BACKGROUND
Understanding Mycobacterium tuberculosis (Mtb) is very important to guide the transmission control strategy efficiently. typing traditional sports do not have enough discriminatory power to overcome the great plague. Here, we examine the potential of using the next-generation genome sequencing to identify the transmission chains associated outbreaks.
RESULTS
Over the long term (1997-2010) prospective, population-based molecular epidemiological surveillance consisting of a total of 2,301 patients, we identified a large outbreak caused by a strain of Mtb lineage Haarlem. The main measure performance results of whole genome sequencing (WGS) is the analysis of the degree of correlation with the analysis WGS contact tracing data and spatio-temporal distribution of plague cases. WGS analysis of 86 isolates revealed 85 single nucleotide polymorphisms (SNPs), grouping plague genome into seven groups (two to 24 isolates each), plus 36 unique SNP profile. WGS Results show that the first outbreak isolates were detected in 1997 were counterfeit clustered by classical genotype.
In 1998, one of the clones (called “Hamburg clone”) began to grow, apparently independently of differences in social environments initial case. genome-based grouping patterns that fit well with contact tracing data and geographic distribution of cases of grouping patterns based on the classic genotype. A maximum of three SNPs identified in the eight confirmed the chain of transmission from human to human, which involved 31 patients. We estimate the Mtb genome evolution rate of 0.4 mutations per genome per year. This level indicates that Mtb grown in natural hosts with a doubling time of about 22 h (400 generations per year). Based on genome variation is found, the emergence of clones Hamburg is dated back to the period between 1993 and 1997, then shortly before the discovery of the outbreak through epidemiological surveillance.
CONCLUSION
Our findings indicate that WGS is superior to conventional genotyping for tracking and investigating Mtb pathogenic micro-epidemics. WGS provides Mtb genome size evolution over time in the context of the natural host.
Highly multiplexed molecular inversion probe genotyping: SNP targeted more than 10,000 genotypes in a single test tube.
Large-scale genetic studies are very dependent on the multiplex SNP tests efficient and scalable. In this study, we report the development of Molecular Inversion Probe technology with four-color, single-array detection, applied to large scale genotyping of up to 12,000 SNPs per reaction. While generating 38 429 SNPs tests using this technology in a population of 30 trios of the family panel Humain Center d’Etude polymorphisms as part of the International HapMap project, we set up a conversion rate of approximately 90% of SNP with a concordance rate of> 99.6% and the level of completeness of> 98% to test the level of multiplexing up to 12,000plex.
Perfringens S.F.P. Supplement ( S.F.P. Supplement ) |
