Integrated multi-omics profiling reveals the role of the cfa gene in mediating penicillin antibiotics resistance and stress adaptability in Shigella sonnei.
Shigella is the pathogen of bacterial dysentery. With the widespread use of antibiotics, the burden of antibiotic resistance in Shigella has become increasingly pronounced. In this study, the cfa gene of ampicillin-resistant strain (Res) was knocked out and back-complemented strains were constructed. The susceptibility of Res and Δcfa strains to ampicillin was compared, and the molecular regulatory mechanisms of cfa gene on antibiotic resistance in Shigella were explored by screening the differentially expressed mRNAs, proteins, and metabolites of the two groups. In addition, we examined differences between the two groups in growth, biofilm formation, environmental stress (including temperature, pH, salt, oxidative stress, and carbon and nitrogen sources), and cytotoxicity. The sensitivity of Δcfa to ampicillin was increased 32-fold compared to the Res strain (64 µg/mL vs. 2 µg/mL). Compared to the Res strain, the Δcfa mutant exhibited a 16-fold increase in susceptibility to amoxicillin, a 16-fold increase in susceptibility to both penicillin and aztreonam, a 4-fold increase in susceptibility to cefotaxime, and a 2-fold increase in susceptibility to cefazolin, ceftazidime, ceftriaxone and tetracycline. The MICs of Δcfa-pcfa complemented strain was elevated to 4, 32, and 16 µg/mL for ampicillin, penicillin, and amoxicillin, respectively. The differential metabolites of the two groups were significantly enriched in the cysteine and methionine metabolic pathways (P < 0.05). Under no antibiotic stress, Δcfa grew faster than the Res strain and had greater biofilm formation capacity and environmental stress adaptation, but there was no significant difference in the virulence effect of the culture supernatant on Vero cell between the two groups. The cfa gene orchestrates sulfur metabolism and coordinates the cysteine-methionine biosynthetic pathway in bacteria. The cfa gene not only mediates penicillin antibiotics resistance mechanisms in Shigella sonnei but also modulates critical physiological processes.