Genomics Approaches to Improve the Recovery of Bacterial Pathogens in Foods

Foods are important vehicles for transmission of infectious bacterial pathogens. Reliable methods for detecting these organisms would ultimately result in fewer contaminated products released into the marketplace. Leveraging genomics tools such as whole genome sequencing (WGS) and metagenomics within the domain of food microbiology presents promising opportunities for enhancing diagnostic methods. This thesis demonstrates the value of genomics-based approaches for improving microbiological methods for foodborne pathogen detection. Two examples of recovery methods developed using WGS-informed antimicrobial resistance (AMR) traits are presented. Furthermore, the application of metabarcoding analysis investigating microbial compositions in food enrichments through 16s rDNA sequencing, is explored to gain a deeper understanding of pathogen growth relative to the background microbiota of food samples. The first case exemplifies a custom (strain-specific) selective enrichment approach for Shigella recovery from outbreak-associated food. This method incorporates enrichment media supplemented with antibiotics chosen based on the WGS-predicted AMR features of the target pathogen. Chapter 2 evaluated the feasibility of the antibiotic-supplemented custom enrichment media in enhancing the recovery of viable drug-resistant Shigella during competition with interfering microorganisms. Chapter 3 further investigated the performance of the custom selective enrichment media for Shigella recovery from baby carrots linked to historical shigellosis outbreak. The addition of the appropriate antibiotics in food enrichment media reduced the relative proportion of competing bacteria in the enrichment cultures and significantly enhanced the recovery of drug-resistant S. sonnei. This demonstrates the potential of genomically-informed selective enrichment in aiding foodborne shigellosis outbreak investigations. To explore whether the application of the genomcally-informed selective enrichment approach could be expanded for an entire pathogen species, the second example (chapter 4) presents an overview of a novel Salmonella selective enrichment broth (Minimal Salts Medium supplemented with amikacin) developed based on a species-specific aminoglycoside resistance genotype (aac(6’)-Iy or aac(6’)-Iaa). The performance of this medium relative to the current enrichment methods by Health Canada was evaluated using chicken feed contaminated with S. Enteritidis. While the novel approach did not provide improved selectivity relative to current methods, 16S rDNA sequencing provided insight into enrichment dynamics in the media evaluated that could be applied to further refinement of this methodology.

Name thesis:degree_name

Doctor of Philosophy (Ph.D.)

Level thesis:degree_level

Doctoral

Discipline thesis:degree_discipline

Biology

Grantor dc:publisher

Carleton University

Year dc:date.issued

2024

Author dc:creator

• Yao, Lang

Statement dc:rights

• Copyright © 2024 the author(s). Theses may be used for non-commercial research, educational, or related academic purposes only. Such uses include personal study, distribution to students, research and scholarship. Theses may only be shared by linking to the Carleton University Institutional Repository and no part may be copied without proper attribution to the author; no part may be used for commercial purposes directly or indirectly via a for-profit platform; no adaptation or derivative works are permitted without consent from the copyright owner.

Language dc:language.iso

en

DOI

10.22215/etd/2024-15928

OAI identifier oai:identifier

oai:carleton.scholaris.ca:20.500.14718/41772