Wound and Genital Tract
Wound, Tissue, and Genital Tract Bacteriology
On this page
- Specimen strategy by lesion type
- Ulcer-associated and bite/scratch organisms
- Nocardia and the aerobic actinomycetes
- Vaginal specimens: bacterial vaginosis and vulvovaginitis
- Endocervical and urethral specimens
- Genital ulcer disease
- Treponema pallidum and the treponematoses
- Chlamydia
- Genital mycoplasmas and Mycoplasma pneumoniae
- Group B Streptococcus screening
Tissue, wound, and genital cultures recover the organism that is actually in the lesion only when the specimen comes from that site and is processed for the pathogens that belong there. Surface swabs of chronic ulcers and unenriched genital cultures recover colonizers as readily as pathogens, so the laboratory result is only as useful as the collection that produced it.1,2
Specimen strategy by lesion type
Surgically obtained tissue, minced and homogenized to a 20% suspension before inoculation to all necessary media, recovers more organisms than a swab with limited absorptive capacity. The surgeon, pathologist, and microbiology laboratory must coordinate so that material is divided appropriately for histopathology and culture.
| Lesion type | Optimal specimen | Processing notes |
|---|---|---|
| Fluid-filled skin lesions (vesicles, pustules, bullae, abscesses) | Aspirated fluid (needle/syringe) | Skin disinfection before aspiration for bacterial/fungal testing; skip disinfection if viral testing is planned (antiseptics inactivate virus). Vesicles suggest HSV/VZV; pustules and generalized bullae suggest bacteria (especially Staphylococcus); foot-limited bullae suggest fungi |
| Wounds | Aspirate, tissue biopsy, or curettage; avoid swabs when possible because surface swabs pick up skin commensals and confuse interpretation | Gram stain plus culture on media appropriate to the suspected organism group |
| Ulcers | Varies by suspected cause (below) | Secondary colonization of chronic ulcers by mixed aerobes/anaerobes is common. Deep tissue or aspirate after debridement is required because surface culture reflects colonizers |
Ulcer-associated and bite/scratch organisms
| Organism | Lesion | Diagnostic approach |
|---|---|---|
| Bacillus anthracis | Cutaneous anthrax (black eschar) | Sentinel rule-out and referral |
| Corynebacterium diphtheriae | Cutaneous diphtheria: membranous ulcer | Methylene-blue smear from the membrane edge; one swab for routine culture, one for cysteine-tellurite selective agar |
| Pseudomonas aeruginosa | Ecthyma gangrenosum (marker of bacteremia) | Gram stain and culture of ulcer-base swabs |
| Francisella tularensis | Ulceroglandular tularemia | Sentinel rule-out and referral |
| Mycobacteria (M. fortuitum, M. abscessus, M. chelonae, M. marinum, M. haemophilum, M. ulcerans) | Chronic cutaneous ulcers/nodules | Aspirate or tissue; do not use a swab because mycobacteria become trapped in swab fibers |
| Fungi | Active ulcer margin | KOH or calcofluor white smear plus culture |
Zoonotic and bite-wound organisms:
| Organism | Reservoir/exposure | Key laboratory features | Disease |
|---|---|---|---|
| Pasteurella multocida and relatives | Oral flora of cats and dogs; cat bites infect more often than dog bites | Grows on blood/chocolate agar, not MacConkey; mouse-like odor; oxidase-, catalase-, indole-positive; wide zone around a penicillin disk | Wound/soft-tissue infection after bite or scratch; can progress to bacteremia, osteomyelitis |
| Capnocytophaga canimorsus/cynodegmi | Dog/cat oral flora | Fusiform gram-negative rods; blood/chocolate agar with 5-10% CO2, slow growth >24 h; may need blind subculture from blood-culture bottles; intrinsically resistant to aminoglycosides | Wound infection, sepsis (especially after splenectomy or in alcoholism), meningitis, endocarditis |
| Oral Capnocytophaga (C. ochraceus, gingivalis, sputigena, granulosa) | Human oral flora | Fusiform, oxidase/catalase-negative | Endogenous periodontal infection, septicemia, endocarditis, osteomyelitis in immunocompromised or immunocompetent hosts |
| Erysipelothrix rhusiopathiae | Swine, fish, poultry; occupational exposure among butchers, fishermen, and veterinarians | Non-hemolytic on blood/chocolate agar (up to 7 days); H2S-positive in TSI; nonmotile; distinctive “pipe cleaner” pattern in gelatin stab at 22 °C; urease/gelatin/esculin-negative; intrinsically resistant to sulfonamides, aminoglycosides, and vancomycin | Erysipeloid: localized violaceous hand/finger cellulitis; rare septicemia |
| Streptobacillus moniliformis | Rat oral flora | String-of-beads filamentous gram-negative rod; L-form colonies (fried-egg) alongside wild type; “puff-ball” growth in broth; requires 15% blood/serum-enriched media, 5-10% CO2; identification needs sequencing or fatty-acid analysis | Rat-bite fever (bite) or Haverhill disease (ingestion of contaminated food/water): fever, migratory polyarthritis, morbilliform rash |
Sentinel recognition and referral of B. anthracis and F. tularensis are covered with the select-agent module.
