RT Journal Article
T1 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
A1 Lamas Freire, Alexandre
A1 Garrido Maestu, Alejandro
A1 Prieto, Alberto
A1 Cepeda Sáez, Alberto
A1 Franco Abuín, Carlos Manuel
K1 Salmonella spp.
K1 Whole genome sequencing
K1 MinION
K1 Flongle
K1 Serotyping
K1 Antimicrobial resistance
K1 Virulence
AB 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.
PB Frontiers
SN 1664-302X
YR 2023
FD 2023-02-10
LK https://hdl.handle.net/10347/43675
UL https://hdl.handle.net/10347/43675
LA eng
NO Lamas A, Garrido-Maestu A, Prieto A, Cepeda A and Franco CM (2023) 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. 14:1254692. doi: 10.3389/fmicb.2023.1254692
DS Minerva
RD 28 abr 2026