Fish eDNA detections in ports mirror fishing fleet activities and highlight the spread of non-indigenous species in the Mediterranean Sea.

Gathering comprehensive marine biodiversity data can be difficult, costly and time consuming, preventing adequate knowledge of diversity patterns in many areas worldwide. We propose fishing ports as "natural" sinks of biodiversity information collected by fishing vessels probing disparate habitats, depths, and environments. By combining rapid environmental DNA metabarcoding (eDNA) surveys and data from public registers and Automatic Identification Systems, we show significant positive relationships between fishing fleet activities (i.e. fishing effort and characteristics of the fishing grounds) and the taxonomic fish assemblage composition in eleven Mediterranean fishing ports. Overall, we identified 160 fish and 123 invertebrate OTUs, including at least seven non-indigenous species, in some instances well beyond their known distribution areas. Our findings suggest that eDNA assessments of fishing harbours' waters might offer a rapid way to monitor marine biodiversity in unknown or under-sampled areas, as well as to reconstruct fishing catches, often underreported in several regions.

All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment.

Monitoring marine resource exploitation is a key activity in fisheries science and biodiversity conservation. Since research surveys are time consuming and costly, fishery-dependent data (i.e., derived directly from fishing vessels) are increasingly credited with a key role in expanding the reach of ocean monitoring. Fishing vessels may be seen as widely ranging data-collecting platforms, which could act as a fleet of sentinels for monitoring marine life, in particular exploited stocks. Here, we investigate the possibility of assessing catch composition of single hauls carried out by trawlers by applying DNA metabarcoding to the dense water draining from fishing nets just after the end of hauling operations (hereafter "slush"). We assess the performance of this approach in portraying ß-diversity and examining the quantitative relationship between species abundances in the catch and DNA amount in the slush (read counts generated by amplicon sequencing). We demonstrate that the assemblages identified using DNA in the slush satisfactorily mirror those returned by visual inspection of net content (about 71% of species and 86% of families of fish) and detect a strong relationship between read counts and species abundances in the catch. We therefore argue that this approach could be upscaled to serve as a powerful source of information on the structure of demersal assemblages and the impact of fisheries.

Environmental DNA effectively captures functional diversity of coastal fish communities.

Robust assessments of taxonomic and functional diversity are essential components of research programmes aimed at understanding current biodiversity patterns and forecasting trajectories of ecological changes. Yet, evaluating marine biodiversity along its dimensions is challenging and dependent on the power and accuracy of the available data collection methods. Here we combine three traditional survey methodologies (underwater visual census strip transects [UVCt], baited underwater videos [BUV] and small-scale fishery catches [SSFc]), and one novel molecular technique (environmental DNA metabarcoding [eDNA]-12S rRNA and cytochrome oxidase subunit 1 [COI]) to investigate their efficiency and complementarity in assessing fish diversity. We analysed 1,716 multimethod replicates at a basin scale to measure the taxonomic and functional diversity of Mediterranean fish assemblages. Taxonomic identities were investigated at species, genus and family levels. Functional identities were assessed using combinations of morphological, behavioural and trophic traits. We show that: (a) SSFc provided the higher taxonomic diversity estimates followed by eDNA, and then UVCt and BUV; (b) eDNA was the only method able to gather the whole spectrum of considered functional traits, showing the most functionally diversified and least redundant fish assemblages; and (c) the effectiveness of eDNA in describing functional structure reflected its lack of selectivity towards any considered functional trait. Our findings suggest that the reach of eDNA analysis stretches beyond taxon detection efficiency and provides new insights into the potential of metabarcoding in ecological studies.

Hooked on you: shape of attachment structures in cymothoid isopods reflects parasitic strategy.

BACKGROUND: Parasite attachment structures are critical traits that influence effective host exploitation and survival. Morphology of attachment structures can reinforce host specificity and niche specialisation, or even enable host switching. Therefore, it is important to understand the determinants of variation in attachment structures. Cymothoid isopods are striking ectoparasites of fishes that include the infamous 'tongue-biters.' They are known to parasitise hosts in one of four qualitatively distinct anatomical regions. Here, we quantify variation in cymothoid attachment structures - hook-like appendages called dactyli - and test whether differences in dactylus shape are correlated with parasite mode (where they attach), allometry, or both, using multivariate ordinary least squares regression. We also assess the influence of shared ancestry on shape using a molecular phylogeny to weight our models using phylogenetic generalised least squares regression. RESULTS: We find clear differences in shape between externally-attaching and internally-attaching cymothoids but also between anterior and posterior dactyli across various species with the same attachment mode. Allometric effects are significant for anterior but not posterior dactyli. Mouth-attaching species show greater shape variability than gill- and mouth-attaching species. We find no evidence that there are clade-specific patterns of association between parasite mode and dactylus shape. CONCLUSIONS: Parasite mode appears to be the main driver of attachment morphology. This likely reflects several components of parasite ecology including feeding and functional demands of attachment in different microhabitats. Geometric morphometric approaches to the quantification of shape variation of simple structures is an effective tool that provides new insights into the evolvability of parasite attachment.

