Figure 3. Diagrammatic representation of cps loci and adjacent regions from donor, recipient and progeny strains depicting serotype switch event for pneumococcal isolates, United States, 2015–2016. Red and green lines in progeny indicate regions of sequence identity or near identity (<2 single-nucleotide polymorphisms/10,000 bp) to the above corresponding donor and recipient sequences, respectively. Rectangles indicate relative locations of PBP gene types for pbp2x and pbp1a. Below each cps locus, a representative reference strain is indicated along with relevant features determined through a bioinformatics pipeline (MLST, PBP type, resistance markers). Junctions between donor and recipient sequences involved in the 2 single recombinational crossovers in the gene replacement event are indicated with blue arrowheads above the progeny diagram, although a single short internal region with sequence identity to the recipient nested within the donor fragment (left coordinates 11349–11839) is also present. Below each green or red segment of the progeny, the level of sequence identity to donor and recipient is provided. The list of each progeny strain, date of isolation, and state is provided. Where MLST is not ST156, its single locus variants (ST9910, ST11584, and ST12921) are included. Two exceptions indicating flanking post-switch recombination within left coordinates 1–6453 are indicated in isolates 20152884 and 20161413 (asterisks): isolate 20152884 had only 99.3%−99.5% identity to recipient and donor over bases 1–3715, and isolate 20161413 had only 99.5%–99.7% identity to recipient and donor over bases 1–2143. Two strains on the right indicate a post-switch deletion event within the wciG putative acetyltransferase gene, which putatively contributes to the acetylation pattern of the serotype 35B polysaccharide (26). MLST, multilocus sequence type; PBP, penicillin-binding protein; ST, sequence type.