Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

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.

Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.
Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

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.

Campylobacter Growth Supplement

MED1538 PK10
EUR 39.44

Bacitracin Selective Supplement

MED1540 PK10
EUR 33.86

Neomycin Selective Supplement

MED1546 PK10
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MED1548 PK10
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Pseudomonas Selective Supplement

MED1558 PK10
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Ampicillin Selective Supplement

MED1562 PK10
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Kanamycin Selective Supplement

MED1564 PK10
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PALCAM Selective Supplement

MED1566 PK10
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B.cepacia Selective Supplement

MED1576 PK10
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Supplement C 5Ml

252710 PK6
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GC LCAT Selective Supplement

MED1524 PK10
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Staph/Strep Selective Supplement

MED1532 PK10
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MRSA Broth Selective Supplement

MED1578 PK10
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Bacillus cereus PEMBA Supplement

MED1580 PK10
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Helicobacter pylori Selective Supplement

MED1674 PK10
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Legionella GVPC Selective Supplement

MED1676 PK10
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Legionella BCYE Growth Supplement

MED1678 PK10
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Exosome-depleted FBS Media Supplement

EXO-FBS-250A-1 250 ml
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Exosome-depleted FBS Media Supplement

EXO-FBS-50A-1 50 ml
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Yersinia CIN Selective Supplement 500mL

MED1582 PK10
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B-27 Serum-Free Supplement (50x)

abx082466-10ml 10 ml
EUR 393.6

Endothelial Cell Growth Supplement (ECGS),From Bovine

CA080-005 5mg Ask for price

Endothelial Cell Growth Supplement (ECGS),From Bovine

CA080-050 50mg Ask for price

Reagent for Total Exosome Isolation (Culture Media Supplement)

EIR-02 50 ml
EUR 2485.2
Description: This product is used for isolating exosomes from culture media supplement based on chemical precipitation isolation method.

Exosome-depleted FBS Media Supplement Heat Inactivated - USA Certified      

EXO-FBSHI-250A-1 250 ml
EUR 1071.6

Exosome-depleted FBS Media Supplement Heat Inactivated - USA Certified      

EXO-FBSHI-50A-1 50 ml
EUR 306

Gibco Resurge CD1 Supplement Without Glucose and L-Glutamine

670011 EACH
EUR 239.4

Gibco Resurge CD2 Supplement Without Glucose and L-Glutamine

670015 EACH
EUR 239.4

Gibco Resurge CD3 Supplement Without Glucose and L-Glutamine

670018 EACH
EUR 238.26

Gibco Resurge CD4 Supplement Without Glucose and L-Glutamine

670021 EACH
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Gibco Resurge CD5 Supplement Without Glucose and L-Glutamine

670024 EACH
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Yeast Extract

abx082370-500g 500 g
EUR 260.4

Yeast Extract

A2540-1000000 1000 g
EUR 259.2
Description: microbial mediawater soluble portion of autolyzed yeast with intact B-complex vitaminsstore at room temperature

Yeast Extract

A2540-500000 500 g
EUR 170.4
Description: microbial mediawater soluble portion of autolyzed yeast with intact B-complex vitaminsstore at room temperature

Yeast Extract

G0961 500g
EUR 97.58

Yeast Extract

Y2007-050 500g
EUR 218.4

Yeast Extract

Y2007-100 1Kg
EUR 295.2

Yeast Extract

Y2007-250 2.5Kg Ask for price

Yeast Extract

Y2007-500 5Kg Ask for price

YEAST EXTRACT

Y25-101-10kg 10 kg
EUR 926.4

YEAST EXTRACT

Y25-101-2Kg 2 Kg
EUR 248.4

YEAST EXTRACT

Y25-101-500g 500 g
EUR 111.6

Yeast Extract

MED1522 EACH
EUR 42.75

Total Exosome RNA Extraction Kit (Biological Fluids/Culture Media Supplement)

EIRK-03 20 reactions
EUR 3380.4
Description: This product is a useful tool for the isolation and efficient total RNA (miRNA and mRNAs) extraction from the total exosome population from human biofluids or cell culture media.

Recombinant Yeast IDH1 Protein, Untagged, Yeast-1mg

QP10670-1mg 1mg
EUR 186

Recombinant Yeast IDH1 Protein, Untagged, Yeast-50mg

QP10670-50mg 50mg
EUR 1251.6

Recombinant Yeast IDH1 Protein, Untagged, Yeast-5mg

QP10670-5mg 5mg
EUR 241.2

Recombinant Yeast GLRX1 Yeast Protein, His, E.coli-10ug

QP11990-10ug 10ug
EUR 186

Recombinant Yeast GLRX1 Yeast Protein, His, E.coli-1mg

QP11990-1mg 1mg
EUR 1873.2

Recombinant Yeast GLRX1 Yeast Protein, His, E.coli-50ug

QP11990-50ug 50ug
EUR 241.2

Recombinant Yeast GLRX2 Yeast Protein, His, E.coli-10ug

QP11991-10ug 10ug
EUR 186

Recombinant Yeast GLRX2 Yeast Protein, His, E.coli-1mg

QP11991-1mg 1mg
EUR 1873.2

Recombinant Yeast GLRX2 Yeast Protein, His, E.coli-50ug

QP11991-50ug 50ug
EUR 241.2

Recombinant Yeast GLC8

7-05266 10µg Ask for price

Recombinant Yeast GLC8

7-05267 50µg Ask for price

Recombinant Yeast GLC8

7-05268 1mg Ask for price

Recombinant Yeast Thioredoxin

7-06895 5µg Ask for price

Recombinant Yeast Thioredoxin

7-06896 20µg Ask for price

Recombinant Yeast Thioredoxin

7-06897 1mg Ask for price

Yeast Thioredoxin Protein

20-abx260628
  • EUR 3650.40
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  • EUR 276.00
  • 1 mg
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  • 5 ug

IL4 Yeast Protein

20-abx262078
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  • EUR 5856.00
  • EUR 276.00
  • 10 ug
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IL2 Yeast Protein

20-abx262079
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  • 10 ug
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  • 2 µg

FNDC5, Yeast Protein

20-abx262686
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  • EUR 276.00
  • 10 ug
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Insulin Yeast Protein

20-abx262991
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  • EUR 276.00
  • 100 mg
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Trypsin, Yeast Protein

20-abx263463
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  • EUR 276.00
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Thioredoxin Reductase, Yeast

LF-P0009 0.5 mg
EUR 242.4
Description: Thioredoxin Reductase, Yeast protein

Thioredoxin 1, Yeast

LF-P0036 0.5 mg
EUR 363.6
Description: Thioredoxin 1, Yeast protein

Thioredoxin 2, Yeast

LF-P0052 0.5 mg
EUR 363.6
Description: Thioredoxin 2, Yeast protein

Glutathione Reductase, Yeast

LF-P0071 0.5 mg
EUR 242.4
Description: Glutathione Reductase, Yeast protein

Yeast extract, powder

GE4420-100G 100 g
EUR 51.6

Yeast extract, powder

GE4420-1KG 1 kg
EUR 132

Yeast extract, powder

GE4420-250G 250 g
EUR 64.8

Yeast extract, powder

GE4420-500G 500 g
EUR 93.6

Y187 Yeast Strains

S0057 100 ul
EUR 438

Y2HGold Yeast Strains

S0058 100 ul
EUR 438

X33 Yeast Strains

S0059 100 ul
EUR 438

KM71 Yeast Strains

S0060 100 ul
EUR 438

INVSC1 Yeast Strains

S0061 100 ul
EUR 438

BY4742 Yeast Strains

S0062 100 ul
EUR 438

AH109 Yeast Strains

S0063 100 ul
EUR 438

Y1HGold Yeast Strains

S0064 100 ul
EUR 438

BY4741 Yeast Strains

S0065 100 ul
EUR 438

GS115 Yeast Strains

S0066 100 ul
EUR 438

NMY51 Yeast Strains

S0094 100 ul
EUR 438

KM71H Yeast Strains

S0100 100 ul
EUR 438

ATCC9080 Yeast Strains

S0109 100 ul
EUR 438

EGY48 Yeast Strains

S0112 100 ul
EUR 438

SMD1168 Yeast Strains

S0116 100 ul
EUR 438

EBY100 Yeast Strains

S0117 100 ul
EUR 438

Yeast AHA1 Protein

SPR-314A 0.05 mg
EUR 313.2
Description: His tagged recombinant yeast AHA1 Protein expressed in E. coli for WB, SDS-PAGE, Functional Assay. The biological activity of this protein has not yet been tested.

Yeast AHA1 Protein

SPR-314B 0.1 mg
EUR 452.4
Description: His tagged recombinant yeast AHA1 Protein expressed in E. coli for WB, SDS-PAGE, Functional Assay. The biological activity of this protein has not yet been tested.

Yeast AHA1 Protein

SPR-314C 2x0.1 mg
EUR 676.8
Description: His tagged recombinant yeast AHA1 Protein expressed in E. coli for WB, SDS-PAGE, Functional Assay. The biological activity of this protein has not yet been tested.

