Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Gregorio Marañón (Madrid)
Hospital Admission Unit Internal medicine
Patient Sex M
Patient Age 64
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation BAL
Infection or Colonization I
Outbreak None
Genus/Species
Klebsiella pneumoniae
Carbapenamase type(s) OXA-48
MLST 405:gapA(2), infB(1), mdh(62), pgi(3), phoE(10), rpoB(4), tonB(110)
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 2 S S
CEF >128 R R
AZT >128 R R
MEM 0.5 S S
IMI 0.5 S S
IMI-RELE ≤0.25 S S
ERT >128 R R
FOSFO 128 I R
GENTA 16 R R
TOBRA 8 I R
AMK 4 S S
CIP 8 R R
COLIS 0.12 WT S
AI2585_v1
AI2585_v1

Sample 3 was assembled with Unicycler_v0.4.6 into 6 scaffolds, 6 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
AI2585_v1_c1 3 405 Browse 32 5122 5536953 1.00
Klebsiella pneumoniae
57.17 Non-mobilizable - - - - MPF_T NC_010726_00014, NC_005814_00013, NC_010726_00011, NC_013284_00016 - - CP021942 0.21089700 1705
AI2585_v1_c2 3 405 Browse 32 240 247179 1.53
Klebsiella pneumoniae
52.54 Conjugative IncFII, IncFIB 000124__KP125893_00142, 000107__CP014778_00094 MOBF NC_021231_00058 MPF_F NC_021502_00150, NC_019165_00034, NC_021654_00016, NC_011281_00082, NC_022609_00081, NC_014312_00128, NC_019389_00068, NC_023332_00154, NC_014312_00118, NC_014312_00116, NC_021502_00131, NC_019155_00032 - - KY271404 0.00199971 770
AI2585_v1_c3 3 405 Browse 1 83 63589 1.75
Klebsiella pneumoniae
51.22 Conjugative IncL/M 000148__NC_021488_00028 MOBP NC_004464_00056 MPF_I NC_004464_00105, NC_005246_00057, NC_019063_00094, NC_019344_00078, NC_004464_00066, NC_004464_00068, NC_019154_00069, NC_005246_00069, NC_004464_00073 - - CP015075 0.00004769 681
AI2585_v1_c4 3 405 Browse 0 47 38000 2.63
Escherichia coli
49.30 Non-mobilizable IncN 000150__JQ996149 - - MPF_T NC_020122_00019, NC_020122_00006, NC_020122_00009, NC_020122_00011, NC_020122_00012 - - CP018988 0.01074050 680
AI2585_v1_c5 3 405 Browse 0 7 8262 29.81
Escherichia coli
52.94 Mobilizable ColRNAI_rep_cluster_1857 000008__AJ627566 MOBP NC_014003_00004 - - MOBP NZ_CP011065 CP011433 0.01471450 259
AI2585_v1_c6 3 405 Browse 0 2 1552 36.31
Escherichia coli
51.87 Mobilizable ColRNAI_rep_cluster_1885 000013__DQ995351_00001 - - - - MOB_unknown JN985534 JN253636 0.05133700 414