Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Clínic (Barcelona)
Hospital Admission Unit Digestive surgery
Patient Sex M
Patient Age 81
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 1 S S
CEF 128 R R
AZT >128 R R
MEM 1 S S
IMI 1 S S
IMI-RELE 1 S S
ERT 2 R R
FOSFO <32 S S
GENTA ≤0.25 S S
TOBRA ≤0.25 S S
AMK 0.5 S S
CIP 8 R R
COLIS 0.25 WT S
AI2840_v1
AI2840_v1

Sample 85 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
AI2840_v1_c1 85 392 Browse 28 4909 5293172 1.00
Klebsiella pneumoniae
57.43 Non-mobilizable - - - - - - - - CP007734 0.20360400 1586
AI2840_v1_c2 85 392 Browse 13 347 336901 1.40
Klebsiella pneumoniae
48.59 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 0.02360200 1530
AI2840_v1_c3 85 392 Browse 28 181 166265 0.98
Klebsiella pneumoniae
51.06 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 0.00351914 770
AI2840_v1_c4 85 392 Browse 1 84 63871 1.56
Klebsiella pneumoniae
51.18 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 0.00016755 681
AI2840_v1_c5 85 392 Browse 0 4 4167 21.46
Klebsiella pneumoniae
41.49 Non-mobilizable ColRNAI_rep_cluster_1987, rep_cluster_2050 001473__CP024541, 000019__CP000651_00005 - - - - - - EU932690 0.00036121 205