CAM 20416

Diagnosis of Vaginitis including Multi-target PCR Testing

Category:Laboratory   Last Reviewed:April 2019
Department(s):Medical Affairs   Next Review:April 2020
Original Date:February 2000    

Vaginitis is defined as inflammation of the vagina with symptoms of discharge, itching and discomfort often due to a disruption of the vaginal microflora. The most common infections are bacterial vaginosis, Candida vulvovaginitis, and trichomoniasis (J. D. Sobel, 1999). Other causes include vaginal atrophy in postmenopausal women, cervicitis, foreign body, irritants and allergens (J. Sobel, 2017a).

Bacterial vaginosis (BV) is characterized by a shift in microbial species from the normally dominant hydrogen-peroxide producing Lactobacillus species to Gardnerella vaginalis and anaerobic commensals (Eschenbach et al., 1989; Hill, 1993; Lamont et al., 2011; Ling et al., 2010; J. Sobel, 2017b).

Vulvovaginal candidiasis (VVC) is characterized by Candida species. It is the second most common cause of vaginitis symptoms (after BV) and accounts for approximately one-third of vaginitis cases (J. Sobel, 2017c; Workowski & Bolan, 2015).

Trichomoniasis is caused by the flagellated protozoan Trichomonas vaginalis, which principally infects the squamous epithelium in the urogenital tract: vagina, urethra, and paraurethral glands (Kissinger, 2015; J. Sobel, 2017d).

The squamous epithelium of the vagina in premenopausal women is rich in glycogen, a substrate for lactobacilli, which create an acidic vaginal environment (pH 4.0 to 4.5). This acidity helps maintain the normal vaginal flora and inhibits growth of pathogenic organisms. Disruption of the normal ecosystem by menstrual cycle, sexual activity, contraceptive, pregnancy, foreign bodies, estrogen level, sexually transmitted diseases, and use of hygienic products or antibiotics can lead development of vaginitis. Bacterial vaginosis, vulvovaginal candidiasis, and trichomoniasis are the three most common infections responsible for vaginitis. Other causes include: vaginal atrophy in postmenopausal women, cervicitis, foreign body, irritants and allergens (J. Sobel, 2017a).

Laboratory documentation of the etiology of vaginitis is important before initiating therapy, given the nonspecific nature considerable overlap of the symptoms (Anderson, Klink, & Cohrssen, 2004; Ellis, Lerch, & Whitcomb, 2001; Landers, Wiesenfeld, Heine, Krohn, & Hillier, 2004) Diagnostic testing enables targeted treatment, increases therapeutic compliance, and increases the likelihood of partner notification (J. Sobel, 2017a; Workowski & Bolan, 2015).

Measurement of vaginal pH is the primary initial finding that drives the diagnostic. The pH of the normal vaginal secretions in premenopausal women with relatively high estrogen levels is 4.0 to 4.5. The pH of normal vaginal secretions in premenarchal and postmenopausal women in whom estrogen levels are low is ≥4.7. An elevated pH in a premenopausal woman suggests infections such as BV (pH>4.5) or trichomoniasis (pH 5 to 6), and helps to exclude Candida vulvovaginitis (pH 4 to 4.5). Vaginal pH may also be altered by lubricating gels, semen, douches, intravaginal medications and in pregnant women, leakage of amniotic fluid (Anderson et al., 2004; J. Sobel, 2017a).

Microscopic examination of normal vaginal discharge reveals a predominance of squamous epithelial cells, rare polymorphonuclear leukocytes (PMNs), and Lactobacillus species. The primary goal of the examination is to look for candidal buds or hyphae, motile trichomonads, epithelial cells studded with adherent coccobacilli (clue cells), and increased numbers of PMNs (J. Sobel, 2017a).

The microscopic evaluation of BV is usually based on Amsel criteria (Amsel et al., 1983). If clinical criteria are used to define infection, then reported sensitivity ranges from 62 to 100 percent (Spiegel, 1991). Using Gram's stain as the standard for diagnosing BV, the sensitivity of Amsel criteria for diagnosis of BV is over 90 percent and specificity is 77 percent (Landers et al., 2004). Because BV represents complex changes in the vaginal flora, vaginal culture has no role in diagnosis. If microscopy is not available, commercial diagnostic testing methods (e.g., rapid antigen and nucleic acid amplification tests) are used for confirming the clinical suspicion of BV. PCR-based assays to quantify BV associated bacteria (Cartwright et al., 2012; Menard, Fenollar, Henry, Bretelle, & Raoult, 2008) have good sensitivity and specificity compared with standard clinical tests (Dumonceaux et al., 2009; Menard et al., 2010); however, they are expensive and of limited utility (J. Sobel, 2017b).