Sponges as natural environmental DNA samplers.

At a time of unprecedented impacts on marine biodiversity, scientists are rapidly becoming persuaded by the potential of screening large swathes of the oceans through the retrieval, amplification and sequencing of trace DNA fragments left behind by marine organisms; an approach known as 'environmental DNA' (eDNA) [1]. In trying to circumvent the many challenges associated with water filtration and DNA isolation from environmental samples, significant investment is being made in high-tech solutions, such as automated underwater vehicles and robots [2]. Here, instead, we explored a simpler, alternative option, based on the recovery of eDNA from sponges (phylum Porifera), the planet's most effective water-filterers. We obtained sponge samples from Mediterranean and Antarctic surveys, extracted total DNA from their tissues, and obtained tens of thousands of fish DNA reads via metabarcoding, which were able to clearly distinguish samples from the two regions. One Antarctic sample yielded hundreds of reads from chinstrap penguin (Pygoscelis antarcticus) and Weddell seal (Leptonychotes weddellii). We argue that this 'natural sampler DNA' (nsDNA) approach is poised to become a powerful, affordable, universal tool for aquatic biodiversity monitoring globally.

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding.

Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focussed on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here, we employed eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea. We screened 68 water samples using a universal eukaryotic COI barcode region and detected highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions. Less than 15% of eukaryotic taxa were assigned to metazoans, most DNA sequences belonged to a variety of planktonic "protists," with over 50% of taxa unassigned at the phylum level, suggesting that the sampled communities host an astonishing amount of micro-eukaryotic diversity yet undescribed or absent from COI reference databases. Although such a predominance of micro-eukaryotes severely reduces the efficiency of universal COI markers to investigate vertebrate and other metazoans from aqueous eDNA, the study contributes to the advancement of rapid biomonitoring methods and brings us closer to a full inventory of extant marine biodiversity.

Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny.

Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical 'best case scenario' by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record-specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus-may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.

A unit-based intervention aimed at improving patient adherence to pharmacological thromboprophylaxis.

BACKGROUND: Pharmacological thromboprophylaxis is necessary among many hospitalised patients to prevent venous thromboembolism (VTE). However, a significant number of clinician-ordered doses are not administered with many doses refused by patients. We aimed to assess the impact and sustainability of a multifaceted intervention to improve medication adherence to pharmacological thromboprophylaxis. The intervention included a standardised nursing response to patient refusal, daily assessment of VTE prophylaxis usage and regular feedback on refusal rates. METHODS: We conducted a quasi-experimental study of patients admitted between January 2010 and November 2012 to one of six hospital intervention units (three medical and three oncology units) or five control units. The primary outcome was the proportion of VTE prophylaxis doses missed for any reason. RESULTS: A total of 20,208 admissions occurred at the six hospital units during the study period. In the pre-post analysis, the rate of missed and refused doses decreased significantly after the intervention (24.7% to 14.7% and 18.3% to 9.4%, respectively; p value <0.01 for both comparisons). In multiple regression models with interrupted time series analysis, the intervention was associated with an immediate and sustained decrease in missed (adjusted OR 0.64; 95% CI 0.55 to 0.74 and 0.98; 95%CI 0.97 to 0.99) and refused doses (adjusted OR per month 0.58; 95% CI 0.48 to 0.71 and 0.97; 95%CI 0.96 to 0.98). No immediate or sustained reduction in missed or refused doses was observed in the control units. CONCLUSIONS: Implementation of a multifaceted intervention resulted in an immediate and sustained decrease in the proportion of missed and refused doses of pharmacological thromboprophylaxis. Efforts aimed at increasing patient adherence are a promising approach to improve rates of VTE thromboprophylaxis administration.

Post-Acute Care Use and Hospital Readmission after Sepsis.

