Fig. 5: Integrating GWAS and DCA to reveal the genetic networks of in vivo virulence in M. abscessus.
From: Mycobacterium abscessus pathogenesis identified by phenogenomic analyses
a, Representative image of Drosophila melanogaster infected with M. abscessus (magenta) resembles mycobacterial infection in other organisms (independently repeated over five times), with infection of phagocytes (green) and formation of granuloma-like structures (inset). b, Genome-wide association (using a linear model and applying Wald test statistics) reveals a putative secretion system protein and a peptide synthetase to be highly associated with Drosophila survival. The black horizontal line marks the multiple hypothesis testing threshold based on the number of independent variants. HP, hypothetical protein. c, Both variants align to clinical isolates with long survival, including a dominant circulating clone, within the subspecies M. a. abscessus. d, Deletion in MAB_0471 was associated with persistent respiratory infection in CF patients (two-sided unpaired t-test). e, CRISPR–dCas9 knockdown of MAB_0471 and MAB_3317 (unlike the essential gene yidC) did not affect growth in liquid culture (left) but in vivo silencing did lead to prolonged survival of infected Drosophila, as shown by Kaplan–Meier survival analysis (log-rank test, P = 7.6 × 10−17) generated from data from at least 18 infected flies per bacterial strain. f, Epistatic gene network, derived from DCA outputs, revealed direct coupling of MAB_0471 with other putative secretion system proteins including MAB_0472 and a distant connection to the peptide synthetase MAB_3317. g, In vivo silencing of MAB_0472 replicated virulence attenuation (log-rank test, P = 3.6 × 10−12).
