Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitari Germans Trias i Pujol (Badalona)
Hospital Admission Unit Vascular surgery
Patient Sex M
Patient Age 82
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation wound
Infection or Colonization I
Outbreak None
Genus/Species
Enterobacter cloacae complex
Carbapenamase type(s) VIM-1
MLST 78:dnaA(8), fusA(9), gyrB(6), leuS(9), pyrG(9), rplB(6), rpoB(8)
EDTA Assay (if any) None
PCR Result (if any) None
Agent MIC CLSI EUCAST
Piper 128 R R
P/T 128 R R
CTX 128 R R
CAZ 128 R R
CAZ-AVI 128 R R
CEF 64 R R
AZT 16 R R
MEM ≤0.25 S S
IMI ≤0.25 S S
IMI-RELE ≤0.25 S S
ERT 0.5 S S
FOSFO 64 S R
GENTA 32 R R
TOBRA 4 S R
AMK 0.5 S S
CIP 16 R R
COLIS <0.06 WT S
AI2620_v1
AI2620_v1

Sample 56 was assembled with Unicycler_v0.4.6 into 6 scaffolds, 6 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
AI2620_v1_c1 56 78 Browse 27 4339 4716089 1.00
Enterobacter cloacae
55.19 Non-mobilizable - - - - - - - - CP008824 0.18226900 966
AI2620_v1_c2 56 78 Browse 3 136 115150 1.57
Enterobacter cloacae
51.80 Non-mobilizable IncFIB 000104__CP010386_00052 - - - - - - CP021897 0.00031257 86
AI2620_v1_c3 56 78 Browse 1 116 103280 1.56
Enterobacter hormaechei
51.39 Mobilizable - - - - - - MOB_unknown NC_014385 CP010385 0.04128450 1109
AI2620_v1_c4 56 78 Browse 0 105 95152 1.71
Citrobacter freundii
54.36 Conjugative IncFII 000114__CP015527, 000122__JQ418538 MOBF NC_021501_00073 MPF_F NC_021501_00097, NC_006323_00096, NC_006323_00097, NC_009378_00101, NC_006323_00105, NC_021501_00085, NC_021501_00084, NC_021501_00083, NC_006323_00113, NC_021501_00076, NC_021501_00074 - - KP900016 0.03923310 621
AI2620_v1_c5 56 78 Browse 11 96 76169 2.09
Escherichia coli
52.60 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 - - JX988621 0.02047890 683
AI2620_v1_c6 56 78 Browse 2 11 9923 19.62
Escherichia coli
57.29 Mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 MOBP NC_001848_00006, NC_011404_00002 - - MOBP NZ_HG941720 AB905284 0.02468310 2178