Multiresistant Arcobacter butzleri NGS

Initially, 30 multiresistant A. butzleri isolates were selected to perform NGS and genomic resistance marker identification. Bacterial DNA was extracted using the MagNA Pure 6 DNA and Viral NA SV Kit, and purification was performed from bacterial lysis on a MagNA Pure 96 System (Roche Applied Science, Manheim, Germany). Spectrophotometry using NanoDrop Technologies (Wilmington, DE, USA) was performed on all DNA samples for quantification and purity checks (260/280 and 260/230 ratios). Following DNA extraction, NGS was performed using an Illumina HiSeq 4000 machine (Integragen, Evry, France), quality tests were run using FastQC v0.11.9 (47 (link)), and raw (.fastq) data were cleaned using Sickle v1.33 (48 ) and assembled using SPAdes v3.10.1 (49 (link)). Species identification of all isolates was also performed using FastANI v1.1 (50 ) against A. butzleri reference genomes NCTC 12481 (51 (link)) and RM4018 (29 (link)). The studied genomes are available in the NCBI database under BioProject PRJNA798874, and the corresponding identifiers are presented in Table 2. Finally, the determination of associated antimicrobial genomic resistance markers was performed using Prokka v1.14.6 (52 (link)) annotation software and the Comprehensive Antibiotic Resistance Database (CARD) Resistance Gene Identifier webtool (card.mcmaster.ca/analyze/rgi) (53 (link)).

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Jehanne Q., Bénéjat L., Ducournau A., Bessède E, & Lehours P. (2022). Molecular Cut-off Values for Aliarcobacter butzleri Susceptibility Testing. Microbiology Spectrum, 10(4), e01003-22.

Publication 2022

Viral NA SV Kit MagNA Pure 96 System

Antibiotic resistance Antimicrobial Bacterial Bacterial dna Gene Genomic Resistance determination Spectrophotometry

Corresponding Organization : Inserm

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Variable analysis

independent variables

DNA extraction using MagNA Pure 6 DNA and Viral NA SV Kit
DNA purification on a MagNA Pure 96 System
Quantification and purity checks using NanoDrop Technologies
Next-generation sequencing (NGS) using Illumina HiSeq 4000 machine
Quality tests using FastQC v0.11.9
Raw data cleaning using Sickle v1.33
Genome assembly using SPAdes v3.10.1
Species identification using FastANI v1.1
Genomic resistance marker identification using Prokka v1.14.6 and CARD Resistance Gene Identifier

dependent variables

Identification of antimicrobial genomic resistance markers

control variables

30 multiresistant Arcobacter butzleri isolates initially selected for the study

positive controls

Reference genomes NCTC 12481 and RM4018 used for species identification

negative controls

No explicit negative controls mentioned

Annotations

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