Recently I assisted a colleague with a patient that was having recurrent UTIs with the same bacteria, E. coli. The concern was that despite appropriate antibiotic therapy the E. coli UTI with Keflex symptoms would improve, but not completely resolve, and return in less than a week after completing therapy. PCR testing would repeatedly show E. coli. There was also some resistance developing with repeated courses of antibiotics.
Finally, the clinician decided to send a sample to MicroGen Dx for DNA sequencing. That sample showed that E. coli only made up 5% of the bioburden. The other 95% of the bioburden was two species of Citrobacter and Enterococcus. All three are not sensitive to Keflex. That explains why symptoms would only partially improve.
Since switching the patient to Augmentin which picked up all of the bacteria associated in this particular infection there has been complete resolution of the patient’s symptoms. The question was why did PCR testing miss 95% of the organisms associated in the particular case?
PCR testing is a valuable tool and is essential in determining the offending organism quickly so that appropriate antibiotic therapy can be administered rapidly. The problem is that PCR testing depends on templates. This limitation can only allow us to identify the most common organisms associated with a particular infection. With UTIs, E. coli is probably the most common bacteria
associated with that type of infection. Unfortunately, with over 30,000 microorganisms identified, PCR testing may miss what is actually going on.
Polymicrobial infections are on the rise for a number of reasons including an increase in antibiotics resistance, more medical procedures being done and more vulnerable patients in society. If all the organisms associated with a particular infection are not identified like in this case, the potential is for the infection to become recalcitrant and not improve with conventional therapy.
DNA sequencing allows for all the organisms in a sample to be identified and allow for better antibiotic choices as in this case. Once switched to Augmentin the patient improved significantly. In addition the clinician is working with the patient to minimize intestinal permeability.
The world is changing, and with more people living longer with chronic illnesses, testing for infections needs to change to meet the demand.
