TABLE 2

Structural variants and plasmid losses in infecting compared to colonizing strains in each patient

PatientStrain typeagr statusaType of eventFragment length (bp)No. of genesEvent description
Cases
    53BloodInsertion4,1567Insertion of 4 paralogs of essI and 4 genes encoding hypothetical proteins in the ess locus
Repeat expansion1201Expansion in gene sdrD
Repeat contraction901Contraction in gene sdrE
Deletion210Deletion in intergenic region
Repeat contraction690350 bp upstream of setC
Repeat expansion570Intergenic region
Repeat contraction560Intergenic region
Deletion1,6740Deletion of 4 genes encoding hypothetical proteins and a partial deletion of 1 gene encoding a hypothetical protein
Repeat expansion590Intergenic region
Deletion43,04666Deletion of a φSa3 prophage containing scn, sak, lytN, dnaC, xerC, and 61 genes encoding hypothetical proteins; excision restores hlb
Repeat contraction1000Intergenic region
Repeat expansion61Expansion in swrC
Insertion1,1520Intergenic region
Repeat expansion1281Expansion in clfB
Plasmid loss23,16024Loss of plasmid containing racA, entD, entA, entG, acuI, ohrR, bin3, cadC, and 16 genes encoding hypothetical proteins
    60BloodNone
    73BloodRepeat expansion901Expansion in gene bbp
Repeat contraction231Expansion in a gene encoding a hypothetical protein
Insertion1,0741Insertion of a gene encoding a hypothetical protein
Insertion600Insertion in the intergenic region
    117Focus+None
    117BloodDeletion271In gene pepF
Deletion301In a gene encoding a hypothetical protein
    135FocusInsertion4621Insertion alters a gene encoding a hypothetical protein
Deletion4621Deletion of a gene encoding a hypothetical protein
Deletion43,75769Prophage deletion; contains atl, dnaC, hin, lytN, pezA, and ssb
Insertion200Insertion of 20 bp in the intergenic region
Deletion1251Deletion alters a gene encoding a hypothetical protein
Repeat contraction221In a gene encoding a hypothetical protein
Insertion1,3322Insertion in dpiB; contains a gene encoding a hypothetical protein
Insertion1,33224Insertion of a gene encoding a hypothetical protein into plasmid pPS00077.1A.1
    135BloodInsertion4621Insertion alters a gene encoding a hypothetical protein
Deletion4621Deletion of a gene encoding a hypothetical protein
Deletion43,75769Prophage deletion; contains atl, dnaC, hin, lytN, pezA, and ssb
Insertion200Insertion of 20 bp in the intergenic region
Deletion1251Deletion alters a gene encoding a hypothetical protein
Repeat contraction221In a gene encoding a hypothetical protein
Insertion1,3322Insertion in dpiB contains a gene encoding a hypothetical protein
Plasmid loss26,24123Loss of a plasmid containing nhaX, dauA, hin, bin, tnsB, blaI, blaR1, blaZ, repB, qacC, norG, and 10 genes encoding hypothetical proteins
Controls
    35Blood+Repeat expansion560238 bp upstream of the hslO gene
Plasmid loss39,35341Loss of a plasmid containing etb, hin, yxlF, ccr, lagD, ltnA2, cadC, and 35 genes encoding hypothetical proteins
    36Blood+Repeat expansion1,5483Alters a gene encoding a hypothetical protein
    45Blood+None
    63Blood+None
    108BloodNone
    152Focus+Insertion1,3322Deletion of gene encoding hypothetical protein alters another gene encoding a hypothetical protein
Deletion1,3321Insertion alters a gene encoding a hypothetical protein
Variable region578/1,330Deletion of a gene encoding a hypothetical protein; the inserted sequence alters another gene encoding a hypothetical protein
Deletion581Partial deletion of the mpr gene
    152Blood+Insertion1,3321Contains a gene encoding a hypothetical protein
Deletion1,3322Deletion of a gene encoding a hypothetical protein; alters another gene encoding a hypothetical protein
    158Blood+Inversion6,9391Contains aphA, aadK, ycgJ, and 6 genes encoding hypothetical proteins
  • a +, functional; −, nonfunctional.