Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of Staphylococcus aureus in an intensive care unit

BACKGROUND  Strategies to prevent Staphylococcus aureus infection in hospitals focus on patient-to-patient transmission. We used whole-genome sequencing to investigate the role of colonized patients as the source of new S. aureus acquisitions, and the reliability of identifying patient-to-patient transmission using the conventional approach of spa typing and overlapping patient stay. METHODS Over 14 months, all unselected patients admitted to an adult intensive care unit (ICU) were serially screened for S. aureus. All available isolates (n = 275) were spa typed and underwent whole-genome sequencing to investigate their relatedness at high resolution. RESULTS Staphylococcus aureus was carried by 185 of 1109 patients sampled within 24 hours of ICU admission (16.7%); 59 (5.3%) patients carried methicillin-resistant S. aureus (MRSA). Forty-four S. aureus (22 MRSA) acquisitions while on ICU were detected. Isolates were available for genetic analysis from 37 acquisitions. Whole-genome sequencing indicated that 7 of these 37 (18.9%) were transmissions from other colonized patients. Conventional methods (spa typing combined with overlapping patient stay) falsely identified 3 patient-to-patient transmissions (all MRSA) and failed to detect 2 acquisitions and 4 transmissions (2 MRSA). CONCLUSIONS Only a minority of S. aureus acquisitions can be explained by patient-to-patient transmission. Whole-genome sequencing provides the resolution to disprove transmission events indicated by conventional methods and also to reveal otherwise unsuspected transmission events. Whole-genome sequencing should replace conventional methods for detection of nosocomial S. aureus transmission

Umbrella species in marine systems: using the endangered humphead wrasse to conserve coral reefs

Extinction risk is closely tied to body size, home range, and species distribution. Quantifying home range is critical for conservation, and can enable the use of concepts such as \u27umbrella species\u27, whose conservation protects other species due to shared habitat. To determine the value of the humphead wrasse as an umbrella species for coral reef conservation, we conducted a multi-year study of humphead wrasse home range at Palmyra Atoll, Central Tropical Pacific, tagging juvenile, female, and male individuals with acoustic transmitters. We quantified home range using 2 metrics, length and area, and determined if these metrics were related to the sex and maturity status of the individual. We recorded individual movements during 5030 fish days, yielding detailed records for 14 individuals comprising 3 juveniles, 5 females, and 6 males. The home range of humphead wrasse measured over a 2 yr study was 0.4 to 14 km and changed with ontogeny. Females had larger home ranges than other reef fishes studied to date (n = 68), indicating value as an umbrella species for coral reefs. We compared the home range of the species to the size distribution of tropical marine protected areas (MPAs), and used a model to estimate the MPA length necessary to retain humphead wrasse. Most MPAs are too small to effectively protect the humphead wrasse

Unlocking Complex Soil Systems as Carbon Sinks: Multi-pool Management as the Key

Much research focuses on increasing carbon storage in mineral-associated organic matter (MAOM), in which carbon may persist for centuries to millennia. However, MAOM-targeted management is insufficient because the formation pathways of persistent soil organic matter are diverse and vary with environmental conditions. Effective management must also consider particulate organic matter (POM). In many soils, there is potential for enlarging POM pools, POM can persist over long time scales, and POM can be a direct precursor of MAOM. We present a framework for context-dependent management strategies that recognizes soils as complex systems in which environmental conditions constrain POM and MAOM formation

Patient safety incident capture resulting from incident reports: a comparative observational analysis

