<b>How much is enough? Optimising sampling frames for genomic surveillance of </b><b><i>Escherichia coli</i></b><b> and </b><b><i>Klebsiella</i></b><b> spp. bloodstream infections – a retrospective study</b> - Supplementary data files.

<p dir="ltr"><b>Background</b>: Optimising sampling frames for genomic surveillance of <i>E. coli</i> and <i>Klebsiella </i>may support interventions to mitigate bloodstream infections (BSIs), but approaches to estimating sample size and how these relate to bacterial population diversity at multiple genetic levels (strain/plasmid/antimicrobial resistance genes</p><p dir="ltr">[ARGs]) are lacking.</p><p dir="ltr"><b>Methods</b>: Using systematically collected, regionally-stratified, whole genome sequencing data from a 6-month genomic survey of English <i>E. coli</i>/<i>Klebsiella</i> BSI isolates (n=1,939; NEKSUS), we used Bayesian approaches to estimate the sample sizes required to capture genetic diversity at strain- (MLST, fastBAPS clusters), plasmid- and ARG-levels, using two diversity measures: ‘coverage’ (i.e. proportion of the bacterial population/plasmids/ARGs represented by features observed in the sample), and the number/proportion of unique features observed at varying surveillance sample sizes.</p><p dir="ltr"><b>Findings</b>: Randomly sampling 1,400 <i>E. coli</i>/<i>Klebsiella</i> BSI isolates each achieved ≥80% coverage of bacterial lineages and ARGs (i.e. capture features constituting ≥80% of the population) at 95% certainty, but captured lower proportions of unique features (28% MLSTs, 59% fastBAPS clusters, 19% plasmid subcommunities, and 57% ARGs for <i>E. coli; </i>49%, 87%, 50% and 83% for <i>Klebsiella</i>, respectively).

Sample sizes required for 80% coverage of <i>E. coli</i> plasmid populations were higher than MLSTs (1,928[95% CrI:1,837–2,025] vs 1,351[1,230–1,472]), while for <i>Klebsiella</i>, estimates were lower for plasmids (1,115[1,052–1,181] vs 1,422[1,331–1,515] for MLSTs). Lower sample sizes adequately captured 80% coverage of fastBAPS clusters and ARGs (649[575 – 727] and 27[23–30], respectively, for <i>E. coli</i>; 113[84–145] and 83[72-96] for <i>Klebsiella</i>), due to feature-specific frequency distributions. <i>Klebsiella</i> BSIs were more diverse than <i>E. coli</i>, with sampling 10.9% vs 3.2% of total annual BSIs in England needed to reach 80% MLST coverage.