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Table 2 Resistome categories for carbapenem-resistant isolates in our prospective collection

From: Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

Resistance mechanism # of CRE isolates # of CSE isolates % of total isolates in this category that are CRE % of CRE isolates with this mechanism
i. Carbapenemases 146 2 98.6% 66.1%
AllblaKPC 124 2 98.4% 56.1%
  blaKPC-3 60 1 98.4% 27.1%
  blaKPC-2 50 1 98.0% 22.6%
  blaKPC-4 11 0 100.0% 5.0%
  blaKPC(read based)a 3 0 100.0% 1.4%
AllblaNDM 14 0 100.0% 6.3%
  blaNDM-1 11 0 100.0% 5.0%
  blaNDM-5 3 0 100.0% 1.4%
AllblaSME 6 0 100.0% 2.7%
  blaSME-1 3 0 100.0% 1.4%
  blaSME-2 3 0 100.0% 1.4%
Other carbapenemases 2 0 100.0% 0.9%
  blaIMP-84andblaKPC-4 1 0 100.0% 0.5%
  blaIMP-4 1 0 100.0% 0.5%
ii. ESBL/AmpC + porin defect(s)b 61 32 65.6% 27.6%
Includes any ESBL 46 11 80.7% 20.8%
  IncludesblaCTX-M-15 34 2 94.4% 15.4%
  IncludesblaSHV-12 11 5 68.8% 5.0%
  Includes other ESBLs 13 5 72.2% 5.9%
Includes any AmpC 31 23 57.4% 14.0%
  IncludesblaEC 19 8 70.4% 8.6%
  IncludesblaCMY-2 12 4 75.0% 5.4%
  Includes other AmpCs 5 12 29.4% 2.3%
iii. ESBL/AmpC without porin defect 6 168 3.4% 2.7%
iv. Porin defect(s) without ESBL/AmpC 8 23 25.8% 3.6%
Defect in both major porins 5 5 50.0% 2.3%
v. No known resistant determinants 0 113 0.0% 0.0%
  1. aThe blaKPC was not present in the whole-genome assembly, but we were able to detect its presence by examining the read data (see Methods)
  2. bStrains may have multiple predicted AmpC and/or ESBL genes. See Additional file 1: Tables S6-S7 for specific resistance determinants predicted for each isolate