|||
| 92096 | Sisco Laboratories | 5 vl | EUR 9.41 |
|
Description: Part D |
|||
Perfringens S.F.P. Supplement ( S.F.P. Supplement ) |
|||
| 92096-1 | Sisco Laboratories | 4 x5 vl | EUR 31.64 |
|
Description: Part D |
|||
Perfringens T.S.C. Supplement (T.S.C Supplement) (200mg/vl) |
|||
| 55688 | Sisco Laboratories | 5 vl | EUR 10.26 |
|
Description: Part D |
|||
Perfringens T.S.C. Supplement (T.S.C Supplement) (200mg/vl) |
|||
| 55688-1 | Sisco Laboratories | 4 x5 vl | EUR 29.08 |
|
Description: Part D |
|||
KV Supplement |
|||
| 70663 | Sisco Laboratories | 5 vl | EUR 13.68 |
|
Description: Part D |
|||
VCN Supplement |
|||
| 34123 | Sisco Laboratories | 5 vl | EUR 19.67 |
|
Description: Part D |
|||
VCN Supplement |
|||
| 34123-1 | Sisco Laboratories | 5 x5 vl | EUR 69.28 |
|
Description: Part D |
|||
CNA Supplement |
|||
| 64078 | Sisco Laboratories | 5 vl | EUR 13.68 |
|
Description: Part D |
|||
CPC Supplement |
|||
| 65165 | Sisco Laboratories | 5 vl | EUR 17.96 |
|
Description: Part D |
|||
CFC Supplement |
|||
| 70984 | Sisco Laboratories | 5 vl | EUR 12.83 |
|
Description: Part D |
|||
CFC Supplement |
|||
| 70984-1 | Sisco Laboratories | 5 x5 vl | EUR 39.34 |
|
Description: Part D |
|||
CBI Supplement |
|||
| 18871 | Sisco Laboratories | 5 vl | EUR 11.97 |
|
Description: Part D |
|||
ITS Supplement |
|||
| 6065031 | Dakewe Biosci | 10 mL | Ask for price |
VCNT Supplement |
|||
| 32249 | Sisco Laboratories | 5 vl | EUR 19.67 |
|
Description: Part D |
|||
VCNT Supplement |
|||
| 32249-1 | Sisco Laboratories | 5 x5 vl | EUR 69.28 |
|
Description: Part D |
|||
Lactic Supplement |
|||
| 84282 | Sisco Laboratories | 5 vl | EUR 11.12 |
|
Description: Part D |
|||
Strepto Supplement |
|||
| 11475 | Sisco Laboratories | 5 vl | EUR 10.26 |
|
Description: Part D |
|||
Strepto Supplement |
|||
| 11475-1 | Sisco Laboratories | 5 x5 vl | EUR 32.5 |
|
Description: Part D |
|||
N-2 Supplement (100x) |
|||
| TBS8081-5ML | Tribioscience | 5mL | EUR 84.5 |
N2 SF Supplement, 100X |
|||
| CC529-0005 | GeneDireX | 5 mL | Ask for price |
Cetrinix Supplement |
|||
| 94532 | Sisco Laboratories | 5 vl | EUR 14.54 |
|
Description: Part D |
|||
Cetrinix Supplement |
|||
| 94532-1 | Sisco Laboratories | 5 x5 vl | EUR 35.92 |
|
Description: Part D |
|||
N-2 Supplement |
|||
| 6065011 | Dakewe Biosci | 5 mL | Ask for price |
HAT Supplement(50X) |
|||
| CA010-010 | GenDepot | 100ml | EUR 151.2 |
NS-27 Supplement |
|||
| 6065021 | Dakewe Biosci | 10 mL | Ask for price |
CDM-XF Supplement |
|||
| abx298010-5ml | Abbexa | 5 ml | EUR 343.2 |
Fraser Supplement (250mg/vl) |
|||
| 97539 | Sisco Laboratories | 5 vl | EUR 9.41 |
|
Description: Part D |
|||
GlutaGO™ Supplement, 100X |
|||
| CC516-0100 | GeneDireX | 100 mL | Ask for price |
Supplement C 5Ml - PK6 |
|||
| 252710 | Scientific Laboratory Supplies | PK6 | EUR 486 |
GTC Supplement (1.25mg/vl) |
|||
| 30963 | Sisco Laboratories | 5 vl | EUR 6.84 |
|
Description: Part D |
|||
MUG Supplement (50mg/vl) |
