Whole genome sequencing in the palm of your hand: how to implement a MinION Galaxy-based workflow in a food safety laboratory for rapid Salmonella spp. serotyping, virulence, and antimicrobial resistance gene identification

Alexandre Lamas; Alejandro Garrido-Maestu; Alberto Prieto; Alberto Cepeda; Carlos Manuel Franco

doi:10.3389/fmicb.2023.1254692

Whole genome sequencing in the palm of your hand: how to implement a MinION Galaxy-based workflow in a food safety laboratory for rapid Salmonella spp. serotyping, virulence, and antimicrobial resistance gene identification

Front Microbiol. 2023 Dec 1:14:1254692. doi: 10.3389/fmicb.2023.1254692. eCollection 2023.

Authors

Alexandre Lamas¹, Alejandro Garrido-Maestu², Alberto Prieto³, Alberto Cepeda¹, Carlos Manuel Franco¹

Affiliations

¹ Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition and Bromatology, Veterinary School, Universidade da Santiago de Compostela, Lugo, Spain.
² Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal.
³ Department of Animal Pathology (INVESAGA Group), Faculty of Veterinary Sciences, Universidade de Santiago de Compostela, Lugo, Spain.

Abstract

Introduction: Whole Genome Sequencing (WGS) implementation in food safety laboratories is a significant advancement in food pathogen control and outbreak tracking. However, the initial investment for acquiring next-generation sequencing platforms and the need for bioinformatic skills represented an obstacle for the widespread use of WGS. Long-reading technologies, such as the one developed by Oxford Nanopore Technologies, can be easily implemented with a minor initial investment and with simple protocols that can be performed with basic laboratory equipment.

Methods: Herein, we report a simple MinION Galaxy-based workflow with analysis parameters that allow its implementation in food safety laboratories with limited computer resources and without previous knowledge in bioinformatics for rapid Salmonella serotyping, virulence, and identification of antimicrobial resistance genes. For that purpose, the single use Flongle flow cells, along with the MinION Mk1B for WGS, and the community-driven web-based analysis platform Galaxy for bioinformatic analysis was used. Three strains belonging to three different serotypes, monophasic S. Typhimurium, S. Grancanaria, and S. Senftenberg, were sequenced.

Results: After 24 h of sequencing, enough coverage was achieved in order to perform de novo assembly in all three strains. After evaluating different tools, Flye de novo assemblies with medaka polishing were shown to be optimal for in silico Salmonella spp. serotyping with SISRT tool followed by antimicrobial and virulence gene identification with ABRicate.

Discussion: The implementation of the present workflow in food safety laboratories with limited computer resources allows a rapid characterization of Salmonella spp. isolates.

Keywords: Flongle; MinION; Salmonella spp.; antimicrobial resistance; serotyping; virulence; whole genome sequencing.