An outbreak case

In silico genotype raw data are available.

Potential AMR prediction

AMR catalog version 20190627

View read mapping using JBrowse (Genome Res. 2009. 19: 1630-1638)

Isoniazid (INH)
ahpCahpC_promoterfabG1_promoterinhAkasAkatGkatG_promoterndh
Rifampicin (RIP)
rpoBrpoC
Pyrazinamide (PZA)
panDpncApncA_promoterrpsA
Streptomycin (STR)
gidrpsLrrs
Ethambutol (EMB)
embAembA_promoterembBembCembR
Ethionamide (ETH)
ethAethRfabG1_promoterinhAndh
Fluoroquinolones (FQ)
gyrAgyrB
Amikacin (AMK)
rrs
Capreomycin (CPM)
rrstlyA
Kanamycin (KM)
eis_promoterrrs
Para-aminosalisylic_acid (PAS)
folCribDthyA
Linezolid (LZD)
rplCrrl
Clofazimine (CFZ)
Rv0678
Bedaquiline (BDQ)
Rv0678

Strain INHRIPPZASTREMBETHFQAMKCPMKMPASLZDCFZBDQ Mutations in candidate genes
JP01_S1_L001 embA (c.228C>T)
embC (c.2781C>T)
gid (c.276A>C, E92D)
gid (c.615A>G)
gyrA (c.61G>C, E21Q)
gyrA (c.284G>C, S95T)
gyrA (c.1212C>G)
gyrA (c.2003G>A, G668D)
katG (c.1388G>T, R463L)
rpoA (c.949C>T, P317S)
rpoB (c.3225T>C)
rpoC (c.1771G>C, E591Q)
rpsA (c.636A>C)
tlyA (c.33A>G)
JP02_S2_L001 embA (c.228C>T)
embC (c.2781C>T)
gid (c.276A>C, E92D)
gid (c.615A>G)
gyrA (c.61G>C, E21Q)
gyrA (c.284G>C, S95T)
gyrA (c.1212C>G)
gyrA (c.2003G>A, G668D)
katG (c.1388G>T, R463L)
rpoA (c.949C>T, P317S)
rpoA_promoter (C-45A)
rpoB (c.3225T>C)
rpoC (c.1771G>C, E591Q)
rpsA (c.636A>C)
tlyA (c.33A>G)
JP03_S3_L001 embA (c.228C>T)
embC (c.2781C>T)
gid (c.276A>C, E92D)
gid (c.615A>G)
gyrA (c.61G>C, E21Q)
gyrA (c.284G>C, S95T)
gyrA (c.1212C>G)
gyrA (c.2003G>A, G668D)
katG (c.1388G>T, R463L)
rpoA (c.949C>T, P317S)
rpoB (c.3225T>C)
rpoC (c.1771G>C, E591Q)
rpsA (c.636A>C)
tlyA (c.33A>G)
JP04_S4_L001 embA (c.228C>T)
embC (c.2781C>T)
gid (c.276A>C, E92D)
gid (c.615A>G)
gyrA (c.61G>C, E21Q)
gyrA (c.284G>C, S95T)
gyrA (c.1212C>G)
gyrA (c.2003G>A, G668D)
katG (c.1388G>T, R463L)
rpoA (c.949C>T, P317S)
rpoB (c.3225T>C)
rpoC (c.1771G>C, E591Q)
rpsA (c.636A>C)
tlyA (c.33A>G)
JP05_S5_L001 embA (c.228C>T)
embC (c.2781C>T)
gid (c.276A>C, E92D)
gid (c.615A>G)
gyrA (c.61G>C, E21Q)
gyrA (c.284G>C, S95T)
gyrA (c.1212C>G)
gyrA (c.2003G>A, G668D)
katG (c.1388G>T, R463L)
rpoA (c.949C>T, P317S)
rpoB (c.3225T>C)
rpoC (c.1771G>C, E591Q)
rpsA (c.636A>C)
tlyA (c.33A>G)
JP06_S6_L001 embA (c.228C>T)
embC (c.2781C>T)
gid (c.276A>C, E92D)
gid (c.615A>G)
gyrA (c.61G>C, E21Q)
gyrA (c.284G>C, S95T)
gyrA (c.1212C>G)
gyrA (c.2003G>A, G668D)
katG (c.1388G>T, R463L)
rpoA (c.949C>T, P317S)
rpoB (c.3225T>C)
rpoC (c.1771G>C, E591Q)
rpsA (c.636A>C)
tlyA (c.33A>G)
JP07_S7_L001 embA (c.228C>T)
embC (c.2781C>T)
gid (c.276A>C, E92D)
gid (c.615A>G)
gyrA (c.61G>C, E21Q)
gyrA (c.284G>C, S95T)
gyrA (c.1212C>G)
gyrA (c.2003G>A, G668D)
katG (c.1388G>T, R463L)
rpoA (c.949C>T, P317S)
rpoB (c.3225T>C)
rpoC (c.1771G>C, E591Q)
rpsA (c.636A>C)
tlyA (c.33A>G)

