Bacteria

Morphology

Cytology:
Basophilic to amphophilic granular intracytoplasmic inclusions in columnar or metaplastic infected epithelial cells; perinuclear halos possible; neutrophil-rich background. In conjunctival smears, follicular response with cytoplasmic inclusions in epithelial cells. 
C. pneumoniae and C. psittaci rarely show diagnostic inclusions on routine cytology (no pictures available); macrophages with fine granular inclusions and neutrophil-poor interstitial pattern in lower airway samples may be helpful.

Histology:
Mild to moderate chronic active mucositis; lymphoid aggregates. In lungs, interstitial pneumonitis with mononuclear infiltrates; organisms usually not seen on HE.

Differential diagnosis:

• Reactive metaplasia with cytoplasmic vacuoles
• Gonorrhea with abundant intracellular diplococci
• HSV cytopathic effect
• Bacterial vaginosis flora 
• Mycoplasma or Ureaplasma
• Fungal elements mimicking granules

Clinical notes

C. trachomatis: Commonly asymptomatic STI causing cervicitis and urethritis; ascending infection may lead to pelvic inflammatory disease and tuboovarian abscess; epididymitis in men; neonatal conjunctivitis and pneumonia. Etiologic agent of lymphogranuloma venereum (LGV) with urogenital or anorectal ulcers, regional lymphadenopathy, fever, and possible inguinal buboes if untreated. Trachoma is a chronic follicular conjunctivitis and a leading cause of preventable blindness worldwide.
C. pneumoniae: Atypical pneumonia, bronchitis, pharyngitis.
C. psittaci: Psittacosis with fever, headache, and atypical pneumonia, typically associated with bird exposure.

Ancillary Testing

NAAT from vaginal, cervical, urethral swab or first-void urine for C. trachomatis. Co-testing for N. gonorrhoeae and BV when clinically indicated. DFA or NAAT on conjunctival swabs in neonatal or trachoma settings. For lower respiratory samples, PCR for C. pneumoniae or C. psittaci. Serology can support psittacosis diagnosis when PCR is unavailable.

Additional Information

Cytology is insufficient for species assignment; NAAT confirmation is required.