Five-Year Outcomes After Implementing a Pain, Agitation, and Delirium Protocol in a Mixed Intensive Care Unit.

Objective: Assess for continued improvements in patient outcomes after updating our institutional sedation and analgesia protocol to include recommendations from the 2013 Society of Critical Care Medicine (SCCM) Pain, Agitation, and Delirium (PAD) guidelines. Methods: Retrospective before-and-after study in a mixed medical/surgical intensive care unit (ICU) at an academic medical center. Mechanically ventilated adults admitted from September 1, 2011 through August 31, 2012 (pre-implementation) and October 1, 2012 through September 30, 2017 (post-implementation) were included. Measurements included number of mechanically ventilated patients, APACHE IV scores, age, type of patient (medical or surgical), admission diagnosis, ICU length of stay (LOS), hospital LOS, ventilator days, number of self-extubations, ICU mortality, ICU standardized mortality ratio, hospital mortality, hospital standardized mortality ratio, medication data including as needed (PRN) analgesic and sedative use, and analgesic and sedative infusions, and institutional savings. Results: Ventilator days (Pre-PAD = 4.0 vs. Year 5 post = 3.2, P < .0001), ICU LOS (Pre-PAD = 4.8 days vs. Year 5 post = 4.1 days, P = .0004) and hospital LOS (Pre-PAD = 14 days vs. Year 5 post = 12 days, P < .0001) decreased after protocol implementation. Hospital standardized mortality ratio (Pre-PAD = 0.69 vs. Year 5 post = 0.66) remained constant; while, APACHE IV scores (Pre-PAD = 77 vs. Year 5 post = 89, P < .0001) and number of intubated patients (Pre-PAD = 1146 vs. Year 5 post = 1468) increased over the study period. Using the decreased ICU and hospital LOS estimates, it is projected the institution saved $4.3 million over the 5 years since implementation. Conclusions: Implementation of an updated PAD protocol in a mixed medical/surgical ICU was associated with a significant decrease in ventilator time, ICU LOS, and hospital LOS without a change in the standardized mortality ratio over a five-year period. These favorable outcomes are associated with a significant cost savings for the institution.

Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.

Shotgun metagenomics is a powerful, high-resolution technique enabling the study of microbial communities in situ. However, species-level resolution is only achieved after a process of 'binning' where contigs predicted to originate from the same genome are clustered. Such culture-independent sequencing frequently unearths novel microbes, and so various methods have been devised for reference-free binning. As novel microbiomes of increasing complexity are explored, sometimes associated with non-model hosts, robust automated binning methods are required. Existing methods struggle with eukaryotic contamination and cannot handle highly complex single metagenomes. We therefore developed an automated binning pipeline, termed 'Autometa', to address these issues. This command-line application integrates sequence homology, nucleotide composition, coverage and the presence of single-copy marker genes to separate microbial genomes from non-model host genomes and other eukaryotic contaminants, before deconvoluting individual genomes from single metagenomes. The method is able to effectively separate over 1000 genomes from a metagenome, allowing the study of previously intractably complex environments at the level of single species. Autometa is freely available at https://bitbucket.org/jason_c_kwan/autometa and as a docker image at https://hub.docker.com/r/jasonkwan/autometa under the GNU Affero General Public License 3 (AGPL 3).

Finding the niche: An interprofessional approach to defining oritavancin use criteria in the emergency department.

INTRODUCTION: Cellulitis is commonly treated in the emergency department (ED). Oritavancin is a novel, broad-spectrum antibiotic which provides an entire treatment course for cellulitis with one dose. However, optimal ED prescribing scenarios for oritavancin have not been well defined. The purpose of this study was to identify a population of ED patients with cellulitis who would be most appropriate to receive oritavancin. METHODS: This was a descriptive, retrospective study conducted at a Midwest healthcare system with two EDs. Over a 1 year period, all adult patients admitted from the ED to an inpatient ward with an ICD-10 diagnosis for cellulitis were reviewed using a priori defined criteria to identify potentially avoidable admissions (PAA). Potentially avoidable admissions were further characterized and compared to the non-avoidable admission population. Identified patient-specific criteria for PAAs were used to develop oritavancin inclusion/exclusion criteria and a case selection flowchart. RESULTS: Eighty-six patients were identified during the study period. Nine patients (10.5%) were deemed a PAA. A majority of the PAA population had at least one risk factor for treatment failure (55% with diabetes mellitus) and this group was significantly younger than the non-PAA group (42.2 vs 58.6 years; P = 0.01). There were no differences between the PAA group and the non-PAA group in regard to non-age demographics, other risk factors for outpatient treatment failure, comorbidities, or length of stay. CONCLUSION: Oritavancin is an outpatient treatment alternative for cellulitis patients whose only justification for planned admission is the presence of one or more risk factors for treatment failure.