Fig. 2: Transmission cluster characterization and source analysis.

a Transmission clusters as determined by phylothresholds (n = 69) represented as boxes, colored according to invasive status (red: invasive clusters; blue: colonizing clusters) and annotated with methicillin resistance status. R indicates methicillin-resistant S. aureus (MRSA) cluster and S indicates methicillin-susceptible S. aureus (MSSA) cluster. Within each cluster, patient status is indicated by colored dots (blue: colonization only; red: infection only; yellow: both colonization and infection), with individual patient IDs shown as numbers. Environmental isolates are marked by gray diamonds. Two bars below each cluster box indicate: (1) the specific NICU section where the cluster was detected, and (2) the assigned treatment team at the time of detection. Among all transmission clusters identified, 19 were classified as invasive. b Temporal comparison of genomic emergence and transmission index cases versus index patient admission dates (n = 48 transmission clusters, each row representing a distinct transmission cluster with ≥4 genomes). Green bars represent 95% confidence intervals for transmission index case dates (bounds: weighted 2.5th and 97.5th percentiles of inferred transmission index dates across posterior samples), and dark green lines indicate medoid dates. Blue bars represent 95% highest posterior density intervals for tMRCA (time to most recent common ancestor) from BEAST2 molecular clock analysis (bounds: lower and upper 95% HPD boundaries from the posterior distribution), and dark blue lines indicate the mean. Purple triangles indicate index patient admission dates, and purple circles indicate collection dates of the earliest cluster genomes. The 95% confidence intervals of transmission index dates overlap with the 95% HPD of tMRCA for all clusters, indicating that tMRCA serves as both a genomic emergence indicator and a reliable proxy for transmission index cases. Index patient admission dates fell within the 95% HPD of tMRCA for 50% (24/48) of clusters, suggesting that admission of pre-colonized index patients represents a major introduction route. Source data are provided as a Source Data file.