Nocardia and the aerobic actinomycetes
Nocardia morphology, identification, susceptibility testing, and pathogenicity are covered in mycobacteriology. Related aerobic actinomycetes include Rhodococcus equi (opportunistic granulomatous pneumonia, typically in severe immunosuppression), Gordonia and Tsukamurella (pathogenic mainly with a foreign body or underlying chronic infection), and Actinomadura/Streptomyces somaliensis (agents of actinomycotic mycetoma, chiefly in barefoot populations of tropical/subtropical regions). Tropheryma whipplei, the agent of Whipple disease, is not culturable by routine methods.
Vaginal specimens: bacterial vaginosis and vulvovaginitis
Bacterial vaginosis (BV) results from overgrowth of Gardnerella vaginalis together with a shift toward anaerobic flora (Mobiluncus, Prevotella, and others) and loss of protective Lactobacillus. Vulvovaginitis is more often caused by Candida spp. or Trichomonas vaginalis. BV is linked to preterm birth, PID, endometritis, and increased acquisition of other sexually transmitted infections, so laboratory results guide treatment.
Gram stain with a standardized scoring system (Nugent score) is the reference laboratory method for BV. Three morphotype categories are scored and summed: large gram-positive rods (Lactobacillus morphotypes) score 0-4 inversely, so abundant Lactobacillus lowers the score; small gram-variable rods/coccobacilli (Gardnerella/Bacteroides morphotypes) score 0-4; and curved gram-variable rods (Mobiluncus morphotypes) score 0-2. The total ranges from 0 to 10: 0-3 is normal, 4-6 is intermediate, and ≥7 is diagnostic of BV.3
Clinical/point-of-care criteria include clue cells (epithelial cells stippled with adherent bacteria at the margin) on wet mount, vaginal pH >4.5, and a fishy amine odor on addition of 10% KOH (“whiff test”); sensitivity and specificity are inferior to a scored Gram stain. Molecular multiplex panels simultaneously target Candida spp., T. vaginalis, and G. vaginalis (or a broader vaginal-microbiome signature) and are now the most sensitive class of test among symptomatic women. Culture of G. vaginalis is not diagnostic for BV, because the organism is recoverable from asymptomatic, healthy women.
G. vaginalis is a thin, gram-variable, catalase-negative rod or coccobacillus. It grows slowly (48 hours in 5% CO2) and is faintly β-hemolytic on rabbit or human blood media. The organism does not produce β-lactamase. No susceptibility-testing guidelines exist for this organism.