|||
| 26834 | Sisco Laboratories | 5 vl | EUR 16.25 |
|
Description: Part D |
|||
Oxford Listeria Supplement |
|||
| 42116 | Sisco Laboratories | 5 vl | EUR 13.68 |
|
Description: Part D |
|||
Pericyte Growth Supplement |
|||
| cAP-09S | Angio Proteomie | 50ml | EUR 113.85 |
Novobiocin Supplement - PK10 |
|||
| MED1556 | Scientific Laboratory Supplies | PK10 | EUR 64.26 |
ITS Cell Culture Supplement（100×） |
|||
| ITSS-10201 | Cyagen | 10mL | EUR 59 |
PEMBA Supplement (10KU/vl) |
|||
| 89858 | Sisco Laboratories | 5 vl | EUR 7.7 |
|
Description: Part D |
|||
Uracil Supplement, 5.6mg/mL |
|||
| 40121138-1 | Bio-WORLD | 25 mL | EUR 25.82 |
Uracil Supplement, 5.6mg/mL |
|||
| 40121138-2 | Bio-WORLD | 50 mL | EUR 43.77 |
Uracil Supplement, 5.6mg/mL |
|||
| 40121138-3 | Bio-WORLD | 100 mL | EUR 66.21 |
Bolton Selective Supplement |
|||
| 55582 | Sisco Laboratories | 5 vl | EUR 13.68 |
|
Description: Part D |
|||
Bolton Selective Supplement |
|||
| 55582-1 | Sisco Laboratories | 5 x5 vl | EUR 61.58 |
|
Description: Part D |
|||
Fraser Selective Supplement |
|||
| 52071 | Sisco Laboratories | 5 vl | EUR 11.97 |
|
Description: Part D |
|||
Kimmig Selective Supplement |
|||
| 42820 | Sisco Laboratories | 5 vl | EUR 17.11 |
|
Description: Part D |
|||
McBride Listeria Supplement |
|||
| 70317 | Sisco Laboratories | 5 vl | EUR 11.12 |
|
Description: Part D |
|||
Perfringens Supplement-II |
|||
| 62598 | Sisco Laboratories | 5 vl | EUR 10.26 |
|
Description: Part D |
|||
Perfringens Supplement-II |
|||
| 62598-1 | Sisco Laboratories | 5 x5 vl | EUR 27.37 |
|
Description: Part D |
|||
B 27 SF Supplement, 50X |
|||
| CC528-0010 | GeneDireX | 10 mL | Ask for price |
Esculin Supplement (0.5gm/vl) |
|||
| 27131 | Sisco Laboratories | 5 vl | EUR 22.24 |
|
Description: Part D |
|||
Listeria UVM Supplement I |
|||
| 51864 | Sisco Laboratories | 5 vl | EUR 8.55 |
|
Description: Part D |
|||
Listeria UVM Supplement II |
|||
| 72547 | Sisco Laboratories | 5 vl | EUR 8.55 |
|
Description: Part D |
|||
N2 NeuroPlex™ Supplement |
|||
| 400-163-005 | GeminiBio | 5 mL | Ask for price |
Tellurite Cefixime Supplement |
|||
| 15297 | Sisco Laboratories | 5 vl | EUR 11.12 |
|
Description: Part D |
|||
Neomycin Supplement (30mg/vl) |
|||
| 77316 | Sisco Laboratories | 5 vl | EUR 9.41 |
|
Description: Part D |
|||
Listeria Moxalactum Supplement |
|||
| 15650 | Sisco Laboratories | 5 vl | EUR 12.83 |
|
Description: Part D |
|||
Novobiocin Supplement(5mg/vl) |
|||
| 18352 | Sisco Laboratories | 5 vl | EUR 10.26 |
|
Description: Part D |
|||
Novobiocin Supplement(5mg/vl) |
|||
| 18352-1 | Sisco Laboratories | 5 x5 vl | EUR 28.22 |
|
Description: Part D |
|||
Vancomycin Supplement (3mg/vl) |
|||
| 26117 | Sisco Laboratories | 5 vl | EUR 13.68 |
|
Description: Part D |
|||
Clostridium Difficile Supplement |
|||
| 93834 | Sisco Laboratories | 5 vl | EUR 10.26 |
|
Description: Part D |
|||
Clostridium Difficile Supplement |
|||
| 93834-1 | Sisco Laboratories | 5 x5 vl | EUR 30.79 |
