Wiki¶

Input data¶

Raw data was transferred from Medmicro's athena server (athena.uct.ac.za) to Ilifu /scratch3/users/katiel/Clinton/

A reference genome for Serratia was downloaded from https://www.ncbi.nlm.nih.gov/genome/?term=Serratia%20marcescens%5bOrganism%5d&cmd=DetailsSearch
GCF_001034395.1_Serr_marc_UCI87_V1_genomic.fna.gz

QC, filtering, trimming¶

Raw data was QCed and filtered using my fastq_QC pipeline as follows

nextflow run kviljoen/fastq_QC --reads '/scratch/users/katiel/Clinton/*_R{1,2}_001.fastq.gz' -profile ilifu

QCed and trimmed reads can be found at

/scratch3/users/katiel/Clinton/2021-05-19-fastq_QC/pipeline_info/fastq_qc_report.html

Assembly¶

Next filtered, trimmed reads were assembled using the assembly module of the UCT-Tychus pipeline:

nextflow /users/katiel/Tychus/assembly.nf -profile assembly --assembly_out_dir /scratch/users/katiel/Clinton/Serratia_assembly/ --read_pairs '/scratch/users/katiel/Clinton/2021-05-19-fastq_QC/bbduk/*L001_trimmed_R{1,2}.fq' -resume

Assembly results, one file per sample (collated in R downstream) here:

/scratch3/users/katiel/Clinton/Serratia_assembly/AnnotatedContigs/

Plasmid detection¶

Info from Clinton:
These strains all exhibited resistance to the carbapenems, so carbapenem resistant Serratia marcescens. These are emerging resistant strains and we wanted to characterise relatedness and identify genes which may be responsible for the resistance, or plasmids carrying the resistance genes. We are not sure which genes are responsible for the phenotype. Previous papers identified blaVIM-1 and blaOXA-48 as the carbapenemase resistance genes, and these were carried on resistance plasmids. I don’t see any of the common carbapenemase genes in the table though (blaGES, blaIMP, blaNDM, blaOXA, blaVIM, blaKPC), so I’m not sure if they’re in the database and not detected or not in the database and not detected, or if there are other genes or mechanisms responsible here? I was thinking we could use a tree to determine which strains are related and which resistance genes they have in common and take it from there? We may also need to screen for plasmid rep types to see if they harbour similar plasmids.