Fig. 3: In-depth strain-level SNP analysis in tracking putative transmission of infant-associated C. perfringens.
a, Number of C. perfringens isolates sequenced from five hospitals. b, Number of infants with two or more longitudinal sampling time points. c, Pairwise SNP distance in longitudinally sampled isolates (n = 209): strains (ANI > 99.9%) versus between strains (ANI < 99.9%). M, mean (SNPs). The statistical analysis was performed using Wilcoxon’s test (two sided). The box in the boxplot represents 50% of the central data, in between the lower and upper quartiles, with a central line representing the median, whereas the whiskers show the most extreme data points. d, Phylogenetics of 272 infant-associated C. perfringens isolates with branches colour coded according to the lineage assigned. The key strains, defined as isolates having highly similar ANI > 99.9%, as indicated on the tree, are further described in e–g. e, Tracking multi-host C. perfringens strain VIf (31 isolates) which involves six individuals in two sister hospitals, A and B, based on clinical metadata. Twin pairs are colour coded. A CPA-NEC infant (N20) was highlighted in red. f, Putative intrahospital circulation of strain Ib. Strain Ib was not detected in a 60-d window in the infant cohort. A CPA-NEC infant (N3) was highlighted in red. g, Comparison of SNP distance trees between isolates from twin pairs, suggesting dissemination of C. perfringens.
