Chapter 22, ‘Diagnosis’, p. 282).Certain infections can be detected or diagnosed within clinics or surgeries, but others require microbiological services, also essential for confirmatory and antimicrobial sensitivity testing. If on-site microscopy is unavailable, the use of air-dried swabs sent for laboratory staining and microscopy should be considered. This is applicable for vaginal discharge (e.g. bacterial vaginosis, candidiasis) and also for ♂ urethral discharge for polymorphonuclear leucocytes (PMNLs) indicating urethritis and Gram –ve intracellular diplococci, which are highly suggestive, but not diagnostic of gonorrhoea.
The optimum minimum time to take swabs for screening from asymptomatic patients following a specific incident has not been established. It will depend on the type of test used, the site screened, and the presence/absence of infected secretions. However, 14 days after a sexual risk is recommended.
The timing of serological tests should take into consideration the ‘window periods’ of the respective infections. Final exclusion tests must be advised at the end of this time. Baseline assays soon after the incident may be useful, especially if subsequent repeat tests are positive.
First-voided 20 mL of urine (especially in ♂ as variable sensitivities in ♀) or ♂ urethra, vagina/vulva (specimen of choice for ♀, 96–98% sensitivity) or endocervix. In addition, rectal samples (although unlicensed) have been shown to be useful in MSM. Important to take if MSM present with anorectal symptoms because of lymphogranuloma venereum. If confirmed, genotype for L1, L2, or L3. Also unlicensed for oropharyngeal sampling due to variable sensitivities, but NAAT is the most sensitive test that is widely available. In medico-legal situations, a +ve NAAT test should be confirmed using a second target.
Rarely used, but are at least 30% less sensitive than NAAT and are now generally not recommended. Not suitable for urine and vulvo-vaginal testing in ♀ and certain kits are not recommended for urine testing in ♂.
Not widely available and due to low sensitivity (60–80%) compared with NAAT testing, not now recommended in medico-legal situations. Available from Sexually Transmitted Bacterial Reference Unit for persistent infection/failed treatment.
Specimens for culture should be kept refrigerated at all times. Storage of NAAT and EIA specimens for >24 hours at room temperature may result in sample degradation, although absolute data are lacking. If delays are anticipated, storage at 4°C is recommended. Manufacturer’s instructions of individual commercial assays should be followed.
Investigation of choice to detect gonorrhoea infection. High sensitivity, >90% for all urogenital specimens (male urine, vulvovaginal, endocervical), except female urine. Single swab or urine as a dual NAAT to detect gonorrhoea and chlamydia widely available. No assay is licensed from extragenital sites, but significantly more sensitive than culture from rectum and oropharynx, and rectal and pharyngeal specimens should be considered if at risk. Positive extra-genital NAATs should ideally be confirmed with a supplementary test on a different nucleic acid target. Positive results need culture primarily for antibiotic sensitivity testing and also confirmation, but the sensitivity is lower. Transport and storage as above for chlamydia NAAT. Testing for gonorrhoea recommended in situations where it is clinically indicated (e.g. sexual history, symptomatic, contacts), whereas screening is only recommended in a population or setting where prevalence ≥1% due to a clear local public health need. NAAT test of cure recommended from positive site 2 weeks post-treatment.
Required, if possible, in all patients with a positive gonococcal NAAT test from the infected site to enable antibiotic sensitivity testing and detection of resistant strains. Culture swabs should be taken before anti-gonococcal antimicrobial therapy initiated, including situations such as treatment of contacts or treatment for microscopic identification of gonorrhoea. Sensitivities differ depending on sites sampled with a greater sensitivity from endocervix and male urethra than extragenital sites
If a carbon dioxide incubator is available, specimens can be plated directly onto selective growth medium (e.g. modified New York City culture medium), although they will need to be transported to the laboratory in a carbon dioxide-enriched environment (e.g. in candle jars).
Otherwise, specimens must be sent in a transport medium (e.g. Amies or Stuart charcoal). Their use only reduces sensitivity by ~10% (compared with direct inoculation) provided that the specimens are refrigerated and received by the laboratory within 48 hours.
Swab from posterior fornix. Prepare air-dried smear from the swab or send in transport medium (Amies, Stuart), requesting a Gram stain for bacterial flora and clue cells. A result suggestive of BV does not necessarily indicate the need for treatment, which must be assessed clinically.
