Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Lucus Augusti (Lugo)
Hospital Admission Unit Internal medicine
Patient Sex F
Patient Age 90
Community/Hospital/LTCF acquisition Hospital
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 64 R R
CAZ-AVI 0.5 S S
CEF >128 R R
AZT >128 R R
MEM 32 R R
IMI 16 R R
IMI-RELE 16 R R
ERT >128 R R
FOSFO <32 S S
GENTA 8 I R
TOBRA 8 I R
AMK 4 S S
CIP >128 R R
COLIS <0.06 WT S
AN2357_v1
AN2357_v1

Sample 492 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
AN2357_v1_c1 492 15 Browse 34 4889 5341432 1.00
Klebsiella pneumoniae
57.42 Non-mobilizable - - - - MPF_T NC_010726_00014, NC_005814_00013, NC_010726_00011, NC_013284_00016 - - CP015754 0.21089700 1583
AN2357_v1_c2 492 15 Browse 41 291 287806 1.79
Klebsiella pneumoniae
52.51 Conjugative IncFII, IncFIB, IncR, rep_cluster_1418 000107__CP014778_00094, 000113__CP022035, 000204__CP008701_00115, 000128__CP023916, 000759__NC_013950_00034 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 - - CP021710 0.01235330 767
AN2357_v1_c3 492 15 Browse 1 84 65498 1.82
Escherichia coli
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 0.00141786 681