Piloting data linkage in a prospective cohort study of a GP referral scheme to avoid unnecessary emergency department conveyance

BACKGROUND: UK Ambulance services are under pressure to safely stream appropriate patients away from the Emergency Department (ED). Even so, there has been little evaluation of patient outcomes. We investigated differences between patients who are conveyed directly to ED after calling 999 and those referred by an ambulance crew to a novel GP referral scheme. METHODS: This was a prospective study comparing patients from two cohorts, one conveyed directly to the ED (n = 4219) and the other referred to a GP by the on-scene paramedic (n = 321). To compare differences in patient outcomes, we include follow-up data of a smaller subset of each cohort (up to n = 150 in each) including hospital admission, history of long-term illness, previous ED attendance, length of stay, hospital investigations, internal transfers, 30-day re-admission and 10-month mortality. RESULTS: Older individuals, females, and those with minor incidents were more likely to be referred to a GP than conveyed directly to ED. Of those patients referred to the GP, only 22.4% presented at ED within 30 days. These patients were more likely to be admitted then than were those initially conveyed directly to ED (59% vs 31%). Those conveyed to ED had a higher risk of death compared to those who were referred to the GP (HR: 2.59; 95% CI 1.14–5.89), however when analyses were restricted to those who presented at ED within 30 days, there was no difference in mortality risk (HR: 1.45; 95% CI 0.58–3.65). CONCLUSIONS: Despite limited data and a small sample size, there were differences between patients conveyed directly to ED and those who were referred into GP care. Initial evidence suggests that referring individuals to a GP may provide an appropriate and safe alternative path of care. This pilot study demonstrated a need for larger scale, methodologically rigorous study to demonstrate the benefits of alternative conveyance schemes and recommend changes to the current system of urgent and emergency care

The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity

New bioinformatic tools are needed to analyze the growing volume of DNA sequence data. This is especially true in the case of secondary metabolite biosynthesis, where the highly repetitive nature of the associated genes creates major challenges for accurate sequence assembly and analysis. Here we introduce the web tool Natural Product Domain Seeker (NaPDoS), which provides an automated method to assess the secondary metabolite biosynthetic gene diversity and novelty of strains or environments. NaPDoS analyses are based on the phylogenetic relationships of sequence tags derived from polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, respectively. The sequence tags correspond to PKS-derived ketosynthase domains and NRPS-derived condensation domains and are compared to an internal database of experimentally characterized biosynthetic genes. NaPDoS provides a rapid mechanism to extract and classify ketosynthase and condensation domains from PCR products, genomes, and metagenomic datasets. Close database matches provide a mechanism to infer the generalized structures of secondary metabolites while new phylogenetic lineages provide targets for the discovery of new enzyme architectures or mechanisms of secondary metabolite assembly. Here we outline the main features of NaPDoS and test it on four draft genome sequences and two metagenomic datasets. The results provide a rapid method to assess secondary metabolite biosynthetic gene diversity and richness in organisms or environments and a mechanism to identify genes that may be associated with uncharacterized biochemistry