RATIONALE: The epidemiology of post-acute care use and hospital readmission after sepsis remains largely unknown. OBJECTIVES: To examine the rate of post-acute care use and hospital readmission after sepsis and to examine risk factors and outcomes for hospital readmissions after sepsis. METHODS: In an observational cohort study conducted in an academic health care system (2010-2012), we compared post-acute care use at discharge and hospital readmission after 3,620 sepsis hospitalizations with 108,958 nonsepsis hospitalizations. We used three validated, claims-based approaches to identify sepsis and severe sepsis. MEASUREMENTS AND MAIN RESULTS: Post-acute care use at discharge was more likely after sepsis, driven by skilled care facility placement (35.4% after sepsis vs. 15.8%; P < 0.001), with the highest rate observed after severe sepsis. Readmission rates at 7, 30, and 90 days were higher postsepsis (P < 0.001). Compared with nonsepsis hospitalizations (15.6% readmitted within 30 d), the increased readmission risk was present regardless of sepsis severity (27.3% after sepsis and 26.0-26.2% after severe sepsis). After controlling for presepsis characteristics, the readmission risk was found to be 1.51 times greater (95% CI, 1.38-1.66) than nonsepsis hospitalizations. Readmissions after sepsis were more likely to result in death or transition to hospice care (6.1% vs. 13.3% after sepsis; P < 0.001). Independent risk factors associated with 30-day readmissions after sepsis hospitalizations included age, malignancy diagnosis, hospitalizations in the year prior to the index hospitalization, nonelective index admission type, one or more procedures during the index hospitalization, and low hemoglobin and high red cell distribution width at discharge. CONCLUSIONS: Post-acute care use and hospital readmissions were common after sepsis. The increased readmission risk after sepsis was observed regardless of sepsis severity and was associated with adverse readmission outcomes.

Usability and impact of a computerized clinical decision support intervention designed to reduce urinary catheter utilization and catheter-associated urinary tract infections.

OBJECTIVE: To evaluate the usability and effectiveness of a computerized clinical decision support (CDS) intervention aimed at reducing the duration of urinary tract catheterizations. DESIGN: Retrospective cohort study. SETTING: Academic healthcare system. PATIENTS: All adult patients admitted from March 2009 through May 2012. INTERVENTION: A CDS intervention was integrated into a commercial electronic health record. Providers were prompted at order entry to specify the indication for urinary catheter insertion. On the basis of the indication chosen, providers were alerted to reassess the need for the urinary catheter if it was not removed within the recommended time. Three time periods were examined: baseline, after implementation of the first intervention (stock reminder), and after a second iteration (homegrown reminder). The primary endpoint was the usability of the intervention as measured by the proportion of reminders through which providers submitted a remove urinary catheter order. Secondary endpoints were the urinary catheter utilization ratio and the rate of hospital-acquired catheter-associated urinary tract infections (CAUTIs). RESULT: The first intervention displayed limited usability, with 2% of reminders resulting in a remove order. Usability improved to 15% with the revised reminder. The catheter utilization ratio declined over the 3 time periods (0.22, 0.20, and 0.19, respectively; P < .001), as did CAUTIs per 1,000 patient-days (0.84, 0.70, and 0.51, respectively; P < .001). CONCLUSIONS: A urinary catheter removal reminder system was successfully integrated within a healthcare system's electronic health record. The usability of the reminder was highly dependent on its user interface, with a homegrown version of the reminder resulting in higher impact than a stock reminder.

Timeliness and quality of surgical discharge summaries after the implementation of an electronic format.

BACKGROUND: As electronic discharge summaries (EDS) become more prevalent and health care systems increase their focus on transitions of care, analysis of EDS quality is important. The objective of this study was to assess the timeliness and quality of EDS compared with dictated summaries for surgical patients, which has not previously been evaluated. METHODS: A retrospective study was conducted of a sample of discharge summaries from surgical patients at an urban university teaching hospital before and after the implementation of an EDS program. Summaries were evaluated on several dimensions, including time to summary completion, summary length, and summary quality, which was measured on a 13-item scoring tool. RESULTS: After the exclusion of 5 patients who died, 195 discharge summaries were evaluated. Discharge summaries before and after EDS implementation were similar in admission types and discharge destinations of the patients. Compared with dictated summaries, EDS had equivalent overall quality (P = .11), with higher or equivalent scores on all specific quality aspects except readability. There was a highly significant statistical and clinical improvement in timeliness for electronic summaries (P < .01). Obvious use of copying and pasting was identified in 8% of discharge summaries and was associated with decreased readability (P = .02). CONCLUSIONS: The implementation of EDS can improve the timeliness of summary completion without sacrificing quality for surgical patients. Excessive copying and pasting can reduce the readability of discharge summaries, and strategies to discourage this practice without the use of appropriate editing should be used.

The readmission risk flag: using the electronic health record to automatically identify patients at risk for 30-day readmission.

