Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Ramón y Cajal (Madrid)
Hospital Admission Unit None
Patient Sex M
Patient Age 60
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation sputum
Infection or Colonization I
Outbreak None
Genus/Species
Klebsiella pneumoniae
Carbapenamase type(s) VIM-1
MLST 15:gapA(1), infB(1), mdh(1), pgi(1), phoE(1), rpoB(1), tonB(1)
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 >256 R R
CAZ-AVI 256 R R
CEF >128 R R
AZT >128 R R
MEM 0.25 S S
IMI 1 S S
IMI-RELE 1 S S
ERT 8 R R
FOSFO <32 S S
GENTA 128 R R
TOBRA 4 S R
AMK 2 S S
CIP 128 R R
COLIS <0.06 WT S
AI3025_v1
AI3025_v1

Sample 148 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
AI3025_v1_c1 148 15 Browse 32 4853 5299795 1.00
Klebsiella pneumoniae
57.49 Non-mobilizable - - - - - - - - CP008932 0.20360400 1226
AI3025_v1_c2 148 15 Browse 21 330 319173 1.30
Klebsiella pneumoniae
47.90 Conjugative rep_cluster_1150 000430__CP020850 MOBH NC_016980_00239 MPF_F NC_016980_00240, NC_018107_00101, NC_016980_00110, NC_016980_00109, NC_016980_00099, NC_018107_00235, NC_023911_00309 - - CP018961 0.02256510 1530
AI3025_v1_c3 148 15 Browse 20 169 178274 0.97
Klebsiella pneumoniae
51.34 Conjugative IncFII, IncFIB 000107__CP014778_00094, 000113__CP022035, 000130__CP023489 MOBF NC_021231_00058 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_021654_00004 - - NC_024992 0.00705245 769
AI3025_v1_c4 148 15 Browse 0 117 109837 0.90
Klebsiella pneumoniae
48.84 Non-mobilizable IncFIB 000100__NZ_CP016161_00012 - - - - - - CP012570 0.00366686 80
AI3025_v1_c5 148 15 Browse 12 56 45820 1.75
Klebsiella pneumoniae
53.01 Non-mobilizable IncR 000204__CP008701_00115 - - - - - - CP018737 0.02564720 726
AI3025_v1_c6 148 15 Browse 0 4 4163 14.79
Klebsiella pneumoniae
45.78 Non-mobilizable ColRNAI_rep_cluster_1987, rep_cluster_2050 001473__CP024541, 000019__CP000651_00005 - - - - - - CP018739 0.06158390 207
AI3025_v1_c7 148 15 Browse 0 2 2077 25.90
Escherichia coli
47.23 Non-mobilizable Inc13 000058__CP000643_00001 - - - - - - CP008719 0.00139189 839
AI3025_v1_c8 148 15 Browse 0 1 2058 34.41
Escherichia coli
56.51 Non-mobilizable ColRNAI_rep_cluster_1993 000024__JX133088 - - - - - - KU302803 0.00048345 78