When it comes to determining relatedness between isolates in an HAI investigation, you know by now that we believe there is no better tool than whole-genome sequencing (WGS). But in some cases, WGS alone may not be enough. Although WGS allows you to see variations of DNA down to the single nucleotide level, comparing sequences of DNA without considering recombination events can prevent you from getting the definitive answers you need when determining clonality.

Recombination events happen when bacteria are being “promiscuous” — i.e., taking in fragments of DNA from other bacteria or the environment and meshing it with their own. Recombination events introduce changes in the genome at a far faster rate and with much higher density than the natural rate of variation that happens with the passage of time (the “molecular clock”). This phenomenon is an important evolutionary mechanism and most commonly takes place between closely related bacterial species.

However, in an HAI investigation, recombinations can confound relatedness estimates in a suspected outbreak and make two infections look less clonal than they really are. Detecting recombination events is particularly important when looking at healthcare-associated transmission chains that may have taken place over longer periods of time. Time increases the chances that one or more recombination events have occurred, resulting in potential false-negative results that can mislead intervention strategies.  

In one study (published in ICHE) involving a Carbapenem-Resistant Acinetobacter baumannii outbreak spanning several months, we used epiXact, our rapid, HAI detection service, to detect pairwise SNP differences between the isolates after identifying and removing several recombination events. A baumannii is a highly promiscuous species known to have frequent recombination events. So without a method for detecting and unmasking recombinations, these isolates could very well have been deemed outside of the cluster that was being investigated, radically changing the scope of the intervention.

CRAB Study

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.