Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario La Paz (Madrid)
Hospital Admission Unit ICU
Patient Sex M
Patient Age 53
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation blood culture
Infection or Colonization I
Outbreak None
Genus/Species
Klebsiella pneumoniae
Carbapenamase type(s) OXA-48
MLST 15:gapA(1), infB(1), mdh(1), pgi(1), phoE(1), rpoB(1), tonB(1)
EDTA Assay (if any) Should have OXA-48
PCR Result (if any) OXA-48 positive x2
Agent MIC CLSI EUCAST
Piper >256 R R
P/T >256 R R
CTX >128 R R
CAZ >128 R R
CAZ-AVI 1 S S
CEF >128 R R
AZT >128 R R
MEM 1 S S
IMI 0.5 S S
IMI-RELE 0.25 S S
ERT 4 R R
FOSFO <32 S S
GENTA >256 R R
TOBRA 256 R R
AMK 8 S S
CIP >128 R R
COLIS 0.12 WT S
AI3024_v1
AI3024_v1

Sample 126 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
AI3024_v1_c1 126 15 Browse 32 4835 5276461 1.00
Klebsiella pneumoniae
57.50 Non-mobilizable - - - - - - - - CP008932 0.20360400 1226
AI3024_v1_c2 126 15 Browse 28 222 227227 0.82
Klebsiella pneumoniae
52.29 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 - - CP021710 0.00617965 767
AI3024_v1_c3 126 15 Browse 6 115 113903 0.70
Klebsiella pneumoniae
52.79 Conjugative IncFII, IncFIB 000113__CP022035, 000097__NC_025166_00051, 000130__CP023489 MOBF NC_021231_00058 MPF_F NC_021502_00150, NC_019165_00034, NC_021654_00016, NC_022609_00081, NC_014312_00128, NC_019389_00068, NC_023332_00154, NC_014312_00118, NC_014312_00116, NC_021502_00131, NC_019389_00080, NC_023905_00125 - - CP000649 0.01198400 1220
AI3024_v1_c4 126 15 Browse 17 73 60602 0.97
Klebsiella pneumoniae
55.16 Non-mobilizable IncR 000204__CP008701_00115 - - - - - - CP006662 0.02206230 728
AI3024_v1_c5 126 15 Browse 0 2 2058 32.26
Klebsiella pneumoniae
56.51 Non-mobilizable ColRNAI_rep_cluster_1993 000024__JX133088 - - - - - - KU302803 0.00058191 78