An 11-day-old neonate has been brought to his paediatrician because the infant has developed a sharp cough. Physical examination also reveals a mild conjunctivitis with some pus; a chest film confirms pneumonia. No organisms are seen on Gram stain of the pus. What is the most likely causative agent?

The presentation is most likely Chlamydia trachomatis conjunctivitis and pneumonia. This obligate intracellular organism is unable to make its own ATP. Choice B (gonococcus) should have been eliminated on Gram stain, and most would have been intracellular but not in phagosomes. Choice C is mycoplasma, which is not intracellular and rarely causes pneumonias in neonates this young. Choice D would be a rickettsia, which is both unlikely and not a good fit for the disease.