Endocervical and urethral specimens
Endocervical specimens target N. gonorrhoeae and C. trachomatis. Collect them with a polyester-tipped swab inserted 1-2 cm past the squamocolumnar junction, after removing surface discharge, and without lubricant. Male urethral specimens, collected ≥2 hours after voiding, target the same organisms. NAAT is the recommended method for both organisms because it is more sensitive and specific than culture. Several FDA-cleared assays detect both simultaneously from swab or first-void urine specimens. When culture is pursued for N. gonorrhoeae, such as for susceptibility testing after treatment failure, direct bedside inoculation of modified Thayer-Martin agar with a CO2-generating supplement is optimal. The organism is fragile and should never be refrigerated in transit.2,4
Genital ulcer disease
| Organism | Disease | Optimal test | Notes |
|---|---|---|---|
| Herpes simplex virus | Vesicular/ulcerative genital lesions | NAAT of vesicle fluid or ulcer-base swab in viral transport medium | DFA on lesion scrapings is an alternative (~70% sensitivity vs. NAAT) |
| Haemophilus ducreyi | Chancroid (painful genital ulcer) | Primarily clinical diagnosis; no FDA-cleared NAAT exists. Culture requires bedside inoculation of chocolate agar and is insensitive | - |
| Treponema pallidum | Primary syphilitic chancre | Darkfield microscopy or serology | Painless, indurated, single ulcer with a clean base is classic |
| C. trachomatis serovars L1-L3 | Lymphogranuloma venereum (LGV) | NAAT of lesion exudate or lymph-node aspirate; complement fixation titer ≥1:64 supports a presumptive diagnosis in a compatible clinical picture | Rectal NAAT is preferred in proctocolitis presentations, common among men who have sex with men |
| Klebsiella granulomatis (formerly Calymmatobacterium granulomatis) | Granuloma inguinale (donovanosis) | Crush preparation from the ulcer margin, Wright or Giemsa stain, looking for intracellular safety-pin-shaped “Donovan bodies” | Does not grow on routine media; molecular assays exist but are not commercially available |
Treponema pallidum and the treponematoses
Treponema pallidum subsp. pallidum causes venereal syphilis; subsp. pertenue causes yaws; subsp. endemicum causes endemic syphilis (bejel); the related species T. carateum causes pinta. Pathogenic treponemes cannot be cultured on artificial media, so diagnosis depends on direct visualization early and serology thereafter.
| Stage | Timing | Findings |
|---|---|---|
| Primary | Median 3 weeks post-inoculation | Painless indurated chancre (may be unnoticed or absent in previously infected patients); regional non-suppurative lymphadenopathy |
| Secondary | ~6 weeks post-inoculation (range 2-12 weeks) | Widespread mucocutaneous rash including palms/soles, condyloma lata, generalized lymphadenopathy, constitutional symptoms; mucous patches |
| Latent | Early (first year) vs. late | Asymptomatic; early latent relapses are possible, late latent relapse is uncommon |
| Tertiary | 10-25 years after infection | Cardiovascular syphilis (ascending aortic aneurysm, aortic insufficiency), gummas, meningovascular/parenchymal neurosyphilis |
| Congenital | Early (<2 years) or late (after a latent period) | Risk and severity correlate with the stage of maternal infection (highest with primary/secondary/early latent disease) and gestational timing |
Darkfield microscopy on serous exudate from a cleaned, abraded primary or secondary lesion visualizes motile spirochetes within about 20 minutes of collection. Motility is required for identification because treponemes are too narrow for conventional light microscopy. Darkfield microscopy is unreliable on oral lesions because morphologically similar commensal oral treponemes are present. Immunohistochemical staining of paraffin-embedded tissue is an alternative where darkfield is unavailable.
Nontreponemal and treponemal serologic testing, algorithm interpretation, and neurosyphilis serologic criteria are covered in Immunology. T. pallidum remains uniformly susceptible to penicillin. A 23S rRNA mutation can confer high-level macrolide resistance.
