Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Clínic (Barcelona)
Hospital Admission Unit Surgery
Patient Sex F
Patient Age 86
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation blood culture
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 0.5 S S
CEF >128 R R
AZT >128 R R
MEM 1 S S
IMI 0.5 S S
IMI-RELE 0.25 S S
ERT 4 R R
FOSFO 128 I R
GENTA ≤0.25 S S
TOBRA ≤0.25 S S
AMK 4 S S
CIP 128 R R
COLIS 0.12 WT S
AI2640_v1
AI2640_v1

Sample 88 was assembled with Unicycler_v0.4.6 into 5 scaffolds, 5 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
AI2640_v1_c1 88 392 Browse 30 4926 5309557 1.00
Klebsiella pneumoniae
57.44 Non-mobilizable - - - - - - - - CP007734 0.21089700 1586
AI2640_v1_c2 88 392 Browse 13 351 341694 1.60
Klebsiella pneumoniae
48.51 Conjugative rep_cluster_1150 000430__CP020850 MOBH NC_016980_00239 MPF_F NC_016980_00240, NC_018107_00101, NC_016980_00110, NC_016980_00109, NC_016980_00099, NC_018107_00235, NC_023911_00309 - - CP015501 0.02421420 1530
AI2640_v1_c3 88 392 Browse 28 183 168173 1.15
Klebsiella pneumoniae
51.14 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 0.00369655 770
AI2640_v1_c4 88 392 Browse 1 85 65498 2.95
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 0.00134007 681
AI2640_v1_c5 88 392 Browse 0 4 4167 24.32
Klebsiella pneumoniae
41.49 Non-mobilizable ColRNAI_rep_cluster_1987, rep_cluster_2050 001473__CP024541, 000019__CP000651_00005 - - - - - - EU932690 0.00028831 205