Improved annotation with <i>de novo</i> transcriptome assembly in four social amoeba species

Background: Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale. This is the first time this has been performed in these eukaryotic species. Results: An initial de novo transcriptome assembly was generated by Trinity for each species and then refined with Program to Assemble Spliced Alignments (PASA). The completeness and quality were assessed with the Benchmarking Universal Single-Copy Orthologs (BUSCO) and Transrate tools at each stage of the assemblies. The final datasets of 11,315-12,849 transcripts contained 5,610-7,712 updates and corrections to >50% of existing gene models including changes to hundreds or thousands of protein products. Putative novel genes are also identified and alternative splice isoforms were observed for the first time in P. pallidum, D. lacteum and D. fasciculatum. Conclusions: In taking a whole transcriptome approach to genome annotation with empirical data we have been able to enrich the annotations of four existing genome sequencing projects. In doing so we have identified updates to the majority of the gene annotations across all four species under study and found putative novel genes and transcripts which could be worthy for follow-up. The new transcriptome data we present here will be a valuable resource for genome curators in the Dictyostelia and we propose this effective methodology for use in other genome annotation projects

La recherche pour mieux soigner, l’exemple Antibioclic

International audienceCommunication orale invitée, plénière recherch

Computerized Decision Support System (CDSS) Use for Surveillance of Antimicrobial Resistance in Urinary Tract Infections in Primary Care

Abstract Background Hospital-based surveillance of antimicrobial resistance may be irrelevant as a guide to antimicrobial use for urinary tract infections (UTIs) in primary care. Objectives To highlight the value of online computerized decision support systems (CDSS) in providing information on the surveillance of antimicrobial resistance in community-acquired UTIs. Methods We collected the susceptibility profile for key antibiotics by type of UTI involving Escherichia coli from 2017 to 2020, using queries for UTI (Q-UTI) submitted to a French CDSS. We compared these results with those from the MedQual French surveillance system for community-acquired UTI and the European Antimicrobial Resistance Surveillance Network (EARS-NET) for invasive infections. Results We collected 43\mkern1mu591 Q-UTI, of which 10\mkern1mu192 (23%) involved E. coli: 40% cystitis, 32% male-UTI, and 27% pyelonephritis. Resistance was 41.3% (95% CI, 40.3%\textendash 42.2%) for amoxicillin, 16.6% (95% CI, 15.9%\textendash 17.3%) for fluoroquinolones, 6.6% (95% CI, 6.1%\textendash 7.0%) for third-generation cephalosporins (3GC), and 5.7% (95% CI, 5.2%\textendash 6.1%) for aminoglycosides. Resistance to amoxicillin was lower than that reported in MedQual (42.7%, P value\mkern1mu=\mkern1mu0.004), and in EARS-NET (55.2%, P value\mkern1mu&lt;\mkern1mu0.001). For fluoroquinolones, resistance was higher than in MedQual (12.0%, P value\mkern1mu&lt;\mkern1mu0.001) and EARS-NET (15.8%, P value\mkern1mu=\mkern1mu0.041). In complicated pyelonephritis and male UTI, fluoroquinolone resistance peaked at ∼20%. For 3GC, all UTI had higher resistance than in MedQual (3.5%, P value\mkern1mu&lt;\mkern1mu0.001), but lower than in EARS-NET (9.5%, P value\mkern1mu&lt;\mkern1mu0.001). Aminoglycoside resistance was not reported by MedQual, and was lower than in EARS-NET (7.1%, P value\mkern1mu&lt;\mkern1mu0.001). Conclusions CDSS can inform prescribers in real-time about the ecology and surveillance of E. coli resistance in community-acquired UTI. In complicated upper UTIs, they can underline the risk of empirical use of fluoroquinolones and suggest preferential use of 3GC

A Computerized Decision Support System (CDSS) for Antibiotic Prescription in Primary Care\textemdashAntibioclic: Implementation, Adoption and Sustainable Use in the Era of Extended Antimicrobial Resistance

