Strain-specific Recovery of S. sonnei from Artificially Contaminated Baby Carrots: Enhancing Food-safety Investigations with a Customized Shigella Detection Method Based on Genomically predicted Antibiotic Resistance Traits

Lang Yao; Ashley Cooper; Calvin Ho-Fung Lau; Alex Wong; Burton W Blais; Catherine D Carrillo

doi:10.1016/j.jfp.2024.100300

Strain-specific Recovery of S. sonnei from Artificially Contaminated Baby Carrots: Enhancing Food-safety Investigations with a Customized Shigella Detection Method Based on Genomically predicted Antibiotic Resistance Traits

J Food Prot. 2024 May 9;87(7):100300. doi: 10.1016/j.jfp.2024.100300. Online ahead of print.

Authors

Lang Yao¹, Ashley Cooper², Calvin Ho-Fung Lau³, Alex Wong⁴, Burton W Blais⁵, Catherine D Carrillo⁶

Affiliations

¹ Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada; Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada. Electronic address: Lang.Yao@inspection.gc.ca.
² Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada. Electronic address: Ashley.Cooper@inspection.gc.ca.
³ Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada. Electronic address: Calvin.Lau@inspection.gc.ca.
⁴ Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada. Electronic address: AlexWong@cunet.carleton.ca.
⁵ Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada; Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada. Electronic address: burton.blais@inspection.gc.ca.
⁶ Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada; Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada. Electronic address: catherine.carrillo@inspection.gc.ca.

PMID: 38734413
DOI: 10.1016/j.jfp.2024.100300

Abstract

Shigella spp. are Gram-negative gastrointestinal bacterial pathogens that cause bacillary dysentery or shigellosis in humans. Isolation of Shigella from outbreak-associated foods is often problematic due to the lack of selectivity of cultural enrichment broths. To facilitate Shigella recovery from foods, we have developed strain-specific enrichment media based on the genomically-predicted antimicrobial resistance (AMR) features of an outbreak-associated Shigella sonnei strain harboring resistance genes for streptomycin (STR) and trimethoprim (TMP). To assess performance of the method, baby carrots were artificially contaminated with the S. sonnei strain at low (2.4 CFU), medium (23.5 CFU), and high levels (235 CFU) along with 10-fold higher levels of a Shigella-inhibiting Escherichia coli strain. The target S. sonnei strain was successfully recovered from artificially-contaminated baby carrots when enriched in modified Tryptone Soya Broth (mTSB) supplemented with TMP, whereas Shigella was not recovered from Shigella broth (SB) or SB supplemented with STR. Quantitative PCR analysis indicated that supplementation of the enrichment broths with TMP or STR increased the relative proportion of S. sonnei in enrichment cultures, except at the lowest inoculation level for STR. Microbiome profiling of the baby carrot enrichment cultures conducted by 16S rRNA gene sequencing indicated that both SB-STR and mTSB-TMP repressed the growth of competing Enterobacteriaceae in the enrichment cultures, relative to SB without supplementation. Overall, improved Shigella recovery was achieved with the addition of the appropriate custom selective agent during cultural enrichments demonstrating that genomically informed custom selective enrichment of Shigella could be a valuable tool for supporting future foodborne shigellosis outbreak investigations.

Keywords: 16S rRNA gene sequencing; Antibiotics; Antimicrobial resistance; Custom enrichment; Shigella sonnei; Whole-genome sequencing.