Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a “minimal” model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously

Epidemiology of Surgical Site Infection in a Community Hospital Network

OBJECTIVE To describe the epidemiology of complex surgical site infection (SSI) following commonly performed surgical procedures in community hospitals and to characterize trends of SSI prevalence rates over time for MRSA and other common pathogens METHODS We prospectively collected SSI data at 29 community hospitals in the southeastern United States from 2008 through 2012. We determined the overall prevalence rates of SSI for commonly performed procedures during this 5-year study period. For each year of the study, we then calculated prevalence rates of SSI stratified by causative organism. We created log-binomial regression models to analyze trends of SSI prevalence over time for all pathogens combined and specifically for MRSA. RESULTS A total of 3,988 complex SSIs occurred following 532,694 procedures (prevalence rate, 0.7 infections per 100 procedures). SSIs occurred most frequently after small bowel surgery, peripheral vascular bypass surgery, and colon surgery. Staphylococcus aureus was the most common pathogen. The prevalence rate of SSI decreased from 0.76 infections per 100 procedures in 2008 to 0.69 infections per 100 procedures in 2012 (prevalence rate ratio [PRR], 0.90; 95% confidence interval [CI], 0.82–1.00). A more substantial decrease in MRSA SSI (PRR, 0.69; 95% CI, 0.54–0.89) was largely responsible for this overall trend. CONCLUSIONS The prevalence of MRSA SSI decreased from 2008 to 2012 in our network of community hospitals. This decrease in MRSA SSI prevalence led to an overall decrease in SSI prevalence over the study period. Infect Control Hosp Epidemiol 2016;37:519–52

Assessment of infectious diseases risks from dental aerosols in real-world settings

BACKGROUND: Infectious diseases physicians are leaders in assessing the health risks in a variety of community settings. An understudied area with substantial controversy is the safety of dental aerosols. Previous studies have used in vitro experimental designs and/or indirect measures to evaluate bacteria and viruses from dental surfaces. However, these findings may overestimate the occupational risks of dental aerosols. The purpose of this study was to directly measure dental aerosol composition to assess the health risks for dental healthcare personnel and patients. METHODS: We used a variety of aerosol instruments to capture and measure the bacterial, viral, and inorganic composition of aerosols during a variety of common dental procedures and in a variety of dental office layouts. Equipment was placed in close proximity to dentists during each procedure to best approximate the health risk hazards from the perspective of dental healthcare personnel. Devices used to capture aerosols were set at physiologic respiration rates. Oral suction devices were per the discretion of the dentist. RESULTS: We detected very few bacteria and no viruses in dental aerosols-regardless of office layout. The bacteria identified were most consistent with either environmental or oral microbiota, suggesting a low risk of transmission of viable pathogens from patients to dental healthcare personnel. When analyzing restorative procedures involving amalgam removal, we detected inorganic elements consistent with amalgam fillings. CONCLUSIONS: Aerosols generating from dental procedures pose a low health risk for bacterial and likely viral pathogens when common aerosol mitigation interventions, such as suction devices, are employed

'To live and die [for] Dixie': Irish civilians and the Confederate States of America

Around 20,000 Irishmen served in the Confederate army in the Civil War. As a result, they left behind, in various Southern towns and cities, large numbers of friends, family, and community leaders. As with native-born Confederates, Irish civilian support was crucial to Irish participation in the Confederate military effort. Also, Irish civilians served in various supporting roles: in factories and hospitals, on railroads and diplomatic missions, and as boosters for the cause. They also, however, suffered in bombardments, sieges, and the blockade. Usually poorer than their native neighbours, they could not afford to become 'refugees' and move away from the centres of conflict. This essay, based on research from manuscript collections, contemporary newspapers, British Consular records, and Federal military records, will examine the role of Irish civilians in the Confederacy, and assess the role this activity had on their integration into Southern communities. It will also look at Irish civilians in the defeat of the Confederacy, particularly when they came under Union occupation. Initial research shows that Irish civilians were not as upset as other whites in the South about Union victory. They welcomed a return to normalcy, and often 'collaborated' with Union authorities. Also, Irish desertion rates in the Confederate army were particularly high, and I will attempt to gauge whether Irish civilians played a role in this. All of the research in this paper will thus be put in the context of the Drew Gilpin Faust/Gary Gallagher debate on the influence of the Confederate homefront on military performance. By studying the Irish civilian experience one can assess how strong the Confederate national experiment was. Was it a nation without a nationalism

An integrated approach to determine three‐dimensional accretion geometries of tidal point bars: Examples from the Venice Lagoon

Low rates of lateral migration (centimetres to decimetres per year) combined with relatively high rates of vertical accretion (millimetres to centimetres per year) recorded in microtidal channels of the Venice Lagoon (Italy) give rise to point‐bar geometries and internal facies arrangements that differ substantially from widely accepted models of point‐bar sedimentary architecture. In this study, field data from the Venice Lagoon are combined with a three‐dimensional forward stratigraphic model, the ‘Point‐Bar Sedimentary Architecture Numerical Deduction’ (PB‐SAND), to predict the stratal geometries of point bars formed in aggradational settings. The PB‐SAND uses a combined geometric and stochastic modelling approach that can be constrained by field evidence. The model applied determines the geometry of four point bars generated by 9 to 11 m wide channels cutting through salt marshes. An iterative best‐fit modelling approach has been used to obtain multiple simulations for each case‐study, each of which fits the observations derived from the analysis of time‐series historical aerial photographs and 44 sedimentary cores. Results demonstrate how the geometry of the bars is determined by the development of two key stratal surfaces: the point‐bar brink and channel‐thalweg surfaces. These surfaces are defined by the progressive translation and vertical shift of the point‐bar brink (i.e. break of slope between bar top and bar slope) and the channel thalweg (i.e. deepest part of the channel) during bar evolution. The approach is used to: (i) reconstruct three‐dimensional point‐bar geometries; (ii) propose alternative reconstructions; (iii) provide insight to drive the acquisition of additional data to better constrain the proposed models; and (iv) provide insight into the mechanism of bar growth for slowly migrating channels in settings subject to relatively high rates of aggradation. This study highlights how interaction between styles of planform transformation and latero‐vertical shifts of meandering channels can determine the geometry of related sedimentary bodies

