Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Puerta del Mar (Cádiz)
Hospital Admission Unit Rehabilitation
Patient Sex F
Patient Age 48
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation urine
Infection or Colonization I
Outbreak None
Genus/Species
Klebsiella pneumoniae
Carbapenamase type(s) VIM-1
MLST 11:gapA(3), infB(3), mdh(1), pgi(1), phoE(1), rpoB(1), tonB(4)
EDTA Assay (if any) None
PCR Result (if any) None
Agent MIC CLSI EUCAST
Piper >256 R R
P/T >256 R R
CTX 128 R R
CAZ >128 R R
CAZ-AVI 64 R R
CEF 32 R R
AZT >128 R R
MEM 0.5 S S
IMI ≤0.25 S S
IMI-RELE ≤0.25 S S
ERT 2 R R
FOSFO >256 R R
GENTA 0.5 S S
TOBRA 8 I R
AMK 2 S S
CIP 128 R R
COLIS 0.25 WT S
AI2626_v1
AI2626_v1

Sample 66 was assembled with Unicycler_v0.4.6 into 3 scaffolds, 3 of which are closed circles. More details can be found in the table below. Raw data such as the assembly FASTA and annotation files can be downloaded from the "Raw Data" box. The assembly can be browsed by clicking on the "Browse" link for each scaffold.

Scaffold Sample ST Jbrowse Resistance Genes All Genes Scaffold length Circular Est. Copy Number Species GC content Mobility Replicon type Replicon type accession Relaxase type Relaxase type accession MPF type Mpf type accession OriT type OriT accession MASH nearest neighbor MASH neighbor distance MASH neighbor cluster
AI2626_v1_c1 66 11 Browse 29 4915 5274880 1.00
Klebsiella pneumoniae
57.40 Non-mobilizable - - - - - - - - CP007734 0.19729200 1586
AI2626_v1_c2 66 11 Browse 39 243 237704 1.26
Klebsiella pneumoniae
53.12 Conjugative IncFII, IncFIB 000107__CP014778_00094, 000113__CP022035, 000132__HG969996 MOBF NC_021231_00058 MPF_F NC_021502_00150, NC_019165_00034, NC_021654_00016, NC_022609_00081, NC_014312_00128, NC_023332_00154, NC_014312_00118, NC_014312_00116, NC_021502_00131, NC_019389_00080, NC_019155_00032, NC_021654_00004 - - CP021713 0.00328537 767
AI2626_v1_c3 66 11 Browse 10 45 39384 2.03
Klebsiella pneumoniae
55.44 Mobilizable IncR 000204__CP008701_00115 MOBP NC_021576_00050 - - - - CP014299 0.00544411 730