INH: Isoniazid; RIP: Rifampicin; PZA: Pyrazinamide; STR: Streptomycin; EMB: Ethambutol; ETH: Ethionamide; FQ: Fluoroquinolones; AMK: Amikacin; CPM: Capreomycin; KM: Kanamycin; PAS: Para-aminosalisylic_acid; LZD: Linezolid; CFZ: Clofazimine; BDQ: Bedaquiline;


TB profiler result

TB profiler AMR catalog used here is not the latest one.
Please refer to the original site for the latest information.
Reference
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Coll F, McNerney R, et al. Genome Med. 2015 May 27;7(1):51. doi: 10.1186/s13073-015-0164-0. TBprofiler website
Strain Lineage MDR XDR INH RIP PZA STR EMB ETH FQ AMK CPM KM Mutations in candidate genes
JP01_S1_L001 lineage2 East-Asian Beijing RD105
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181
gyrA, 7362, Glu21Gln
gyrA, 7585, Ser95Thr
gyrA, 8513, Val404Val
gyrA, 9304, Gly668Asp
rpoB, 763031, Ala1075Ala
rpoC, 765140, Glu591Gln
rpsA, 1834177, Arg212Arg, lineage2
tlyA, 1917972, Leu11Leu
katG, 2154724, Arg463Leu
embC, 4242643, Arg927Arg
embA, 4243460, Cys76Cys
JP02_S2_L001 lineage2 East-Asian Beijing RD105
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181
gyrA, 7362, Glu21Gln
gyrA, 7585, Ser95Thr
gyrA, 8513, Val404Val
gyrA, 9304, Gly668Asp
rpoB, 763031, Ala1075Ala
rpoC, 765140, Glu591Gln
rpsA, 1834177, Arg212Arg, lineage2
tlyA, 1917972, Leu11Leu
katG, 2154724, Arg463Leu
embC, 4242643, Arg927Arg
embA, 4243460, Cys76Cys
JP03_S3_L001 lineage2 East-Asian Beijing RD105
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181
gyrA, 7362, Glu21Gln
gyrA, 7585, Ser95Thr
gyrA, 8513, Val404Val
gyrA, 9304, Gly668Asp
rpoB, 763031, Ala1075Ala
rpoC, 765140, Glu591Gln
rpsA, 1834177, Arg212Arg, lineage2
tlyA, 1917972, Leu11Leu
katG, 2154724, Arg463Leu
embC, 4242643, Arg927Arg
embA, 4243460, Cys76Cys
JP04_S4_L001 lineage2 East-Asian Beijing RD105
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181
gyrA, 7362, Glu21Gln
gyrA, 7585, Ser95Thr
gyrA, 8513, Val404Val
gyrA, 9304, Gly668Asp
rpoB, 763031, Ala1075Ala
rpoC, 765140, Glu591Gln
rpsA, 1834177, Arg212Arg, lineage2
tlyA, 1917972, Leu11Leu
katG, 2154724, Arg463Leu
embC, 4242643, Arg927Arg
embA, 4243460, Cys76Cys
JP05_S5_L001 lineage2 East-Asian Beijing RD105
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181
gyrA, 7362, Glu21Gln
gyrA, 7585, Ser95Thr
gyrA, 8513, Val404Val
gyrA, 9304, Gly668Asp
rpoB, 763031, Ala1075Ala
rpoC, 765140, Glu591Gln
rpsA, 1834177, Arg212Arg, lineage2
tlyA, 1917972, Leu11Leu
katG, 2154724, Arg463Leu
embC, 4242643, Arg927Arg
embA, 4243460, Cys76Cys
JP06_S6_L001 lineage2 East-Asian Beijing RD105
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181
gyrA, 7362, Glu21Gln
gyrA, 7585, Ser95Thr
gyrA, 8513, Val404Val
gyrA, 9304, Gly668Asp
rpoB, 763031, Ala1075Ala
rpoC, 765140, Glu591Gln
rpsA, 1834177, Arg212Arg, lineage2
tlyA, 1917972, Leu11Leu
katG, 2154724, Arg463Leu
embC, 4242643, Arg927Arg
embA, 4243460, Cys76Cys
JP07_S7_L001 lineage2 East-Asian Beijing RD105
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181
gyrA, 7362, Glu21Gln
gyrA, 7585, Ser95Thr
gyrA, 8513, Val404Val
gyrA, 9304, Gly668Asp
rpoB, 763031, Ala1075Ala
rpoC, 765140, Glu591Gln
rpsA, 1834177, Arg212Arg, lineage2
tlyA, 1917972, Leu11Leu
katG, 2154724, Arg463Leu
embC, 4242643, Arg927Arg
embA, 4243460, Cys76Cys

