Tuberculosis is changing

Walker, Timothy M; Cruz, Ana Lúıza Gibertoni; Pető, Tünde; Smith, E. Grace; Esmail, Hanif; Crook, Derrick W.

doi:10.1016/s1473-3099(17)30123-8

Cited by 51 publications

(59 citation statements)

References 7 publications

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“…This may cause a small improvement in cost-effectiveness, as we would now expect a higher yield of LTBI per case, as more contacts will be tested for LTBI, provided it is not accompanied by lower rates of PT enrolment and completion. The introduction in 2017 of whole genome sequencing (WGS) in the UK39 may also affect our conclusions. While a study of the current strain typing service found no impact on contact tracing,23 it is plausible that faster turnaround times and improved targeting available with WGS may affect contact tracing yields.…”

Section: Discussionmentioning

confidence: 99%

Should NICE reconsider the 2016 UK guidelines on TB contact tracing? A cost-effectiveness analysis of contact investigations in London

Cavany

Vynnycky

Anderson

et al. 2018

Thorax

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Section: Discussionmentioning

confidence: 99%

Should NICE reconsider the 2016 UK guidelines on TB contact tracing? A cost-effectiveness analysis of contact investigations in London

Cavany

Vynnycky

Anderson

et al. 2018

Thorax

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“…All mycobacterial positive cultures sent to the PHE reference laboratory undergo WGS, with reports returned to clinicians within five to seven days detailing mycobacterial species, and predicting drug susceptibility and genetic relatedness for the Mycobacterium tuberculosis complex. 14 It is anticipated that this will have profound impacts upon treatment and control of TB in the UK, including individually tailored anti-tuberculosis therapy according to the susceptibility of the specific mycobacterium causing infection. 15…”

Section: Molecular Diagnostics For Detection Of Mycobacteriamentioning

confidence: 99%

Current recommended management of tuberculosis

Rogers¹,

Kennedy²,

Wiselka³

et al. 2018

Prescriber

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“…Its utility increases with the proportion of genome obtained; from detection, to speciation and antimicrobial resistance prediction, to phylogenetic and evolutionary insights. This allows whole genome sequencing (WGS) to out-perform other rapid molecular methods (such as GeneXpert MTB/RIF, Cepheid, Solna, Sweden) due to susceptibility predictions to multiple drugs, and its combination with classical epidemiological methods which informs transmission (5–8).…”

Section: Introductionmentioning

confidence: 99%

“…WGS of MTB from early positive cultures offers markedly faster results than traditional culture-based methods which take ≤80 days. The national implementation of Illumina sequencing of Mycobacteria from early positive cultures in England provides WGS in three to four weeks, together with antimicrobial resistance predictions (5, 9). Time to WGS could be reduced further if routine sequencing could be performed direct-from-sample.…”

Section: Introductionmentioning

confidence: 99%

DNA Thermo-Protection Facilitates Whole Genome Sequencing of Mycobacteria Direct from Clinical Samples by the Nanopore Platform

George

Rodger

et al. 2020

Preprint

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22Mycobacterium tuberculosis (MTB) is the leading cause of death from bacterial infection. 23 Improved rapid diagnosis and antimicrobial resistance determination, such as by whole 24 genome sequencing, are required. Our aim was to develop a simple, low-cost method of 25 preparing DNA for Oxford Nanopore Technologies (ONT) sequencing direct from MTB 26 positive clinical samples (without culture). Simultaneous sputum liquefaction, bacteria heat-27 inactivation (99ºC/30min) and enrichment for Mycobacteria DNA was achieved using an 28 equal volume of thermo-protection buffer (4M KCl, 0.05M HEPES buffer pH7.5, 0.1% 29 DTT). The buffer emulated intracellular conditions found in hyperthermophiles, thus 30 protecting DNA from rapid thermo-degradation, which renders it a poor template for 31 sequencing. Initial validation employed Mycobacteria DNA (extracted or intracellular). Next, 32 mock clinical samples (infection-negative human sputum spiked 0-10 5 BCG cells/ml) 33 underwent liquefaction in thermo-protection buffer and heat-inactivation. DNA was extracted 34 and sequenced. Human DNA degraded faster than Mycobacteria DNA, resulting in target 35 enrichment. Four replicate experiments each demonstrated detection at 10 1 BCG cells/ml, 36 with 31-59 MTB complex reads. Maximal genome coverage (>97% at 5x-depth) was 37 achieved at 10 4 BCG cells/ml; >91% coverage (1x depth) at 10 3 BCG cells/ml. Final 38 validation employed MTB positive clinical samples (n=20), revealed initial sample volumes 39 ≥1ml typically yielded higher mean depth of MTB genome coverage, the overall range 0.55-40 81.02. A mean depth of 3 gave >96% one-fold TB genome coverage (in 15/20 clinical 41 samples). A mean depth of 15 achieved >99% five-fold genome coverage (in 9/20 clinical 42 samples). In summary, direct-from-sample sequencing of MTB genomes was facilitated by a 43 low cost thermo-protection buffer.44 48 Report 2019; https://www.who.int/tb/publications/global_report/en/). In addition, 5-10% of 49 an estimated 1.7 billion people with latent TB infections are at risk of progressing to active 50 disease. The greatest burden occurs in under-resourced regions of South-East Asia, Africa 51 and the Western Pacific. There are large discrepancies between the estimated annual number 52 of new cases (10 million) and the number reported (7 million) (WHO report 53 https://www.who.int/tb/publications/global_report/en/). Consequently, diagnostic methods for 54 use at the point of care, to identify 'missing' cases are a global priority (1, 2). Rapid diagnosis 55 and antimicrobial resistance determination are essential to ensure appropriate TB treatment 56 and control, particularly in light of increasing drug resistance (3, 4). In 2018, approximately 57 500,000 cases of rifampicin-resistant TB were identified, 78% of which were also isoniazid 58 resistant (multi-drug resistant) (https://www.who.int/tb/publications/global_report/en/). 59 60The application of DNA sequencing to TB molecular diagnostics yields clinically valuable 61 information. Its utility inc...

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Tuberculosis is changing

Cited by 51 publications

References 7 publications

Should NICE reconsider the 2016 UK guidelines on TB contact tracing? A cost-effectiveness analysis of contact investigations in London

Should NICE reconsider the 2016 UK guidelines on TB contact tracing? A cost-effectiveness analysis of contact investigations in London

Current recommended management of tuberculosis

DNA Thermo-Protection Facilitates Whole Genome Sequencing of Mycobacteria Direct from Clinical Samples by the Nanopore Platform

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