Using Technology to Understand Antibiotic Resistance in Salmonella

Last April 7 and 8, in the framework of PANDOMIC exchange visits, the Institutul Național de Sănătate Publică (INSP) welcomed members from the Laboratoire national de santé and the Institutul Național de Cercetare-Dezvoltare Medico-Militară Cantacuzino (IC), in Bucharest, Romania.

The aim of the visit was to introduce the newly implemented long read sequencing workflow and bioinformatics tools, used to reconstruct genomic entities (from LNS). The purpose is to analyze multidrug resistance bacteria like Salmonella, addressing antibiotic resistant genes and their transferability.

The visit started with a laboratory tour at INSP and a team meeting. It was followed by wet-lab sessions – focused on technical laboratory activities – which provided insightful information regarding long read sequencing and tools relevant to the project. This way, INSP and IC learned more about the QIAgen MagAttract kit – an extraction technique enabling to extract and purify high molecular weight DNA – and the Oxford Nanopore rapid barcoding protocol – a technique to quickly labelling long DNA fragments to be sequenced in a single run.

The dry-lab session focused on computational workflows designed for generating high-quality circular assemblies from long read sequencing data. Considering that sequencing activities generate big data analytics, the semi-automated workflow aims to obtain a complete, contiguous genome composed of the main chromosome and plasmids – small transferable genomic entities that can carry antibiotic resistance – thanks to long read assembly.

This visit enabled to strengthen the collaboration among the consortium by sharing learning experiences.

Participants of this visit included: Arnaud Muller (LNS), Noémie Berg (LNS), Laura-Ioana Popa (IC), Daniela Cristea (IC), Mihaela Oprea (IC), Sorin Dinu (IC), Grigore-Mihaita Stan (IC), Teodora Vremera (INSP), Raluca Gatej (INSP), Ciprian Ilie (INSP), Mihaela Leustean (INSP), and Adina Gatea (INSP).