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Table 3 Overview of chromosome structural variants

From: Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

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
  1. Bp base pair