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InFocus: Neisseria gonorrhoeae: Laboratory Testing

Roberts, James R. MD

doi: 10.1097/01.EEM.0000424139.74146.8f

Dr. Robertsis the chairman of emergency medicine and the director of the division of toxicology at Mercy Catholic Medical Center, and a professor of emergency medicine and toxicology at the Drexel University College of Medicine, both in Philadelphia.

The collection system for urine (star) and endocervical and vaginal swab (diamond) nucleic acid amplification testing is highly accurate for detecting GC and Chlamydia in the same sample

The collection system for urine (star) and endocervical and vaginal swab (diamond) nucleic acid amplification testing is highly accurate for detecting GC and Chlamydia in the same sample



Neisseria gonorrhea (GC) has mutated to the point where it is now considered a superbug, cured only by a combination of an increased dose of ceftriaxone over prior recommendations (now 250 mg) plus 1 g of azithromycin orally. It is still sensitive to this regimen, but this is the last bastion of our antimicrobial weapons, and GC may become untreatable.

Much has changed over the past decade in laboratory testing for identifying GC. Technology has evolved to allow for rapidly identifying it and Chlamydia through DNA amplification tests, but the downside, an unexpected consequence of our own science of relegating the standard GC culture to antiquity, has been our inability to follow antibiotic resistance patterns. You can identify an infected individual quite easily with a rapid DNA test, but we currently have no way to evaluate drug sensitivity except through CDC surveillance data, but those data are alarming.

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Systematic Review: Noninvasive Testing for Chlamydia trachomatis and Neisseria gonorrhoeae

Cook RL, Hutchinson SL, et al

Ann Intern Med


Traditional methods for screening for GC and Chlamydia involved sending an endocervical specimen obtained by a speculum exam in women and a urethral swab in men for culture. These methods are time-consuming, embarrassing, and require trained personnel and an exam room. Cultures have been universally replaced with nucleic acid testing of material obtained via a swab or by applying a similar technique to urine. Techniques employ nucleic acid amplification methods on urine or on urethral, endocervical, or vaginal secretions directly obtained with a specialized swab. Noninvasive urine screening has overcome many of the direct swab-related barriers, although they have not totally replaced the traditional swab.

The authors reviewed published evidence to analyze if urine DNA testing could totally replace cervical or urethral swabbing. The highly accurate direct swab technique of searching for bacteria nucleic acid for both organisms with one sampling has now been applied to noninvasive urine testing. Most EDs are moving toward urine testing only for GC and Chlamydia, the easiest and most patient-friendly noninvasive way of identification.

All reports of urine and traditional swab sample testing for Chlamydia and GC evaluated involved testing with nucleic acid amplification techniques. The results for GC vs. Chlamydia were slightly different. The authors concluded that results from urine sampling for Chlamydia in men and women are nearly identical to those obtained on swab samples collected directly from the cervix or urethra. Although likely quite accurate, the sensitivity for N. gonorrhoeae in urine with this technique is too low to recommend it over swab testing in women. The urine test for GC in men is highly accurate.

Comment: Most EDs now send a DNA/RNA-based test to the lab, results of which can be obtained in a few hours but which are generally not available for a day or two. This is not because the test is so complicated; it's because we haven't gotten our act together to perform it while the patient is still in the ED. One might argue why test or culture at all if you are going to treat, so some eschew testing and just treat. This tactic is much more efficient, but does not allow for reporting or confirming the infection. My thinking is that testing without onsite empiric treatment is ill advised, and involves patient callback, additional expense, and a lot of resources to ensure that a positive test was treated adequately. I see no reason to test an asymptomatic exposed partner seeking empiric treatment; simply treat for GC and Chlamydia.

Modern DNA testing procedures can be utilized on cervical, vaginal, urethral swab, and urine specimens. The nucleic acid amplification tests are highly sensitive, more sensitive than traditional cultures. Nucleic acid amplification technology (NAAT) consists of amplifying the DNA or RNA sequence using PCR or other identification techniques. It is actually more sensitive than culturing, and may detect as little as one organism per sample. Antibiotic sensitivity cannot be determined with these tests. A few variations exist, but the CDC currently recommends the use of a nucleic acid amplification test as the preferred testing modality, and it is best applied to urine in men and to an endocervical swab in women. Vaginal swab testing, usually self-obtained, is occasionally used.

