Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Marqués de Valdecilla (Santander)
Hospital Admission Unit None
Patient Sex F
Patient Age 87
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 5000:gapA(3), infB(3), mdh(113), 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 2 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 0.12 S S
FOSFO >256 R R
GENTA 8 I R
TOBRA 8 I R
AMK 0.12 S S
CIP 16 R R
COLIS <0.06 WT S
AI2740_v1
AI2740_v1

Sample 368 was assembled with Unicycler_v0.4.6 into 5 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
AI2740_v1_c1 368 5000 Browse 32 5012 5341489 1.00
Klebsiella pneumoniae
57.43 Non-mobilizable - - - - MPF_T NC_010726_00014, NC_005814_00013, NC_010726_00011, NC_013284_00016 - - CP015754 0.20360400 1583
AI2740_v1_c2 368 5000 Browse 32 214 212171 1.24
Klebsiella pneumoniae
52.85 Non-mobilizable IncFII, IncFIB 000107__CP014778_00094, 000113__CP022035, 000132__HG969996 - - MPF_F 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 0.00274254 767
AI2740_v1_c3 368 5000 Browse 1 84 65498 2.43
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
AI2740_v1_c4 368 5000 Browse 1 12 12355 4.06
Klebsiella pneumoniae
53.35 Non-mobilizable - - - - - - - - CP011334 0.06482500 3836
AI2740_v1_c5 368 5000 Browse 0 1 1475 1.00
-
33.36 Non-mobilizable - - - - - - - - KX756454 0.01880530 3836