Swabs of vesicular fluid or from ulcers
NAAT is the investigation of choice to determine genital herpes. Highly sensitive (detects 11–77% more cases than culture), specific, allows typing, and is rapid. Confirmatory testing of +ve PCR samples is not recommended. Manufacturer’s instructions should be consulted for transport, but less stringent storage and transport conditions required than for virus culture.
Will miss ~30% of PCR +ve samples (usually late or mild recurrent episodes). Must be sent in transport medium. Standard viral transport systems should be kept refrigerated, but some commercial systems (e.g. Virocult®) can be maintained at ambient temperature as HSV will survive for up to 12 days at up to 23°C. Local laboratory or manufacturer’s instructions should be consulted.
• Immunofluorescent antigen detection: provided by some laboratories using material (sample in viral transport medium).
• Type-specific serology: of little diagnostic value ( Chapter 22, ‘Diagnosis’, p. 282).
Swab from posterior fornix or urethra/sub-preputial sac (if indicated) in growth medium (e.g. Feinberg–Whittington incubated at 37°C) or transport medium (Amies/Stuart charcoal), refrigerated, and received within 24–48 hours. Although some laboratories provide a culture service, most diagnose on slides prepared from the swabs. Newer culture systems (InPouch TV; BioMed Diagnostics, USA) offer advantages over previous media, negating the need to prepare wet preparations on a daily basis and also allowing the entire pouch to be read microscopically, rather than a proportion of the culture medium.
Test of choice where resources allow, vaginal or endocervical swabs in women, and urine samples from men demonstrate sensitivities of 88–97% and specificities of 98–99%. Becoming increasingly available.
Swab from vaginal wall or vulva, glans penis, prepuce, anus, etc., if indicated, in transport medium (Amies, Stuart) without any special precautions. Candida spp. are common skin and genital commensals and, therefore, the need to treat must be based on clinical findings.
Routine NAAT testing is not performed in UK Sexual Health clinics, but validated commercially available assays may become more widely available in the future.
Clotted blood is required with no special arrangements needed for transport. Baseline assays are useful, especially if subsequent repeat tests are positive.
• Syphilis and HIV: seroconversion usually occurs within 2–6 weeks, but may take up to 3 months. However, 4th-generation HIV assays are now routinely used, detecting both HIV antibody and HIV p24 antigen, which can shorten the duration of detection to 4 weeks post-HIV infection. Guidelines now recommend that an HIV test at 4 weeks post-exposure is highly likely to exclude infection, but those at high risk should be retested at 3 months.
• Hepatitis B core antibody and/or surface antigen, and hepatitis C antibody: can usually be detected within 3 months of infection although occasionally may take longer. In high-risk situations a further test at 6 months is advisable. Additional investigations for e-Ag/eAb are performed on this sample if the initial hepatitis B surface antigen test is positive. Hepatitis C RNA test may be positive within 2 weeks and can be used to detect early infection in possible high risk exposure.
More detailed information on testing in specific situations and less common infections can be found in the relevant chapters.
See Box 5.1.
Box 5.1 Frequently asked questions about laboratory tests
• ♂: Usually we only need to do a urine test, but if you have a discharge then we also use a swab to send for gonorrhoea culture and smear onto a microscope slide. You will feel some discomfort, but it should not be painful. The swabs only take a few seconds to take. You may notice slight discomfort on urinating the first time after the swab and/or loop has been taken.
• ♀: If you have no symptoms then you may wish to do your own vulvovaginal swab placed about 2 inches into the vagina and rotated for just over 10 seconds. If you have symptoms, then we use a speculum inserted into the vagina to take the swabs, similar to when having a smear taken.
We may advise that swabs be taken from your throat or rectum for gonorrhoea and chlamydia, depending on certain circumstances (e.g. sexual activity at these sites). You may be able to do some of these tests yourself.
No. This is an old instrument used for ♂ >40 years ago. Modern swabs are taken with very fine swabs or we use a small loop to sample secretions.
No. You will not get all your results today.
If you are ♀, microscopy at the time of your appointment may show thrush, bacterial vaginosis, or trichomoniasis. We can also sometimes detect gonorrhoea, but this needs to be confirmed by swabs taken at the same time and sent to the laboratory. One of the swabs will detect both gonorrhoea and chlamydia, another is to see if gonorrhoea can be grown in the laboratory to ensure the correct antibiotics are been given. The results for chlamydia and gonorrhoea are usually available within a week.
