Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario La Princesa (Madrid)
Hospital Admission Unit Urology
Patient Sex M
Patient Age 84
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 392:gapA(3), infB(4), mdh(6), pgi(1), phoE(7), rpoB(4), tonB(40)
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 8 R I
IMI 8 R R
IMI-RELE 8 R R
ERT 2 R R
FOSFO >256 R R
GENTA 64 R R
TOBRA 16 R R
AMK 2 S S
CIP 128 R R
COLIS 4 NWT R
AI3028_v1
AI3028_v1

Sample 200 was assembled with Unicycler_v0.4.6 into 4 scaffolds, 4 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
AI3028_v1_c1 200 392 Browse 32 4995 5394027 1.00
Klebsiella pneumoniae
57.34 Non-mobilizable - - - - - - - - CP007734 0.20360400 1586
AI3028_v1_c2 200 392 Browse 31 205 195692 0.57
Klebsiella pneumoniae
51.67 Conjugative IncFII, IncFIB 000124__KP125893_00142, 000107__CP014778_00094 MOBF NC_021231_00058 MPF_F NC_021502_00150, NC_014312_00141, NC_019165_00034, NC_021654_00016, NC_011281_00082, NC_022609_00081, NC_014312_00128, NC_019389_00068, NC_023332_00154, NC_014312_00118, NC_014312_00116, NC_021502_00131 - - CP010390 0.00002383 770
AI3028_v1_c3 200 392 Browse 1 84 65499 2.81
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
AI3028_v1_c4 200 392 Browse 0 1 2927 22.43
Klebsiella pneumoniae
46.53 Non-mobilizable ColRNAI_rep_cluster_1987, rep_cluster_2050 001473__CP024541, 000019__CP000651_00005 - - - - - - CP011643 0.00026408 199