' ambivalence on caring for patients with multidrug-resistant bacteria at their end of life: A qualitative study.

AIMS AND OBJECTIVES: To explore healthcare professionals' personal experiences, feelings and attitudes about caring for hospitalised patients with multidrug-resistant bacteria in palliative and geriatric care. BACKGROUND: Working in end-of-life care involves at times burdening demands that affect not only healthcare professionals personally but also their actions. It is suggested that multidrug-resistant bacteria and their consequences for colonised or infected patients in hospitals are among the challenges for all professionals in end-of-life care. Little is known about the feelings and experiences of staff members during healthcare activities with regard to these bacteria. DESIGN: A qualitative interview study in two German hospitals. METHODS: We interviewed 35 staff members from a German palliative care unit and a geriatric unit about their experiences with multidrug-resistant bacteria in end-of-life care and the management of colonised or infected patients. Semistructured interviews were transcribed verbatim and analysed using grounded theory. RESULTS: Interviewees represented two interdisciplinary teams with 40% nurses, 26% physicians and 34% other professionals. Salient themes that were identified included impact of multidrug-resistant bacteria on staff members' personal actions, feelings and attitudes towards the bacteria and the required isolation measures. Besides higher workload and consequences for working routines, the patients' palliative care needs were recognised, as well as the necessary protection measures to avoid contaminations in hospital. Healthcare professionals reported a dilemma that they experienced when facing these diverse demands. CONCLUSIONS: Findings point to emotional and behavioural ambivalence in end-of-life care among staff members because necessary isolation measures and particular situation in end-of-life care create unsolvable conflicts for healthcare professionals. Possible strategies to cope with ambivalence are discussed. RELEVANCE TO CLINICAL PRACTICE: Healthcare professionals in palliative and geriatric care have to deal with multidrug-resistant bacteria and have to face contradictory feelings while trying to fulfil patients' needs as well as isolation requirements.

Thermal Synthesis of Perchlorinated Oligosilanes: A Fresh Look at an Old Reaction.

A combined experimental and theoretical study of the high-temperature reaction of SiCl4 and elemental silicon is presented. The nature and reactivity of the product formed upon rapid cooling of the gaseous reaction mixture is investigated by comparison with the defined model compounds cyclo-Si5 Cl10 , n-Si5 Cl12 and n-Si4 Cl10 . A DFT assessment provides mechanistic insight into the oligosilane formation. Experimental 29 Si NMR investigations, supported by quantum-chemical 29 Si NMR calculations, consistently show that the reaction product is composed of discrete molecular perchlorinated oligosilanes. Low-temperature chlorination is an unexpectedly selective means for the transformation of cyclosilanes to acyclic species by endocyclic Si-Si bond cleavage, and we provide a mechanistic rationalization for this observation. In contrast to the raw material, the product obtained after low-temperature chlorination represents an efficient source of neo-Si5 Cl12 or the amine-stabilized disilene EtMe2 N⋅SiCl2 Si(SiCl3 )2 through reaction with aliphatic amines.

Generic expansion of the Jastrow correlation factor in polynomials satisfying symmetry and cusp conditions.

Jastrow correlation factors play an important role in quantum Monte Carlo calculations. Together with an orbital based antisymmetric function, they allow the construction of highly accurate correlation wave functions. In this paper, a generic expansion of the Jastrow correlation function in terms of polynomials that satisfy both the electron exchange symmetry constraint and the cusp conditions is presented. In particular, an expansion of the three-body electron-electron-nucleus contribution in terms of cuspless homogeneous symmetric polynomials is proposed. The polynomials can be expressed in fairly arbitrary scaling function allowing a generic implementation of the Jastrow factor. It is demonstrated with a few examples that the new Jastrow factor achieves 85%-90% of the total correlation energy in a variational quantum Monte Carlo calculation and more than 90% of the diffusion Monte Carlo correlation energy.

Genetic factors affecting storage and utilization of lipids during dormancy in Mycobacterium tuberculosis.

