Salmonella enterica virulence databases and bioinformatic analysis tools development.
| Title: | Salmonella enterica virulence databases and bioinformatic analysis tools development. |
|---|---|
| Authors: | Han, Jing1,2 (AUTHOR) jing.han1@fda.hhs.gov, Tang, Hailin3 (AUTHOR), Zhao, Shaohua4 (AUTHOR), Foley, Steven L.1,2 (AUTHOR) Steven.Foley@fda.hhs.gov |
| Source: | Scientific Reports. 10/24/2024, Vol. 14 Issue 1, p1-16. 16p. |
| Subject Terms: | *FOODBORNE diseases, *WHOLE genome sequencing, *FOOD pathogens, *DATABASES, *GENETIC variation |
| Abstract: | Salmonella enterica, a prominent foodborne pathogen, contributes significantly to global foodborne illnesses annually. This species exhibits significant genetic diversity, potentially impacting its infectivity, disease severity, and antimicrobial resistance. Whole genome sequencing (WGS) offers comprehensive genetic insights that can be utilized for virulence assessment. However, existing bioinformatic tools for studying Salmonella virulence have notable limitations. To address this gap, a Salmonella Virulence Database with a non-redundant, comprehensive list of putative virulence factors was constructed. Two bioinformatic analysis tools, Virulence Factor Profile Assessment and Virulence Factor Profile Comparison tools, were developed. The former provides data on similarity to the reference genes, e-value, and bite score, while the latter assesses the presence/absence of virulence genes in Salmonella isolates and facilitates comparison of virulence profiles across multiple sequences. To validate the database and associated bioinformatic tools, WGS data from 43,853 Salmonella isolates spanning 14 serovars was extracted from GenBank, and WGS data previously generated in our lab was used. Overall, the Salmonella Virulence database and our bioinformatic tools effectively facilitated virulence assessment, enhancing our understanding of virulence profiles among Salmonella isolates and serovars. The public availability of these resources will empower researchers to assess Salmonella virulence comprehensively, which could inform strategies for pathogen control and risk evaluations associated with human illnesses. [ABSTRACT FROM AUTHOR] |
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| Items | – Name: Title Label: Title Group: Ti Data: Salmonella enterica virulence databases and bioinformatic analysis tools development. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Han%2C+Jing%22">Han, Jing</searchLink><relatesTo>1,2</relatesTo> (AUTHOR)<i> jing.han1@fda.hhs.gov</i><br /><searchLink fieldCode="AR" term="%22Tang%2C+Hailin%22">Tang, Hailin</searchLink><relatesTo>3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Zhao%2C+Shaohua%22">Zhao, Shaohua</searchLink><relatesTo>4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Foley%2C+Steven+L%2E%22">Foley, Steven L.</searchLink><relatesTo>1,2</relatesTo> (AUTHOR)<i> Steven.Foley@fda.hhs.gov</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Scientific+Reports%22">Scientific Reports</searchLink>. 10/24/2024, Vol. 14 Issue 1, p1-16. 16p. – Name: Subject Label: Subject Terms Group: Su Data: *<searchLink fieldCode="DE" term="%22FOODBORNE+diseases%22">FOODBORNE diseases</searchLink><br />*<searchLink fieldCode="DE" term="%22WHOLE+genome+sequencing%22">WHOLE genome sequencing</searchLink><br />*<searchLink fieldCode="DE" term="%22FOOD+pathogens%22">FOOD pathogens</searchLink><br />*<searchLink fieldCode="DE" term="%22DATABASES%22">DATABASES</searchLink><br />*<searchLink fieldCode="DE" term="%22GENETIC+variation%22">GENETIC variation</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Salmonella enterica, a prominent foodborne pathogen, contributes significantly to global foodborne illnesses annually. This species exhibits significant genetic diversity, potentially impacting its infectivity, disease severity, and antimicrobial resistance. Whole genome sequencing (WGS) offers comprehensive genetic insights that can be utilized for virulence assessment. However, existing bioinformatic tools for studying Salmonella virulence have notable limitations. To address this gap, a Salmonella Virulence Database with a non-redundant, comprehensive list of putative virulence factors was constructed. Two bioinformatic analysis tools, Virulence Factor Profile Assessment and Virulence Factor Profile Comparison tools, were developed. The former provides data on similarity to the reference genes, e-value, and bite score, while the latter assesses the presence/absence of virulence genes in Salmonella isolates and facilitates comparison of virulence profiles across multiple sequences. To validate the database and associated bioinformatic tools, WGS data from 43,853 Salmonella isolates spanning 14 serovars was extracted from GenBank, and WGS data previously generated in our lab was used. Overall, the Salmonella Virulence database and our bioinformatic tools effectively facilitated virulence assessment, enhancing our understanding of virulence profiles among Salmonella isolates and serovars. The public availability of these resources will empower researchers to assess Salmonella virulence comprehensively, which could inform strategies for pathogen control and risk evaluations associated with human illnesses. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Scientific Reports is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1038/s41598-024-74124-x Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 16 StartPage: 1 Subjects: – SubjectFull: FOODBORNE diseases Type: general – SubjectFull: WHOLE genome sequencing Type: general – SubjectFull: FOOD pathogens Type: general – SubjectFull: DATABASES Type: general – SubjectFull: GENETIC variation Type: general Titles: – TitleFull: Salmonella enterica virulence databases and bioinformatic analysis tools development. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Han, Jing – PersonEntity: Name: NameFull: Tang, Hailin – PersonEntity: Name: NameFull: Zhao, Shaohua – PersonEntity: Name: NameFull: Foley, Steven L. IsPartOfRelationships: – BibEntity: Dates: – D: 24 M: 10 Text: 10/24/2024 Type: published Y: 2024 Identifiers: – Type: issn-print Value: 20452322 Numbering: – Type: volume Value: 14 – Type: issue Value: 1 Titles: – TitleFull: Scientific Reports Type: main |
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