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Table 3 Illustrative quotes selected from the qualitative survey data, Belgium, 2019

From: 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

Topic Subtopic Illustrative quotes
Public health activities, other than those provided within the survey, that will benefit from the implementation of pathogen genomics Environmental monitoring “drinking water quality”
“air quality, home environmental quality”
Metagenomics “metagenomics for patients with no identified cause of illness using conventional methods”
“identification and characterization of new strains”
“insights in dysbiosis”
“microbiome analysis”
Other “discovery of a causal relation between a pathogen and a clinical disease (e.g. cancer)”
“vaccine development”
“phage therapy”
“early diagnostics of diseases due to slow growing pathogens”
“international tracking”
“monitoring of antiviral resistance”
Concerns, other than those provided within the survey, related to the implementation of pathogen genomics for public health practice Contextual data “harmonization of epidemiological data – most of the epidemiological data is very ‘messy’ or inconsistent, which makes systematic integration and surveillance unfeasible”
“data collection is already limited so newer technologies will not automatically improve this process but be redundant if the basics are not met”
Interpretation and education “how to interpret the result at clinical level”
“[…] they need to have a basic understanding (education) it order to understand and see cost/benefit of the whole picture”
“appropriate training of personnel for execution and interpretation”
“interpretation across sectors”
“multidisciplinary knowledge”
Ethics “[…] healthcare workers integrity concerns”
“in the HIV field, the phylogenetic analyses of virus permit to have an hindsight in paths of transmission – it is a very tricky topic in ethical and potentially legal aspects”
Other “does the identification prove that the pathogen poses a risk?”
“the fear that some actors in the field will try to abuse their power and monopolize this new technology – to be really valuable to patient management and public health it is required to offer access to all laboratories”
“high inter-laboratory variability”
“[…] standardization and facilities for data sharing need to be improved”
“the perceived utility and feasibility of pathogen genomics by public health practitioners is the biggest bottleneck of all – all the other concerns listed above can be tackled given the drive within the field to solve them in the first place”
Reasons, other than those provided within the survey, for not taking a training/course in the field of pathogen genomics   “lack of training adapted to public health needs”
“not applicable for a clinician”
“not my priority”
“not relevant for my practice”
Key drivers for implementation of pathogen genomics   “depends on the evolution in phenotypic typing”
“[…] the main driver the pressure by ECDC rather than a real need for public health […] the first and main driver should be clinical significance: improve quality of care for the patient”
“for bacteria, NGS will never fully replace classical methods for resistance testing, but would offer important complementary data”
“cost-effectiveness (e.g. replacing multiple tests): not particularly true for viruses, but obvious for bacteria”
Laboratory workflow integration Centralization “[…] should be overall coordinated and controlled by the federal public health authority”
“[…] in any scenario it will be important that sequence data are brought together in one databank for surveillance purposes”
Data sharing Organizational aspects “no central BE or EU organization”
“no central database, no clear guidelines on how and what to share”
“the bureaucracy involved in the transmission of data”
“the structure of public health in Belgium will not help sharing data”
“the required technical infrastructure”
Priority to publication “it is really a pity that priority to publication is an obstacle in the scientific world as it functions now”
One Health   “A better collaboration between the veterinary and human side might increase the use of NGS on the veterinary side”
“Monitoring the emergence and spread of zoonotic pathogens has been impacted negatively, by the introduction of WGS at the human side only”