Phylodynamic estimation of the within-host evolutionary rate of extended-spectrum beta-lactamase-producing...

Despite their clinical relevance, the within-host evolution of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales is still poorly understood. To estimate the within-host evolutionary rates of ESBL-producing Escherichia coli and Klebsiella pneumoniae species complex, we fitted phylodynamic models to genomic sequence data of longitudinally collected rectal swabs from 63 colonized hospital patients. We estimated an average within-host evolutionary rate of 7.71e-07 [4.60e-07,1.10e-06] mutations/site/year for E. coli and 4.20e-07 [1.57e-07,7.14e-07] mutations/site/year for the K. pneumoniae species complex, with limited variation observed across patients and sequence types. These estimates are presumably the most accurate reported so far and are useful for future epidemiological and evolutionary studies.