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

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 <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> 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 <i>E. coli</i> and 4.20e-07 [1.57e-07,7.14e-07] mutations/site/year for the <i>K. pneumoniae</i> 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.