Chlamydia
Chlamydiae are obligate intracellular bacteria that depend on the host cell for replication. They have been called energy parasites because reticulate bodies draw on host ATP and metabolites, although they can also generate ATP from imported glucose-6-phosphate. Two morphologic forms alternate through the developmental cycle: the infectious, metabolically inert elementary body and the intracellular, metabolically active reticulate body. Three species infect humans: Chlamydia trachomatis, C. psittaci, and C. pneumoniae (the latter two formerly placed in Chlamydophila).
| Category | Disease | Notes |
|---|---|---|
| Classic trachoma | Recurrent conjunctival infection → scarring → entropion/trichiasis → corneal blindness | Endemic where sanitation and hygiene are poor |
| Sexually transmitted, non-LGV | Urethritis/cervicitis, often asymptomatic; ascending disease (PID, salpingitis, perihepatitis/Fitz-Hugh-Curtis syndrome); reactive arthritis | - |
| Lymphogranuloma venereum (LGV, serovars L1-L3) | Genital ulcer → suppurative regional lymphadenopathy → fibrotic strictures; proctocolitis with rectal transmission | Only C. trachomatis disease with prominent systemic/multisystem involvement |
| Perinatal | Inclusion conjunctivitis (up to 2-5 weeks after birth); interstitial pneumonitis (2 weeks-3 months, staccato cough, no fever) | Acquired during vaginal delivery through an infected birth canal |
NAAT is the diagnostic method of choice for genital, rectal, and oropharyngeal C. trachomatis infection in symptomatic and asymptomatic patients, from swab or urine specimens. For suspected sexual assault/abuse in prepubertal children, CDC 2021 STI guidelines allow culture or an FDA-cleared, CLIA-validated NAAT, with confirmation of any positive result. Routine test-of-cure is not advised for nonpregnant patients treated with a recommended regimen; if test-of-cure is indicated (pregnancy, or concern for treatment failure), NAAT is used no earlier than 4 weeks after therapy. Direct fluorescent antibody (DFA) staining is the only nonculture FDA-cleared method for conjunctival C. trachomatis as of August 31, 2026; NAATs are not FDA-cleared for conjunctival swabs and require CLIA verification if used. DFA should not substitute for NAAT in genital specimens. Serology has little diagnostic value for genital infection (antibody persists long after resolution) but is useful for infant pneumonitis (a single IgM titer ≥1:32 by microimmunofluorescence supports the diagnosis) and, historically, for C. psittaci and C. pneumoniae infection.4,5
C. psittaci (psittacosis, an occupational/exposure-related pneumonia from infected birds) and C. pneumoniae (community respiratory infection) are now most often diagnosed by NAAT rather than serology, though the current CDC/CSTE (2010) case definition confirms psittacosis by culture or a fourfold IgG rise (complement fixation or microimmunofluorescence) and classifies a single IgM titer ≥1:32, or PCR detection, as probable.
Genital mycoplasmas and Mycoplasma pneumoniae
Ureaplasma spp. and Mycoplasma hominis may colonize the vagina and cervix. Colonization itself does not signify disease, but their presence in placental membranes or amniotic fluid is consistently associated with chorioamnionitis, preterm birth, and neonatal pneumonia/sepsis. M. genitalium is a cause of non-gonococcal, non-chlamydial urethritis in men and cervicitis in women.
| Organism | Best diagnostic method | Notes |
|---|---|---|
| M. hominis | Culture (grows on sheep blood agar as nonhemolytic pinpoint colonies; also grows in broth blood-culture media without visible turbidity) or NAAT | Metabolizes arginine, producing a broth color shift |
| Ureaplasma spp. | Culture on specialized agar (urea-CaCl2 color development within 5 minutes) or NAAT | Requires acidic pH (5.5-6.5) for optimal growth, versus 6-8 for M. hominis. Separate media were used historically; combined systems now exist |
| M. genitalium | NAAT only | Culture is impractical because the organism grows as slowly and fastidiously as M. pneumoniae |
| M. pneumoniae | NAAT (single or multiplex respiratory panel) is optimal; culture is rarely offered (3+ weeks, “fried egg” colonies) | Serology (IgM for acute infection; paired IgG for a fourfold rise) and nonspecific cold-agglutinin titers (≥1:32 correlates with severe pneumonia) remain available but are largely superseded by molecular testing |
Macrolide resistance in M. genitalium arises from 23S rRNA mutations at positions 2058/2059; fluoroquinolone resistance arises from parC mutations. M. pneumoniae macrolide resistance is also 23S rRNA-mediated. M. hominis is intrinsically macrolide-resistant and Ureaplasma is intrinsically clindamycin-resistant.