Minor peccadillos of testing have not yet allowed urine testing to be exclusively used for men and women. Extragenital infections in the rectum or pharynx, for example, are still best detected by culture. Information is lacking on the efficacy or applicability of NAAT swab testing in these areas, and there is no FDA approval for these anatomic sites. Apparently the nonpathogenic Neisseria species in the rectum and pharynx may cause cross-reactivity or a false-positive NAAT test.

Formal cultures, which can isolate the bacteria from genital and nongenital sites, require immediate plating on special medium (Thayer-Martin agar), CO2 enrichment, 48 hours of incubation, and personnel to read the results. It will be foreign to today's house staff, but I can remember carrying the agar and a CO2 tablet into the patient's room and directly inoculating the plate. The greatest advantage of a culture is that antibiotic susceptibilities can be identified. Until recently, antibiotic sensitivity has not been an issue, so clinicians rarely take cultures anymore. The reported sensitivity of GC cultures range from 70 percent to 95 percent. The sensitivity declines in asymptomatic infections to 65 percent to 85 percent. All in all, NAAT testing is a giant step forward.

Likewise, gram staining for GC is simply not performed in the ED. The gram stain, once a stalwart task of all interns, is also a clinical dinosaur. Regulations have made it essentially impossible for physicians to perform gram stains in the ED. Most don't even do urine microscopy anymore, and even ED Hemoccult testing for stool blood has roadblocks, including verification of color blindness in the ED staff. A gram stain has low sensitivity in women compared with men because of the presence of other gram-negative diplococci in cervical secretions; it's a worthless endeavor in women. Likewise, a gram stain of pharyngeal or rectal specimen is not recommended.

A few technique issues regarding urine and swab NAAT testing require comment. The patient should not have urinated for at least an hour prior to urine NAAT testing (now advocated as the first test for men). This is a first catch rather than a midstream sample, not an aseptically prepped procedure as used for routine urine culture. Only the first 20 to 30 mL of the initial urine stream is collected, and larger volumes can reduce test sensitivity. No cleaning methods are suggested prior to providing the urine sample. Excess mucus should be removed and the swab should be rotated in the endocervical canal for 10 to 30 seconds for endocervical swabs specimens, which are still recommended as the standard for women. Using a two- to three-second swabbing in the male urethra should also ensure adequate sampling. Swab collection should be done on men who have not urinated for at least an hour prior to the swab sample collection.

Summary: The current recommendation to confirm GC and Chlamydia is to apply nucleic acid amplification testing on urine in men and on an endocervical, not vaginal, swab in women. Urine can be used in women with slightly less accuracy compared with swabbing. NAAT may be used, but culturing is still the gold standard for nongenital areas such as the pharynx, rectum, and conjunctiva.

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Reader Feedback: Readers are invited to ask specific questions and offer personal experiences, comments, or observations on InFocus topics. Pertinent responses will be published in a future issue. Please send comments to

Dr. Roberts: I am starting to see a lot of prehospital EMS algorithms using ketamine for the “agitated” patient. That being said, what do you do after the ketamine? At some point, they will wake up and possibly have horrible emergence reactions. Is the ketamine a bridge to intubating in the ED? What about in the prehospital setting? Is it just a bridge to get them to the ED? Thoughts? — Scott Goldstein, DO, Philadelphia

Dr. Roberts responds: The safety and efficacy of ketamine was demonstrated more than 15 years ago as an adjunct to intubation for agitated injured soldiers being transported by air ambulance in Israel, even for those with head trauma. (Injury 1997;28[1]:41.) Except for sedation in children where it is uniformly successful, ketamine use outside the OR has been poor. It has a great safety profile as an easily administered agent with little downside for the rapid control of agitation or for intubation, but ketamine is still underused in the ED. I would be happy if EDs would use it more often or at least study it more. Prehospital use sounds like a great idea to me, but I am not aware of its frequent use or acceptance there either. Lots of talk, little use. Go figure. Concerns for secretions and emergence reactions are way overblown, as pediatric emergency physicians can tell you. I always give a generous dose of a benzodiazepine when I use it for agitation or intubation. It seems to help when the drug wears off. But in my experience, severe emergence has not been a problem. Why don't you lobby for Philadelphia EMS to give it a try?

