Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Gregorio Marañón (Madrid)
Hospital Admission Unit Nephrology
Patient Sex M
Patient Age 45
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 4 S S
CEF >128 R R
AZT >128 R R
MEM ≤0.25 S S
IMI ≤0.25 S S
IMI-RELE ≤0.25 S S
ERT 4 R R
FOSFO <32 S S
GENTA 4 S R
TOBRA 2 S S
AMK 8 S S
CIP >128 R R
COLIS 0.5 WT S
AI2822_v1
AI2822_v1

Sample 23 was assembled with Unicycler_v0.4.6 into 4 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
AI2822_v1_c1 23 392 Browse 61 5131 5517947 1.00
Klebsiella pneumoniae
57.26 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 0.13239900 770
AI2822_v1_c2 23 392 Browse 1 84 65499 1.21
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
AI2822_v1_c3 23 392 Browse 0 1 2927 22.16
Klebsiella pneumoniae
46.53 Non-mobilizable ColRNAI_rep_cluster_1987, rep_cluster_2050 001473__CP024541, 000019__CP000651_00005 - - - - - - CP011643 0.00016755 199
AI2822_v1_c4 23 392 Browse 0 3 2495 18.50
Enterobacter hormaechei
51.46 Mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 - - - - MOB_unknown NC_017722 CP010389 0.00098187 215