Dataset Information

NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test

ABSTRACT: Whole genome sequencing (WGS) enables high resolution typing of bacteria up to the single nucleotide polymorphism (SNP) level. WGS is used in clinical microbiology laboratories for infection control, molecular surveillance and outbreak analyses. Given the large palette of WGS reagents and bioinformatics tools, the Swiss clinical bacteriology community decided to conduct a ring trial (RT) to foster harmonization of NGS-based bacterial typing. The RT aimed at assessing methicillin-susceptible Staphylococcus aureus strain relatedness from WGS and epidemiological data. The RT was designed to disentangle the variability arising from differences in sample preparation, SNP calling and phylogenetic methods. Nine laboratories participated. The resulting phylogenetic tree and cluster identification were highly reproducible across the laboratories. Cluster interpretation was, however, more laboratory dependent, suggesting that an increased sharing of expertise across laboratories would contribute to further harmonization of practices. More detailed bioinformatic analyses unveiled that while similar clusters were found across laboratories, these were actually based on different sets of SNPs, differentially retained after sample preparation and SNP calling procedures. Despite this, the observed number of SNP differences between pairs of strains, an important criterion to determine strain relatedness given epidemiological information, was similar across pipelines for closely related strains when restricting SNP calls to a common core genome defined by S. aureus cgMLST schema. The lessons learned from this pilot study will serve the implementation of larger-scale RT, as a mean to have regular external quality assessments for laboratories performing WGS analyses in a clinical setting.

SUBMITTER: Dylus D

PROVIDER: S-EPMC7793906 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:INTRODUCTION:Hospital and ambulatory care systems are rapidly building their virtual care capacity in response to the novel coronavirus (COVID-19) pandemic. The use of resident trainees in telemedicine is one area of potential development and expansion. To date, however, training opportunities in this field have been limited, and residents may not be adequately prepared to provide high-quality telemedicine care. AIM:This study evaluates the impact of an adapted telemedicine Objective Structured Clinical Examination (OSCE) on telemedicine-specific training competencies of residents. SETTING:Primary Care Internal Medicine residents at a large urban academic hospital. PROGRAM DESCRIPTION:In March 2020, the New York University Grossman School of Medicine Primary Care program adapted its annual comprehensive OSCE to a telemedicine-based platform, to comply with distance learning and social distancing policies during the COVID-19 pandemic. A previously deployed in-person OSCE on the subject of a medical error was adapted to a telemedicine environment and deployed to 23 primary care residents. Both case-specific and core learning competencies were assessed, and additional observations were conducted on the impact of the telemedicine context on the encounter. PROGRAM EVALUATION:Three areas of telemedicine competency need were identified in the OSCE case: technical proficiency; virtual information gathering, including history, collateral information collection, and physical exam; and interpersonal communication skills, both verbal and nonverbal. Residents expressed enthusiasm for telemedicine training, but had concerns about their preparedness for telemedicine practice and the need for further competency and curricular development. DISCUSSION:Programs interested in building capacity among residents to perform telemedicine, particularly during the COVID-19 pandemic, can make significant impact in their trainees' comfort and preparedness by addressing key issues in technical proficiency, history and exam skills, and communication. Further research and curricular development in digital professionalism and digital empathy for trainees may also be beneficial.

Dataset Information

NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets