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How sequence analysis programs are better prepared for the threat of antimicrobial resistance.

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Dr. Kirsten Miller-Duys 25/02/2022

Antimicrobial resistance (AMR) is an international public health emergency as identified by the WHO (see references). If no action is taken, we could be spending an additional 1,2 trillion dollars per year on health by 2050 due to the impact of AMR. Much work has been done in the public health space to try and bring attention to this pandemic, however it remains an under recognised and poorly addressed threat. Drug resistance places a substantial and increasing cost on all societies, but is particularly threatening to lower-middle-income countries (LMICs).

One of the key tenets in tackling the AMR crisis lies in the use of sequencing technology. Next Generation Sequencing (NGS) capacity and technology has improved exponentially in the last 10 years. This has been enabled by advancing NGS data analysis capabilities including the development of specialist bioinformatics software.

There are three key areas of AMR that NGS sequencing technologies and sequence analysis programs can address:

  1. Quick identification of pathogens and parallel prediction of susceptibility to antimicrobials. We have seen this in addressing M.tuberculosis where sequencing and NGS data analysis of the mycobacteria to identify resistance is much faster than with conventional culture methods.
  2. Development of new vaccines, antimicrobials and diagnostics. Sequencing and bioinformatics software enables research and development efforts as the pathogen is better understood. It also enhances monitoring of efficacy in diverse populations.
  3. Genomic surveillance to track disease outbreaks. Effective NGS data analysis using end-to-end bioinformatics solutions enables early detection of resistance patterns and disease threats allowing focused national policy and resource interventions and local responses such as adaptation of prescription guidelines. Sharing surveillance data at a global scale is important to identify early threats and understand and act on long-term trends.

One of the positive outcomes from the SARS-CoV-2 pandemic is that we have seen an impressive international focus on genomic data generation, as we all become aware of our collective vulnerability to new variants of the virus. This has meant it has fast-tracked the capacity for genomic surveillance in LMICs. For example, the African CDC (see references), amongst others, tracks and displays SARS-CoV-2 sequences and variants.

However NGS data analysis remains one of the key challenges for LMICs due to limited resources and skills constraints. Making routine NGS data analysis easy and accessible is one of the key focuses for Hyrax Biosciences. Removing the need for limited, specialist resources to have to run step-by-step sequence analysis programs frees them up to focus on downstream tasks. This can assist resource limited labs to capitalise on the power of sequencing in addressing AMR.

We at Hyrax Biosciences are experts in both NGS data analysis and resistance testing in infectious diseases, as well as the genomic surveillance efforts for SARS-CoV-2 . Our experiences and skills in developing bioinformatics software in these areas make us best placed to work with you in taking on the antimicrobial resistance challenge. To partner in the fight, contact us today!