| dc.description.abstract | In order to counteract disease outbreaks, monitor pathogen populations, and allow preventive
measures to be put in place against pathogens, pathogens need to be attributed to putative sources.
To this extent source attribution may look at phenotypical and genotypical characteristics of the
pathogen to link it to a source. Proper designation to a source requires overcoming problems related
to the pathogen and sources characteristic, which may erase recognizable patterns differentiating
one serovar strain from another. However, no standard approach to source attribution exists, which
overcomes the problems and limitations inherent therein. No standard approach to all source
attribution tasks is likely to exist, however by combining different genotyping approaches using WGS
data pathogens can be attributed with a higher resolution. Here biological problems and technical
problems associated with source attribution, among which host range, host switching behavior,
genome plasticity, source designation, metadata annotation, problems with data, and
spatio-temporal dynamics are evaluated. These technical and biological problems are placed in
context of different phenotyping, genotyping and genotype-based microbial source attribution
approaches to give an intuitive overview of the strengths and weaknesses of the aforementioned
approaches. Agreeing with previous papers, we find that a combination of genotyping approaches is
the best way forward. However, WGS genotyping approaches require standardization before
universal application. We hope to highlight possible research directions, such as to what extent
genetic signals are associated with adaptation, and by proxy attributable to a source. Additionally, we
stressed the relevance of spatio-temporal data to expand source attribution capabilities. | |
