Tag Archives: molecular testing

“Gatecrashing: Neisseria meningitidis as a genital pathogen.”

Neisseria meningitidis is more classically known as the cause of meningococcal sepsis and meningococcal meningitis. However its role as a cause of urethritis/cervicitis has been the subject of ongoing speculation over the years, and several studies have backed such a link up. For example, check this study out, and this one.

A recent study has added more weight to this hypothesis, backing the assertion up with DNA studies of the N. meningitidis isolates showing adaptation to a genital environment. (loss of outer capsules, and acquisition of enzymes facilitating survival in a low oxygen environment)

So what does this all mean for clinical microbiology laboratories?

I guess it shows the inherent weakness of molecular diagnosis. There could be a widespread outbreak of urethritis due Neisseria meningitidis urethritis in your local area, but the laboratory would be completely naïve to it, if it only performs molecular testing for C. trachomatis and N. gonorrhoeae. Particularly in the Sexual Health Clinic setting, adjunctive culture of STI samples is important, and not just to obtain the N. gonorrhoeae susceptibilities.

It is also possible that the selective molecular diagnosis and treatment of N. gonorrhoeae will therefore create a “niche” for organisms like Neisseria meningitidis to adapt physiologically and “gatecrash” the party. (I will talk more about “selective pressure by diagnosis” in the next post.)

And finally on this topic, there is also intriguing data coming out that suggests that some meningococcal vaccines may have a protective effect for N. gonorrhoeae infection. Suspected for some time, this suggestion has been backed up by some observational data in this study. More research is obviously needed. We are still a bit away I suspect from a gonococcal vaccine.

The physiological and evolutionary relationship between Neisseria meningitidis and Neisseria gonorrhoeae is a fascinating one.  We shouldn’t think too much about one without considering the other…



“Molecular diagnosis of wound infections: The Holy Grail.”

The slice of pie taken by the molecular department in the microbiology laboratory is increasing, slowly but surely.

On the contrary, the proportion of culture based microbiology is inexorably declining.

Many clinical microbiology laboratories are now switching, or looking at switching over to molecular diagnosis of enteric pathogens.

Molecular diagnosis of pathogens causing vaginitis and pharyngitis will not be far behind, and a few labs have already moved in this direction.

However diagnosis of wound infections remains firmly culture based. There is not even much in the literature with regards to molecular diagnosis of wound infections…

Is it even possible?

So what are the difficulties?:

  • Potential number of pathogens: There are several pathogens or putative pathogens that are able to cause wound infections. This makes PCR based molecular diagnosis more difficult. However, on the flip side, 95% of wound infections in a general clinical setting are caused by two pathogens, Staphylococcus aureus and Streptococcus pyogenes (Group A streptococcus).
  • Lack of susceptibility information: Molecular diagnosis of resistance determinants is still a little behind phenotypic culture based testing. However with regards to the two main pathogens as above, PCR analysis can easily differentiate between MSSA and MRSA, and susceptibility data for Streptococcus pyogenes is only required for a small proportion of patients who have anaphylactic reactions to penicillin.
  • “Over-sensitivity”: It is always nice to know which are the dominant organisms within a wound. Culture is relatively good at this. However molecular methods are starting to be able to quantify to some extent (e.g by playing with the cycle threshold cut-off).
  • Cost: The culture of a standard wound swab might cost $10 or so, even when overheads are included. In my experience molecular tests have to be performed in very large volumes to even get close to this kind of price. However wound swabs do arrive into the laboratory in very large volumes!

If it was easy it would have been done by now… I suspect it is the 4 things above acting together as a “bundle”, as opposed to any one insurmountable barrier which has contributed to the lack of progress up until now.

However it will come in some form or other, you can be sure of that…

Here is a potential solution I have thought of:

  • Any wound swab accompanied with clinical details suggesting an unusual pathogen e.g. animal bites (Pasteurella), water exposure (vibrios, aeromonas), immunocompromise,  would still undergo routine “catch-all” bacterial culture.
  • The rest (the vast majority) would be subjected to a multiplex PCR for the detection of MSSA, MRSA and Streptococcus pyogenes (and possibly Group G streptococcus also). A positive result would be reported routinely. A  negative result would have an accompanying comment to suggest contacting the laboratory if the patient’s symptoms were persisting, or if further susceptibilities are required, so that culture could be set up if necessary.

In this way molecular diagnostics could be performed on (a good proportion of) wound swabs at a relatively low cost.

In addition multiplex PCRs could be developed specifically for infections in specific clinical situations, e.g. post animal bite,  etc., etc.

Automated bacteriology culture systems like Kiestra TLA would not have happened if the industry didn’t think that there was at least another 20 years or so of culture based bacteriology left, and they are probably right. But I don’t think it will be too long before commercial laboratory diagnostics companies start looking closely at “wholesale” molecular options as above.

And who knows, whole genome sequencing might come in and completely disrupt PCR based molecular diagnostics, and the picture might change again…

The future’s uncertain and the end is alway near


“Creating a rod for your own back”

la34808Treatment of sexually transmitted diseases in most places in the world is empiric in nature, based on the presenting clinical syndrome of the patient. A generation ago, the laboratory diagnosis of STDs was fairly rudimentary. No NAAT testing, viral culture and serology only for HSV, etc. Add this to the fact that getting some of the patients back for a second visit isn’t always easy and it is easy to understand why the Sexual Health community have traditionally gone for this model of care.

However things are changing, and changing fast… 

Our ability to accurately diagnose STDs has increased markedly over the past decade. C. trachomatis, N. gonorrhoeae, HSV are now all routinely diagnosed by NAAT testing in most laboratories. “Emerging” organisms such as Mycoplasma genitalium are now coming onto the radar of STD clinicians, primarily because we can now diagnose it…

Whilst empiric treatment works (most of the time anyway), it does have its downsides. Empiric therapy on a population basis usually leads to overtreatment. Resistance to N. gonorrhoeae has reached worrying levels for both fluoroquinolones and ceftriaxone. Resistance of M. genitalium to macrolides has been increasing, most probably in areas where azithromycin is used empirically for urethritis.

We need to be careful we don’t create a rod for our own back…

It may be that Sexual Health needs to start exploiting the progress in laboratory diagnostics that has been made over the past few years and start moving away from empiric based management of STIs. Some NAAT tests are now available (e.g. Cepheid CT/NG) that can give a result in around 90 minutes. Thus it could theoretically be possible to see the patient, take the samples, send the patient away for a coffee, test the samples in the clinic with an automated benchtop PCR analyser, and see the patients back in an hour or two with the results and directed management.

This might well be the future of STD clinics…