Table 3.
Overview of chromosome structural variants
| Patient code | Type of variant | Reference (position) | Annotation | Isolate with variant |
|---|---|---|---|---|
| P_27 | Plasmid loss | S. aureus TW20 | 29,585 bp-plasmid containing the chlorhexidine tolerance determinant qacA and cadmium resistance genes | Index, paired invasive, one paired colonising (second paired colonising like reference) |
| P_30 | Plasmid loss | S. aureus SA564 | 27,272 bp-plasmid containing the beta-lactamase operon | Index (paired invasive like reference) |
| P_05 | Deletion | S. aureus NCTC_8325 (2188042) | 861 bp-deletion (fructose bisphosphate aldolase) | Paired invasive |
| P_12 | Deletion | S. aureus NCTC_8325 (1502725) | 261 bp-deletion (phage protein) | Index (paired invasive like reference) |
| P_14 | Deletion | S. aureus FORC_001 (1953000) | 597 bp-deletion (hypothetical protein) | Paired invasive |
| P_21 | Deletion | S. aureus SA564 (798999) | 15,622 bp deletion of pathogenicity island SaPi2 | Paired invasive |
| P_54 | Deletion | S. aureus AUS0325 (1191813) | 495 bp-deletion (serine/threonine-protein phosphatase) | Index (paired colonising like reference) |
| P_19 | Recombination | S. aureus CA-347 (1577530) | Phage Sa phi3 recombination | Index (paired colonising like reference) |
| P_22 | Insertion | S. aureus TW20 (2243085) | IS256 insertion (prophage phiSPbeta-like) | Paired invasive |
| P_27 | Insertion | S. aureus TW20 (173671) | IS256 insertion (putative DNA-binding protein) | Index and one paired invasive |
| P_27 | Insertion | S. aureus TW20 (1223135) | IS256 (putative membrane protein) | Index, paired invasive (paired colonising like reference) |
| P_27 | Insertion | S. aureus TW20 (1971406) | IS256 insertion (lantibiotic immunity protein, genomic island niSa beta) | Index, paired invasive, one paired colonising (second paired colonising like reference) |
| P_27 | Insertion | S. aureus TW20 (173,671, 173,626) | IS256 insertion (putative DNA-binding protein) | Index and one paired invasive |
| P_34 | Insertion | S. aureus TW20 (1619645) | IS256 insertion (hypothetical protein) | Index (paired invasive like reference) |
| P_39 | Insertion | S. aureus TW20 (1955676) | IS256 insertion (genomic island niSa beta) | Index (paired invasive like reference) |
| P_46 | Insertion | S. aureus TW20 (24644) | IS256 insertion (upstream of walKR operon) | Paired invasive |
| P_46 | Insertion | S. aureus TW20 (528848) | IS256 insertion (exotoxin, genomic island niSa alpha) | Paired invasive |
| P_46 | Insertion | S. aureus TW20 (2306594) | IS256 insertion (phage protein) | Paired invasive |
| P_47 | Insertion | S. aureus str._JKD6008 (1914213) | IS256 insertion (genomic island niSa beta) | Paired invasive |
| P_47 | Insertion | S. aureus str._JKD6008 (2227509) | IS256 insertion (P-ATPase superfamily P-type ATPase potassium (K+) transporter subunit A) | Paired invasive |
| P_49 | Insertion | S. aureus str._JKD6008 (702665) | IS256 insertion (upstream of sodium/hydrogen exchanger family protein) | Paired invasive |
| P_52 | Insertion | S. aureus TW20 (1955675) | IS256 insertion (genomic island niSa beta) | Paired colonising |
Bp base pair