PCR testing in bacterial vaginosis, aerobic vaginitis, and other vaginal infections

PCR testing

PCR testing can help weed out the real cause of bacterial vaginosis (BV), aerobic vaginitis (AV), or other mixed or undetectable infections that may be causing unpleasant vaginal symptoms. Polymerase chain reaction (PCR) testing is a form of microbial detection that looks for bacterial RNA and DNA, instead of trying to grow the bacteria in a lab (culturing).

Before you get any antibiotics, you should ask for both an extensive culture and PCR test, since many bacteria associated with bacterial vaginosis (BV) have natural and/or acquired antibiotic resistance, or are very quick to develop resistance. This can lead to failed treatments and ongoing issues that not even strong antibiotics can resolve.

When your symptoms are not just bacterial vaginosis

You may also have aerobic vaginitis or desquamative inflammatory vaginitis, or something else entirely, as opposed to just straight bacterial vaginosis. Only a test will clear it up. If your symptoms are not simply fishy odour and discharge, then you have something else – classic BV does not cause itching, irritation or inflammation. That’s one of its features.

Aerobic vaginitis, on the other hand, involves other types of bacteria, and does cause inflammation. It can be very useful to be sure what is in your vagina before you do any treatments, particularly antibiotics, but other treatments too. Microbes all have a list of treatments that work very well, depending on the microbe’s nature, with some treatments completely ineffective on certain bugs. If you have tried a treatment and it failed, it’s very likely because the microbe was not susceptible to that treatment.

Wrong antibiotics for short time

If you are given antibiotics, you may be given the wrong sort for too short of a time, and cause antibiotic resistance in undetected bacteria, thus creating a bigger problem. Antibiotic resistance means you’ll have recurrent BV that will not respond to regular treatments, and will get harder and harder to treat with every failed attempt.

What to do if your doctor doesn’t know where to get PCR testing

Some doctors will not know about these tests/how to get hold of them. There are plenty of labs around that do PCR testing, and usually your doctor will already be doing these tests for other microbes. The equipment these special labs use to do these tests are capable of many tests at the same time.

Make sure your doctor has these lists, and the full spectrum of tests is performed both with culture and multiplex PCR (or nucleic acid assay – just as good) as is applicable to your symptoms – not all of these bacteria will match your symptoms, but do your homework and establish a basic understanding so you are informed.

Many doctors will baulk at this and say you don’t need it, but if you believe that you do – as in, your BV just won’t go away and/or you have symptoms that don’t match classic BV – then fight for it or find a new doctor. BV as we know it is changing, and bacteria that used to be considered commensal – harmless and normal – are now revealing themselves as just as much an opportunistic pathogen as the usual suspects.

What to get tested for

When getting multiplex PCR tested, you want to ensure you get the full swathe of appropriate tests (including for STIs if applicable) for your circumstances. This is easier said than done, however, because these companies that make the tests make kits, so a doctor can request the STI profile, or the BV profile, but neither of these covers, for example, E. coli.

The bacteria to be tested for might include (but is not limited to) the following:

Healthy flora test
  1. Lactobacillus (BV & AV Panel, tests for L. crispatus, L. jensenii, L. gasseri, L. iners, all healthy flora)

Important note on L. iners: if your PCR test comes back positive for L. iners, don’t be fooled into thinking you have healthy flora – L. iners can adapt to life with bad bacteria quite quickly, while other lactobacilli do not survive the fight. If your vagina (pre- and during BV) has a presence of L. iners, this can be a predictor of BV, not a sign of a recovering vagina. Do not trust L. iners!