In ♂ we can diagnose some conditions, such as non-specific urethritis (NSU) or gonorrhoea on the day if microscopy is performed (usually in someone with a urethral discharge). A urine test also needs to be sent away, however, as a second test for gonorrhoea and to check for chlamydia, as do any swabs taken from other parts of your body (rectal or throat). All results should be available within a week.
Blood tests results take up to 7 days. However, if there is a particular concern we can obtain a preliminary result within 24 hours.
Yes if gonorrhoea is detected we advise the patient to return in 2 weeks for a repeat urine (♂) or vaginal swab (♀), and other swabs if it was detected at other sites (throat, rectum) to check the antibiotics have worked. We rarely need to do tests of cure for chlamydia. You will be told if you may need a test of cure. Tests do not need repeating unless the first tests were taken too soon after a risk (within 2 weeks), there is a high infection risk, symptoms persist, or there is a risk of re-infection/new infection. If your test was positive and you were treated for an infection you may be invited to come back in 3–6 months for some routine repeat tests; this is good practice to ensure infections are detected and treated early.
Yes. We can still take tests while you are menstruating. However, some prefer to wait until their period has finished.
Two microscopes are usually required, one for direct light and phase contrast illumination, and the other for dark ground microscopy.
• ×10, ×40 (low power): provide overall magnification of ×100 and ×400. Suitable for screening for clue cells, trichomoniasis and candidiasis, and fungal infection, although may require high power to confirm. Also used to identify scabies mites and threadworm ova.
• ×100 (high power): provides overall magnification of ×1000. Must be used with immersion oil. Used to examine specimens for PMNLs, gonococci, and other bacteria, including treponemes.
• Separate objectives are required for direct light/phase contrast and dark ground illumination.
See Fig. 5.1.
• Phase contrast (must match with the same Ph code on the objective).
• Dark ground (used with immersion oil between lens and under surface of the slide).
Fig. 5.1 Condensers.
• Ensure lenses are wiped clean of immersion oil and dust with a lens tissue after use.
• To avoid lens damage, ensure that high-power objective lens is not aligned when slides are moved to and from the microscope.
• When using dark ground microscopy, place a drop of oil on the condenser and raise until it just touches the slide.
• When using phase contrast, ensure that the Ph codes on the condenser and objective match.
• Start with low power to identify a good wide field, and approximate focus before moving to high power.
See Box 5.2.
Box 5.2 Slide preparation techniques
• Fix the smear by heating the slide or submerging it in 95% methanol for 2 minutes.
• Apply crystal violet, methyl violet, or gentian violet (a combination of the first two) for 15 seconds.
• Apply an aqueous solution of iodine for 15 seconds.
• Decolorize slide with acetone for 3 seconds.
• Apply red counterstain (e.g. carbol fuchsin, basic fuchsin, or neutral red) for 15 seconds.
See Chapter 7, ‘Diagnosis and investigation’, pp. 125–129.
• Clean the ulcer with a swab soaked in sterile saline.
• Squeeze the lesion gently to release serum.
• Collect serum with the edge of a cover-slip and mount in normal saline.
• ♂ urethral discharge/urine threads: PMNLs, Gram –ve intracellular diplococci.
• Glans penis/sub-preputial sac: yeast spores ± hyphae, mixed Gram +ve and –ve cocco-bacilli ± curved rods (generally anaerobes).
• ♀ cervix: PMNLs, Gram –ve intracellular diplococci.
• Vagina: lactobacilli (Plate 1), PMNLs, mixed Gram +ve and –ve cocco-bacilli ± curved rods (generally anaerobes), Gram +ve cocci, yeast spores ± hyphae.
• Rectum: PMNLs, Gram –ve intracellular diplococci.
• Ulcers: Gram –ve coccobacillus in shoals (Haemophilus ducreyi)—unusual finding.
Plate 1 Gram stain lactobacilli (5).
• Vagina or sub-preputial sac/glans penis—clue cells/motile curved rods, T. vaginalis, yeast spores ± hyphae;
• Vagina or sub-preputial sac/glans penis—clue cells/motile curved rods, T. vaginalis, yeast spores ± hyphae’
• Burrow material for scabies mite.
• Skin scales in 10% potassium hydroxide for mycelia (tinea/ringworm).
• Perianal transparent adhesive tape strip: threadworm ova.
• ‘Whiff test’: addition of 10% potassium hydroxide releases pungent amines; rarely used now in clinical practice.
Both are indicators of BV. Unnecessary if Hay–Ison diagnostic criteria used ( Chapter 15, ‘Diagnosis’, p. 220).
