Fig. 2: Serial passaging experiments and TraDIS analysis in human serum using a non-HMV-Kp SMKP838. | Nature Communications

Fig. 2: Serial passaging experiments and TraDIS analysis in human serum using a non-HMV-Kp SMKP838.

From: Rapid and Integrated Bacterial Evolution Analysis unveils gene mutations and clinical risk of Klebsiella pneumoniae

Fig. 2

a, b Serial passaging experiments with the parent (wild-type, WT) and mutS mutant (ΔmutS) strains in the presence of human serum. The red circles indicate the wells in which the strains/mutants grew. The geometric means and geometric standard deviations from three independent experiments are given. c Venn diagram of the gene mutations accumulated in SMKP838ΔmutS clones (#1 to #3) during the serial passaging experiments in the presence of human serum after 20 days. The accumulated gene mutations are listed in Supplemental Dataset 1. d Schematic of the TraDIS analysis. e Volcano plots of SMKP838 genomes determined via TraDIS analysis in the presence of 40 mg/L SPA (blue) and 4% (green) and 8% (red) human serum. The x-axis shows the change in abundance of each SMKP838 gene compared with that in the control (a log2-fold change). The y-axis shows the p values of the detected SMKP838 genes compared with the control. f The number of genes detected via TraDIS with significantly increased or decreased detection in human serum compared with the control (FDRp < 0.05). g Venn diagram representing the integration of a total of 140 mutant genes identified in the serial passaging experiment in the presence of human serum in (c) and the genes associated with serum resistance derived from TraDIS analysis performed in the presence of 4% (620 genes) and 8% serum (794 genes) in (f). Putative genes involved in serum resistance when mutations enhance their function in blue, and genes involved in serum resistance when their function is disrupted/decreased are marked in red (less or more than a 2-fold difference in detection in the presence of human serum vs. without human serum in TraDIS, FDRp < 0.05, respectively). h Serum susceptibility of the SMKP838 pORTMAGE mutants. These mutants possessed gene mutation(s) identified in the serial passage experiments in the presence of serum, as shown in (b). PORTserumA (LOCUS_14270: p.Ala293Thr + ramA: p.Tyr34His), PORTserumB (LOCUS_21770: p.Leu113Pro + ramA: p.Tyr34His and a spontaneous mutation: glnD:p.Gly841Glu), PORTserumC (LOCUS_21770: p.Leu113Pro + ramA: p.Tyr34His), PORTserumD (LOCUS_39850: p.Val134Ala + ramA: p.Tyr34His), PORTserumE (ramA: p.Tyr34His and a spontaneous mutation: LOCUS_21770: p.Leu181Pro), and PORTserumF (ramA: p.Cys78Arg).

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