Trichomoniasis can be diagnosed by the presence of motile trichomonads on wet mount, but they are identified in only 60 to 70 percent of culture-confirmed cases. Culture on Diamond's medium was considered the gold standard method for diagnosing T. vaginalis infection (Workowski & Bolan, 2015) however, nucleic acid amplification tests (Baron et al., 2013) have become the accepted gold standard for the diagnosis of T. vaginalis. One study found the sensitivities for T. vaginalis using wet mount, culture, rapid antigen testing, and transcription-mediated amplification testing were 65, 96, 90, and 98 percent, respectively(Huppert et al., 2007). Coexistence of T. vaginalis and BV pathogens is common, with coinfection rates of 60 to 80 percent (J. Sobel, 2017d; J. D. Sobel, Subramanian, Foxman, Fairfax, & Gygax, 2013).

Microscopy is negative in up to 50 percent of patients with culture confirmed VVC (J. D. Sobel, 1985). There are no reliable point of care tests for Candida available in the United States (Abbott, 1995; Chatwani et al., 2007; Dan, Leshem, & Yeshaya, 2010; Hopwood, Evans, & Carney, 1985; Marot-Leblond et al., 2009; Matsui et al., 2009), a culture must be obtained. Polymerase chain reaction (PCR) methods have high sensitivity and specificity and a shorter turn-around time than culture (Diba, Namaki, Ayatolahi, & Hanifian, 2012; Mahmoudi Rad, Zafarghandi, Amel Zabihi, Tavallaee, & Mirdamadi, 2012; Tabrizi, Pirotta, Rudland, & Garland, 2006; Weissenbacher et al., 2009), but are costly and offer no proven benefit over culture in symptomatic women (J. Sobel, 2017c).


  1. Testing of pH, testing for the presence of amines, saline wet mount, hydrogen peroxide (KOH) wet mount and microscopic examination of vaginal fluids is considered MEDICALLY NECESSARY in patients with symptoms of vaginitis.
  2. Direct Probe DNA-based identification of  Gardnerella, Trichomonas, and Candida is considered MEDICALLY NECESSARY in patients with symptoms of vaginitis.
  3. Vaginal cultures for Candida species are considered MEDICALLY NECESSARY for the diagnosis of vulvovaginal candidiasis in patients with clinical signs and symptoms of vaginitis and negative findings on wet-mount preparations and a normal pH test.
  4. Measurement of sialidase activity in vaginal fluid is considered MEDICALLY NECESSARY for the diagnosis of bacterial vaginosis in women with symptoms of vaginitis.
  5. Nucleic Acid Amplification Test (NAAT) or Polymerase Chain Reaction (PCR)-based identification of Trichomonas is considered MEDICALLY NECESSARY in patients with symptoms of vaginitis.
  6. Polymerase Chain Reaction (PCR) based identification of Candida species is considered INVESTIGATIONAL for any indication.
  7. Screening for Trichomonas is considered MEDICALLY NECESSARY for women with risk factors including: new or multiple partners; history of sexually transmitted diseases (STDs); exchange of sex for payment; or injection drug use.
  8. Screening for trichomoniasis and bacterial vaginosis is considered NOT MEDICALLY NECESSARY in asymptomatic patients, including asymptomatic pregnant patients at average or high risk for premature labor.
  9. Rapid identification of Trichomonas by enzyme immunoassay is INVESTIGATIONAL in patients with symptoms of vaginitis.
  10. PCR testing and Multitarget polymerase chain reaction (PCR) testing for diagnosis of bacterial vaginosis is INVESTIGATIONAL.
  11. Using molecular-based panel testing, including, but not limited to, testing such as SmartJane™, to test for microorganisms involved in vaginal flora imbalance and/or infertility is INVESTIGATIONAL.