Urine haze in ♂ (not cleared by addition of 5% acetic acid) ± threads in first pass suggests anterior urethritis. A second specimen [mid-stream specimen of urine (MSSU)] may be of value in suggesting posterior urethritis or UTI (if turbid), and is essential for culture and sensitivity. Urine may also be required for pregnancy testing (see Box 5.3).
• Glucose, ketones: diabetes (recurrent candidiasis, balanitis).
• Leucocytes, nitrites, blood: UTI.
• Persistent proteinuria and haematuria: refer to nephrology.
• Persistent haematuria: discuss with Urology team.
• Leucocytes ≥1 only; with symptoms of urethritis (microscopy unavailable): non-gonococcal urethritis (NGU).
Box 5.3 Pregnancy test (immunoassay), urine, and serum
First documented in Egypt (1350 bc) when ♀ suspecting pregnancy urinated on wheat or barley seeds for 7 days. Seed germination (probably due to 
levels of oestrogen) indicated pregnancy (70% accuracy demonstrated in 1963).
Pregnancy testing can be performed on urine or serum. Both tests detect β-human chorionic gonadotrophin (hCG), a hormone produced by the placental trophoblastic cells shortly after implantation. A positive result usually indicates the presence of a viable foetus.
Urine sampling kits give only a +ve or –ve result. Samples can detect hCG levels >25–50 mIU/mL. Levels of urinary hCG average 100 mIU/mL following the first missed menstrual period and up to 200,000 mIU/mL at 10–12 weeks of pregnancy, after which time levels fall. Test read after 3 minutes.
• Unable to distinguish between uterine and ectopic pregnancy.
• Occasional false-negative results in ectopic pregnancy.
• Inability to distinguish between pituitary hCG (secreted by gonadotrophs of anterior pituitary) and placental hCG.
• Positive result may be obtained in the presence of gestational trophoblastic disease.
• Certain non-trophoblastic neoplasms (e.g. testicular, liver, neuroendocrine, breast, ovarian, pancreatic, cervical, gastric) can cause higher levels of hCG, but rises are usually modest.
• 10% of pregnancies are undetectable on the first day of missed menses.
• False-positive results estimated at up to 10%.
• False-negative results may be due to dilute urine.
More accurate and should be considered if urine testing is –ve, but there is a pregnancy risk. Tests can detect hCG levels above 5–10 mIU/mL. Positive results may be obtained within 7–10 days of conception. Quantitative tests are available that allow exact measurement of serum hCG, useful in assessing the stage of pregnancy. Serum hCG doubles every 36–48 hours in the early stages. A subnormal response may indicate miscarriage or ectopic pregnancy. Extremely high levels of hCG may suggest multiple pregnancy.
See Fig. 5.2.
Fig. 5.2 Algorithm for analysing results on a vaginal Gram-stained smear.
Variable depending on menstrual cycle, sexual activity, and contraception (often with hormonal methods). >30 per high-power field correlates best with gonococcal or chlamydial infections.
Examine cervical smear for intracellular GNDC. Urethral smear of doubtful value if cervix examined and now rarely performed. Finding extracellular GNDC sensitivity by 20% but 
specificity by 4%.
• Switch light source to phase contrast (or dark ground).
• Screen slide (low power) for motile protozoa, spores ± hyphae.
• If necessary, switch to high power. Place a drop of immersion oil on to cover-slip before examining. Can also be used to identify clue cells and motile vibrios (Mobiluncus spp.) often found in bacterial vaginosis.
Non-gonococcal urethritis diagnosed by finding:
• ≥5 PMNLs per high-power field (averaged over five fields with the greatest concentration of PMNLs)
If seen, allows a working diagnosis of gonorrhoea. Generally associated with numerous PMNLs.
Useful if urine threads in first voided urine (FVU) specimen and no urethral material to sample directly. The slide can be prepared from threads or centrifuged FVU. Ideally, urine should not be passed for at least 3–4 hours before assessment.
Non-gonococcal urethritis diagnosed by finding:
• ≥10 PMNLs per high-power field (averaged over five fields with the greatest concentration of PMNLs)
Allows a working diagnosis of gonorrhoea.
If balanitis/balanoposthitis check for:
• clue cells (anaerobic balanitis).
A Gram-stained smear can also be used.
