Through the looking glass: Genome, phenome, and interactome of salmonella enterica

Authors: Guard, Jean

Submitted to: Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/11/2022
Publication Date: 5/14/2022
Citation: Guard, J.Y. 2022. Through the looking glass: Genome, phenome, and interactome of salmonella enterica. Pathogens. 11(5):581. https://doi.org/10.3390/pathogens11050581.
DOI: https://doi.org/10.3390/pathogens11050581

Interpretive Summary: This review revisits previous concepts on biological phenomenon contributing to the success of Salmonella enterica subspecies I as a pathogen and expands upon them to include progress in epidemiology based on whole genome sequencing (WGS). Discussion goes beyond epidemiological uses of WGS to consider how phenotype, which is the biological character of an organism, can be correlated with its genotype to develop a knowledge of the interactome. Deciphering genome interactions with proteins, impact of metabolic flux, epigenetic modifications, and other complex biochemical processes will lead to new therapeutics, control measures, environmental remediations, and improved design of vaccines.

Technical Abstract: Progress in controlling and reducing foodborne illness from pathogens such as S. enterica subspecies I is critical for protecting public health and assuring the security of the food supply as the world encounters threats from climate change, supply issues, and an increasing population. Whole genome sequencing (WGS) of bacterial pathogens is now a commonly applied epidemiological tool used in outbreaks to identify sources, investigate trends in antibiotic resistances, remove contaminated product, and to limit sickness in people. However, WGS has not yet been fully integrated with molecular biology. Applied research intended to improve vaccines, avoid emergence of antibiotic resistance, and to eliminate pathogens within production systems requires biological confirmation prior to implementation. Therefore, subject areas such as biochemistry, molecular biology, environmental remediation, and pharmaceutical development will remain important, perhaps even more so, as promising information is gleaned from large WGS databases. Thus, biologists grounded in the ability to transfer bioinformatics system data to real world applications will be needed. Algorithms designed to include controls for biological considerations rather than pure mathematical prowess will be a challenge to develop because experts in several specialties will need to input parameters. The potential for alternative modes of gene expression from one genome poses a limit to how WGS can be applied for solving biological issues.