Recently, we received multiple requests to help with Nontuberculous Mycobacteria (NTM) healthcare-associated infection (HAI) investigations from hospitals located in different parts of the country, all within a short period of time. It’s not the first time we’ve been contacted to help with an NTM investigation, but we’ve been surprised at how routine the requests seem to be. And it got us wondering, what is up with NTM?

NTM are a heterogeneous group of microorganisms and extremely diverse within species. NTM outbreaks are not typically a result of person-to-person transmission, except possibly in specific vulnerable populations like cystic fibrosis patients but have been implicated in outbreaks that are often sourced to medical equipment or other environmental reservoirs.

One of the challenges in these investigations is that it can be extremely difficult to determine clonality to aid in root cause determination. NTM are highly varied but have a limited set of reference genomes in public databases making it difficult to conduct SNP analysis (single-nucleotide polymorphism). Selecting the most closely matched high-quality reference genome is a critical step for accurate SNP calling and relatedness estimates. If a reference genome is not available, you lose a large amount of the genome which limits resolution and can provide inaccurate results.

Fortunately, epiXact® was built for just this type of challenge. EpiXact selects the most closely related genome for the most accurate results by using a combined reference genome and de novo assembly approach. The automated epiXact pipeline uses an in-house algorithm we developed to select the most similar available reference genome for each isolate pair. However, when no suitable reference is available, the pipeline uses the de novo assemblies generated from the samples themselves as references, enabling analysis that is agnostic to strain or species type.

Additionally, since NTM can last a long time in the right environmental conditions, they can accumulate SNPs and recombinations which can confound relatedness estimates. This is particularly important when looking at transmission events that may have taken place over longer periods of time. EpiXact detects and removes recombination events and mobile genetic elements.

If you are facing an NTM transmission investigation, please contact our HAI experts and see how epiXact can help you. EpiXact, our rapid turnaround WGS service for HAI investigations, uses the highest resolution SNP-based analysis to provide you with a simple, reliable answer about the relatedness of samples within 48 hours.

Contact our HAI experts to learn if epiXact® is right for you so that you can be prepared for any HAI situation that may arise in the future.