Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Central de Asturias (Oviedo)
Hospital Admission Unit Internal medicine
Patient Sex M
Patient Age 76
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation urine
Infection or Colonization I
Outbreak None
Genus/Species
Citrobacter freundii
Carbapenamase type(s) OXA-48
MLST 22:aspC(15), clpX(12), fadD(20), mdh(15), arcA(5), dnaG(11), lysP(17)
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 4 R I
IMI 2 I S
IMI-RELE 1 S S
ERT 8 R R
FOSFO 256 R R
GENTA 32 R R
TOBRA 4 S R
AMK 2 S S
CIP >128 R R
COLIS <0.06 WT S
AI2661_v1
AI2661_v1

Sample 234 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
AI2661_v1_c1 234 22 Browse 35 4876 5150246 1.00
Citrobacter freundii
51.81 Non-mobilizable - - - - - - - - CP007734 0.21953100 1586
AI2661_v1_c2 234 22 Browse 13 271 205393 1.19
Citrobacter freundii
48.84 Non-mobilizable rep_cluster_404 001726__CP019987_00074 - - - - - - CP019987 0.01420090 1876
AI2661_v1_c3 234 22 Browse 1 157 149443 1.80
Citrobacter freundii
51.98 Conjugative IncFII, IncFIB 000111__NZ_CP011595_00114, 000101__NZ_CP012345_00042, 000123__CP000858 MOBF NC_019125_00139 MPF_F NC_021817_00020, NC_021871_00015, NC_019125_00135, NC_021817_00013, NC_019342_00064, NZ_AGTD01000004_00091, NC_021871_00025, NZ_AGTD01000004_00094, NC_021871_00022, NC_021817_00023, NC_021817_00021 MOBP NZ_CP016040 CP011610 0.01561600 748
AI2661_v1_c4 234 22 Browse 1 86 63570 3.13
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 0.00000000 681
AI2661_v1_c5 234 22 Browse 0 4 3576 20.50
Klebsiella variicola
44.99 Non-mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 - - - - - - CP006637 0.13386400 179