Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Gregorio Marañón (Madrid)
Hospital Admission Unit Primary care
Patient Sex M
Patient Age 69
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 11:gapA(3), infB(3), mdh(1), pgi(1), phoE(1), rpoB(1), tonB(4)
EDTA Assay (if any) None
PCR Result (if any) None
Agent MIC CLSI EUCAST
Piper 64 I R
P/T 16 S ATU
CTX 128 R R
CAZ 128 R R
CAZ-AVI 2 S S
CEF 128 R R
AZT 128 R R
MEM ≤0.25 S S
IMI 1 S S
IMI-RELE 1 S S
ERT 4 R R
FOSFO 256 R R
GENTA ≤0.25 S S
TOBRA ≤0.25 S S
AMK 8 S S
CIP 64 R R
COLIS 32 NWT R
AI2861_v1
AI2861_v1

Sample 18 was assembled with Unicycler_v0.4.6 into 3 scaffolds, 3 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
AI2861_v1_c1 18 11 Browse 31 5005 5343517 1.00
Klebsiella pneumoniae
57.44 Non-mobilizable - - - - MPF_T NC_010726_00014, NC_005814_00013, NC_010726_00011, NC_013284_00016 - - CP015754 0.20360400 1583
AI2861_v1_c2 18 11 Browse 32 215 214202 1.15
Klebsiella pneumoniae
53.15 Conjugative IncFII, IncFIB 000107__CP014778_00094, 000113__CP022035, 000132__HG969996 MOBF NC_021231_00058 MPF_F NC_021502_00150, NC_019165_00034, NC_021654_00016, NC_022609_00081, NC_014312_00128, NC_023332_00154, NC_014312_00118, NC_014312_00116, NC_021502_00131, NC_019389_00080, NC_019155_00032, NC_021654_00004 - - CP009777 0.00181236 767
AI2861_v1_c3 18 11 Browse 1 84 65499 2.08
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 0.00007159 681