Similar protocols

Pipeline publication

[…] Bioanalyser (Agilent Technologies, Diegem, Belgium). The DNA band patterns were analysed by means of DiversiLab web-based software using Pearson correlation coefficient pairwise pattern matching and the unweighted pair group method with arithmetic mean (UPGMA) clustering algorithm to create dendrograms., The samples were fully sequenced using next-generation sequencing on the Illumina MiSeq platform (San Diego, CA, USA). The Nextera XT DNA protocol was followed using 1–1.5 ng of starting DNA and a v3 kit (600 cycles). The paired-end reads were barcode de-multiplexed into separate samples, and quality checked in order to remove adapter sequences and bases with a quality score of <25 using FastQC and Sickle software [, ]. The reads were de novo assembled into contigs using Abyss-pe, version 1.5.2 (k parameter = 63) [], with contigs of >500 bp being selected by means of an ad hoc script, and kept for further analysis., The in silico MLST analysis was made by comparing the whole-genome sequences against the Klebsiella pneumoniae Pub MLST database (http://bigsdb.pasteur.fr/klebsiella/klebsiella.html) in order to assign allelic numbers to all ST loci. Phyloviz software based on the goeBURST algorithm was used to visualise the evolutionary relationships among the isolates [, ]., The resistome of antimicrobial resistance genes was analysed using ResFinder-2.1 software (default identity thresholds [ID] 98%) provided by the Center for Genomic Epidemiology (http://www.genomicepidemiology.org) and the resources of the Pasteur MLST K. pneumoniae database, and by locally running the BLAST program. Previously described genes relating to AcrAB-TolC efflux pump-dependent and pump-independent tigecycline resistance mechanisms (acrR, ramR, marR, soxR, lon, rpsJ and rpoC) [, ], and chromosomal (mgrB, pmrA/pmrB, phoP/phoQ) and plasmidic (mcr-1 and mcr-2 […]

Pipeline specifications

Software tools FastQC, ABySS, BIGSdb, PHYLOViZ
Databases ResFinder
Organisms Klebsiella pneumoniae, Homo sapiens, Bacteria
Diseases Cerebrovascular Disorders, CADASIL, Brain Diseases
Chemicals Aminoglycosides, Heterocyclic Compounds, 2-Ring, Antimicrobial Cationic Peptides, Membrane Proteins, Peptides, Cyclic, Polymyxins, Transition Elements, Metals, Heavy, Naphthacenes, Hydrocarbons, Cyclic, Pyrimidines, Heterocyclic Compounds, 2-Ring, Heterocyclic Compounds, 2-Ring, Peptides, Cyclic