T. vaginalis: may occasionally be seen with urethritis.
See Table 5.1
Table 5.1 Accuracy of microscopy by infection and site
| Infection and site | Sensitivity (%) | Specificity (%) |
| Gonorrhoea | ||
| Urethral Gram stain, symptomatic ♂ | 90–95 | 95–99* |
| Urethral Gram stain, asymptomatic ♂ | 50–75 | |
| Rectal Gram stain from MSM | 35–80† | 95–100* |
| Cervical Gram stain | 23–65 | 88–100* |
| Bacterial vaginosis (Hay–Ison criteria) | ||
| Vaginal Gram-stained specimen | 97.5 | 96 |
| Trichomoniasis (saline suspension) | ||
| Suspension of vaginal discharge | 40–80 | If motile protozoa seen 100 |
| Suspension of male urethral/ sub-preputial material | 30 | |
| Candidiasis | ||
| Vaginal Gram stain if symptomatic | 65 | No data |
| Vaginal saline suspension | 40–60 | |
| Primary syphilis | ||
| Dark ground examination of ulcer material in saline | 79–86 | 77–100 |
* Excludes Neisseria meningitidis, which may rarely be found (indistinguishable morphologically from N. gonorrhoeae). †Higher level if rectal pus.
Near patient, rapid medical diagnostic testing, usually performed by non-lab staff, and results used to inform immediate clinical decisions. Useful in resource-limited settings, where expensive laboratory facilities are not available. Some may also be used by the patient at home (see Box 5.4 for properties of an ideal POCT).
Studies have demonstrated that POCTs can lead to the treatment of a greater number of infected patients as they often do not re-attend for results assuming that results will be negative.
Box 5.4 Properties of an ideal POCT
• Easy to store, long shelf-life.
• Sampling acceptable to the patient.
Significant advances have been made in rapid real-time cartridge-based NAAT testing with results available within 90 minutes for chlamydia/gonorrhoea, 40 minutes for trichomonas and <60 minutes for HIV. They enable patients to receive results and be treated on the same day. These tests have high sensitivities and specificities. Non-NAAT POCT for chlamydia and gonorrhoea are commercially available for home use, but have been largely superseded by newer NAAT tests.
Immunoassays for chlamydial antigen (usually lipopolysaccharide) using anti-chlamydial monoclonal antibody. A number are commercially available for testing first-catch urine, endocervical, or vaginal swabs. Sensitivities 77–93%, specificities 97.5–100%, and result time ranges from 12 to 30 minutes. Examples include Clearview® Chlamydia MF, Alere™, Biostar® OIA® Quidel® Quickvue® Chlamydia, Chlamydia Rapid Test (Diagnostics for the Real World Ltd). Because of the low sensitivities of tests, it is important to obtain a confirmatory sample for NAAT testing if facilities are available.
Rarely ever used in clinical settings with the advent of NAAT testing. Some commercially available, e.g. Biostar® Optical Immunoassay and the double-sandwich immunoassay OneStep Rapicard™ Instatest (Cortez Diagnostics). The Biostar® OIA® Gonorrhoea test identifies the L7/L12 ribosomal protein marker, which only occurs in the gonococcus and not other Neisseria spp. (sensitivity 87.8%, specificity 98.5%). Uses endocervical swab in ♀ and urine in ♂, results in 24 minutes. Confirmatory NAAT + culture to determine antibiotic sensitivities prior to treatment essential.
POCTs based on antigen detection are available, which offer quick diagnosis compared with culture, with sensitivities as high as 83–95.5% compared with culture, e.g. OSOM® Trichomonas Rapid Test, Sekisui Diagnostics.
Used widely in clinical practice. Over 60 different products are produced. Recommended in the following settings:
• Community settings/home testing.
• Source testing in exposure/needlestick incidents.
• High-risk situations in which venepuncture is refused.
• When rapid results are required.
POCTs use oral fluid, finger-prick, plasma, whole-blood, or urine.
In low-prevalence settings false-positive rates are relatively higher, with poor positive predictive value of some tests. Therefore, all positive results should be confirmed by laboratory tests. Results may not be reliable if patient is within the ‘window period’.
Examples of rapid assays include particle agglutination on latex particles, immunochromatography (lateral flow) strips, and immunoconcentration (rapid vertical flow) using HIV antigens to immobilize Ab on porous membrane:
• 1st generation: HIV antigen coated on latex particles detects HIV specific IgG. No longer used in UK.
• 2nd generation: Synthetic peptide or recombinant antigen has sensitivity for HIV1 group O and HIV2. Used in some rapid tests.
