The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data
Open accessAbstract
Serotyping forms the basis of national and international surveillance networks for Salmonella , one of the most prevalent foodborne pathogens worldwide (1 – 3). Public health microbiology is currently being transformed by whole-genome sequencing (WGS), which opens the door to serotype determination using WGS data. SeqSero ( www.denglab.info/SeqSero ) is a novel Web-based tool for determining Salmonella serotypes using high-throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants ( rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing (i) raw reads from genomes of 308 Salmonella isolates of known serotype; (ii) raw reads from genomes of 3,306 Salmonella isolates sequenced and made publicly available by GenomeTrakr, a U.S. national monitoring network operated by the Food and Drug Administration; and (iii) 354 other publicly available draft or complete Salmonella genomes. We also demonstrated Salmonella serotype determination from raw sequencing reads of fecal metagenomes from mice orally infected with this pathogen. SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization.
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Cites
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Self-citation
Cited by
Reimschuessel, R., Grabenstein, M., Guag, J., Nemser, S. M., Song, K., Qiu, J., Clothier, K. A., Byrne, B. A., Marks, S. L., Cadmus, K., et al. (2017) · Journal of Clinical Microbiology · doi:10.1128/jcm.02137-16 · Cited by 105
Self-citationHigh Throughput Sequencing for Detection of Foodborne Pathogens
Sekse, C., Holst-Jensen, A., Dobrindt, U., Johannessen, G. S., Li, W., Spilsberg, B., & Shi, J. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02029 · Cited by 98
Park, S. E., Pham, D. T., Pak, G. D., Panzner, U., Maria Cruz Espinoza, L., von Kalckreuth, V., Im, J., Mogeni, O. D., Schütt-Gerowitt, H., Crump, J. A., et al. (2021) · BMJ Global Health · doi:10.1136/bmjgh-2021-005659 · Cited by 50
Kagambèga, A., Hiott, L. M., Boyle, D. S., McMillan, E. A., Sharma, P., Gupta, S. K., Ramadan, H., Cho, S., Humayoun, S. B., Woodley, T. A., et al. (2021) · BMC Microbiology · doi:10.1186/s12866-021-02085-6 · Cited by 15
Metadata
- Authors
- Zhang, S., Yin, Y., Jones, M. B., Zhang, Z., Deatherage Kaiser, B. L., Dinsmore, B. A., Fitzgerald, C., Fields, P. I., & Deng, X.
- Venue
- Journal of Clinical Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2015-05
- Volume
- 53
- Issue
- 5
- Pages
- 1685-1692
- ISSN
- 0095-1137 (ISSN-L)
- 1098-660X
- OpenAlex
- W2164868452
- Cited by
- 423
- References
- 30
- FWCI
- 40.56
- Type
- journal article
- Language
- en
- Open access
- green
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- Zhang, S., Yin, Y., Jones, M. B., Zhang, Z., Deatherage Kaiser, B. L., Dinsmore, B. A., Fitzgerald, C., Fields, P. I., & Deng, X. (2015). Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data. Journal of Clinical Microbiology. https://doi.org/10.1128/jcm.00323-15
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