Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Gregorio Marañón (Madrid)
Hospital Admission Unit Primary care
Patient Sex F
Patient Age 83
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
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) None
Agent MIC CLSI EUCAST
Piper >256 R R
P/T >256 R R
CTX 64 R R
CAZ 64 R R
CAZ-AVI 1 S S
CEF 64 R R
AZT 64 R R
MEM ≤0.25 S S
IMI ≤0.25 S S
IMI-RELE ≤0.25 S S
ERT 2 R R
FOSFO >256 R R
GENTA 32 R R
TOBRA 8 I R
AMK 4 S S
CIP 64 R R
COLIS 1 WT S
AI2594_v1
AI2594_v1

Sample 14 was assembled with Unicycler_v0.4.6 into 7 scaffolds, 7 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
AI2594_v1_c1 14 15 Browse 31 4763 5206222 1.00
Klebsiella pneumoniae
57.46 Non-mobilizable - - - - - - - - CP007734 0.23011000 1586
AI2594_v1_c2 14 15 Browse 26 214 201175 1.41
Klebsiella pneumoniae
50.89 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 0.02795550 770
AI2594_v1_c3 14 15 Browse 0 122 123571 2.35
Klebsiella pneumoniae
52.90 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 0.02699070 476
AI2594_v1_c4 14 15 Browse 19 90 82171 2.01
Klebsiella pneumoniae
52.56 Non-mobilizable IncR, IncFIA, rep_cluster_1418 000204__CP008701_00115, 000093__KX023259_00112, 000759__NC_013950_00034 - - - - - - CP021953 0.00631659 728
AI2594_v1_c5 14 15 Browse 1 83 63589 2.00
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
AI2594_v1_c6 14 15 Browse 0 53 53928 3.81
Klebsiella pneumoniae
52.33 Non-mobilizable rep_cluster_1 000232__CP012429 - - - - - - CP018314 0.01340360 1705
AI2594_v1_c7 14 15 Browse 0 4 3751 22.09
Klebsiella pneumoniae
52.15 Mobilizable ColRNAI_rep_cluster_1291 000001__EU090225_00001 MOBQ NC_019783_00003 - - - - CP003226 0.00134007 509