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Research Project: Monitoring and Molecular Characterization of Antimicrobial Resistance in Foodborne Bacteria

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Title: Serotyping of sub-Saharan Africa Salmonella strains isolated from poultry feces using multiplex PCR and whole genome sequencing

Author
item KAGAMBEGA, ASSETA - Institute Of Science
item Hiott, Lari
item BOYLE, DAVID - Path
item McMillan, Elizabeth
item SHARMA, POONAM - Orise Fellow
item GUPTA, SUSHIM - Orise Fellow
item RAMADAN, HAZEM - Mansoura University
item CHO, SOHYUN - Orise Fellow
item Humayoun, Shaheen
item Woodley, Tiffanie
item BARRO, NICOLAS - Joseph Ki-Zerbo University
item Jackson, Charlene
item Frye, Jonathan

Submitted to: BMC Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/1/2021
Publication Date: 1/19/2021
Citation: Kagambega, A., Hiott, L.M., Boyle, D., Mcmillan, E.A., Sharma, P., Gupta, S., Ramadan, H., Cho, S., Humayoun, S.B., Woodley, T.A., Barro, N., Jackson, C.R., Frye, J.G. 2021. Serotyping of sub-Saharan Africa Salmonella strains isolated from poultry feces using multiplex PCR and whole genome sequencing. BMC Microbiology. 21(29):e2021. https://doi.org/10.1186/s12866-021-02085-6.
DOI: https://doi.org/10.1186/s12866-021-02085-6

Interpretive Summary: Salmonella enterica is a leading cause of food-borne diseases worldwide. Salmonella isolates are serotyped to allow tracking of outbreaks. This information is then used in food safety and public health activities to reduce cases of salmonellosis. This study compares two methods of seoryping on 225 clinical, environmental, food ,and veterinary isolates of Salmonella from Burkina Faso. The methods are SMART PCR which detects genes associated with serotypes, and Whole Genome Sequencing (WGS) followed by serotype prediction using SeqSero 2.0. Among the 225 Salmonella isolates, serotypes for 48 (21.33%) were determined by SMART PCR. One hundred and seventy-six new SMART codes were developed for serotypes found in Burkina Faso. Serotypes of 205 (91.1%) isolates were identified using SeqSero 2.0 for serovar prediction based on WGS data. This study determined that SeqSero 2.0 was more comprehensive for identifying serotypes from Burkina Faso than SMART PCR. WGS and SeqSero 2.0 analysis quickly and accurately determines Salmonella serotypes which can improve outbreak tracking and the rapid application of food safety and public health measures to stop outbreaks.

Technical Abstract: Salmonella enterica remains a leading cause of food-borne diseases worldwide. Serotype information is important in food safety and public health activities to reduce the burden of salmonellosis. In the current study, two methods were used to determine serotypes of 225 clinical, environmental, food and veterinary isolates of Salmonella from Burkina Faso. First, SMART PCR was used to determine the serovars of the S. enterica isolates. Second, serovar prediction based on whole genome sequencing (WGS) data was performed using SeqSero 2.0. Among the 225 Salmonella isolates, serotypes for 48 (21.33%) isolates were identified based on comparison to a panel of representative SMART codes previously determined for the 50 most common serovars in the United States. One hundred and seventy-six new SMART codes were developed for common and uncommon serotypes. WGS followed by SeqSero 2.0 determined the serotype for 205 (91.1%) isolates. This study determined that SeqSero 2.0 was more comprehensive for identifying serotypes from Burkina Faso than SMART PCR.