BACKGROUND: Patient safety incident (PSI) discovery is an essential component of quality improvement. When submitted, incident reports may provide valuable opportunities for PSI discovery. However, little objective information is available to date to quantify or demonstrate this value. The objective of this investigation was to assess how often Emergency Department (ED) incident reports submitted by different sources led to the discovery of PSIs. METHODS: A standardized peer review process was implemented to evaluate all incident reports submitted to the ED. Findings of the peer review analysis were recorded prospectively in a quality improvement database. A retrospective analysis of the quality improvement database was performed to calculate the PSI capture rates for incident reports submitted by different source groups. RESULTS: 363 incident reports were analyzed over a period of 18 months; 211 were submitted by healthcare providers (HCPs) and 126 by non-HCPs. PSIs were identified in 108 resulting in an overall capture rate of 31%. HCP-generated reports resulted in a 44% capture rate compared to 10% for non-HCPs (p \u3c 0.001). There was no difference in PSI capture between sub-groups of HCPs and non-HCPs. CONCLUSION: HCP-generated ED incident reports were much more likely to capture PSIs than reports submitted by non-HCPs. However, HCP reports still led to PSI discovery less than half the time. Further research is warranted to develop effective strategies to improve the utility of incident reports from both HCPs and non-HCPs

Draft genome sequence of Neurospora crassa strain FGSC 73

Citation: Baker, S. E., Schackwitz, W., Lipzen, A., Martin, J., Haridas, S., LaButti, K., . . . McCluskey, K. (2016). Draft genome sequence of Neurospora crassa strain FGSC 73. Genome Announcements, 3(2). doi:10.1128/genomeA.00074-15Citation: Baker, S., Schackwitz, W., Lipzen, A., . . . McCluskey, K. (2015). Draft Genome Sequence of Neurospora crassa Strain FGSC 73. Genome Announcements, 3(2), e00074-15. https://doi.org/10.1128/genomeA.00074-15We report the elucidation of the complete genome of the Neurospora crassa (Shear and Dodge) strain FGSC 73, a mat-a, trp-3 mutant strain. The genome sequence around the idiotypic mating type locus represents the only publicly available sequence for a mat-a strain. 40.42 Megabases are assembled into 358 scaffolds carrying 11,978 gene models. © 2015 Baker et al

Emergency department patient safety incident characterization: an observational analysis of the findings of a standardized peer review process

BACKGROUND: Emergency Department (ED) care has been reported to be prone to patient safety incidents (PSIs). Improving our understanding of PSIs is essential to prevent them. A standardized, peer review process was implemented to identify and analyze ED PSIs. The primary objective of this investigation was to characterize ED PSIs identified by the peer review process. A secondary objective was to characterize PSIs that led to patient harm. In addition, we sought to provide a detailed description of the peer review process for others to consider as they conduct their own quality improvement initiatives. METHODS: An observational study was conducted in a large, urban, tertiary-care ED. Over a two-year period, all ED incident reports were investigated via a standardized, peer review process. PSIs were identified and analyzed for contributing factors including systems failures and practitioner-based errors. The classification system for factors contributing to PSIs was developed based on systems previously reported in the emergency medicine literature as well as the investigators\u27 experience in quality improvement and peer review. All cases in which a PSI was discovered were further adjudicated to determine if patient harm resulted. RESULTS: In 24 months, 469 cases were investigated, identifying 152 PSIs. In total, 188 systems failures and 96 practitioner-based errors were found to have contributed to the PSIs. In twelve cases, patient harm was determined to have resulted from PSIs. Systems failures were identified in eleven of the twelve cases in which a PSI resulted in patient harm. CONCLUSION: Systems failures were almost twice as likely as practitioner-based errors to contribute to PSIs, and systems failures were present in the majority of cases resulting in patient harm. To effectively reduce PSIs, ED quality improvement initiatives should focus on systems failure reduction

