TABLE 1

blaKPC-containing structures ascertained from long-read PacBio sequencing of 17 randomly chosen isolates

IsolateSpeciesPatienthDateblaKPC plasmidSize (bp)GroupaWithin-group genetic change(s)bTn4401 variantFlanking sequencescTn2-like elementd
CAV1344K. pneumoniaeEPDec 2010pKPC_CAV1344176,497SingletonNAiTn4401b-1GTTCT…GTTCTYes
CAV1392K. pneumoniaeEUMar 2011pKPC_CAV139243,621pKPC_UVA011 SNVTn4401b-2GTTCT…GTTCTYes
NA (chromosomal)NANANATn4401b-2AGATA…AGATANo
CAV1596K. pneumoniaeFKApr 2012pKPC_CAV1596-7877,801SingletonNATn4401b-2GTTCT…GTTCTYes
pKPC_CAV1596-9796,702SingletonNATn4401b-2TATCG…TATCGNo
CAV1099K. oxytocaAUApr 2009pKPC_CAV1099113,105pKPC_UVA020 SNVsTn4401b-1ATGCA…GGCCAeNo
CAV1335K. oxytocaEQDec 2010pKPC_CAV1335113,105pKPC_UVA020 SNVsTn4401b-1ATGCA…GGCCAeNo
CAV1374K. oxytocaEDAug 2010pKPC_CAV1374332,956SingletonNATn4401b-1GTTCT…GTTCTYes
CAV1043E. asburiaeLMar 2008pKPC_CAV104359,138SingletonNATn4401b-2GTTCT…GTTCTYes
CAV1176E. cloacaeDNMay 2010pKPC_CAV117690,452pKPC_CAV11760 SNVsTn4401novel-1GTTCT…GTTCTYes
CAV1311E. cloacaeEOJan 2011pKPC_CAV131190,452pKPC_CAV11760 SNVsTn4401novel-1GTTCT…GTTCTYes
CAV1411E. cloacaeFCJun 2011pKPC_CAV141190,452pKPC_CAV11761 SNV, 40-kb inversionTn4401novel-1GTTCT…GTTCTYes
CAV1669E. cloacaeHVAug 2012pKPC_CAV166990,452pKPC_CAV117640-kb inversionTn4401novel-1GTTCT…GTTCTYes
CAV1668E. cloacaeHQAug 2012pKPC_CAV166843,433pKPC_UVA011 SNV, 188-bp deletionTn4401novel-1GTTCT…GTTCTYes
CAV1321C. freundiiEGNov 2010pKPC_CAV1321-4544,846pKPC_UVA011,225-bp insertionTn4401b-1GTTCT…GTTCTYes
pKPC_CAV1321-244243,709SingletonNATn4401b-1GTTCT…GTTCTYes
CAV1741C. freundiiEROct 2012pKPC_CAV1741129,196pKPC_UVA0114,960-bp duplication, 70,615-bp insertionTn4401b-1fGTTCT…GTTCTYes
CAV1151K. intermediaCDSep 2009pKPC_CAV115143,621pKPC_UVA010 SNVsgTn4401b-1GTTCT…GTTCTYes
CAV1320E. aerogenesELNov 2010pKPC_CAV132013,981SingletonNATn4401b-1TTGTT…TTGTTNo
CAV1492S. marcescensGLDec 2011pKPC_CAV149269,158SingletonNATn4401b-8TTTTT…TTTTTNo
  • a Plasmids are defined as belonging to the same group if the sequences are largely identical, allowing for a small number of substitutions and/or rearrangements that may be expected to occur within the outbreak time frame. Different groups have very limited homology outside the Tn4401 region, indicative of independent integrations into distinct plasmid structures. “Singleton” indicates a plasmid backbone that is distinct from all of the others shown.

  • b Difference(s) from the reference sequence of that plasmid group, as specified in the previous column.

  • c Sequences immediately flanking Tn4401; generally expected to be identical because of 5-bp target site duplication during transposition (28).

  • d Tn4401 integrated into the tnpA gene of a Tn2-like element.

  • e No evidence of target site duplication.

  • f Two copies.

  • g It is noteworthy that this plasmid from K. intermedia CAV1151 is exactly identical to pKPC_UVA01 from K. pneumoniae CAV1016, with isolation dates 2 years apart.

  • h Anonymized patient identifiers are used; they do not represent initials or any other personal information.

  • i NA, not applicable.