|
Description: Part D |
|||
Tributyrin Supplement (10ml/vl) |
|||
| 87704 | Sisco Laboratories | 5 vl | EUR 13.68 |
|
Description: Part D |
|||
Tributyrin Supplement (10ml/vl) |
|||
| 87704-1 | Sisco Laboratories | 5 x5 vl | EUR 54.74 |
|
Description: Part D |
|||
Ticarcillin Supplement (1mg/vl) |
|||
| 67819 | Sisco Laboratories | 5 vl | EUR 10.26 |
|
Description: Part D |
|||
Ampicillin Supplement (10mg/vl) |
|||
| 78162 | Sisco Laboratories | 5 vl | EUR 11.97 |
|
Description: Part D |
|||
Gem21 NeuroPlex™ Supplement |
|||
| 400-160-010 | GeminiBio | 10 mL | Ask for price |
Tetracycline Selective Supplement |
|||
| 40873 | Sisco Laboratories | 5 vl | EUR 11.97 |
|
Description: Part D |
|||
Enterococcus Selective Supplement |
|||
| 47082 | Sisco Laboratories | 5 vl | EUR 12.83 |
|
Description: Part D |
|||
Enterococcus Selective Supplement |
|||
| 47082-1 | Sisco Laboratories | 5 x5 vl | EUR 43.62 |
|
Description: Part D |
|||
Pseudomonas C.N. Supplement - PK10 |
|||
| MED1530 | Scientific Laboratory Supplies | PK10 | EUR 42.66 |
B.P. Sulpha Supplement (50mg/vl) |
|||
| 15097 | Sisco Laboratories | 5 vl | EUR 9.41 |
|
Description: Part D |
|||
Streptococcus Selective Supplement |
|||
| 35140 | Sisco Laboratories | 5 vl | EUR 13.68 |
|
Description: Part D |
|||
Streptococcus Selective Supplement |
|||
| 35140-1 | Sisco Laboratories | 5 x5 vl | EUR 33.36 |
|
Description: Part D |
|||
Lactobacilli Supplement (50mg/vl) |
|||
| 39785 | Sisco Laboratories | 5 vl | EUR 12.83 |
|
Description: Part D |
|||
Lactobacilli Supplement (50mg/vl) |
|||
| 39785-1 | Sisco Laboratories | 5 x5 vl | EUR 39.34 |
|
Description: Part D |
|||
Vitamin K1 Supplement (10mg/vl) |
|||
| 34326 | Sisco Laboratories | 5 vl | EUR 9.41 |
|
Description: Part D |
|||
Genta-Oxy Selective Supplement |
|||
| 50084 | Sisco Laboratories | 5 vl | EUR 12.83 |
|
Description: Part D |
|||
Genta-Oxy Selective Supplement |
|||
| 50084-1 | Sisco Laboratories | 5 x5 vl | EUR 29.93 |
|
Description: Part D |
|||
Non-Spore Anaerobic Supplement |
|||
| 34350 | Sisco Laboratories | 5 vl | EUR 11.97 |
|
Description: Part D |
|||
Yersinia Selective (C.I.N.) Supplement |
|||
| 15061 | Sisco Laboratories | 5 vl | EUR 11.97 |
|
Description: Part D |
|||
Yersinia Selective (C.I.N.) Supplement |
|||
| 15061-1 | Sisco Laboratories | 5 x5 vl | EUR 35.07 |
|
Description: Part D |
|||
PALCAM Selective Supplement - PK10 |
|||
| MED1566 | Scientific Laboratory Supplies | PK10 | EUR 90.45 |
Rosolic Acid Supplement (0.1gm/vl) |
|||
| 57672 | Sisco Laboratories | 5 vl | EUR 10.26 |
|
Description: Part D |
|||
B.cepacia Selective Supplement - PK10 |
|||
| MED1576 | Scientific Laboratory Supplies | PK10 | EUR 162 |
Neomycin Selective Supplement - PK10 |
|||
| MED1546 | Scientific Laboratory Supplies | PK10 | EUR 44.55 |
B28 Neuron culture supplement（50×） |
|||
| BNCS-50101 | Cyagen | 5/10mL | Ask for price |
Kanamycin Selective Supplement - PK10 |
|||
| MED1564 | Scientific Laboratory Supplies | PK10 | EUR 64.94 |
