Simple SummaryStreptococcus agalactiae (GBS) is a serious threat to farmed tilapia, which results in high mortality and seriously hinders tilapia farming development. The pathogenic mechanism of tilapia infected with GBS which die rapidly in production remains unknown. We provided a comprehensive comparative analysis of the tilapias infected with fish-derived GBS attenuated strain YM001 and its parental virulent strain HN016. The present study indicates that the interaction between phagocytes and GBS mediated by the activated complement system is key to GBS inducing tilapia acute bacterial meningitis. The low survival ability caused by reduced β-lactam antibiotics resistance is one of the important reasons YM001 lost its pathogenicity to tilapia. Our study provided a comprehensive cognition of the mechanism of acute bacterial meningitis caused by GBS.AbstractStreptococcus agalactiae is an important pathogen for tilapia meningitis. Most of the infected tilapia die rapidly in production, when the way to study the pathogenic mechanism of bacteria on host through chronic infection in laboratory is not comprehensive and accurate enough to elucidate the real pathogenic mechanism. The objective of this study was to investigate the mechanism of acute bacterial meningitis of tilapia caused by Streptococcus agalactiae (GBS), and provide a theoretical basis for its prevention and treatment. Duel RNA-seq, proteome analysis, histopathological analysis, plasma biochemical indexes, and blood routine examination were performed on tilapias infected with fish-derived GBS attenuated strain YM001 and its parental virulent strain HN016. The results showed that the contents of white blood cell (WBC), monocytes (MON), and neutrophil (NEU) were significantly lower in the HN016 group compared to that in the YM001 group (p < 0.05). Histopathological examination showed that there were partially lesions in the examined tissues of tilapia infected by HN016, while no obvious histopathological changes occurred in the YM001 group. The differential expressed genes (DEGs) and differential expressed proteins (DEPs) between YM001 and HN016 were mainly enriched in the beta-lactam resistance pathway (oppA1, oppA2, oppB, oppC, oppD, oppF, and mrcA). The DEGs DEPs between YM001-brain and HN016-brain were mainly enriched in the complement and coagulation cascades signaling pathway (C2a, c4b, c3b, c7, CD59, ITGB2, and ITGAX). The present study indicates that the interaction between phagocytes and GBS mediated by the activated complement system is the key to GBS inducing tilapia acute bacterial meningitis. The low survival ability caused by reduced β-lactam antibiotics resistance is one of the important reasons for why YM001 lost its pathogenicity to tilapia.