Predicting antimicrobial susceptibility from the bacterial genome: A new paradigm for one health resistance monitoring
Abstract
The laboratory identification of antibacterial resistance is a cornerstone of infectious disease medicine. In vitro antimicrobial susceptibility testing has long been based on the growth response of organisms in pure culture to a defined concentration of antimicrobial agents. By comparing individual isolates to wild‐type susceptibility patterns, strains with acquired resistance can be identified. Acquired resistance can also be detected genetically. After many decades of research, the inventory of genes underlying antimicrobial resistance is well known for several pathogenic genera including zoonotic enteric organisms such as Salmonella and Campylobacter and continues to grow substantially for others. With the decline in costs for large scale DNA sequencing, it is now practicable to characterize bacteria using whole genome sequencing, including the carriage of resistance genes in individual microorganisms and those present in complex biological samples. With genomics, we can generate comprehensive, detailed information on the bacterium, the mechanisms of antibiotic resistance, clues to its source, and the nature of mobile DNA elements by which resistance spreads. These developments point to a new paradigm for antimicrobial resistance detection and tracking for both clinical and public health purposes.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Oct 03, 2020
- Source ID
- 10.1111/jvp.12913
Entities
People
- James J. Davis
- Patrick F McDermott
Organizations
- Argonne National Laboratory
- Defense Advanced Research Projects Agency
- Food and Drug Administration
- University of Chicago