Perfect timing! Tonight I watched Richard Goodman’s London Calling 2022 session titled “The bacterial black market: utilising sequencing to study the inter-cellular and intra-cellular transfer of AMR genes in bacteria.” I have been working on an AMR detection protocol using digital PCR for class today. Goodman is at the Liverpool School of Tropical Medicine in the UK. They began describing the impact of antimicrobial resistance (AMR) and what would happen if there we don’t intervene. The burden of antimicrobial resistance is carried by developing countries. Goodman explained that antimicrobial resistance can occur by two mechanisms: acquisition of mutations in DNA or acquisition of DNA via horizontal gene transfer. Horizontal gene transfer is what Goodman referred to as a the bacterial black market. Transfer can occur through transformation, transduction, or conjugation. Bacteria can become antibiotic resistant and survive drug treatment while others treated with that antibiotic die. This results, Goodman noted, often in monocultures of highly resistant bacteria. Colistin resistance is what Goodman studied. They developed an “entrapment vector” with the goal of identifying resistance movements. They took an E. coli strain with the entrapment vector and used this to identify movements of colistin resistance. However, Goodman noted they needed sequencing to learn about transposon insertion. Their sequence analysis consisted of pre-processing, assembling with Flye, polishing with short reads, and annotation wist rast and resfinder. Interestingly, the entrapment vector became a transposon! They now have a system to track antibiotic resistance genetic movements. Their capture system can trap transposable elements. Whole-genome sequencing can help identify precise locations of insertion and reconfiguration of genetic elements. Goodman noted that Nanopore sequencing helps facilitate rapid sequencing allowing for a new understanding of AMR transfer.
