Overview Gram stain Gram-positive bacteria have a thick peptidoglycan layer in their cell walls that holds the crystal violet stain Gram-negative bacteria cannot hold the crystal violet stain and are counterstained by safranin Giemsa stain Borrelia Plasmodium trypanosomes Chlamydia Periodic acid-Schiff stain (PAS) glycogen mucopolysaccharides used to diagnose Whipple's disease (Tropheryma whippelii) Carbolfuscin acid-fast stain Ziehl-Neelsen acid-fast organisms Mycobacterium Nocardia (partially acid fast) Cryptosporidum oocysts India ink Cryptococcus neoformans stain is not taken up by polysaccharide capsule, creating a transparent halo mucicarmine can also be used to stain capsule red Silver stain fungi e.g. Pneumocystis, Legionella Bugs that Gram stain poorly Treponema to thin to be visualized use darkfield microscopy or fluorescent antibodies Rickettsia Mycobacteria high-lipid-content cell wall use acid-fast stain Legionella pneumophila intracellular parasite use silver stain Mycoplasma no cell wall Ureaplasma no cell wall Chlamydia intracellular parasite has a cell wall but the cell wall does not contain peptidoglycan