Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Univeristario de Bellvitge (Barcelona)
Hospital Admission Unit Emergencies
Patient Sex M
Patient Age 68
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation urine
Infection or Colonization I
Outbreak None
Genus/Species
Klebsiella pneumoniae
Carbapenamase type(s) Conflict with PCR
MLST 147:gapA(3), infB(4), mdh(6), pgi(1), phoE(7), rpoB(4), tonB(38)
EDTA Assay (if any) None
PCR Result (if any) Positivo NDM y Negativo OXA-48
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 >128 R R
AZT >128 R R
MEM 64 R R
IMI 32 R R
IMI-RELE 16 R R
ERT >128 R R
FOSFO 64 S R
GENTA >256 R R
TOBRA >256 R R
AMK >128 R R
CIP 64 R R
COLIS 0.12 WT S
AI3000_v1
AI3000_v1

Sample 418 was assembled with Unicycler_v0.4.6 into 9 scaffolds, 9 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
AI3000_v1_c1 418 147 Browse 32 4932 5334591 1.00
Klebsiella pneumoniae
57.39 Non-mobilizable - - - - MPF_T NC_010726_00014, NC_005814_00013, NC_010726_00011, NC_013284_00016 - - CP015754 0.19729200 1583
AI3000_v1_c2 418 147 Browse 4 120 117442 0.75
Klebsiella pneumoniae
53.21 Conjugative IncFII, rep_cluster_1418 000759__NC_013950_00034, 000118__KJ958926_00047 MOBP NC_021198_00256 MPF_I NC_021198_00230, NC_021198_00234, NC_021198_00235, NC_021198_00236, NC_021198_00238, NC_021198_00239, NC_021198_00240, NC_021198_00243, NC_021198_00249 - - CP021758 0.00105797 1713
AI3000_v1_c3 418 147 Browse 9 69 65762 1.63
Klebsiella pneumoniae
52.52 Mobilizable IncR 000204__CP008701_00115 MOBP NC_021576_00050 - - - - CP021761 0.00604372 727
AI3000_v1_c4 418 147 Browse 1 83 63589 1.64
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
AI3000_v1_c5 418 147 Browse 0 51 53996 4.60
Klebsiella pneumoniae
52.92 Non-mobilizable rep_cluster_3 001607__CP009878 - - - - - - CP021760 0.01335470 1705
AI3000_v1_c6 418 147 Browse 0 8 7926 13.33
-, Citrobacter freundii, Enterobacter cloacae, Enterobacter hormaechei, Escherichia coli
48.20 Non-mobilizable ColRNAI_rep_cluster_1987, rep_cluster_2050 001473__CP024541, 000019__CP000651_00005 - - - - - - CP000651 0.01807090 206
AI3000_v1_c7 418 147 Browse 0 4 4715 23.96
Klebsiella pneumoniae
41.12 Mobilizable ColRNAI_rep_cluster_1857 000008__AJ627566 - - - - MOBP, MOB_unknown NC_019986, AP017298 DQ286390 0.00260250 33
AI3000_v1_c8 418 147 Browse 0 4 4167 37.09
Klebsiella pneumoniae
41.49 Non-mobilizable rep_cluster_2050 001473__CP024541 - - - - - - EU932690 0.00048345 205
AI3000_v1_c9 418 147 Browse 0 1 2674 12.86
Klebsiella pneumoniae
31.19 Non-mobilizable - - - - - - - - 1.00000000