Abstract Objectives To describe the implementation and use of a computerized decision support system (CDSS) for antibiotic prescription in primary care in France (Antibioclic). The CDSS targets 37 infectious diseases and has been freely available on a website since 2011. Methods Description and implementation of the architecture of a CDSS for antibiotic prescription in general practice. Analysis of the queries made between 2012 and 2018 on the CDSS by GPs. Analysis of two cross-sectional studies of users in 2014 and 2019. Results The number of queries increased from a median of 796/day [IQR, 578\textendash 989] in 2012 to 11\,125/day [5592\textendash 12\,505] in 2018. Unique users increased from 414/day [245\textendash 494] in 2012 to 5365/day [2891\textendash 5769] in 2018. Time taken to make a query was 2\,min [1.9\textendash 2.1]. Among 3\,542\,347 queries in 2018, 78% were for adults. Six situations accounted for ≥q50% of queries: cystitis; acute otitis media; acute sinusitis; community-acquired pneumonia; sore throat; and pyelonephritis. Queries concerned pathologies for which antibiotic prescription was necessary (64%), was conditional on additional clinical steps (34%) or was not recommended (2%). Most users (81%) were GPs, with median age of 38\,years [31\textendash 52] and 58% were female. Among the 4016 GPs who responded to the surveys, the vast majority (96%) reported using the CDSS during the consultation, with 24% systematically using Antibioclic to initiate an antibiotic course and 93% having followed the CDSS recommendation for the latest prescription. Most GPs were comfortable using the CDSS in front of a patient. Conclusions Antibioclic has been adopted and is widely used in primary care in France. Its interoperability could allow its adaptation and implementation in other countries

Paving the Way for the Implementation of a Decision Support System for Antibiotic Prescribing in Primary Care in West Africa: Preimplementation and Co-Design Workshop With Physicians

International audienceBackground: Suboptimal use of antibiotics is a driver of antimicrobial resistance (AMR). Clinical decision support systems (CDSS) can assist prescribers with rapid access to up-to-date information. In low- and middle-income countries (LMIC), the introduction of CDSS for antibiotic prescribing could have a measurable impact. However, interventions to implement them are challenging because of cultural and structural constraints, and their adoption and sustainability in routine clinical care are often limited. Preimplementation research is needed to ensure relevant adaptation and fit within the context of primary care in West Africa.Objective: This study examined the requirements for a CDSS adapted to the context of primary care in West Africa, to analyze the barriers and facilitators of its implementation and adaptation, and to ensure co-designed solutions for its adaptation and sustainable use.Methods: We organized a workshop in Burkina Faso in June 2019 with 47 health care professionals representing 9 West African countries and 6 medical specialties. The workshop began with a presentation of Antibioclic, a publicly funded CDSS for antibiotic prescribing in primary care that provides personalized antibiotic recommendations for 37 infectious diseases. Antibioclic is freely available on the web and as a smartphone app (iOS, Android). The presentation was followed by a roundtable discussion and completion of a questionnaire with open-ended questions by participants. Qualitative data were analyzed using thematic analysis.Results: Most of the participants had access to a smartphone during their clinical consultations (35/47, 74%), but only 49% (23/47) had access to a computer and none used CDSS for antibiotic prescribing. The participants considered that CDSS could have a number of benefits including updating the knowledge of practitioners on antibiotic prescribing, improving clinical care and reducing AMR, encouraging the establishment of national guidelines, and developing surveillance capabilities in primary care. The most frequently mentioned contextual barrier to implementing a CDSS was the potential risk of increasing self-medication in West Africa, where antibiotics can be bought without a prescription. The need for the CDSS to be tailored to the local epidemiology of infectious diseases and AMR was highlighted along with the availability of diagnostic tests and antibiotics using national guidelines where available. Participants endorsed co-design involving all stakeholders, including nurses, midwives, and pharmacists, as central to any introduction of CDSS. A phased approach was suggested by initiating and evaluating CDSS at a pilot site, followed by dissemination using professional networks and social media. The lack of widespread internet access and computers could be circumvented by a mobile app with an offline mode.Conclusions: Our study provides valuable information for the development and implementation of a CDSS for antibiotic prescribing among primary care prescribers in LMICs and may, in turn, contribute to improving antibiotic use, clinical outcomes and decreasing AMR