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Edge Implementation with Intel® NUC Mini PCs for MDR, XDR and XXDR Tuberculosis Genome Informatics Pipeline

MaryT_Intel
Community Manager
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Key Takeaways

  • High proportion of drug resistance in Tuberculosis (TB) patients in India1 and elsewhere2 necessitates early and rapid drug susceptibility testing in TB diagnostic facilities. Genomic analysis of TB whole genome sequencing (WGS) data has emerged as the gold standard for comprehensive drug susceptibility testing (DST) for TB worldwide3–6. However, the need for high performance computing (HPC) for genomic analysis using validated analytical pipelines is a bottleneck for the uptake of WGS based TB DST. Here we describe the edge implementation of automated genomic DST for TB samples by ΩTB® software created by HaystackAnalytics® using Intel® NUC Mini PCs.

Combating Tuberculosis Drug Resistance is Essential for the Success of the National Tuberculosis Elimination Program

Tuberculosis (TB) patients who do not respond to therapy due to drug resistance actively transmit the disease in the community. By recent estimates 75% of drug resistant (DR) TB remain undiagnosed⁶ and each of the undiagnosed DR-TB patients can cause on an average 2 to 3 percent new DR-TB cases⁷.

Despite an aggressive TB control program in India, DR TB has risen sharply over the past decade.

The most worrying aspect is the increase in the number of antibiotics to which resistance has been detected, wherein Multidrug Resistant (MDR) TB has been overshadowed by the increase in Extensively Drug Resistant (XDR), Extremely Drug Resistant (XXDR) TB and Totally Drug Resistant (TDR)  TB⁸.

The inability to diagnose DR-TB early in the diagnostic cycle is the most challenging part of treating DR-TB. It can take longer than 3 weeks and up to 3 months for all existing approaches in the Programmatic Management of DR-TB (PMDT⁹) to detect DR-TB, causing poor outcomes in diagnosis and significantly increasing the proportion of DR-TB.  Therefore, until an efficient and comprehensive diagnostic test is adopted nationally, all existing procedures would not be able to allow the achievement of TB elimination goals.

TB Genomics - The Global Gold Standard for Drug Resistant Tuberculosis Diagnosis

Genomic prediction of TB drug resistance has revolutionized DR-TB diagnosis globally. The National Health Services (in UK) employed genomics in TB diagnosis in 201510, after which the World Health Organization released the technical guidelines for using genomics for DR-TB diagnosis.

While current methods used 11 different tests to detect drug resistance to 13 drugs over a period of several months, genomics can provide a drug resistance profile of 17 antibiotics in one test within eight hours11. Clinical studies from Mumbai have already shown the use of genomics can significantly reduce the TB burden in India5.

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Notices and Disclaimers

Performance varies by use, configuration and other factors. Learn more at www.Intel.com/PerformanceIndex.

Performance results are based on testing as of December 2020 and may not reflect all publicly available updates.  See backup for configuration details.

No product or component can be absolutely secure. Your costs and results may vary.

Intel technologies may require enabled hardware, software or service activation.

Intel does not control or audit third-party data.  You should consult other sources to evaluate accuracy.

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Intel disclaims all express and implied warranties, including without limitation, the implied warranties of merchantability, fitness for a particular purpose, and non-infringement, as well as any warranty

arising from course of performance, course of dealing, or usage in trade.

HaystackAnalytics® disclaims all express and implied warranties whatsoever, including without limitation, the implied warranties of merchantability, non-infringement and fitness for any particular

purpose. Further, HaystackAnalytics® will not be liable for any direct, indirect, special, incidental, punitive, or consequential damages of any kind.

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About the Author
Mary is the Community Manager for this site. She likes to bike, and do college and career coaching for high school students in her spare time.