Whole-genome sequencing of bacterial strains

Genomic DNA from an overnight culture of each of the two strains was prepared using the QIAamp DNA minikit (Qiagen, Hilden, Germany) and was then subjected to whole-genome sequencing using the HiSeq X10 sequencing platform (Illumina, San Diego, CA, USA) with an approximate 250× coverage. Reads were de novo assembled into contigs using the program SPAdes v3.15.1 (44 (link)). Potential contaminations of WCHAc060012^T and WCHAc060115^T genomes were checked using CheckM v1.1.3 (45 (link)). Antimicrobial resistance genes were identified from genome sequences using the ABRicate program (https://github.com/tseemann/abricate) to query the ResFinder database 4.1 (https://cge.cbs.dtu.dk/services/ResFinder/).

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Qin J., Feng Y., Lü X, & Zong Z. (2021). Precise Species Identification for Acinetobacter: a Genome-Based Study with Description of Two Novel Acinetobacter Species. mSystems, 6(3), e00237-21.

Publication 2021

QIAamp DNA minikit HiSeq X10 sequencing platform

Antimicrobial Genes Genome Strains

Corresponding Organization : West China Hospital of Sichuan University

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Variable analysis

independent variables

Genomic DNA from overnight cultures of two strains

dependent variables

Whole-genome sequences of the two strains
Antimicrobial resistance genes identified from the genome sequences

control variables

Genomic DNA preparation using the QIAamp DNA minikit
Whole-genome sequencing using the HiSeq X10 sequencing platform
De novo assembly of reads into contigs using the SPAdes v3.15.1 program
Checking for potential contaminations of the genomes using CheckM v1.1.3
Identification of antimicrobial resistance genes using the ABRicate program and the ResFinder database 4.1

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