Treatment of Neonatal Conjunctivitis Systemic, topical, or combined antimicrobial therapy Neonates with conjunctivitis and known maternal gonococcal infection or with gram-negative intracellular diplococci identified in conjunctival exudates should be treated with ceftriaxone or cefotaxime (see Table: Recommended Dosages of Selected Parenteral Antibiotics for Neonates) before results of confirmatory tests are available.