TABLE 2

Tn4401 variations

Tn4401 variantaStructural isoform (29)SNV(s)bblaKPC variantNo. of:
PatientsIsolatesStrains
Tn4401b-1cbblaKPC-212117642
Tn4401b-2b8015C→TdblaKPC-3224019
Tn4401b-3b8015C→T, 9621T→CblaKPC-3132
Tn4401b-4b7199T→A, 8015C→T, 9621T→CblaKPC-3111
Tn4401b-5b8015NeblaKPC-2/blaKPC-3121
Tn4401b-6b7509C→G, 7917T→GfblaKPC-4111
Tn4401b-7b6800T→C, 7509C→G, 7917T→GblaKPC-4141
Tn4401b-8b9663T→CblaKPC-2131
Tn4401a-1a (del 7020-7118)blaKPC-2581
Tn4401novel-1Novel (del 6919-7106)blaKPC-228392
Tn4401trunc-1Truncated (del 1-6654)blaKPC-2231
Tn4401trunc-2Truncated (del 1-6727)6800NgblaKPC-2111
  • a Variants are named such that letters indicate previously described structural isoforms and numbers indicate nucleotide level variations (SNVs) within an isoform (apart from the truncated Tn4401 structures, where numbers are used to indicate different truncation locations).

  • b With respect to Tn4401b-1, which was considered the reference Tn4401 sequence in this study.

  • c Tn4401b-1 differs from the reference isoform b sequence in EU176013.1 by the following 14 SNVs: 4939C→G, 4989C→T, 5099A→T, 5131A→G, 5154T→G, 5185G→C, 5255C→A, 5361G→C, 5375C→G, 5390A→C, 5996G→A, 5998G→C, 8112C→A, 8113A→C.

  • d This substitution converts blaKPC-2 to blaKPC-3.

  • e Quality filters failed at this position because of a mixture of reads supporting C and T (i.e., Tn4401b-5 actually represents a mixture of Tn4401b-1 and Tn4401b-2).

  • f These two substitutions convert blaKPC-2 to blaKPC-4.

  • g Quality filters failed at this position because of a lack of reads mapped in the reverse direction. All of the reads mapped in the forward direction supported a reference (T) call.