BV / AV / UTI panel
  1. Atopobium vaginae (hard to culture, fastidious bacteria, associated with BV, some strains metronidazole resistant, creates biofilms/contributes to biofilms)
  2. Bacteroides spp. (strongly correlated with BV, can cause ammonia odour)
  3. Dialister spp. (relatively low virulence)
  4. Enterococcus faecalis (normal in bowel flora, can be cause of abnormal vaginal flora and faecal odour from vagina, very hardy, very antibiotic resistant, creates biofilms)
  5. Escherichia coli (normal in bowel flora, cause of UTIs and abnormal vaginal flora, can contribute to BV/aerobic vaginitis with odour and discharge, creates biofilms)
  6. Eggerthella sp. (relatively low virulence)
  7. Fusobacterium nucleatum
  8. Gardnerella vaginalis (potential STI, directly involved in BV, causes fishy odour, watery discharge, creates thick biofilms)
  9. Group B Streptococcus (GBS) (can be involved in abnormal flora, controversial as to involvement in BV or vaginitis, creates biofilms)
  10. Leptotrichia amnioni
  11. Mobiluncus curtisii (possibly involved in BV, antibiotic resistant, creates/contributes to biofilms)
  12. Mobiluncus mulieris (possibly involved in BV, antibiotic resistant, creates/contributes to biofilms)
  13. Megasphaera species (type 1 and type 2, may be new species, normally present, associated with BV, type 1 worst, PCR test only)
  14. Mycoplasma genitalium (possibly involved in BV, antibiotic resistant. creates biofilms)
  15. Staphylococcus aureus and MRSA (fishy/foul odour, vulvovaginitis, discharge, itch, small pimples/boils, transmissible, antibiotic resistant, causes biofilms)
  16. Ureaplasma urealyticum (may be involved in BV and abnormal flora, antibiotic resistant, creates biofilms)
  17. Ureaplasma parvum (may be involved in BV and abnormal flora, antibiotic resistant, creates biofilms)
  18. BV-associated bacterium (BVAB-1, BVAB-2 and BVAB-3) (novel bacteria in the Clostridiales Order highly specific for BV, relatively low virulence)
  19. Sneathia amnii and Sneathia sanguinegens (formerly Leptotrichia sanguinegens(heavily related to BV, not found in healthy vaginas, cause of BV, thick biofilms, very adherent)
  1. Candida albicans (common yeast, can overgrow causing yeast infections with itching, thick cottage cheese discharge, treated with antifungals, responds to boric acid, causes biofilms)
  2. Candida glabrata (less severe symptoms than C. albicans, burns, very antifungal resistant, responds to boric acid, causes biofilms)
  3. Candida parapsilosis (Similar or the same as other yeast infections, discharge, may cause UTIs, itch, burning, pain after sex, stinging, antifungal resistant, causes biofilms)
  4. Candida tropicalis (Similar or the same as other yeast infections, itch, burning, pain after sex, stinging, fluconazole resistant, causes biofilms)
STI panel
  1. Chlamydia trachomatis chlamydia (STI, causes discharge, urinary tract symptoms, antibiotic resistant strains appearing, creates biofilms)
  2. Herpes simplex virus types 1 and 2 – genital herpes virus (STI, causes genital sores, flu-like symptoms, no odour, no discharge, may utilise other species’ biofilms to hide in)
  3. Neisseria gonorrhoeae – gonorrhoea (STI, maybe no symptoms, discharge, burning urination, foul odour, treated with antibiotics, some strains antibiotic resistant, creates biofilm)
  4. Trichomonas vaginalis – trich (STI, causes fishy odour and abnormal discharge, usually one of first BV tests)
  5. Treponema pallidum – syphilis (STI)
Other bacteria, fungi and viruses
  1. Epstein-Barr virus (EBV) (vulvar ulcers, urinary tract symptoms, vulvar pain, itching, discharge)
  2. Haemophilus ducreyi (cause of painful genital sores/ulcers)
  3. Haemophilus influenzae (discharge, itch, antibiotic resistant, often found in children from nose picking-crotch itching, antibiotic resistance developing)
  4. Human adenovirus (can cause urethritis, genital sores that look like herpes)
  5. Neisseria meningitidis (vaginal bleeding, discharge, urethral symptoms, vulvovaginitis, irritation, inflammation, antibiotic resistance developing)
  6. Streptococcus pneumoniae (serious infection in respiratory tract, can cause pelvic organ infection)
  7. Helicobacter pylori (maybe STI, possibly associated with BV or vulvovaginal infections)

