Collection SERGAS
Isolation Year 2017
Isolation Location Hospital de Guadalajara (Guadalajara)
Hospital Admission Unit Long-term care facility
Patient Sex F
Patient Age 56
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation wound
Infection or Colonization I
Outbreak None
Genus/Species
Klebsiella pneumoniae
Carbapenamase type(s) OXA-48
MLST 307:gapA(4), infB(1), mdh(2), pgi(52), phoE(1), rpoB(1), tonB(7)
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 32 R R
CAZ-AVI ≤0.25 S S
CEF 4 SDD I
AZT 32 R R
MEM 32 R R
IMI 8 R R
IMI-RELE 8 R R
ERT 32 R R
FOSFO <32 S S
GENTA 32 R R
TOBRA 16 R R
AMK 2 S S
CIP 64 R R
COLIS 0.25 WT S
AI3039_v1
AI3039_v1

Sample 292 was assembled with Unicycler_v0.4.6 into 10 scaffolds, 10 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
AI3039_v1_c1 292 307 Browse 28 4988 5374704 1.00
Klebsiella pneumoniae
57.42 Non-mobilizable - - - - - - - - CP007734 0.21953100 1586
AI3039_v1_c2 292 307 Browse 9 313 308562 1.25
Klebsiella pneumoniae
47.53 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 - - CP015501 0.01937140 1530
AI3039_v1_c3 292 307 Browse 32 236 240138 1.03
Klebsiella pneumoniae
52.43 Conjugative IncFII, IncFIB 000124__KP125893_00142, 000107__CP014778_00094 MOBF NC_021231_00058 MPF_F NC_021502_00150, NC_019165_00034, NC_021654_00016, NC_011281_00082, NC_022609_00081, NC_014312_00128, NC_019389_00068, NC_023332_00154, NC_014312_00118, NC_014312_00116, NC_021502_00131, NC_019155_00032 - - KY271404 0.00194597 770
AI3039_v1_c4 292 307 Browse 1 83 63589 2.05
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
AI3039_v1_c5 292 307 Browse 0 4 3991 30.27
Klebsiella pneumoniae
44.35 Non-mobilizable ColRNAI_rep_cluster_1987, rep_cluster_2050 001473__CP024541, 000019__CP000651_00005 - - - - - - CP012558 0.08624910 195
AI3039_v1_c6 292 307 Browse 0 3 3670 24.25
Klebsiella pneumoniae
55.64 Mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 MOBP NC_001848_00006 - - MOBP CP018941 CP018740 0.04874130 95
AI3039_v1_c7 292 307 Browse 0 3 3516 30.70
Enterobacter hormaechei
55.29 Mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 MOBP NC_001848_00006, NC_019986_00002 - - MOBP NC_010936 CP008845 0.02315240 192
AI3039_v1_c8 292 307 Browse 0 2 2058 39.09
Klebsiella pneumoniae, Proteus mirabilis
56.51 Non-mobilizable ColRNAI_rep_cluster_1993 000024__JX133088 - - - - - - KU302803 0.00048345 78
AI3039_v1_c9 292 307 Browse 0 1 1949 17.14
Salmonella enterica
50.03 Mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 - - - - MOBP KT693145 CP019997 0.03870850 141
AI3039_v1_c10 292 307 Browse 0 1 1551 32.46
Escherichia coli
51.64 Mobilizable ColRNAI_rep_cluster_1885 000013__DQ995351_00001 - - - - MOBP, MOB_unknown JN985534, AB027308 JN253636 0.04734430 414