Mycobacterium tuberculosis (Mtb) can adopt a non-growing dormant state during infection that may be critical to both active and latent tuberculosis. During dormancy, Mtb is widely tolerant toward antibiotics, a significant obstacle in current anti-tubercular drug regimens, and retains the ability to persist in its environment. We aimed to identify novel mechanisms that permit Mtb to survive dormancy in an in vitro carbon starvation model using transposon insertion sequencing and gene expression analysis. We identified a previously uncharacterized component of the lipid transport machinery, omamC, which was upregulated and required for survival during carbon starvation. We show that OmamC plays a role both in increasing fatty acid stores during growth in rich media and enhancing fatty acid utilization during starvation. Besides its involvement in lipid metabolism, OmamC levels affected the expression of the anti-anti-sigma factor rv0516c and other genes to improve Mtb survival during carbon starvation and increase its tolerance toward rifampicin, a first-line drug effective against non-growing Mtb. Importantly, we show that Mtb can be eradicated during carbon starvation, in an OmamC-dependent manner, by inhibiting lipid metabolism with the lipase inhibitor tetrahydrolipstatin. This work casts new light into the survival processes of non-replicating, drug-tolerant Mtb by identifying new proteins involved in lipid metabolism required for the survival of dormant bacteria and exposing a potential vulnerability that could be exploited for antibiotic discovery.IMPORTANCETuberculosis is a global threat, with ~10 million yearly active cases. Many more people, however, live with "latent" infection, where Mycobacterium tuberculosis survives in a non-replicative form. When latent bacteria activate and regrow, they elicit immune responses and result in significant host damage. Replicating and non-growing bacilli can co-exist; however, non-growing bacteria are considerably less sensitive to antibiotics, thus complicating treatment by necessitating long treatment durations. Here, we sought to identify genes important for bacterial survival in this non-growing state using a carbon starvation model. We found that a previously uncharacterized gene, omamC, is involved in storing and utilizing fatty acids as bacteria transition between these two states. Importantly, inhibiting lipid metabolism using a lipase inhibitor eradicates non-growing bacteria. Thus, targeting lipid metabolism may be a viable strategy for treating the non-growing population in strategies to shorten treatment durations of tuberculosis.

Accurate and rapid antibiotic susceptibility testing using a machine learning-assisted nanomotion technology platform.

Antimicrobial resistance (AMR) is a major public health threat, reducing treatment options for infected patients. AMR is promoted by a lack of access to rapid antibiotic susceptibility tests (ASTs). Accelerated ASTs can identify effective antibiotics for treatment in a timely and informed manner. We describe a rapid growth-independent phenotypic AST that uses a nanomotion technology platform to measure bacterial vibrations. Machine learning techniques are applied to analyze a large dataset encompassing 2762 individual nanomotion recordings from 1180 spiked positive blood culture samples covering 364 Escherichia coli and Klebsiella pneumoniae isolates exposed to cephalosporins and fluoroquinolones. The training performances of the different classification models achieve between 90.5 and 100% accuracy. Independent testing of the AST on 223 strains, including in clinical setting, correctly predict susceptibility and resistance with accuracies between 89.5% and 98.9%. The study shows the potential of this nanomotion platform for future bacterial phenotype delineation.

The cost of virulence: retarded growth of Salmonella Typhimurium cells expressing type III secretion system 1.

Virulence factors generally enhance a pathogen's fitness and thereby foster transmission. However, most studies of pathogen fitness have been performed by averaging the phenotypes over large populations. Here, we have analyzed the fitness costs of virulence factor expression by Salmonella enterica subspecies I serovar Typhimurium in simple culture experiments. The type III secretion system ttss-1, a cardinal virulence factor for eliciting Salmonella diarrhea, is expressed by just a fraction of the S. Typhimurium population, yielding a mixture of cells that either express ttss-1 (TTSS-1(+) phenotype) or not (TTSS-1(-) phenotype). Here, we studied in vitro the TTSS-1(+) phenotype at the single cell level using fluorescent protein reporters. The regulator hilA controlled the fraction of TTSS-1+ individuals and their ttss-1 expression level. Strikingly, cells of the TTSS-1(+) phenotype grew slower than cells of the TTSS-1(-) phenotype. The growth retardation was at least partially attributable to the expression of TTSS-1 effector and/or translocon proteins. In spite of this growth penalty, the TTSS-1(+) subpopulation increased from <10% to approx. 60% during the late logarithmic growth phase of an LB batch culture. This was attributable to an increasing initiation rate of ttss-1 expression, in response to environmental cues accumulating during this growth phase, as shown by experimental data and mathematical modeling. Finally, hilA and hilD mutants, which form only fast-growing TTSS-1(-) cells, outcompeted wild type S. Typhimurium in mixed cultures. Our data demonstrated that virulence factor expression imposes a growth penalty in a non-host environment. This raises important questions about compensating mechanisms during host infection which ensure successful propagation of the genotype.

