Genomic DNA of clinical M. abscessus strains

Introduction. Mycobacterium abscessus (Mab) is a pathogenic bacterium that can cause severe lung infections, particularly in individuals with cystic fibrosis. Mab colonies can exhibit either a smooth (S) or rough (R) morphotype, influenced by the presence or absence of glycopeptidolipids (GPL) on their surface, respectively. Despite the clinical significance of these morphotypes, the relationship between GPL levels, morphotype, and the pathogenesis of Mab infections remains poorly understood.
Gap Statement. The mechanisms and implications of GPL production and morphotypes in clinical Mab infections are unclear. There is a gap in understanding their correlation with infectivity and pathogenicity, particularly in patients with underlying lung disease.
Aim. This study aimed to investigate the correlation between Mab morphology, GPL, and infectivity by analysing strains from cystic fibrosis patients' sputum samples.
Methodology. Mab was isolated from patient sputum samples and categorised b..., DNA extraction and sequencing
Unseparated isolates were grown in 7H9OADCT on a shaker at 37 °C to an OD600 of 1.0-2.0. Genomic DNA was extracted with the CTAB method, eluted into 50µL of sterile water and stored at -20 °C.
Samples were transferred to the Genome Sciences Centre (UBC, Vancouver, Canada) for sequencing on the Illumina MiSeq platform (Illumina, San Diego, CA, USA). Each genome was sequenced to a 100-fold depth of coverage. FASTQ files of the paired-end reads were inspected for overall quality using the FastQC program and assembled using SPAdes v.3.9.0. Assembled genomes were aligned to the reference strain ATCC19977/ CIP104536 S through conserved genomic regions with Parsnp. Core genome single nucleotide polymorphisms (SNPs) identified from the alignment were then used to construct a phylogenetic tree, which was visualised with FigTree v.1.4.4., , # Genomic DNA of clinical M. abscessus strains

[https://doi.org/10.5061/dryad.7m0cfxq3r](https://doi.org/10.5061/dryad.7m0cfxq3r)

Sequence data of each sample have been uploaded as forward (R1) and reverse (R2) fastq files.\
Files are labelled with the sample name and forward/reverse designation e.g., Mab10_R1.fastq.gz (SampleName_ForwardRead.fastq.gz).

**DNA extraction and sequencing**

Unseparated isolates were grown in 7H9OADCT on a shaker at 37 °C to an OD600 of 1.0-2.0.  Genomic DNA was extracted with the CTAB method, eluted into 50µL of sterile water and stored at -20 °C.

Samples were transferred to the Genome Sciences Centre (UBC, Vancouver, Canada) for sequencing on the Illumina MiSeq platform (Illumina, San Diego, CA, USA). Each genome was sequenced to a 100-fold depth of coverage. FASTQ files of the paired-end reads were inspected for overall quality using the FastQC program and assembled using SPAdes v.3.9.0. Assembled genomes were aligned to tthe reference strain ATCC199...