FGTC Antibiotic Supplement (2.5mg/vl) |
|||
| 78507 | Sisco Laboratories | 5 vl | EUR 9.41 |
|
Description: Part D |
|||
Leucine Supplement, 16.8mg/mL, Sterile |
|||
| 40120866-1 | Bio-WORLD | 10x50 mL | EUR 334.43 |
GC LCAT Selective Supplement - PK10 |
|||
| MED1524 | Scientific Laboratory Supplies | PK10 | EUR 56.7 |
Listeria Selective Supplement (PALCAM) |
|||
| 90345 | Sisco Laboratories | 5 vl | EUR 9.41 |
|
Description: Part D |
|||
Staph-Strepto Selective Supplement |
|||
| 18247 | Sisco Laboratories | 5 vl | EUR 12.83 |
|
Description: Part D |
|||
Staph-Strepto Selective Supplement |
|||
| 18247-1 | Sisco Laboratories | 5 x5 vl | EUR 31.64 |
|
Description: Part D |
|||
Campylobacter Growth Supplement - PK10 |
|||
| MED1538 | Scientific Laboratory Supplies | PK10 | EUR 56.7 |
Bacitracin Selective Supplement - PK10 |
|||
| MED1540 | Scientific Laboratory Supplies | PK10 | EUR 48.6 |
Bordetella Selective Supplement - PK10 |
|||
| MED1548 | Scientific Laboratory Supplies | PK10 | EUR 59.4 |
Ampicillin Selective Supplement - PK10 |
|||
| MED1562 | Scientific Laboratory Supplies | PK10 | EUR 49.95 |
Perfringens Supplement-I (50mg/vl) |
|||
| 11976 | Sisco Laboratories | 5 vl | EUR 7.7 |
|
Description: Part D |
|||
Perfringens Supplement-I (50mg/vl) |
|||
| 11976-1 | Sisco Laboratories | 5 x5 vl | EUR 20.53 |
|
Description: Part D |
|||
Pseudomonas Selective Supplement - PK10 |
|||
| MED1558 | Scientific Laboratory Supplies | PK10 | EUR 160.65 |
Yersinia CIN Selective Supplement 500mL - PK10 |
|||
| MED1582 | Scientific Laboratory Supplies | PK10 | EUR 93.15 |
Bromothymol Blue Supplement (20mg/vl) |
|||
| 46172 | Sisco Laboratories | 5 vl | EUR 4.28 |
|
Description: Part D |
|||
B-27 Serum-Free Supplement (50x) |
|||
| abx082466-10ml | Abbexa | 10 ml | EUR 393.6 |
Tryptophan Supplement, 11.2mg/mL, Sterile |
|||
| 40121134-1 | Bio-WORLD | 500 mL | EUR 279.45 |
MRSA Broth Selective Supplement - PK10 |
|||
| MED1578 | Scientific Laboratory Supplies | PK10 | EUR 44.55 |
Shigella Selective Supplement (0.55mg/vl) |
|||
| 45290 | Sisco Laboratories | 5 vl | EUR 9.41 |
|
Description: Part D |
|||
Oxytetra Selective Supplement (50mg/vl) |
|||
| 51521 | Sisco Laboratories | 5 vl | EUR 7.7 |
|
Description: Part D |
|||
Oxytetra Selective Supplement (50mg/vl) |
|||
| 51521-1 | Sisco Laboratories | 5 x5 vl | EUR 24.8 |
|
Description: Part D |
|||
Aeromonas Selective Supplement (2.5mg/vl) |
|||
| 63013 | Sisco Laboratories | 5 vl | EUR 10.26 |
|
Description: Part D |
|||
Bromocresol Purple Supplement (15mg/vl) |
|||
| 26384 | Sisco Laboratories | 5 vl | EUR 6.84 |
|
Description: Part D |
|||
Staph/Strep Selective Supplement - PK10 |
|||
| MED1532 | Scientific Laboratory Supplies | PK10 | EUR 47.25 |
Bacillus cereus PEMBA Supplement - PK10 |
|||
| MED1580 | Scientific Laboratory Supplies | PK10 | EUR 48.6 |
Oxacillin Resistant Selective Supplement |
|||
| 57253 | Sisco Laboratories | 5 vl | EUR 11.12 |
|
