Public health researchers have only a poor understanding of how infectious diseases spread. The specific organisms that cause outbreaks often go undiscovered, and the ecologies of respiratory and other pathogens are hard to study. Accordingly, researchers would like better tools to trace the causes and track the spread of infectious disease outbreaks. A widely used method for distinguishing bacterial strains involves PCR amplification of conserved or variable gene fragments followed by sequencing to identify variations in those fragments. But the sequencing work can take days or weeks, and is targeted to specific bacterial species.