MDR: Multi drug resistance, INH + RFP; XDR: Extremely drug resistance, MDR + FQ + (AMK or CPM or KM); INH: Isoniazid; RIP: Rifampicin; PZA: Pyrazinamide; STR: Streptomycin; EMB: Ethambutol; ETH: Ethionamide; FQ: Fluoroquinolones; AMK: Amikacin; CPM: Capreomycin; KM: Kanamycin;

KvarQ MTBC analysis result

Reference
KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes. Steiner A, Stucki D, Coscolla M, Borrell S, Gagneux S. BMC Genomics. 2014 Oct 9;15(1):881. doi:10.1186/1471-2164-15-881. http://www.swisstph.ch/kvarq.
  • KvarQ modified version: Coverage torelance was changed: std 1.5 -> 2.0
    (Around line 446 in file genes.py, std limitation was changed to 2.0).
  • MTBC analysis version: MTBC.niid.3.20150403 about license
SamplePhyloResistance
JP01_S1_L001 lineage 2/beijing sublineage
No resistance found
JP02_S2_L001 lineage 2/beijing sublineage
No resistance found
JP03_S3_L001 lineage 2/beijing sublineage
No resistance found
JP04_S4_L001 lineage 2/beijing sublineage
No resistance found
JP05_S5_L001 lineage 2/beijing sublineage
No resistance found
JP06_S6_L001 lineage 2/beijing sublineage
No resistance found
JP07_S7_L001 lineage 2/beijing sublineage
No resistance found

Core genome phylogenetic tree

ML tree generated by RAxML ver. 8.2.0 [Strain]...[SRA ID]...[lineage]
R SVG Plot! H37Rv...NC 000962...lineage 4 S00017318...ERR330651...lineage 4 S00013760...ERR294180...lineage 4.8 Bir 426...ERR072039...lineage 4.9 S00013201...ERR270699...lineage 4.4.1 S00013203...ERR270701...lineage 4.4.1.1 Bir 79...ERR038282...lineage 4.4.1.2 S00013126...ERR270624...lineage 4.4.2 S00018378...ERR351925+ERR386857...lineage 4.4 S00017375...ERR330708...lineage 4.2.2 S00009367...ERR228222...lineage 4.2.2.1 S00009328...ERR228183...lineage 4.2.1 Bir 74...ERR038277...lineage 4.1.1 S00007348...ERR117732...lineage 4.1.1.3 S00007381...ERR114477...lineage 4.1.1.1 MT0016...SRR058116...lineage 4.1.1.2 Haarlem...NC 022350...lineage 4.1.2.1 S00018390...ERR351937+ERR386869...lineage 4.1.2.1 ATCC 35801...NC 020559...lineage 4.1.2.1 7199-99...NC 020089...lineage 4.1.2.1 S00013476...ERR278597+ERR386956...lineage 4.1.2 L4 DY195...ERR234201...lineage 4.1 S00007361...ERR114513...lineage 3 S00007291...ERR114453...lineage 3.1.1 S00007295...ERR117696...lineage 3.1.2.1 S00018322...ERR351869+ERR386801...lineage 3.1.2 S00007298...ERR114442...lineage 3.1.2.2 GX 450708...SRR1710066...lineage 2.1 GX 451017...SRR1710070...lineage 2.1 proto-Beijing 10 0554...SRR1710083...lineage 2.2.2 SJ649...SRR1710111...lineage 2.2.2 MG1 Shanghai 09-1608...SRS790114...lineage 2.2.2 MG1 GQ366...ERR234133...lineage 2.2.1 PG1 2533E...ERR234658...lineage 2.2.1 PG1 08 0205...SRR1710073...lineage 2.2.1 MG2 SJ432...SRR1710110...lineage 2.2.1 MG3 L2 GQ-1343...ERR234121...lineage 2.2.1.1 hlj100113...SRS475367...lineage 2.2.1 -NA-...ERR019574...lineage 2.2.1 MG3 CCDC5180...NC 017522...lineage 2.2.1 L2 N0130...ERR234263...lineage 2.2.1.2 M08 14556...ERR015616...lineage 2.2.1 MG3 0710Y...ERR117454...lineage 2.2.1 MG3 MTB GT 333...ERR234208...lineage 2.2.1 MG3 L2 GQ1164...ERR234116...lineage 2.2.1 PG2 JP02 S2 L001 JP01 S1 L001 JP05 S5 L001 JP06 S6 L001 JP03 S3 L001 JP04 S4 L001 JP07 S7 L001 Mt256...ERR181435...lineage 7 S00013829...ERR294249...lineage 5 S00019848...ERR387001...lineage BOV L6 N0091...ERR234254...lineage 6 Bir 270...ERR046881...lineage 1.2.2 S00013408...ERR278529+ERR386888...lineage 1.2.1 EAI5...NC 021740...lineage 1.1.2 S00007273...ERR114427...lineage 1.1.2 S00018368...ERR351915+ERR386847...lineage 1.1.3 S00019855...ERR387008...lineage 1.1.1.1 S00007279...ERR117694...lineage 1.1.1 FFUL KAUST MTB26...ERR275206...lineage 4.3.4.2 S00013762...ERR294182...lineage 4.3.4.2.1 S00013422...ERR278543+ERR386902...lineage 4.3.4.1 S00013459...ERR278580+ERR386939...lineage 4.3.4 KZN 4207...NC 016768...lineage 4.3.3 KZN 605...NC 018078...lineage 4.3.3 KZN 1435...NC 012943...lineage 4.3.3 CTRI-2...NC 017524...lineage 4.3.3 S00013400...ERR278521+ERR386880...lineage 4.3.3 S00019824...ERR386977...lineage 4.3.1 S00018339...ERR351886+ERR386818...lineage 4.3.2.1 F11...NC 009565...lineage 4.3.2.1 S00013789...ERR294209...lineage 4.3.2 S00017336...ERR330669...lineage 4.5 S00007213...ERR123915...lineage 4.6.2.2 Bir 225...ERR046839...lineage 4.6.2.1 S00013416...ERR278537+ERR386896...lineage 4.6.2 S00018392...ERR351939+ERR386871...lineage 4.6 S00007206...ERR123926...lineage 4.6.1.2 S00019843...ERR386996...lineage 4.6.1.1 S00017343...ERR330676...lineage 4.7 H37Ra ATCC 25177...NC 009525...lineage 4 Root 100 100 100 100 100 100 79 100 100 100 100 36 100 100 100 100 100 84 100 62 70 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 40 50 54 100 98 98 95 100 47 72 75 19 23 100 100 100 100 99 100 100 81 100 100 100 100 100 100 100 100 100 25 100 100 100 100 100 100 100 100 100 0 0.01 0.02 0.03 0.04 0.05 0.06 0.07

