A metagenomics-based workflow for the detection and genomic characterization of GBS in raw freshwater fish

• Published in: Microbiology spectrum Vol. 12; no. 6; p. e0327623
• Main Authors: Sim, Kae Hwan, Ho, Jiaying, Lim, Jia Qi, Chan, Sheot Harn, Li, Angela, Chng, Kern Rei
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 07.05.2024
• Subjects: biosurveillance; Food Microbiology; food safety; foodborne pathogen; group B Streptococcus; metagenomics; Methods and Protocols; food safety; group B Streptococcus; biosurveillance; foodborne pathogen; metagenomics
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/spectrum.03276-23

The unexpected foodborne outbreak in Singapore in 2015 has accentuated Group B (GBS, ) sequence type 283 as an emerging foodborne pathogen transmitted via the consumption of contaminated raw freshwater fish. Isolation-based workflows utilizing conventional microbiological and whole-genome sequencing methods are commonly used to support biosurveillance efforts critical for the control management of this emerging foodborne pathogen. However, these isolation-based workflows tend to have relatively long turnaround times that hamper a timely response for implementing risk mitigation. To address this gap, we have developed a metagenomics-based workflow for the simultaneous detection and genomic characterization of GBS in raw freshwater fish. Notably, our validation results showed that this metagenomics-based workflow could achieve comparable accuracy and potentially better detection limits while halving the turnaround time (from 2 weeks to 5 days) relative to an isolation-based workflow. The metagenomics-based workflow was also successfully adapted for use on a portable long-read nanopore sequencer, demonstrating its potential applicability for real-time point-of-need testing. Using GBS in freshwater fish as an example, this work represents a proof-of-concept study that supports the feasibility and validity of metagenomics as a rapid and accurate test methodology for the detection and genomic characterization of foodborne pathogens in complex food matrices. The need for a rapid and accurate food microbiological testing method is apparent for a timely and effective foodborne outbreak response. This is particularly relevant for emerging foodborne pathogens such as Group B (GBS) whose associated food safety risk might be undercharacterized. By using GBS in raw freshwater fish as a case example, this study describes the development of a metagenomics-based workflow for rapid food microbiological safety testing and surveillance. This study can inform as a working model for various foodborne pathogens in other complex food matrices, paving the way for future methodological development of metagenomics for food microbiological safety testing.