Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Gregorio Marañón (Madrid)
Hospital Admission Unit Traumatology
Patient Sex M
Patient Age 42
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation biopsy
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 >256 R R
P/T >256 R R
CTX >128 R R
CAZ >128 R R
CAZ-AVI 4 S S
CEF >128 R R
AZT >128 R R
MEM 0.5 S S
IMI 1 S S
IMI-RELE ≤0.25 S S
ERT 4 R R
FOSFO 256 R R
GENTA 8 I R
TOBRA 4 S R
AMK 4 S S
CIP >128 R R
COLIS 32 NWT R
AI2824_v5
AI2824_v5

Sample 26 was assembled with Unicycler_v0.4.6 into 4 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
AI2824_v5_c1 26 11 Browse 33 5030 5362998 1.00
Klebsiella pneumoniae
57.40 Non-mobilizable - - - - MPF_T NC_010726_00014, NC_005814_00013, NC_010726_00011, NC_013284_00016 - - CP015754 0.20360400 1583
AI2824_v5_c2 26 11 Browse 34 233 230081 1.02
Klebsiella pneumoniae
53.17 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
AI2824_v5_c3 26 11 Browse 1 83 63589 1.98
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
AI2824_v5_c4 26 11 Browse 7 53 51084 1.34
Klebsiella pneumoniae
50.43 Conjugative IncR 000204__CP008701_00115 MOBF, MOBP NC_015599_00019, NC_021576_00050 MPF_T NC_022375_00024 MOBF NZ_CP012928 CP014299 0.02572920 730