Pangenome Analysis of a Salmonella Enteritidis Population Links a Major Outbreak to a Gifsy-1-Like Prophage Containing Anti-Inflammatory Gene
            <i>gogB</i>

Svahn, Adam J.; Suster, C. J. E.; Chang, Sheryl L.; Rockett, Rebecca; E, Sim; Cliff, Oliver M.; Wang, Qinning; Arnott, Alicia; Ramsperger, Marc; Sorrell, Tania C.; Sintchenko, Vitali; Prokopenko, Mikhail

doi:10.1128/spectrum.02791-22

Microbiol Spectr

2023

DOI: 10.1128/spectrum.02791-22

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Pangenome Analysis of a Salmonella Enteritidis Population Links a Major Outbreak to a Gifsy-1-Like Prophage Containing Anti-Inflammatory Gene gogB

Adam J. Svahn

C. J. E. Suster

Sheryl L. Chang

et al.

Abstract: We examined 5 years of genomic and epidemiological data for the significant global foodborne pathogen, Salmonella enterica . Although Salmonella enterica subspecies enterica serovar Enteritidis ( S. Enteritidis ) is the leading cause of salmonellosis in the USA and Europe, prior to 2018 it was not endemic in the southern states of Australia.

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Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis

Schadron,

van den Beld,

Mughini-Gras

et al. 2024

Front. Microbiol.

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Improvements in sequencing quality, availability, speed and costs results in an increased presence of genomics in infectious disease applications. Nevertheless, there are still hurdles in regard to the optimal use of WGS for public health purposes. Here, we discuss the current state (“status quo”) and future directions (“quo vadis”) based on literature regarding the use of genomics in surveillance, hazard characterization and source attribution of foodborne pathogens. The future directions include the application of new techniques, such as machine learning and network approaches that may overcome the current shortcomings. These include the use of fixed genomic distances in cluster delineation, disentangling similarity or lack thereof in source attribution, and difficulties ascertaining function in hazard characterization. Although, the aforementioned methods can relatively easily be applied technically, an overarching challenge is the inference and biological/epidemiological interpretation of these large amounts of high-resolution data. Understanding the context in terms of bacterial isolate and host diversity allows to assess the level of representativeness in regard to sources and isolates in the dataset, which in turn defines the level of certainty associated with defining clusters, sources and risks. This also marks the importance of metadata (clinical, epidemiological, and biological) when using genomics for public health purposes.

show abstract

Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis

Schadron,

van den Beld,

Mughini-Gras

et al. 2024

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

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Pangenome Analysis of a Salmonella Enteritidis Population Links a Major Outbreak to a Gifsy-1-Like Prophage Containing Anti-Inflammatory Gene gogB

Cited by 1 publication

References 16 publications

Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis

Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis

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