Fig. 3: Role of different plasmid genes in pOXA-48 biology.
From: Dissecting pOXA-48 fitness effects in clinical Enterobacterales using plasmid-wide CRISPRi screens
Identification of pOXA-48 genes producing significant fitness effects and their effect on plasmid stability. A Volcano plots obtained from two-sided permutation test assays in absence of selection (left) and in the presence of ertapenem (right). The Y axis shows the logarithmic transformation of the adjusted P value (FDR) from the permutation test, while the x axis indicates the median gene score (log2 fold-change values for sgRNAs targeting each gene from CRISPRi screens). Grey points indicate genes and intergenic regions which silencing was non-significant (i.e., −0.5 < gene score < 0.5; and P > 0.05). Genes and intergenic regions which silencing was detrimental in each condition are indicated in red, whereas genes which silencing was beneficial are coloured in blue. The labels of genes encoding hypothetical proteins are shown in grey. B pOXA-48 stability after 24 h of CRISPRi gene silencing of individual plasmid genes (X axis) in a subset of 5 strains (Y axis; 2 E. coli: EC22 and C288; and 3 K. pneumoniae: KPN18, KPN11 and KPN10) from our screenings (in presence of apramycin to select for pFR56apm). C pOXA-48 Copy Number measured silencing individual plasmid genes relative to control guide values for each strain tested (Log10 scale). Negative values indicate PCN decrease when silencing the indicated gene. Each point shows an individual replicate (n = 6). Bars correspond to median relative PCN values for all the replicates in each of the strains tested. Bars shaded in blue correspond to K. pneumoniae strains, and in pink to E. coli strains.