X33 Yeast Strain

STR0059 100 ul
EUR 369.6

Recombinant (yeast) Hirudin

RP-820 10 ug
EUR 343.2

YEAST NITROGEN BASE

Y25-104-10kg 10 kg
EUR 6818.4

YEAST NITROGEN BASE

Y25-104-2kg 2kg
EUR 1528.8

YEAST NITROGEN BASE

Y25-104-500g 500 g
EUR 459.6

Yeast Extract Agar

MED1080 PK6
EUR 51.98

Yeast Extract Agar

MED1480 EACH
EUR 83.22

Gibco Yeast Extract

211929 EACH
EUR 112.06

Gibco Yeast Extract

211930 EACH
EUR 495.9

Yeast buffer kit

28944045 EACH
EUR 124.26

Insulin-Transferrin-Selenium ITS, Insulin-Transferrin-Selenium Supplement (100X), in Earle's Balanced Salts.

ITL03-10ML 10 ml
EUR 134.4
Description: ITS, Insulin-Transferrin-Selenium Supplement (100X), in Earle's Balanced Salts.

Recombinant Human Insulin Yeast

7-01120 2mg Ask for price

Recombinant Human Insulin Yeast

7-01121 10mg Ask for price

Recombinant Human Insulin Yeast

7-01122 100mg Ask for price

Insulin, human recombinant (Yeast)

4773-25
EUR 1305.6

Insulin, human recombinant (Yeast)

4773-5
EUR 477.6

Recombinant Human Trypsin, Yeast

7-06736 1mg Ask for price

Recombinant Human Trypsin, Yeast

7-06737 5mg Ask for price

Recombinant Human Trypsin, Yeast

7-06738 50mg Ask for price

Recombinant Yeast Glutaredoxin 1

7-02842 10µg Ask for price

Recombinant Yeast Glutaredoxin 1

7-02843 50µg Ask for price

Recombinant Yeast Glutaredoxin 1

7-02844 1mg Ask for price

Recombinant Yeast Glutaredoxin 2

7-02848 10µg Ask for price

Recombinant Yeast Glutaredoxin 2

7-02849 50µg Ask for price

Recombinant Yeast Glutaredoxin 2

7-02850 1mg Ask for price

Recombinant Yeast Thioredoxin Reductase

7-03685 5µg Ask for price

Recombinant Yeast Thioredoxin Reductase

7-03686 20µg Ask for price

Recombinant Yeast Thioredoxin Reductase

7-03687 1mg Ask for price

Yeast Cell Ag antibody

20R-YG001 1 ml
EUR 678
Description: Goat polyclonal Yeast Cell Ag antibody

Yeast Mitochondria (Pichia pastoris)

1111-200 200 ug
EUR 354.24
Description: Mitochondria are the power house of the cells as they generate most of the supply of energy in the form of adenosine tri-phosphate (ATP). Mitochondria are double membrane organelles comprising of an outer membrane and a folded inner membrane called cristae. Isolated mitochondria are a useful tool to study mitochondrial respiration, assembly of the respiratory complexes, apoptosis, mtDNA, mtRNA, protein profiling, and as a loading control. Highly pure yeast mitochondria are purified using standard protocol as mentioned in the Yeast Mitochondria Isolation Kit - Cat # K259-100 from Pichia pastoris.

Yeast Mitochondria (Pichia pastoris)

1111-50 50 ug
EUR 174.24
Description: Mitochondria are the power house of the cells as they generate most of the supply of energy in the form of adenosine tri-phosphate (ATP). Mitochondria are double membrane organelles comprising of an outer membrane and a folded inner membrane called cristae. Isolated mitochondria are a useful tool to study mitochondrial respiration, assembly of the respiratory complexes, apoptosis, mtDNA, mtRNA, protein profiling, and as a loading control. Highly pure yeast mitochondria are purified using standard protocol as mentioned in the Yeast Mitochondria Isolation Kit - Cat # K259-100 from Pichia pastoris.

Yeast Mitochondria (S. cerevisiae)

1222-200
EUR 510

Yeast Mitochondria (S. cerevisiae)

1222-50
EUR 248.4

Yeast Glutaredoxin 2 (Recombinant)

20-abx073039
  • EUR 276.00
  • EUR 2364.00
  • EUR 393.60
  • 10 ug
  • 1 mg
  • 50 ug

Yeast Glutaredoxin 1 (Recombinant)

20-abx073040
  • EUR 276.00
  • EUR 2364.00
  • EUR 393.60
  • 10 ug
  • 1 mg
  • 50 ug

Yeast Thioredoxin Reductase (Recombinant)

20-abx073523
  • EUR 4803.60
  • EUR 393.60
  • EUR 276.00
  • 1 mg
  • 20 ug
  • 5 ug

Poly(A) Polymerase Yeast

M1215-100
EUR 333.6

Native Yeast Aldehyde Dehydrogenase

NATE-0901 100u
EUR 453.6

Native Yeast Alcohol dehydrogenase

NATE-0975 50KU
EUR 324

Yeast Nuclei Isolation Kit

K289-50
EUR 470.4

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.