  Cholera continues to be a global health threat. Understanding how cholera
spreads between locations is fundamental to the rational, evidence-based design
of intervention and control efforts. Traditionally, cholera transmission models
have utilized cholera case count data. More recently, whole genome sequence
data has qualitatively described cholera transmission. Integrating these data
streams may provide much more accurate models of cholera spread, however no
systematic analyses have been performed so far to compare traditional
case-count models to the phylodynamic models from genomic data for cholera
transmission. Here, we use high-fidelity case count and whole genome sequencing
data from the 1991-1998 cholera epidemic in Argentina to directly compare the
epidemiological model parameters estimated from these two data sources. We find
that phylodynamic methods applied to cholera genomics data provide comparable
estimates that are in line with established methods. Our methodology represents
a critical step in building a framework for integrating case-count and genomic
data sources for cholera epidemiology and other bacterial pathogens.