Siemens Reloaded: Chloride-Assisted Selective Hydrodechlorination of SiCl4 to HSiCl3.

Trichlorosilane is the key intermediate for the large-scale production of polycrystalline silicon in the Siemens and Union Carbide processes. Both processes, however, are highly inefficient, and over two thirds of the trichlorosilane employed is converted to unwanted silicon tetrachloride accumulating in millions of tons per year on a global scale. In this combined experimental and theoretical study we report an energetically and environmentally benign synthetic protocol for the highly selective conversion of SiCl4 to HSiCl3 using organohydridosilanes as recyclable hydrogen transfer reagents in combination with onium chlorides as efficient catalysts. We put the same protocol to further use demonstrating the quantitative conversion of higher oligosilane residues, which form as another unwanted and potentially hazardous byproduct of Siemens processes, to HSiCl3 in a low-temperature recycling step.

Nanomotion technology in combination with machine learning: a new approach for a rapid antibiotic susceptibility test for Mycobacterium tuberculosis.

Nanomotion technology is a growth-independent approach that can be used to detect and record the vibrations of bacteria attached to cantilevers. We have developed a nanomotion-based antibiotic susceptibility test (AST) protocol for Mycobacterium tuberculosis (MTB). The protocol was used to predict strain phenotype towards isoniazid (INH) and rifampicin (RIF) using a leave-one-out cross-validation (LOOCV) and machine learning techniques. This MTB-nanomotion protocol takes 21 h, including cell suspension preparation, optimized bacterial attachment to functionalized cantilever, and nanomotion recording before and after antibiotic exposure. We applied this protocol to MTB isolates (n = 40) and were able to discriminate between susceptible and resistant strains for INH and RIF with a maximum sensitivity of 97.4% and 100%, respectively, and a maximum specificity of 100% for both antibiotics when considering each nanomotion recording to be a distinct experiment. Grouping recordings as triplicates based on source isolate improved sensitivity and specificity to 100% for both antibiotics. Nanomotion technology can potentially reduce time-to-result significantly compared to the days and weeks currently needed for current phenotypic ASTs for MTB. It can further be extended to other anti-TB drugs to help guide more effective TB treatment.

Investigating nanomotion-based technology (Resistell AST) for rapid antibiotic susceptibility testing among adult patients admitted to a tertiary-care hospital with Gram-negative bacteraemia: protocol for a prospective, observational, cross-sectional, single-arm study.

INTRODUCTION: Effective treatment of bloodstream infections (BSIs) is relying on rapid identification of the causing pathogen and its antibiotic susceptibility. Still, most commercially available antibiotic susceptibility testing (AST) methods are based on monitoring bacterial growth, thus impacting the time to results. The Resistell AST is based on a new technology measuring the nanomotion caused by physiologically active bacterial cells and detecting the changes in nanomotion caused by the exposure to a drug. METHODS AND ANALYSIS: This is a single-centre, prospective, cross-sectional, single-arm diagnostic accuracy study to determine the agreement of the Resistell AST on Gram-negative bacteria isolated from blood cultures among patients admitted to a tertiary-care hospital with the reference method. Up to 300 patients will be recruited. Starting with a pilot phase, enrolling 10%-20% of the subjects and limited to Escherichia coli BSI tested for ceftriaxone susceptibility, the main phase will follow, extending the study to Klebsiella pneumoniae and ciprofloxacin. ETHICS AND DISSEMINATION: This study has received ethical approval from the Swiss Ethics Committees (swissethics, project 2020-01622). All the case report forms and clinical samples will be assigned a study code by the local investigators and stored anonymously at the reference centre (Lausanne University Hospital). The results will be broadly distributed through conference presentations and peer-reviewed publications. TRIAL REGISTRATION NUMBER: ClinicalTrials.gov Registry (NCT05002413).

A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients.

The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.

An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium.

In this work we consider the regulation system present on the SPI1 pathogenicity island of Salmonella enterica serovar Typhimurium. It is well-known that HilA is the central regulator in the overall scheme of SPI1 regulation and directly binds to virulence operons and activates their expression. The regulation of the expression of HilA is via a complex feed-forward loop involving three transcriptional activators: HilC, HilD and RtsA, and the negative regulator HilE. Our aim is to model this regulation network and study its dynamical behavior. We show that this regulatory system can display a bistable behavior relevant to the biology of Salmonella, and that noise can be a driving force in this system.