A Tabletop X-Ray Tomography Instrument for Nanometer-Scale Imaging: Integration of a Scanning Electron Microscope with a Transition-Edge Sensor Spectrometer

X-ray nanotomography is a powerful tool for the characterization of nanoscale materials and structures, but is difficult to implement due to competing requirements on X-ray flux and spot size. Due to this constraint, state-of-the-art nanotomography is predominantly performed at large synchrotron facilities. Compact X-ray nanotomography tools operated in standard analysis laboratories exist, but are limited by X-ray optics and destructive sample preparation techniques. We present a laboratory-scale nanotomography instrument that achieves nanoscale spatial resolution while changing the limitations of conventional tomography tools. The instrument combines the electron beam of a scanning electron microscope (SEM) with the precise, broadband X-ray detection of a superconducting transition-edge sensor (TES) microcalorimeter. The electron beam generates a highly focused X-ray spot in a metal target, while the TES spectrometer isolates target photons with high signal-to-noise. This combination of a focused X-ray spot, energy-resolved X-ray detection, and unique system geometry enable nanoscale, element-specific X-ray imaging in a compact footprint. The proof-of-concept for this approach to X-ray nanotomography is demonstrated by imaging 160 nm features in three dimensions in a Cu-SiO2 integrated circuit, and a path towards finer resolution and enhanced imaging capabilities is discussed.Comment: The following article has been submitted to Physical Review Applie

PROPHETIC: Prospective Identification of Pneumonia in Hospitalized Patients in the Intensive Care Unit

BACKGROUND: Pneumonia is the leading infection-related cause of death. Using simple clinical criteria and contemporary epidemiology to identify patients at high risk of nosocomial pneumonia should enhance prevention efforts and facilitate development of new treatments in clinical trials. RESEARCH QUESTION: What are the clinical criteria and contemporary epidemiology trends helpful in identifying patients at high risk of nosocomial pneumonia? STUDY DESIGN AND METHODS: Within the intensive care units of 28 United States hospitals, we conducted a prospective cohort study among adults hospitalized more than 48 hours and considered high risk for pneumonia (defined as treatment with invasive or noninvasive ventilatory support or high levels of supplemental oxygen). We estimated the proportion of high-risk patients developing nosocomial pneumonia. Using multivariable logistic regression, we identified patient characteristics and treatment exposures associated with increased risk of pneumonia development during the intensive care unit admission. RESULTS: Between February 6, 2016 and October 7, 2016, 4613 high-risk patients were enrolled. Among 1464/4613 (32%) high-risk patients treated for possible nosocomial pneumonia, 537/1464 (37%) met the study pneumonia definition. Among high-risk patients, a multivariable logistic model was developed to identify key patient characteristics and treatment exposures associated with increased risk of nosocomial pneumonia development (c-statistic 0.709, 95% confidence interval 0.686 to 0.731). Key factors associated with increased odds of nosocomial pneumonia included an admission diagnosis of trauma or cerebrovascular accident, receipt of enteral nutrition, documented aspiration risk, and receipt of systemic antibacterials within the preceding 90 days. INTERPRETATION: Treatment for nosocomial pneumonia is common among intensive care unit patients receiving high levels of respiratory support, yet more than half of patients treated do not fulfill standard diagnostic criteria for pneumonia. Application of simple clinical criteria may improve the feasibility of clinical trials of pneumonia prevention and treatment by facilitating prospective identification of patients at highest risk

Short Operative Duration and Surgical Site Infection Risk in Hip and Knee Arthroplasty Procedures

OBJECTIVE To determine the association (1) between shorter operative duration and surgical site infection (SSI) and (2) between surgeon median operative duration and SSI risk among first-time hip and knee arthroplasties. DESIGN Retrospective cohort study SETTING A total of 43 community hospitals located in the southeastern United States. PATIENTS Adults who developed SSIs according to National Healthcare Safety Network criteria within 365 days of first-time knee or hip arthroplasties performed between January 1, 2008 and December 31, 2012. METHODS Log-binomial regression models estimated the association (1) between operative duration and SSI outcome and (2) between surgeon median operative duration and SSI outcome. Hip and knee arthroplasties were evaluated in separate models. Each model was adjusted for American Society of Anesthesiology score and patient age. RESULTS A total of 25,531 hip arthroplasties and 42,187 knee arthroplasties were included in the study. The risk of SSI in knee arthroplasties with an operative duration shorter than the 25 th percentile was 0.40 times the risk of SSI in knee arthroplasties with an operative duration between the 25 th and 75 th percentile (risk ratio [RR], 0.40; 95% confidence interval [CI], 0.38–0.56; P <.01). Short operative duration did not demonstrate significant association with SSI for hip arthroplasties (RR, 1.04; 95% CI, 0.79–1.37; P =.36). Knee arthroplasty surgeons with shorter median operative durations had a lower risk of SSI than surgeons with typical median operative durations (RR, 0.52; 95% CI, 0.43–0.64; P <.01). CONCLUSIONS Short operative durations were not associated with a higher SSI risk for knee or hip arthroplasty procedures in our analysis. Infect. Control Hosp. Epidemiol. 2015;36(12):1431–143