Perceived utility and feasibility of pathogen genomics for public health practice: a survey among public health professionals working in the field of infectious diseases, Belgium, 2019

Abstract

Background: Pathogen genomics is increasingly being translated from the research setting into the activities of public health professionals operating at different levels. This survey aims to appraise the literacy level and gather the opinions of public health experts and allied professionals working in the field of infectious diseases in Belgium concerning the implementation of next-generation sequencing (NGS) in public health practice. Methods: In May 2019, Belgian public health and healthcare professionals were invited to complete an online survey containing eight main topics including background questions, general attitude towards pathogen genomics for public health practice and main concerns, genomic literacy, current and planned NGS activities, place of NGS in diagnostic microbiology pathways, data sharing obstacles, end-user requirements, and key drivers for the implementation of NGS. Descriptive statistics were used to report on the frequency distribution of multiple choice responses whereas thematic analysis was used to analyze free text responses. A multivariable logistic regression model was constructed to identify important predictors for a positive attitude towards the implementation of pathogen genomics in public health practice.

Next-generation sequencing: what are the needs in routine clinical microbiology? A survey among clinicians involved in infectious diseases practice

“…The potential application of NGS as a routine diagnostic tool in CML, has been recently reviewed ( 1 , 3 , 4 , 6 , 7 ). However, most of these publications did not explore the expectations of the end-users that are field clinicians.…”

“…In human microbiology, NGS use is indeed mostly limited to academic or reference laboratories. Most published NGS applications in microbiology relate to research studies, applying either metagenomics (mNGS) to explore microbiota or whole genome NGS to characterize specific microorganisms or analyze molecular epidemiology ( 2 , 4 ). Molecular epidemiological studies have certainly already improved several public health domains such as outbreak management, guidance of vaccination strategies and antibiotic stewardship.…”

The New Precision Stewards?

“…As pathogen genomics advance, what happens when existing roles (e.g., that of microbiologists) are expanded or new forms of expertise (e.g., computational biology) are added to the team? Van Goethem and colleagues (2020) anticipate this challenge, describing differing attitudes of pathogen genomics data providers and end-users in Belgium, capturing both existing knowledge gaps and accompanying gulfs in expectations for clinical and population health impact [ 146 ]. The study of attitudes and behavior, both individual and collective, will be needed to help IPC and ASP teams expand.…”

Using Genomics to Understand the Epidemiology of Infectious Diseases in the Northern Territory of Australia

“…As public health genomics is implemented, the monitoring and evaluation of the use of this technology is needed to maximise its impact [150,[156][157][158][159][160]. A framework for evaluation of public health genomics has recently been developed, including three phases: (i) the pre-analysis and analysis phase, including quality control, analysis of individual genomes, the number of specimens processed, turnaround times, and costings; (ii) the reporting and communication phase, including analysis of groups of isolates, the timing and utility of reports, and engagement with end-users to ensure processes are fit for purpose; and (iii) the implementation phase, including qualitative and quantitative assessment of public health impact [156].…”