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Laboratory Testing for Chlamydia trachomatis and Neisseria gonorrhoeae

A number of available nucleic acid application tests (NAAT) are available and recommended for diagnosing genital tract infections caused by N. gonorrhoeae and C. trachomatis, frequent co-pathogens. Pharyngeal and rectal sites are still culture candidates. Both infections may be present in men and women with and without symptoms, and one sample identifies both pathogens. The sensitivity of NAAT techniques in swab specimens is 98 percent to 100 percent. These new techniques are actually more accurate than cultures, which require complicated handling and identification by a lab tech. The NAAT technique can be used on vaginal and endocervical samples, and applied to urine samples from men and women. Consensus opinion holds that the optimal specimen for NAAT testing is urine for men and an endocervical swab for women. Self-obtained vaginal swabs and clinician-obtained cervical swabs perform almost equally well. The following protocols apply to urine sample collection and endocervical and male urethral swab specimens using the Gen-Probe APTIMA collection device.

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GC and Chlamydia Collection Kits

Urine Specimens

  • Store collection kit at room temperature (15° to 30°).
  • The patient should not have urinated for at least one hour prior to sampling.
  • Direct the patient to provide a first-catch urine (approximately 20–30 mL of the initial urine stream) into a urine collection cup. Collection of larger volumes of urine may reduce test sensitivity. Female patients should not clean the labial area before providing the specimen.
  • Remove the cap and transfer 2 mL of urine into the urine specimen transport tube using the disposable pipette provided. The correct volume of urine has been added when the fluid level is between the black lines on the urine specimen transport tube label.
  • Recap the urine specimen transport tube tightly. This is now known as the processed urine specimen.
  • Urine specimens can be transported to the laboratory at 2°C-30°C in the primary collection device (urine cup) or in the urine specimen transport tube. Urine specimens must be maintained at 2°C-30°C, and must be transferred into the specimen transport tube within 24 hours of collection. Processed urine specimens must be tested within 30 days of collection.
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Unisex Swab for Endocervical and Male Urethral Swab Specimens

  • Store collection kit at room temperature (15° to 30°).
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Endocervical Swab Specimens

  • Remove excess mucus from the cervical os and surrounding mucosa using the cleaning swab (white shaft). Discard this swab. Remove excess mucus from the cervical os with a large-tipped cleaning swab (not provided).
  • Insert the specimen collection swab (blue shaft) into the endocervical canal.
  • Gently rotate the swab clockwise for 10–30 seconds in the endocervical canal to ensure adequate sampling.
  • Withdraw the swab carefully; avoid any contact with the vaginal mucosa.
  • Remove the cap from the swab specimen transport tube and immediately place the specimen collection swab into the transport tube.
  • Carefully break the swab shaft at the score line; use care to avoid splashing the contents.
  • Re-cap the swab specimen transport tube tightly.
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Male Urethral Swab Specimens

  • The patient should not have urinated for at least one hour prior to sample collection.
  • Insert the specimen collection swab (blue shaft) 2–4 cm into the urethra.
  • Gently rotate the swab clockwise for 2–3 seconds in the urethra to ensure adequate sampling.
  • Withdraw the swab carefully.
  • Remove the cap from the swab specimen transport tube and immediately place the specimen collection swab into the transport tube.
  • Carefully break the swab shaft at the score line; use care to avoid splashing of contents.
  • Re-cap the swab specimen transport tube tightly.
  • Transport and store the swab specimen transport tube at 2°C-30°C. Assay within 60 days of collection.
© 2012 Lippincott Williams & Wilkins, Inc.