Fig. 2: pOXA-48-encoded genes produce similar fitness effects across clinical strains.

Representation of the fitness effects associated with silencing each gene in pOXA-48 individually in the presence and absence of antibiotic pressure, and how conserved those effects are amongst strains. A Heatmap of CRISPRi gene scores at the end of the screening (t = 72 h, ~85 generations). Fitness effects associated with silencing each individual gene / intergenic region in the absence of selection (top panel) and in the presence of ertapenem (bottom panel). The score for each gene / intergenic region corresponds to the median log₂ fold-change of the sgRNAs targeting the element in the population (see “Methods”). Blue shades indicate those genes which silencing is detrimental (i.e., genes that are beneficial in that condition), whereas yellow shades correspond to genes which silencing is beneficial during the experiment (i.e., genes that are costly in that condition). Coding regions of pOXA-48 are shown with different colours indicating common functional clusters as shown on top. Genes and surrounding intergenic regions showing a significant deviation in the gene scores in both conditions are highlighted in the top. A fully annotated version of the figure is available in SFig. 7. B Pearson correlation matrices between strains’ gene scores at the end of the screening without (left) and with ertapenem (right). Blue shades indicate positive Pearson correlation coefficients, meaning similar tendencies in the overall screening results between the strains. Circle sizes indicate correlation absolute values from 0 to 1 (blue) or −1 to 0 (red).