Description: Part D |
|||
Nalidixic Selective Supplement (15mg/vl) |
|||
| 67124 | Sisco Laboratories | 5 vl | EUR 9.41 |
|
Description: Part D |
|||
Legionella BCYE Growth Supplement - PK10 |
|||
| MED1678 | Scientific Laboratory Supplies | PK10 | EUR 120.15 |
Bordetella Selective Supplement (20mg/vl) |
|||
| 66006 | Sisco Laboratories | 5 vl | EUR 11.12 |
|
Description: Part D |
|||
Gentamicin Selective Supplement (20mg/vl) |
|||
| 78334 | Sisco Laboratories | 5 vl | EUR 7.7 |
|
Description: Part D |
|||
Klebsiella Selective Supplement (25mg/vl) |
|||
| 29760 | Sisco Laboratories | 5 vl | EUR 10.26 |
|
Description: Part D |
|||
Endothelial Cell Growth Supplement (ECGS) |
|||
| cAP-20 | Angio Proteomie | 50mg | EUR 178.2 |
Endothelial Cell Growth Supplement (ECGS) |
|||
| MBS634714-10x15mg | MyBiosource | 10x15mg | EUR 1090 |
Endothelial Cell Growth Supplement (ECGS) |
|||
| MBS634714-50mg | MyBiosource | 50mg | EUR 790 |
B-27 Supplement (50x) with Vitamin A |
|||
| TBS8079-10ML | Tribioscience | 10mL | EUR 117 |
Bacteroides Selective Supplement (50mg/vl) |
|||
| 83141 | Sisco Laboratories | 5 vl | EUR 9.41 |
|
Description: Part D |
|||
B-27 Supplement (50x), minus Vitamin A |
|||
| TBS8080-10ML | Tribioscience | 10mL | EUR 117 |
Legionella GVPC Selective Supplement - PK10 |
|||
| MED1676 | Scientific Laboratory Supplies | PK10 | EUR 98.55 |
Campylobacter Antimicrobic Supplement, Blaser |
|||
| MBS652931-10x5mL | MyBiosource | 10x5mL | EUR 880 |
Campylobacter Antimicrobic Supplement, Blaser |
|||
| MBS652931-5x5mL | MyBiosource | 5x5mL | EUR 635 |
Potassium Tellurite 3.5% Supplement (1ml/vl) |
|||
| 99482 | Sisco Laboratories | 5 vl | EUR 6.84 |
|
Description: Part D |
|||
Potassium Tellurite 1% Supplement (1ml/vl) |
|||
| 91488 | Sisco Laboratories | 5 vl | EUR 6.84 |
|
Description: Part D |
|||
Potassium Tellurite 1% Supplement (1ml/vl) |
|||
| 91488-1 | Sisco Laboratories | 5 x5 vl | EUR 23.09 |
|
Description: Part D |
|||
Grace's supplement medium for insect cells |
|||
| PM152012 | Elabscience Biotech | 500mL | EUR 55 |
|
Description: Others |
|||
Polymyxin B Selective Supplement (50KU/vl) |
|||
| 35980 | Sisco Laboratories | 5 vl | EUR 7.7 |
|
Description: Part D |
|||
Polymyxin B Selective Supplement (50KU/vl) |
|||
| 35980-1 | Sisco Laboratories | 5 x5 vl | EUR 26.51 |
|
Description: Part D |
|||
Insulin-Transferrin-Sodium Selenite Supplement (100X) |
|||
| TM052 | ABM | 10 ml | EUR 140 |
Furthermore, these individual metrics can be “traded off” and, at the expense of a small portion of the conversion rates, the accuracy can be improved to a very high level. No loss of performance seen when the scale of 6,000plex to 12,000plex the test, it validates the technological capability to suppress cross-reactivity at high multiplex level. These results indicate the suitability of this technology for a comprehensive association study using targeted SNPs in linkage disequilibrium studies indirectly or directly screen for the mutation causes.