BackgroundI was awarded the Mike and Carole Ralston award in 2013, which enabled me to go to England and acquire bacterial whole genome analysis skills at the Oxford Genomics Centre, Oxford University.MethodsThrough this collaboration, 139 Enterococcus faecium bacteraemia isolates (collected between ...
Sharma P, Gupta SK, Rolain JM. Whole genome sequencing of bacteria in cystic fibrosis as a model for bacterial genome adaptation and evolution. ExpertRev Anti. Infect Ther. 2014; 12:343-55. doi: 10. 1586/14787210.2014.887441Sharma P, Gupta SK, Rolain JM. 2014. Whole genome sequencing ...
Whole genome CRISPRi screening identifies druggable vulnerabilities in an isoniazid resistant strain of Mycobacterium tuberculosis In this work, authors utilise genome-wide CRISPRi screening to identify vulnerabilities in isoniazid-resistant strains of Mycobacterium tuberculosis. XinYue Wang , William J. Jow...
1.3.3 Changing landscape of bacterial genetics: whole genome sequencing (WGS) and linking phenotype to genotype Characterization of known pathogens encompasses defining the pathogen’s virulence and other adaptive features and establishing a link between the phenotype and the genotype. Bacterial genetics,...
Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DN
There was no difference in the length of the 16S rDNA sequences of 76 paired genome assemblies (Fig. 2A). Figure 2 Sequence similarity of 16S rRNA genes and whole genomes, and mutation detection. (A) Sequence alignment and length of 16S rRNA genes. (B) Genome distance analysis using the...
Whole genome sequencing and bioinformatic analysis To identify the polymorphisms associated with TCS resistance evolution, we sequenced 13 TRMs obtained from day 7 (4× MIC) to day 10 (16× MIC), exhibiting high resistance to TCS. Bacterial DNA was extracted using genomic DNA (gDNA) extraction ...
TORMES is an open-source, user-friendly pipeline for whole bacterial genome sequencing (WGS) analysis directly from raw Illumina paired-end sequenceing data. Sinceversion 1.1TORMES can also analyze already assembled genomes, alone or in combination with raw sequencing data. TORMES work with every ba...
As macrolide use continues to select for increased resistance inN. gonorrhoeae, both the RplD G70D and rarer binding site mutations should be targets for surveillance in future whole-genome sequencing studies. The rapid increase in the prevalence of strains with mosaicmtralleles conferring azithromycin...
In our dispersal assay, the most striking mutant was Tn5_13, which was entirely dispersal deficient on bothMucornetworks (Fig.3d) and low-agar medium (Supplementary Fig.5), suggesting a loss of motility. Using whole-genome sequencing, we discovered that the Tn5 transposon had disrupted thefliS...