Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Gregorio Marañón (Madrid)
Hospital Admission Unit Urology
Patient Sex F
Patient Age 58
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 ≤0.25 S S
IMI ≤0.25 S S
IMI-RELE ≤0.25 S S
ERT 64 R R
FOSFO <32 S S
GENTA ≤0.25 S S
TOBRA ≤0.25 S S
AMK 4 S S
CIP >128 R R
COLIS 1 WT S
AI2819_v5
AI2819_v5

Sample 10 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
AI2819_v5_c1 10 15 Browse 31 4937 5365759 1.00
Klebsiella pneumoniae
57.35 Non-mobilizable - - - - - - - - CP007734 0.21953100 1586
AI2819_v5_c2 10 15 Browse 27 204 212774 0.92
Klebsiella pneumoniae
51.57 Conjugative IncFII, IncFIB 000107__CP014778_00094, 000113__CP022035, 000128__CP023916 MOBF NC_021231_00058 MPF_F NC_021502_00150, NC_014312_00141, 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 - - CP015135 0.01364960 768
AI2819_v5_c3 10 15 Browse 0 118 109087 0.67
Klebsiella pneumoniae
49.36 Non-mobilizable IncFIB 000100__NZ_CP016161_00012 - - - - - - MF144193 0.01153130 80
AI2819_v5_c4 10 15 Browse 1 84 65499 1.39
Klebsiella pneumoniae
51.43 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 - - KX523901 0.00011950 681
AI2819_v5_c5 10 15 Browse 3 28 31167 2.01
Escherichia coli
53.77 Non-mobilizable IncR 000204__CP008701_00115 - - - - - - LC155908 0.02129230 731
AI2819_v5_c6 10 15 Browse 0 1 2255 23.64
Morganella morganii
42.79 Non-mobilizable ColRNAI_rep_cluster_1885 000013__DQ995351_00001 - - - - - - CP008717 0.10933100 427