Using botanic gardens and arboreta to help identify urban trees for the future

Societal Impact StatementDiversification of urban forests is essential to enhance their resilience to future biotic threats as well as those posed by a changing climate. Arboreta and botanic gardens host a wide range of plant material that can be evaluated to inform tree selection policy. This study demonstrates that plant functional traits, such as the water potential at leaf turgor loss, can be highly instructive when developing evidence-based recommendations for urban environments. However, if botanic collections are to fulfil a critical role in understanding plant response to environment, they should not be managed solely as visitor attractions but must have scientific objectives at the forefront of management policy.SummaryArboreta and botanic gardens host a multitude of species that can be utilized in research focused on improving diversity within urban forests. Higher tree species diversity will enhance the resilience of urban forests to abiotic and biotic threats and help deliver strategies that foster sustainable communities. Consequently, this study aims to demonstrate the value of botanic collections as a resource for research into tree species selection for more resilient urban landscapes. As water stress is a major constraint for trees in urban environments, understanding the drought tolerance of species is essential for urban tree selection. This study evaluates a key functional trait relating to drought tolerance. Using vapor pressure osmometry, the water potential at leaf turgor loss was evaluated for 96 species using plant material from seven botanic collections in North America and Europe. Leaf turgor loss contrasted widely in the temperate deciduous trees evaluated and, in summer, ranged from -1.7 MPa to -3.9 MPa. Significant differences in drought tolerance were also apparent across genera and closely related cultivars. Osmotic adjustment was shown to be a major physiological factor driving leaf turgor loss. A meta-analysis also demonstrated that leaf turgor loss was closely related to a drought-tolerance scale based on observations of tree performance under drought. Arboreta and botanic collections can play a vital role in the evaluation of plant material for urban environments, provided they are curated with scientific objectives at the forefront of management policy and are not managed purely as visitor attractions

Lithium protects against anaesthesia neurotoxicity in the infant primate brain

Exposure of infant animals, including non-human primates (NHPs), to anaesthetic drugs causes apoptotic death of neurons and oligodendrocytes (oligos) and results in long-term neurodevelopmental impairment (NDI). Moreover, retrospective clinical studies document an association between anaesthesia exposure of human infants and significant increase in NDI. These findings pose a potentially serious dilemma because millions of human infants are exposed to anaesthetic drugs every year as part of routine medical care. Lithium (Li) at clinically established doses is neuroprotective in various cerebral injury models. We therefore investigated whether Li also protects against anaesthesia neurotoxicity in infant NHPs. On postnatal day 6 NHPs were anaesthetized with the widely used anaesthetic isoflurane (ISO) for 5 h employing the same standards as in a human pediatric surgery setting. Co-administration of Li completely prevented the acute ISO-induced neuroapoptosis and significantly reduced ISO-induced apoptosis of oligodendroglia. Our findings are highly encouraging as they suggest that a relatively simple pharmacological manipulation might protect the developing primate brain against the neurotoxic action of anaesthetic drugs while not interfering with the beneficial actions of these drugs. Further research is needed to determine Li’s potential to prevent long-term NDI resulting from ISO anaesthesia, and to establish its safety in human infants

TOP2A and EZH2 Provide Early Detection of an Aggressive Prostate Cancer Subgroup.

Purpose: Current clinical parameters do not stratify indolent from aggressive prostate cancer. Aggressive prostate cancer, defined by the progression from localized disease to metastasis, is responsible for the majority of prostate cancer–associated mortality. Recent gene expression profiling has proven successful in predicting the outcome of prostate cancer patients; however, they have yet to provide targeted therapy approaches that could inhibit a patient\u27s progression to metastatic disease. Experimental Design: We have interrogated a total of seven primary prostate cancer cohorts (n = 1,900), two metastatic castration-resistant prostate cancer datasets (n = 293), and one prospective cohort (n = 1,385) to assess the impact of TOP2A and EZH2 expression on prostate cancer cellular program and patient outcomes. We also performed IHC staining for TOP2A and EZH2 in a cohort of primary prostate cancer patients (n = 89) with known outcome. Finally, we explored the therapeutic potential of a combination therapy targeting both TOP2A and EZH2 using novel prostate cancer–derived murine cell lines. Results: We demonstrate by genome-wide analysis of independent primary and metastatic prostate cancer datasets that concurrent TOP2A and EZH2 mRNA and protein upregulation selected for a subgroup of primary and metastatic patients with more aggressive disease and notable overlap of genes involved in mitotic regulation. Importantly, TOP2A and EZH2 in prostate cancer cells act as key driving oncogenes, a fact highlighted by sensitivity to combination-targeted therapy. Conclusions: Overall, our data support further assessment of TOP2A and EZH2 as biomarkers for early identification of patients with increased metastatic potential that may benefit from adjuvant or neoadjuvant targeted therapy approaches. ©2017 AACR