Examining the multitude of available methods for attributing sources to molecular infection and antimicrobial resistance

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.