Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Gregorio Marañón (Madrid)
Hospital Admission Unit Nephrology
Patient Sex F
Patient Age 71
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 >128 R R
CAZ >128 R R
CAZ-AVI 1 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 8 R R
FOSFO >256 R R
GENTA 16 R R
TOBRA 8 I R
AMK 8 S S
CIP >128 R R
COLIS 64 NWT R
AI2818_v1
AI2818_v1

Sample 9 was assembled with Unicycler_v0.4.6 into 5 scaffolds, 5 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
AI2818_v1_c1 9 15 Browse 51 4972 5413730 1.00
Klebsiella pneumoniae
57.25 Non-mobilizable - - - - MPF_T NC_010726_00014, NC_005814_00013, NC_010726_00011, NC_013284_00016 - - CP014763 0.17817300 1525
AI2818_v1_c2 9 15 Browse 0 90 75339 0.75
Klebsiella pneumoniae
52.80 Conjugative IncFII, rep_cluster_1418 000127__CP009275, 000759__NC_013950_00034 MOBF NC_021231_00058 MPF_F NC_021502_00150, NC_019165_00034, NC_021654_00016, NC_022609_00081, NC_014312_00128, NC_019389_00068, NC_023332_00154, NC_014312_00118, NC_014312_00116, NC_021502_00131, NC_019389_00080, NC_019155_00032 - - LK391770 0.02980310 1585
AI2818_v1_c3 9 15 Browse 1 83 63589 1.14
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
AI2818_v1_c4 9 15 Browse 10 52 42353 1.08
-, Enterobacter cloacae, Enterobacter sp., Escherichia coli, Salmonella enterica
51.81 Mobilizable IncR 000204__CP008701_00115 MOBP NC_021576_00050 - - - - KF954150 0.01404920 731
AI2818_v1_c5 9 15 Browse 0 2 2058 33.46
Klebsiella pneumoniae
56.51 Non-mobilizable ColRNAI_rep_cluster_1993 000024__JX133088 - - - - - - KU302803 0.00053260 78