If you are like most professionals in the HAI space, you probably spend your days (hopefully not your nights) thinking about AMR outbreaks driven by clonal bacterial transmission. While these outbreaks certainly represent the majority, there is a growing concern for transmission carried by mobile genetic elements, especially plasmids. Plasmids can spread resistance markers across various strains and species, making the task of investigating an outbreak extremely tricky. When unusual resistance patterns surface across different bacterial strains and species, such as the emergence of CRE (Carbapenem resistant Enterobacterales) phenotypes in different species, it’s time to consider plasmid transmission as the perpetrator.

The challenge in pinpointing these elusive elements lies in their detection. Traditional short-read whole-genome sequencing (WGS) can accurately identify clonal bacterial transmission, but comes up short in recovering plasmid sequences. Similarly, elements like transposons, integrons, or gene cassettes, which play a role in gene mobilization, are challenging for short reads to reconstruct. Long-read WGS enables you to circularize plasmid sequences and comprehensively analyze bacterial isolates. This method allows consideration of both clonal bacterial transmission and mobile genetic elements as potential routes of AMR, providing a comprehensive understanding of the transmission dynamics at play.

Recently, a client asked us for help with a persistent critical resistance phenotype they were seeing across multiple bacterial species. We recommended sequencing their samples with Oxford Nanopore sequencing for an HAI analysis. While the pathogens were not found to be clonal, ONT long-read sequencing identified multiple plasmids common across these non-clonal isolates, including plasmids carrying resistance genes of interest. Leveraging our recently announced partnership with ONT, our client was able to look at a more complete picture of their problem and gather evidence for an unlikely transmission event causing their observed uptick in a critical resistant phenotype. Any other strategy would’ve cost more time, resources, and likely more infected individuals.

If you’re stuck on finding the source of your hospital’s HAI outbreak or individual transmission event, or you’d like to be proactive with comprehensive preventative HAI surveillance, check out our website and contact our experts via email, LinkedIn, or X, maybe we can help.