Fig. 5

Non-culture-based Amplicon sequencing of the plyNCR marker for pneumococcal strain resolution. Nasal swabs (NS) are illustrated as crosses (“x”; lytA < 10 copies) or circles (lytA ≥ 10 copies) for pneumococcal absence and presence during the first year of life, respectively. Infants with only negative pneumococcal swabs were omitted. Each unique amplicon sequence variant (ASV) recovered by DADA2 after plyNCR sequencing represents a pneumococcal strain and is denoted as a single count (1–30) within the dark brown circles. The major (most abundant) plyNCR ASV is shown first, followed by minor (lower abundant) plyNCR ASVs. Swabs where pneumococci were expected (lytA ≥ 10 copies), but having no plyNCR ASV (due to failed/sub-optimal amplification, low QC quality, failed sequencing, or no DADA2 output) are illustrated as empty tan circles. Serotypes/serogroups identified via conventional multiplex PCR (cPCR) are shown at the top of each circle. Question mark (?) indicates an expected, but indeterminable serotype or non-typeable (NT) S. pneumoniae in a co-colonizing sample, due to the limitations of the multiplex panel