Things to know about these bacteria

Many of these bacteria are antibiotic resistant and do not appear on cultures, being slow-growing or otherwise hard to culture. PCR testing is not a replacement for culturing, which is an excellent method of detection for many bacteria, so both should be done with as many suspect bacteria as possible.

Get a copy of all of your test results every time you get tested so you can see exactly for what and how you have been tested, and record any treatments you are given including antibiotic name, dose and treatment duration. This matters if treatment fails.

Research into PCR testing for bacterial vaginosis

    1. J Clin Microbiol. 2016 June 24; 54(7): 1930. Development and Validation of a Highly Accurate Quantitative Real-Time PCR Assay for Diagnosis of Bacterial Vaginosis, David W. Hilbert, William L. Smith, and Scott E. Gygax
    2. doi: 10.1128/JCM.00506-12. Epub 2012 Apr 25. Development and validation of a semiquantitative, assay for diagnosis of bacterial vaginosis. Cartwright CP, Lembke BD, Ramachandran K, Body BA, Nye MB, Rivers CA, Schwebke JR
    3. May;48(5):1812-9. doi: 10.1128/JCM.00851-09. Epub 2010 Mar 19. Quantitative PCR assessments of bacterial species in women with and without bacterial vaginosis. Zozaya-Hinchliffe M, Lillis R, Martin DH, Ferris MJ
    4. Appl Environ Microbiol. 2013 Jul; 79(13): 4181–4185.  Novel PCR-Based Methods Enhance Characterization of Vaginal Microbiota in a Bacterial Vaginosis Patient before and after Treatment doi:  10.1128/AEM.01160-13 Janet A. Lambert, Apoorv Kalra, Cristina T. Dodge, Susan John, Jack D. Sobel, and Robert A. Akins
    5. Twin, J., Bradshaw, C. S., Garland, S. M., Fairley, C. K., Fethers, K., & Tabrizi, S. N. (2013). The potential of metatranscriptomics for identifying screening targets for bacterial vaginosis. PLoS One8(9)
    6. Sex Transm Infect 2013;89:A88. Evaluation of a Real-Time PCR-Based Test For Bacterial Vaginosis, J. G. Kusters, E. A. Reuland, and J. W. Dorigo-Zetsma
    7. J Clin Microbiol. 2014 August; 52(8): 3137Changes in Vaginal Bacterial Concentrations with Intravaginal Metronidazole Therapy for Bacterial Vaginosis as Assessed by Quantitative PCR David N. Fredricks, Tina L. Fiedler, and Jeanne M. Marrazzo
    8. Srinivasan S, Hoffman NG, Morgan MT, et al. Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria. Ratner AJ, ed. PLoS ONE. 2012;7(6):e37818. doi:10.1371/journal.pone.0037818.
Jessica Lloyd - Naturopathic Practitioner, BHSc(N)

Jessica Lloyd - Naturopathic Practitioner, BHSc(N)

Jessica is a degree-qualified naturopath (BHSc) specialising in vulvovaginal health and disease, based in Melbourne, Australia.

Jessica is the owner and lead naturopath of My Vagina, and is a member of the:

  • International Society for the Study of Vulvovaginal Disease (ISSVD)
  • International Society for the Study of Women's Sexual Health (ISSWSH)
  • National Vulvodynia Association (NVA) Australia
  • New Zealand Vulvovaginal Society (ANZVS)
  • Australian Traditional Medicine Society (ATMS)
Read more about Jessica and My Vagina's origin story.
Jessica Lloyd - Naturopathic Practitioner, BHSc(N)

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