Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Ramón y Cajal (Madrid)
Hospital Admission Unit None
Patient Sex M
Patient Age 92
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation urine
Infection or Colonization I
Outbreak None
Genus/Species
Klebsiella pneumoniae
Carbapenamase type(s) OXA-48, KPC
MLST 15:gapA(1), infB(1), mdh(1), pgi(1), phoE(1), rpoB(1), tonB(1)
EDTA Assay (if any) None
PCR Result (if any) OXA-48 positive, KPC positive
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 4 R I
IMI 8 R R
IMI-RELE 0.5 S S
ERT 16 R R
FOSFO >256 R R
GENTA 32 R R
TOBRA 0.5 S S
AMK 2 S S
CIP 128 R R
COLIS <0.06 WT S
AI2888_v1
AI2888_v1

Sample 156 was assembled with Unicycler_v0.4.6 into 4 scaffolds, 4 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
AI2888_v1_c1 156 15 Browse 32 4822 5259432 1.00
Klebsiella pneumoniae
57.41 Non-mobilizable - - - - - - - - CP007734 0.23011000 1586
AI2888_v1_c2 156 15 Browse 26 211 201961 0.96
Klebsiella pneumoniae
51.05 Conjugative IncFII, IncFIB 000107__CP014778_00094, 000127__CP009275 MOBF NC_021231_00058 MPF_F NC_021502_00150, NC_014312_00141, 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 - - CP009879 0.02760060 770
AI2888_v1_c3 156 15 Browse 0 91 84462 0.91
Klebsiella pneumoniae
50.35 Conjugative IncI1 000145__HE610900_00001 MOBP NC_019097 MPF_I NC_019097_00056, NC_022267_00057, NC_019111_00038, NC_023290_00086, NC_015965_00072, NC_019097_00075, NC_022267_00069, NZ_CM001473_00069, NC_019097_00085 MOBP JN253636 CP019215 0.01689630 476
AI2888_v1_c4 156 15 Browse 1 83 63589 0.88
Escherichia coli, 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 0.00000000 681