Capsular Typing Method for Streptococcus agalactiae Using Whole-Genome Sequence Data.

Group B streptococcus (GBS) capsular serotypes are major determinants of virulence and affect potential vaccine coverage. Here we report a whole-genome-sequencing-based method for GBS serotype assignment. This method shows strong agreement (kappa of 0.92) with conventional methods and increased serotype assignment (100%) to all 10 capsular types

From Genotype to Phenotype: Linking Bioinformatics and Medical Informatics Ontologies

A small group of around 40 people came together at the Chancellors Conference Centre in Manchester for the Ontologies Workshop, chaired by Alan Rector and Robert Stevens. The workshop was, rather strangely, spread over 2 half days. In hindsight, this programme worked very well as it gave people the opportunity to chat over a drink on the Saturday evening and share ideas, before launching into the second half on the following day. The participants were from various walks of life, all with a common interest in finding out more about ontologies and promoting collaborations between the medical informatics and bioinformatics ontology communities

Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

Escherichia colisequence type 131 (ST131) has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined. This study of the largest worldwide collection (n= 215) of sequenced ST131E. coliisolates to date demonstrates that the clonal expansion of two previously recognized antimicrobial-resistant clades, C1/H30R and C2/H30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to have emerged in the United States, with the expansion of the C2/H30Rx clade driven by the acquisition of ablaCTX-M-15-containing IncFII-like plasmid that has subsequently undergone extensive rearrangement. Several other evolutionary processes influencing the trajectory of this drug-resistant lineage are described, including sporadic acquisitions of CTX-M resistance plasmids and chromosomal integration ofblaCTX-Mwithin subclusters followed by vertical evolution. These processes are also occurring for another family of CTX-M gene variants more recently observed among ST131, theblaCTX-M-14/14-likegroup. The complexity of the evolutionary history of ST131 has important implications for antimicrobial resistance surveillance, epidemiological analysis, and control of emerging clinical lineages ofE. coli These data also highlight the global imperative to reduce specific antibiotic selection pressures and demonstrate the important and varied roles played by plasmids and other mobile genetic elements in the perpetuation of antimicrobial resistance within lineages.IMPORTANCEEscherichia coli, perennially a major bacterial pathogen, is becoming increasingly difficult to manage due to emerging resistance to all preferred antimicrobials. Resistance is concentrated within specificE. colilineages, such as sequence type 131 (ST131). Clarification of the genetic basis for clonally associated resistance is key to devising intervention strategies. We used high-resolution genomic analysis of a large global collection of ST131 isolates to define the evolutionary history of extended-spectrum beta-lactamase production in ST131. We documented diverse contributory genetic processes, including stable chromosomal integrations of resistance genes, persistence and evolution of mobile resistance elements within sublineages, and sporadic acquisition of different resistance elements. Both global distribution and regional segregation were evident. The diversity of resistance element acquisition and propagation within ST131 indicates a need for control and surveillance strategies that target both bacterial strains and mobile genetic elements

Internet Resources for Curriculum Development in Medical Education: An Annotated Bibliography

Curriculum development in medical education should be a methodical and scholarly, yet practical process that addresses the needs of trainees, patients, and society. To be maximally efficient and effective, it should build upon previous work and use existing resources. A conventional search of the literature is necessary, but insufficient for this purpose. The internet provides a rich source of information and materials. This bibliography is a guide to internet resources that are of use to curriculum developers, organized into 1) medical accreditation bodies, 2) topic-oriented resources, 3) general educational resources within medicine, and 4) general education resources beyond medicine

Accuracy of identifying incident stroke cases from linked healthcare data in UK Biobank

Objective: In UK Biobank (UKB), a large population-based prospective study, cases of many diseases are ascertained through linkage to routinely collected, coded national health datasets. We assessed the accuracy of these for identifying incident strokes. Methods: In a regional UKB sub-population (n=17,249), we identified all participants with ≥1 code signifying a first stroke after recruitment (incident stroke-coded cases) in linked hospital admission, primary care or death record data. Stroke physicians reviewed their full electronic patient records (EPRs) and generated reference standard diagnoses. We evaluated the number and proportion of cases that were true positives (i.e. positive predictive value, PPV) for all codes combined and by code source and type. Results: Of 232 incident stroke-coded cases, 97% had EPR information available. Data sources were: 30% hospital admission only; 39% primary care only; 28% hospital and primary care; 3% death records only. While 42% of cases were coded as unspecified stroke type, review of EPRs enabled a pathological type to be assigned in >99%. PPVs (95% confidence intervals) were: 79% (73%-84%) for any stroke (89% for hospital admission codes, 80% for primary care codes) and 83% (74%-90%) for ischemic stroke. PPVs for small numbers of death record and hemorrhagic stroke codes were low but imprecise. Conclusions: Stroke and ischemic stroke cases in UKB can be ascertained through linked health datasets with sufficient accuracy for many research studies. Further work is needed to understand the accuracy of death record and hemorrhagic stroke codes and to develop scalable approaches for better identifying stroke types.Rannikmae, Kristiina (2021). Accuracy of identifying incident stroke cases from linked healthcare data in UK Biobank [Dataset]. Dryad. https://doi.org/10.5061/dryad.w9ghx3fk