BACKGROUND: Identification of patients at high risk for readmission is a crucial step toward improving care and reducing readmissions. The adoption of electronic health records (EHR) may prove important to strategies designed to risk stratify patients and introduce targeted interventions. OBJECTIVE: To develop and implement an automated prediction model integrated into our health system's EHR that identifies on admission patients at high risk for readmission within 30 days of discharge. DESIGN: Retrospective and prospective cohort. SETTING: Healthcare system consisting of 3 hospitals. PATIENTS: All adult patients admitted from August 2009 to September 2012. INTERVENTIONS: An automated readmission risk flag integrated into the EHR. MEASURES: Thirty-day all-cause and 7-day unplanned healthcare system readmissions. RESULTS: Using retrospective data, a single risk factor, ≥ 2 inpatient admissions in the past 12 months, was found to have the best balance of sensitivity (40%), positive predictive value (31%), and proportion of patients flagged (18%), with a C statistic of 0.62. Sensitivity (39%), positive predictive value (30%), proportion of patients flagged (18%), and C statistic (0.61) during the 12-month period after implementation of the risk flag were similar. There was no evidence for an effect of the intervention on 30-day all-cause and 7-day unplanned readmission rates in the 12-month period after implementation. CONCLUSIONS: An automated prediction model was effectively integrated into an existing EHR and identified patients on admission who were at risk for readmission within 30 days of discharge.

Clinical predictors of urgent findings on abdominopelvic CT in emergency department patients with Crohn's disease.

BACKGROUND: Patients with Crohn's disease (CD) are frequently exposed to diagnostic radiation in emergency departments (EDs). We aimed to examine clinical predictors of urgent abdominopelvic computed tomography (APCT) findings in this population. METHODS: A retrospective cross-sectional study was performed among adults with CD presenting to 2 emergency departments with a gastrointestinal chief complaint. The outcome, APON (abscess, perforation, obstruction, new or worsening non-CD-related findings), included APCTs with new or worsening CD-related or non-CD-related urgent findings. Variables with P < 0.05 in bivariate analyses were included in a multivariable logistic regression model, which was also used to develop a risk score for APON. RESULTS: A total of 481 APCTs were performed and 166 (34.5%) identified APON. Variables retained in the final model were history of intestinal obstruction (odds ratio [OR]: 3.78, 95% confidence interval [CI]: 2.27-6.28), history of intraabdominal abscess (OR: 2.64, 95% CI: 1.43 to 4.88), current hematochezia (OR: 0.38, 95% CI: 0.21 to 0.68), and white blood cell count >12,000/µL (OR: 2.49, 95% CI: 1.63 to 3.84). The c-statistic was 0.72. The risk score subtracts 1 point for hematochezia, and adds 1 point for each of the other variables. Among patients with a risk score of -1, the predicted and observed risk for APON was 9% and 6%, respectively. Any score greater than -1 had a predicted and observed risk of 19.8% and higher. CONCLUSIONS: An APON risk score of -1 is associated with a low risk of urgent APCT findings in patients with CD in the emergency department. Implementation of such a tool may support clinical decision-making in the ED setting.

The complexity and cost of drug regimens of older patients hospitalized with heart failure in the United States, 1998-2001.

BACKGROUND: Polypharmacy-the concurrent prescription of multiple medications-is a salient consideration in the care of older patients with heart failure. Little is known, however, about the complexity and financial burden of medical therapy in this population. METHODS: This is a study of the chronic medications prescribed at hospital discharge to patients 65 years or older hospitalized for heart failure in 2 cohorts separated by 27 months (April 1998-March 1999, n = 31 602; July 2000-June 2001, n = 30,774). Three utilization measures were assessed: the number of drugs, the estimated number of doses per day, and the estimated annual costs using the same cost standard (2003 average wholesale prices) for both samples. Utilization associated with population characteristics and between time frames was assessed in multivariable models. RESULTS: In 1998-1999, the mean number of drugs was 6.8, representing 10.1 doses daily at a cost of 3142 dollars/y, increasing to 7.5 drugs, 11.1 doses daily and 3823 dollars/y in 2000-2001 (P<.001 for all comparisons). After adjustment, the number of drugs increased by 12% and costs by 24% between samples. Factors associated with greater complexity and cost included diabetes (1.6 additional drugs and 1094 dollars/y additional cost), prior revascularization (1.3 drugs, 1154 dollars/y), and chronic lung disease (1.2 drugs, 814 dollars/y). Younger age and white race were also associated with more drugs and higher costs. CONCLUSIONS: The drug treatment of older patients with heart failure is characterized by rapidly increasing complexity and cost. Efforts should be directed toward optimizing the complex drug regimens of elderly patients with heart failure and multiple comorbidities.