Centers for Disease Control and Prevention (CDC)
The CDC published recommendations for the evaluation of diseases characterized by vaginal discharge in the 2015 Sexually Transmitted Diseases Treatment Guidelines (CDC, 2015). They state that: "Various diagnostic methods are available to identify the etiology of an abnormal vaginal discharge." "In the clinician’s office, the cause of vaginal symptoms might be determined by pH, a potassium hydroxide (KOH) test, and microscopic examination of fresh samples of the discharge" and "In settings where pH paper, KOH, and microscopy are not available, alternative commercially available point-of-care tests or clinical laboratory testing can be used to diagnose vaginitis." 

For the evaluation of BV they recommend: "BV can be diagnosed by the use of clinical criteria (i.e., Amsel’s Diagnostic Criteria) (Amsel et al., 1983) or Gram stain" and state that "Other tests, including Affirm VP III (Becton Dickinson, Sparks, MD), a DNA hybridization probe test for high concentrations of G.vaginalis, and the OSOM BV Blue test (Sekisui Diagnostics, Framingham, MA), which detects vaginal fluid sialidase activity, have acceptable performance characteristics compared with Gram stain. Although a prolineaminopeptidase card test is available for the detection of elevated pH and trimethylamine, it has low sensitivity and specificity and therefore is not recommended. PCR has been used in research settings for the detection of a variety of organisms associated with BV, but evaluation of its clinical utility is still underway. Detection of specific organisms might be predictive of BV by PCR (Cartwright et al., 2012; Fredricks, Fiedler, Thomas, Oakley, & Marrazzo, 2007). Additional validation is needed before these tests can be recommended to diagnose BV. Culture of G. vaginalis is not recommended as a diagnostic tool because it is not specific. Cervical Pap tests have no clinical utility for the diagnosis of BV because of their low sensitivity and specificity." They also found that "evidence is insufficient to recommend routine screening for BV in asymptomatic pregnant women at high or low risk for preterm delivery for the prevention of preterm birth (USPSTF, 2008)."

For the evaluation of vulvovaginal candidiasis they recommend: "Examination of a wet mount with KOH preparation should be performed for all women with symptoms or signs of VVC, and women with a positive result should be treated. For those with negative wet mounts but existing signs or symptoms, vaginal cultures for Candida should be considered." And that "PCR testing for yeast is not FDA-cleared; culture for yeast remains the gold standard for diagnosis." They do not address DNA hybridization probe tests.

For the evaluation of Trichomoniasis they recommend: "Diagnostic testing for T. vaginalis should be performed in women seeking care for vaginal discharge." And "The use of highly sensitive and specific tests is recommended for detecting T. vaginalis. Among women, NAAT is highly sensitive, often detecting three to five times more T. vaginalis infections than wet-mount microscopy, a method with poor sensitivity (51%–65%) (Hollman, Coupey, Fox, & Herold, 2010; Roth et al., 2011)." Regarding point of care testing, they state that "Other FDA-cleared tests to detect T. vaginalis in vaginal secretions include the OSOM Trichomonas Rapid Test (Sekisui Diagnostics, Framingham, MA), an antigen-detection test using immunochromatographic capillary flow dipstick technology that can be performed at the point of care, and the Affirm VP III (Becton Dickinson, Sparks, MD), a DNA hybridization probe test that evaluates for T. vaginalis, G. vaginalis, and Candida albicans. The results of the OSOM Trichomonas Rapid Test are available in approximately 10 minutes, with sensitivity 82%–95% and specificity 97%–100% (Campbell, Woods, Lloyd, Elsayed, & Church, 2008; Huppert et al., 2007). Self-testing might become an option, as a study of 209 young women aged 14–22 years found that >99% could correctly perform and interpret her own self-test using the OSOM assay, with a high correlation with clinician interpretation (96% agreement, κ = 0.87) (Huppert et al., 2010). The results of the Affirm VP III are available within 45 minutes. Sensitivity and specificity are 63% and 99.9%, respectively, compared with culture and TMA; sensitivity might be higher among women who are symptomatic (Andrea & Chapin, 2011; Brown, Fuller, Jasper, Davis, & Wright, 2004)."

American Academy of Family Physicians 
The AAFP published an article (Hainer & Gibson, 2017) on the diagnosis of vaginitis which states that: "Physicians traditionally diagnose vaginitis using the combination of symptoms, physical examination, pH of vaginal fluid, microscopy, and the whiff test. When combined, these tests have a sensitivity and specificity of 81 and 70 percent, respectively, for BV; 84 and 85 percent for vulvovaginal candidiasis; and 85 and 100 percent for trichomoniasis when compared with the DNA probe standard (Lowe, Neal, & Ryan-Wenger, 2009)."

