Transcriptome responses in enrofloxacin-resistant strains of Aeromonas hydrophila exposed to Forsythia suspensa

Abstract Forsythia suspensa is a traditional Chinese medicine with antibacterial and anti-inflammatory effects. In this study, the transcriptomes of enrofloxacin (ENR)-resistant strains of Aeromonas hydrophila (ATCC7966-RS) and ENR-resistant A. hydrophila treated with F. suspensa (ATCC7966-RL) were obtained from 9,647,670 and 8,352,378 raw sequence reads, respectively. After the raw sequence reads were filtered and quality checked, the results showed that 8,576,608 and 7,482,820 clean reads were obtained from the ATCC7966-RS and ATCC7966-RL groups, respectively. The average read length was 125 bp for both strains, indicating successful sequencing of the A. hydrophila transcriptome. Furthermore, 829 genes were upregulated, and 214 genes were downregulated in the ATCC7966-RL group. The enrichment results showed that the significantly expressed genes were significantly enriched in map00280, valine, leucine and isoleucine degradation, and map00071, fatty acid degradation. The biological process enrichment of GO showed that the differentially expressed genes were significantly enriched in metabolic processes, including carboxylic acid decomposition, organic acid decomposition, amino acid decomposition, decomposition of organic nitrogen compounds and fatty acid oxidation. Single nucleotide polymorphisms (SNPs) in 82 genes with missense mutations were upregulated, and 31 genes with missense mutations were downregulated in the ATCC7966-RS and ATCC7966-RL groups. This study will provide information to recognize the differential expression of genes and the specific metabolic pathways associated with the resistance of A. hydrophila after F. suspensa treatment.