| Organism | Typical specimen | Representative gene targets | Legacy method |
|---|---|---|---|
| Treponema pallidum | Genital ulcer, blood, CSF, placenta/fetal tissue | polA, 16S rRNA, membrane protein genes | Serology, darkfield, DFA |
| Neisseria gonorrhoeae | Urine, urethral/cervical swab | opa, cytosine methyltransferase, site-specific recombinase genes | Culture |
| Chlamydia trachomatis | Urine, urethral/cervical/conjunctival swab | Major outer membrane protein (MOMP) gene, 16S rRNA | Culture, EIA, DFA |
| Mycoplasma genitalium | Urine, urethral/vaginal/cervical swab | MgPa adhesin gene, rDNA | Culture (essentially unavailable) |
| Mycoplasma hominis, Ureaplasma urealyticum | Genital tract, amniotic fluid | 16S rRNA, urease gene | Culture |
| Haemophilus ducreyi | Genital ulcer | groEL, 16S-23S intergenic spacer | Gram stain, culture, serology |
Group B Streptococcus screening
Universal antepartum screening for Streptococcus agalactiae (group B Streptococcus, GBS) colonization is performed at 36 0/7 to 37 6/7 weeks of gestation. The specimen is a single swab that samples the lower vagina and then the rectum (through the anal sphincter) without a speculum; vaginal sampling alone under-detects colonization.6
The swab is inoculated into a selective enrichment broth, either Lim broth (Todd-Hewitt broth with colistin and nalidixic acid) or the commercial equivalent, TransVag broth, and incubated 18-24 hours before subculture to blood agar. This enrichment allows a small initial inoculum of GBS to outgrow competing vaginal and rectal flora and is required for the antepartum screen.
S. agalactiae forms gray-white colonies with a narrow zone of beta-hemolysis (occasionally nonhemolytic) and appears on Gram stain as catalase-negative, gram-positive cocci in chains. Presumptive identification is confirmed by a positive hippurate hydrolysis test and a positive CAMP test. In the CAMP test, enhanced hemolysis occurs where an S. agalactiae streak meets a Staphylococcus aureus streak because of synergistic action of the CAMP factor on staphylococcal beta-hemolysin. Group B-specific latex agglutination or MALDI-TOF MS can confirm the identification directly without these biochemical tests. Chromogenic GBS-selective media differentiate GBS by colony color after enrichment. NAAT, performed either directly on the swab or after broth enrichment to improve sensitivity, is also an acceptable alternative to conventional culture.
A positive screen documents maternal colonization. For a patient at high anaphylaxis risk to penicillin, the laboratory must test the isolate for clindamycin and erythromycin susceptibility, including a D-test for inducible clindamycin resistance. The D-test method is covered with antimicrobial susceptibility testing. The screening result guides intrapartum prophylaxis to prevent early-onset neonatal GBS disease.
References
- Tille PM. Bailey & Scott's Diagnostic Microbiology. 15th ed. Elsevier; 2021.
- Miller JM, Binnicker MJ, Campbell S, et al. Guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2024 update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin Infect Dis. Published online March 5, 2024. doi:10.1093/cid/ciae104
- Workowski KA, Bachmann LH, Chan PA, et al. Sexually transmitted infections treatment guidelines, 2021. MMWR Recomm Rep. 2021;70(4):1-187. Bacterial vaginosis. Accessed August 31, 2026.
- Workowski KA, Bachmann LH, Chan PA, et al. Sexually transmitted infections treatment guidelines, 2021. MMWR Recomm Rep. 2021;70(4):1-187. Chlamydial infections. Accessed August 31, 2026.
- US Food and Drug Administration. Nucleic acid based tests. Updated June 23, 2025. Accessed August 31, 2026.
- American College of Obstetricians and Gynecologists. Prevention of group B streptococcal early-onset disease in newborns. ACOG Committee Opinion No. 797. Obstet Gynecol. 2020;135(2):e51-e72. Accessed August 31, 2026.