Fig. 6: Features of common lineages, and contribution of common and transmitted lineages to infection burden.

a Genetic and patient characteristics associated with common lineages (identified in ≥3 patients), across n = 294 unique infection episodes. Circles indicate odds ratios estimated in a single multivariable logistic regression model with all 10 predictors; lines indicate 95% confidence intervals for those odds ratios; unadjusted p-values are shown, significant (p < 0.05) associations are coloured black. Binary variables: ESBL (extended spectrum beta-lactamase detected); Kp spp (K. pneumoniae species); Mannose+ KL (K locus includes man operon); Yersiniabactin (ybt detected); Onset day 3+ (isolated from specimen collected on day 3 or later); Patient sex (male); Mannose+ OL (O locus includes man operon); Aerobactin (iuc detected); Rhamnose+ KL (K locus includes rml operon). Continuous variable: Patient age (years). b Transmission network showing 12 clusters, defined as infection episodes in different patients identified less than 45 days apart with isolate genomes separated by ≤25 SNVs (mean 0.7 SNVs) and with plausible epidemiology (onset of non-index case occurred during hospital stay, at least 2 days after index case, and patients spent time in same hospital). Details of clusters are given in Supplementary Table 2. c Infections of different classes (ESBL+/−, ybt+/−) stratified by lineage type (transmission cluster, as defined in b; other common lineage, identified in ≥3 patients; lineage identified in 2 patients; or singleton lineage identified in 1 patient). d Monthly frequencies of ESBL+ and/or transmission-linked isolates. These analyses were completed using one isolate per unique infection episode (n = 294); where there were ESBL+ and ESBL- variants of the same strain associated with the same infection episode, the ESBL+ variant was included in order to best reflect the nature of the ESBL infection burden.