Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Clínic (Barcelona)
Hospital Admission Unit Nephrology
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 1401:gapA(2), infB(1), mdh(1), pgi(1), phoE(9), 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 ≤0.25 S S
CEF >128 R R
AZT >128 R R
MEM 0.5 S S
IMI 1 S S
IMI-RELE 0.5 S S
ERT 32 R R
FOSFO <32 S S
GENTA ≤0.25 S S
TOBRA ≤0.25 S S
AMK 32 I R
CIP 64 R R
COLIS 0.12 WT S
AI2842_v1
AI2842_v1

Sample 90 was assembled with Unicycler_v0.4.6 into 8 scaffolds, 8 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
AI2842_v1_c1 90 1401 Browse 26 4788 5147685 1.00
Klebsiella pneumoniae
57.52 Non-mobilizable - - - - - - - - CP007734 0.21953100 1586
AI2842_v1_c2 90 1401 Browse 24 257 252398 1.28
Klebsiella pneumoniae
52.67 Conjugative IncFIB 000107__CP014778_00094 MOBF, MOBP NC_021231_00058, NC_021576_00050 MPF_F NC_021502_00150, 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_021231_00085 - - JX424424 0.01813130 768
AI2842_v1_c3 90 1401 Browse 0 109 103488 1.31
Klebsiella pneumoniae
51.32 Conjugative IncFII, rep_cluster_1418 000124__KP125893_00142, 000759__NC_013950_00034 MOBF NC_021231_00058 MPF_F NC_021502_00150, 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, NC_019155_00032 - - CP020843 0.02322680 1585
AI2842_v1_c4 90 1401 Browse 1 84 63589 1.81
Escherichia coli, Klebsiella pneumoniae
51.22 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 0.00002383 681
AI2842_v1_c5 90 1401 Browse 0 44 33838 2.23
Escherichia coli
50.50 Conjugative IncN 000151__NC_019163_00001 MOBF NC_015872_00034 MPF_T NC_015872_00033, NC_015872_00005, NC_015872_00006, NC_015872_00007, NC_015872_00010, NC_015872_00011 - - CP022277 0.01471450 938
AI2842_v1_c6 90 1401 Browse 0 7 6647 10.30
Escherichia coli
48.62 Mobilizable ColRNAI_rep_cluster_1857 000008__AJ627566 MOBP NC_019076_00002 - - MOBP MF083142 CP012628 0.00019163 23
AI2842_v1_c7 90 1401 Browse 0 6 5450 16.76
Escherichia coli, Salmonella enterica
38.11 Non-mobilizable - - - - - - - - NC_019062 0.29598100 825
AI2842_v1_c8 90 1401 Browse 0 4 5167 20.89
Klebsiella pneumoniae
47.53 Mobilizable ColRNAI_rep_cluster_1291 000001__EU090225_00001 MOBQ NC_019783_00003 - - - - CP006786 0.00305472 502