"A cost-effectiveness analysis of diagnostic strategies for vaginitis undiagnosed by pelvic examination, wet-mount preparation, and related office tests showed that the least expensive strategy was to perform yeast culture, gonorrhea and chlamydia probes at the initial visit, and Gram stain and Trichomonas culture only when the vaginal pH exceeded 4.9. Other strategies cost more and increased duration of symptoms by up to 1.3 days (Carr, Rothberg, Friedman, Felsenstein, & Pliskin, 2005)." 

U.S. Preventive Services Task Force Recommendations
The USPSTF published recommendations (USPSTF, 2008) on screening for BV in pregnancy which state: "The USPSTF recommends against screening for BV in asymptomatic pregnant women at low risk for preterm delivery". And "The USPSTF concludes that the current evidence is insufficient to assess the balance of benefits and harms of screening for BV in asymptomatic pregnant women at high risk for preterm delivery."

American College of Obstetrics and Gynecology
ACOG published recommendations (ACOG, 2006) for the evaluation of vaginitis in 2006 which state: "Evaluation of women with vaginitis should include a focused history about the entire spectrum of vaginal symptoms, including change in discharge, vaginal malodor, itching, irritation, burning, swelling, dyspareunia, and dysuria." "During speculum examination, samples should be obtained for vaginal pH, amine ("whiff") test, and saline (wet mount) and 10% potassium hydroxide (KOH) microscopy. The pH and amine testing can be performed either through direct measurement or by colorimetric testing." "In selected patients, vaginal cultures or polymerase chain reaction tests for trichomonas or yeast are helpful. A vaginal Gram stain for Nugent scoring of the bacterial flora may help to identify patients with BV. Other currently available ancillary tests for diagnosing vaginal infections include rapid tests for enzyme activity from BV-associated organisms, Trichomonas vaginalis antigen, and point-of care testing for DNA of G vaginalis, T vaginalis, and Candida species; however, the role of these tests in the proper management of patients with vaginitis is unclear. Depending on risk factors, DNA amplification tests can be obtained for Neisseria gonorrheae and Chlamydia trachomatis."


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Coding Section

Code Number Description
CPT  0068U

Candida species panel (C. albicans, C. glabrata, C. parapsilosis, C. kruseii, C tropicalis, and C. auris), amplified probe technique with qualitative report of the presence or absence of each species 


Amines, vaginal fluid, qualitative

  83986 Ph; body fluid, not otherwise specified
  87070 Culture, bacterial; any other source except urine, blood or stool, aerobic, with isolation and presumptive identification of isolates 
  87149 Culture, typing; identification by nucleic acid (DNA or RNA) probe, direct probe technique, per culture or isolate, each organism probed
  87150 Culture, typing; identification by nucleic acid (DNA or RNA) probe, amplified probe technique, per culture or isolate, each organism probed
  87210  Smear, primary source with interpretation; wet mount for infectious agents (eg, saline, India ink, KOH preps)  
  87480 Infectious agent detection by nucleic acid (dna or rna); candida species, direct probe technique
  87481 Infectious agent detection by nucleic acid (dna or rna); candida species, amplified probe technique 
  87482  Infectious agent detection by nucleic acid (dna or rna); candida species, quantification technique 
  87510  Infectious agent detection by nucleic acid (dna or rna); gardnerella vaginalis, direct probe technique 

Infectious agent detection by nucleic acid (DNA or RNA); Gardnerella vaginalis, amplified probe technique 

  87512  Infectious agent detection by nucleic acid (DNA or RNA); Gardnerella vaginalis, quantification 
  87660  Infectious agent detection by nucleic acid (dna or rna); trichomonas vaginalis, direct probe technique 
  87661  Infectious agent detection by nucleic acid (dna or rna); trichomonas vaginalis, amplified probe technique 
  87800  Infectious agent detection by nucleic acid (dna or rna), multiple organisms; direct probe(s) technique 
  87808 Infectious agent antigen detection by immunoassay with direct optical observation; trichomonas vaginalis 
  87905 Infectious agent enzymatic activity other than virus (eg, sialidase activity in vaginal fluid) 
ICD-10-CM  A56.11

