Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Lucus Augusti (Lugo)
Hospital Admission Unit Geriatrics
Patient Sex F
Patient Age 94
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation wound
Infection or Colonization I
Outbreak None
Genus/Species
Klebsiella pneumoniae
Carbapenamase type(s) NDM-1
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) 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 >128 R R
AZT >128 R R
MEM 16 R R
IMI 8 R R
IMI-RELE 8 R R
ERT 8 R R
FOSFO <32 S S
GENTA >256 R R
TOBRA >256 R R
AMK >128 R R
CIP 64 R R
COLIS <0.06 WT S
AI2830_v1
AI2830_v1

Sample 52 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
AI2830_v1_c1 52 147 Browse 38 4985 5387387 1.00
Klebsiella pneumoniae
57.30 Non-mobilizable - - - - MPF_T NC_010726_00014, NC_005814_00013, NC_010726_00011, NC_013284_00016 - - KX636095 0.19173100 770
AI2830_v1_c2 52 147 Browse 5 122 121034 1.13
Klebsiella pneumoniae
53.25 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 0.00002383 1713
AI2830_v1_c3 52 147 Browse 0 84 70767 1.31
Citrobacter sp.
52.46 Conjugative IncFII, IncR 000124__KP125893_00142, 000204__CP008701_00115 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_023332_00154, NC_014312_00118, NC_014312_00116, NC_021502_00131, NC_021231_00085, NC_022609_00095 - - CP008791 0.03681860 1233
AI2830_v1_c4 52 147 Browse 0 52 54404 3.98
Klebsiella pneumoniae
53.17 Non-mobilizable rep_cluster_1 000232__CP012429 - - - - - - CP021760 0.00000000 1705
AI2830_v1_c5 52 147 Browse 0 4 4715 25.81
Klebsiella pneumoniae
41.12 Mobilizable ColRNAI_rep_cluster_1857 000008__AJ627566 - - - - MOBP, MOB_unknown NC_019986, AP017298 DQ286390 0.00257463 33
AI2830_v1_c6 52 147 Browse 0 3 4167 20.49
Klebsiella pneumoniae
41.49 Non-mobilizable ColRNAI_rep_cluster_1987, rep_cluster_2050 001473__CP024541, 000019__CP000651_00005 - - - - - - EU932690 0.00036121 205