Transcriptional responses to tetracycline differ in highly syntenous strains of probiotic Bifidobacterium animalis subsp. lactis.. Bifidobacterium animalis subsp. lactis strain:Bl-04 or HN019

Commercial probiotic bacteria must be tested for acquired antibiotic resistance elements to avoid potential transfer to pathogens. The European Food Safety Authority (EFSA) recommends testing resistance using microdilution culture techniques, which have been used to establish inhibitory thresholds for the Bifidobacterium genus. Many Bifidobacterium animalis subsp. lactis strains exhibit increased resistance to tetracycline, historically attributed to the ribosomal protection gene tet(W). However, some strains that harbor genetically identical tet(W) genes exhibit various inhibition levels suggesting that other genetic elements contribute as well. In this report, we adapted several molecular assays to confirm the inhibition of B. lactis strains Bl-04 and HN019, and then employed RNA-seq to assess the transcriptional differences related to genomic polymorphisms. We detected specific stress responses to the antibiotic by correlating ATP concentration to viable genome copies from droplet digital PCR, and found that the bacteria were still metabolically active in high concentrations of the drug. Transcriptional analyses revealed that several polymorphic regions, particularly a novel multi-drug efflux transporter, were differentially expressed between the strains in each experimental condition, likely having phenotypic effects. We also found that the tet(W) gene was upregulated only during sub-inhibitory concentrations of tetracycline, while two novel tetracycline resistance genes were upregulated during high concentrations. Furthermore, many genes involved in amino acid metabolism and transporter function were upregulated while genes for complex carbohydrate utilization, protein metabolism, and CRISPR-Cas were down-regulated. These results provide high-throughput means for assessing antibiotic resistance and show the network of genetic elements that contribute to the global tetracycline response between two highly related probiotic strains.