Chlamydial female pelvic inflammatory disease

  A59  Trichomoniasis 
  A59.0 Urogenital trichomoniasis  
  A59.00 Urogenital trichomoniasis, unspecified 
  A59.01  Trichomonal vulvovaginitis
  B37.3  Candidiasis of vulva and vagina 
  B96.89  Other specified bacterial agents as the cause of diseases classified elsewhere [Gardnerella vaginitis]
  F11.10-F11.99  Opioid related disorders [injecting drug users] 
  F13.10-F13.99  Sedative, hypnotic, or anxiolytic related disorders [injecting drug users] 
  F14.10-F14.99  Cocaine related disorders [injecting drug users] 
  F15.10-F15.99  Other stimulant related disorders [injecting drug users] 
  L29.0  Pruritus ani 
  L29.2  Pruritus vulvae 
  L29.8  Other pruritus 
  L29.9  Pruritus, unspecified 
  N72  Inflammatory disease of cervix uteri 
  N73  Other female pelvic inflammatory diseases 
  N73.9  Female pelvic inflammatory disease, unspecified 
  N76  Other inflammation of vagina and vulva 
  N76.0  Acute vaginitis 
  N76.1  Subacute and chronic vaginitis 
  N76.2  Acute vulvitis
  N76.3  Subacute and chronic vulvitis 
  N76.89  Other specified inflammation of vagina and vulva 
  N77.1  Vaginitis, vulvitis and vulvovaginitis in diseases classified elsewhere 
  N89.0  Mild vaginal dysplasia 
  N89.1  Moderate vagina dysplasia 
  N89.8  Other specified noninflammatory disorders of vagina 
  N90.89   Other specified noninflammatory disorders of vulva and perineum 
  N93  Other abnormal uterine and vaginal bleeding 
  N94.11  Superficial (introital) dyspareunia 
  N94.89  Other specified conditions associated with female genital organs and menstrual cycle 
  O09.211  Suprvsn of preg w history of pre-term labor, first trimester 
  O09.212  Suprvsn of preg w history of pre-term labor, second tri 
  O09.213  Suprvsn of preg w history of pre-term labor, third trimester 
  O09.219  Suprvsn of preg w history of pre-term labor, unsp trimester 
  R10.2  Pelvic and perineal pain 
  Z01.411  Encounter for gynecological examination (general) (routine) with abnormal findings 
  Z11.2  Encounter for screening for other bacterial diseases 
  Z11.3  Encounter for screening for infections with a predominantly sexual mode of transmission 
  Z11.8  Encounter for screening for other infectious and parasitic diseases [High risk screening for Trichomonas only] 
  Z13.89  Encounter for screening for genitourinary disorders 
  Z20.2  Contact with and (suspected) exposure to infections with a predominantly sexual mode of transmission 
  Z20.9  Contact with and (suspected) exposure to unspecified communicable disease 
  Z33.1  Pregnant state, incidental 
  Z72.5  High risk sexual behavior 
  Z86.19  Personal history of other infectious and parasitic diseases 

Procedure and diagnosis codes on Medical Policy documents are included only as a general reference tool for each Policy. They may not be all-inclusive.

This medical policy was developed through consideration of peer-reviewed medical literature generally recognized by the relevant medical community, U.S. FDA approval status, nationally accepted standards of medical practice and accepted standards of medical practice in this community, Blue Cross and Blue Shield Association technology assessment program (TEC) and other non-affiliated technology evaluation centers, reference to federal regulations, other plan medical policies and accredited national guidelines.

"Current Procedural Terminology© American Medical Association.  All Rights Reserved" 

History From 2014 Forward     


Updating coding section with N89.8 ICD 10 code. No other changes made. 


Annual review, adding one additional policy statement 


Interim review with change to month of annual review, no other changes made. 


Annual review with a major revision to all aspects of the policy for clarity and expanded testing criteria. 


Updating Coding Section with Code N89.8. No change to policy intent. 


Corrected typo in Coding section. No other changes. 


Updated category to Laboratory. No other changes. 


Updated coding to add Z20.2. 


Annual review, no change to policy intent. 


Interim review adding coding: 87512 and 87999. No change to policy intent.


Annual review, no changes made. 


Annual review. Updated title, rationale, references. Added verbiage related to multitarget PCR testing.

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