World Aquaculture Singapore 2022

November 29 - December 2, 2022

Singapore

A METAGENOMICS WORKFLOW FOR RAPID DETECTION AND CHARACTERIZATION OF Group B Streptococcus IN FISH

Kae Hwan SIM*, Sri Harminda HARTANTYO, Jiaying HO, Vijitha MANOGARAN, Jia Qi LIM, Angela LI, and Kern Rei CHNG

National Centre for Food Science

Singapore Food Agency

TechQuest, 7 International Business Park Singapore 609919.

sim_kae_hwan@sfa.gov.sg

 



Group B Streptococcus (GBS), also known as Streptococcus agalactiae, is a versatile animal pathogen responsible for bovine mastitis and massive fish kill. Since the 2015 outbreak in Singapore, GBS Sequence Type (ST) 283 was shown to be a foodborne pathogen that can be transmitted via consumption of contaminated freshwater fish. The findings had subsequently led to the updated policy and guidelines on the sale of ready-to-eat (RTE) raw freshwater fish dishes in Singapore and the implementation of biosurveillance and risk analysis on this pathogenic bacterium. To support rapid screening and characterization of GBS ST283 in food samples, we have investigated the application of metagenomics sequencing to facilitate simultaneous detection and subtyping of GBS in a single proposed workflow. Without the need for isolation, metagenomic analytics can potentially shorten the turnaround time (TAT) for detection and sequencing typing of GBS in food samples from approximately 12 working days using a conventional approach to around 6 working days. Toman fish samples, which were not contaminated with GBS, were artificially spiked with GBS ST283 and used to benchmark the proposed metagenomics workflow. Our preliminary results suggest that the limit of detection (LOD) for GBS associated with the proposed metagenomics workflow is approximately at 2 log colony-forming unit (CFU) per 25 gram of fish sample. Notably, we were able to show that the proposed metagenomics workflow is able to concurrently detect and sequence type the GBS strain in the fish sample without the need for bacterial isolation and purification. In addition, the proposed metagenomics workflow was also successfully applied on one toman fish sample naturally contaminated by GBS (confirmed by the conventional approach) for parallel detection and sequence typing of GBS. Our preliminary results have clearly demonstrated the potential of the proposed metagenomics analytical workflow to support rapid screening of GBS in fish to facilitate and strengthen survey efforts for biosurveillance and risk assessment. More research and extensive validation are in progress to further develop and optimize the proposed workflow.