IS6110 insert positions

Depth filter:
%
Lightblue: forward. Red: reverse
Length shows % depth for average.
Dots show number of the insertions
(Neighboring dots are shown at different vertical positions)


[, ] H37Ra_ATCC_25177-NC_009525
[, ] F11-NC_009565
[, ] CTRI-2-NC_017524
[, ] KZN_1435-NC_012943
[, ] KZN_605-NC_018078
[, ] KZN_4207-NC_016768
[, ] EAI5-NC_021740
[, ] JP07_S7_L001
[, ] JP04_S4_L001
[, ] JP03_S3_L001
[, ] JP06_S6_L001
[, ] JP05_S5_L001
[, ] JP01_S1_L001
[, ] JP02_S2_L001
[, ] CCDC5180-NC_017522
[, ] 7199-99-NC_020089
[, ] ATCC_35801-NC_020559
[, ] Haarlem-NC_022350
[, ] H37Rv-NC_000962

Spoligotyping


H37Ra_ATCC_25177-NC_009525
F11-NC_009565
CTRI-2-NC_017524
KZN_1435-NC_012943
KZN_605-NC_018078
KZN_4207-NC_016768
EAI5-NC_021740
JP07_S7_L001
JP04_S4_L001
JP03_S3_L001
JP06_S6_L001
JP05_S5_L001
JP01_S1_L001
JP02_S2_L001
CCDC5180-NC_017522
7199-99-NC_020089
ATCC_35801-NC_020559
Haarlem-NC_022350
H37Rv-NC_000962

VNTR

Download our customised 43 VNTR loci list in PDF or Excel format.
Coloring setting of TRs
Min: Max:
Depth Filter: %
Gray box () indicates lower than the depth filter setting (%).
Black box () indicates no detection TR.
Stripe patterned box () indicates possible mixed number of TR.

Example
Number: Tandem repeats (TRs).
Blue horizontal line: Read depth ratio to avg. depth.
Box color: Corresponds to the TRs.
Lower than the depth filter setting.



H37Ra_ATCC_25177-NC_009525
F11-NC_009565
CTRI-2-NC_017524
KZN_1435-NC_012943
KZN_605-NC_018078
KZN_4207-NC_016768
EAI5-NC_021740
JP07_S7_L001
JP04_S4_L001
JP03_S3_L001
JP06_S6_L001
JP05_S5_L001
JP01_S1_L001
JP02_S2_L001
CCDC5180-NC_017522
7199-99-NC_020089
ATCC_35801-NC_020559
Haarlem-NC_022350
H37Rv-NC_000962