• 3rd generation: Synthetic peptide or recombinant protein in immunometric sandwich. Detects IgG and IgM with sensitivity during early seroconversion.
• 4th generation: 3rd generation Ab detection + monoclonal antibodies to detect p24 Ag. Detects HIV infection before seroconversion (preferred method).
Antigens vary with individual assay, often from viral envelope (glycoprotein (gp)41, 120, 160). Some include p24 core antigen. Tests have been developed that, in addition to HIV-1, will identify HIV-2 (using gp36 antigen), appearing positive at a different location on the strip or membrane. Difficulty in some tests identifying Group O subtypes and certain HIV-2 strains. Sensitivities of 3rd and 4th generation POCTs range between 93 and 98% (oral fluid: OraQuick) 87–100% (blood: Uni-Gold Ab, INSTI HIV1/2Ab, SD Bioline Combo and Determine Combo) and specificities are similarly high, >99%, for POCTs using oral fluid and blood.
Kits became legal to purchase in the UK in April 2014; currently, the only approved CE marked POCT in the UK is the HIV Self-Test from Biosure Ltd, which can be read in 15 minutes using a finger-prick blood sample. Sensitivity 99.7%, specificity of 99.9%, and detects HIV antibody only.
Some companies or agencies offer STI home sampling. The customer purchases a test kit, conducts sampling at home, then posts it back. The customer receives results, usually by text or secure online site. For some infections, e.g. chlamydia, the company may sell treatment or refers to a local sexual health clinic for treatment. Some NHS and voluntary sector initiatives now offer a free home-sampling service in parts of the UK.
A variety of other POCTs have been developed for syphilis (e.g. Determine® TP assay, INSTITM Multiplex Syphilis/HIV1/HIV2 assay) and for hepatitis B and C.
Genital specimens include various micro-organisms, which may not be pathogenic. These include hydrogen peroxide producing Lactobacillus spp., which indicate normality, and other organisms, usually commensal, but pathogenic under certain conditions. Therefore, results of routine genital specimens should be interpreted in the clinical context and inappropriate antibiotic treatment should be avoided.
Elongated chain of lactobacilli that may be mistaken for Candida spp. on microscopy. Usually, not clinically significant, but may be associated with vaginitis caused by candida or TV.
Vaginal carriage rates in ♀ attending GUM clinics 12–36%; usually, not clinically significant, except in late pregnancy. Antenatal services should be informed if isolated in a pregnant woman ( Chapter 32, ‘Group B β-haemolytic streptococci’, pp. 374–375).
Found in 3% of ♀ genital specimens—4% if using intrauterine device (IUD). Detectable on cervical cytology, vaginal wet mount, and Gram-stained smears. If asymptomatic, no intervention is required. However, removal (and culture) of IUD and treatment with prolonged courses of antibiotics may be indicated if otherwise unexplained symptoms, e.g. intermenstrual bleeding, dyspareunia, and pelvic pain.
Actinomycosis (suppurative upper-genital tract infection) is a rare complication, especially associated with long-term use of plastic IUDs ( Chapter 11, ‘Aetiology’, p. 171).
Rates of nasopharyngeal carriage in MSM and those practising orogenital sex, reporting multiple sexual partners, or diagnosed with anogenital gonococcal infection (>20% in these groups compared with a general rate of 5–15%). High rates also found in university students (up to 34%). Anogenital carriage in up to 2% of MSM, 0.2% of heterosexual ♂, and 0.1% ♀. May rarely cause urethritis in ♂and there are case reports of symptomatic disease in women
• Gardnerella vaginalis, Prevotella melaninogenica, Peptostreptococci, and other anaerobic organisms may be detected in genital specimens because of low-level colonization without bacterial vaginosis.
• Ureaplasma urealyticum, Bacterioides urealyticum, and Mycoplasma hominis may also be found without any clinical manifestations but may cause local inflammation.
• Corynebacterium species, Escherichia coli, and coagulase-negative staphylococci in genital specimens are usually of no clinical significance, but rarely may be implicated in vaginitis.
• Spirochaetes: Brachyspira aalborgi and Brachyspira pilosicoli colonize colorectal epithelium in up to 30% of people in some developing countries and a similar proportion of MSM or those with HIV infection in the developed countries. In addition, Treponema denticola, Treponema vincentii, and other similar treponemes associated with periodontal infections and Treponema refringens, Treponema phagedenis, and Treponema minutum, found as commensals in the genitalia, need to be distinguished from T. pallidum in rectal, oral, or genital specimens.