Antibiotic Sensitivities & Viable vs Non-viable bacteria

1. NGS technology can’t replace traditional culture because it doesn’t provide Antibiotic Sensitivities.

  • We do provide antibiotic resistance by detection of the resistant gene for the antibiotic classes.
  • Culture sensitivities can only be performed if you can “grow” the microbe.
  • Being able to culture “grow” a microbe is not the determining factor to verify if the species is a problem for the host.
  • Only 1% of all known microorganisms can be grown in culture. Most physicians have only seen 30-50 species on C&S reports their entire medical career.
  • We currently know the sequence codes for more than 25,000 species.
  • You will not get from your micro lab the sensitivities of the more than 4,000 species we have detected in human samples.
  • ECSMID guidelines make the point that antibiotic sensitivities have no clinical value when treating a biofilm infection.
  • Breakpoints to determine S-I-R have been established for planktonic bacteria however, breakpoints haven’t been established for the biofilm or community of microorganisms.

2. How do you determine if the bacteria species are Viable?

Dead or Non Viable bacteria DNA degrades within 24 hours within the host environment.

Viable or Live bacteria once removed from the host environment it will take about 5 days for the DNA to die or degrade and become non-viable.

  • If you refrigerate the sample it will be good for weeks. If you freeze the sample, the DNA will not degrade, and will be good forever.
  • Due to the rapid degradation of DNA in dead bacterial cells it becomes extremely challenging for the technology to reach the threshold of DNA reads. If we don’t achieve enough DNA reads we can not detect the species.
  • If the bacterial species is listed in our report it has met our criteria for DNA reads.

3. Interpretation of the Lab Report - What Does All This Mean?

Detecting multiple species in a sample may be overwhelming, especially seeing species that you do not recognize. We are providing a complete picture of the microorganisms at the site the sample was taken from.  If the sample was taken from an area of the host which has an established microbiome, (sinus cavity, mouth) interpretation can be more of a challenge. The following are points you should consider when reviewing our report.

  • When treating a chronic infection you are dealing with biofilm phenotype.
  • CDC and NIH “have estimated that biofilm infections now constitute 65% to 80% (respectively) of bacterial infections treated by physicians in the developed world.
  • All bacteria / microorganisms will move to a biofilm phenotype.
  • If we detect multiple species from a host site that is normally sterile, there is a high probability you are dealing with a Biofilm.

4. Questions on Species Detected:

A: What do I treat?
Answer: Treatment decisions are based on multiple diagnostic criteria. Our report is not to be used in isolation. A common approach is to treat the dominant species when there is a concern for using multiple antimicrobials.

B. Is there a cut off of which species to treat?
Answer: No. Multiple species identified could be interpreted as a biofilm. In the case of biofilm infections the microorganisms are a “collaborative community” and are highly synergistic. When the sample is taken from a site other than the mouth, sinus cavity, gut, or areas in the body where we have an established microbiome, there are no commensal bacteria (Good Bacteria). Commensals need specific host related mechanisms and those host dependent processes are not possible in wounds, RTI, UTI, or joint infections.

5. What is found in non-infected patients?

You will find microorganism DNA in healthy people BUT you are going to have other diagnostic information to indicate infection. We give you precise information on what was detected at the site.

6. Why don’t the % of species add up to 100%?

We only report species that make up greater than 2% of the DNA detected.