Collection SERGAS
Isolation Year 2017
Isolation Location Complejo Asistencial Universitario de Salamanca (Salamanca)
Hospital Admission Unit ICU
Patient Sex F
Patient Age 59
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation peritoneal fluid
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 >256 R R
P/T >256 R R
CTX 128 R R
CAZ >128 R R
CAZ-AVI >128 R R
CEF 64 R R
AZT 128 R R
MEM 1 S S
IMI 0.5 S S
IMI-RELE 0.25 S S
ERT 8 R R
FOSFO 64 S R
GENTA ≤0.25 S S
TOBRA 2 S S
AMK 0.25 S S
CIP 64 R R
COLIS <0.06 WT S
AI2615_v1
AI2615_v1

Sample 46 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
AI2615_v1_c1 46 78 Browse 29 4377 4740944 1.00
Enterobacter cloacae
55.13 Non-mobilizable - - - - - - - - CP008824 0.18226900 966
AI2615_v1_c2 46 78 Browse 3 137 115150 1.46
Enterobacter cloacae
51.81 Non-mobilizable IncFIB 000104__CP010386_00052 - - - - - - CP021897 0.00023990 86
AI2615_v1_c3 46 78 Browse 9 139 108267 2.58
Enterobacter hormaechei
49.71 Conjugative IncX3 000221__NC_025130_00012 MOBP NC_020552_00059 MPF_T NC_023277_00163, NC_019157_00030, NC_019083_00030, NC_017624_00009, NC_012885_00167, NC_019083_00032 - - CP012168 0.05499660 964
AI2615_v1_c4 46 78 Browse 0 6 5413 8.60
Escherichia coli
51.38 Mobilizable ColRNAI_rep_cluster_1987 000020__CP023920 MOBP NC_021293_00005, NC_001848_00006 - - MOBP CP008720 CP011049 0.04142620 98
AI2615_v1_c5 46 78 Browse 0 8 4995 15.48
Klebsiella oxytoca
51.77 Mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 MOBP NC_011404_00002 - - MOBP CP008720 NC_011404 0.00173271 102
AI2615_v1_c6 46 78 Browse 0 5 3223 14.99
Citrobacter freundii, Salmonella enterica, Serratia marcescens
56.35 Mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 MOBP NC_013090_00004 - - MOBP CP018941 CP016867 0.00065615 133