Definition
- First-line lab test in bacterial identification. Bacteria with thick peptidoglycan layer retain crystal violet dye (gram positive); bacteria with thin peptidoglycan layer turn red/pink dye (gram negative) with counterstain.
- These bugs do not Gram stain well (These Little Microbes May Unfortunately Lack Real Color But Are Everywhere)
Organism | Reason for poor Gram staining |
Treponema, Leptospira | Too thin to be visualized |
Mycobacteria | Cell wall has high lipid content |
Mycoplasma, Ureaplasma | No cell wall |
Legionella, Rickettsia, Chlamydia, Bartonella, Anaplasma, Ehrlichia | Primarily intracellular; also, Chlamydia lack classic peptidoglycan due to ↓ muramic acid |
Key stains
Stain type
Target/details
Mnemonics/notes
Images
Giemsa stain
Chlamydia, Rickettsia, Trypanosomes, Borrelia, Helicobacter pylori, Plasmodium.
Clumsy Rick Tripped on a Borrowed Helicopter Plastered in Gems
Periodic acid-Schiff stain
Stains glycogen, mucopolysaccharides; diagnosis for Whipple disease (Tropheryma whipplei).
PaSs the sugar
Ziehl-Neelsen stain (carbol fuchsin)
Acid-fast bacteria (e.g. Mycobacteria, Nocardia; stains mycolic acid in cell wall); protozoa (e.g. Cryptosporidium oocysts).
Auramine-rhodamine often used for screening (inexpensive, more sensitive).
India ink stain
Cryptococcus neoformans (mucicarmine can also be used to stain thick polysaccharide capsule red).
Silver stain
Helicobacter pylori, Legionella, Bartonella henselae, and fungi (e.g. Coccidioides, Pneumocystis jirovecii, Aspergillus fumigatus).
HeLiCoPters Are silver
Fluorescent antibody stain
Identifies many bacteria, viruses, Pneumocystis jirovecii, Giardia, Cryptosporidium
Example is FTA-ABS for syphilis
Whipple disease (Tropheryma whipplei)
Multisystem disorder involving bowel and CNS infection
- CNS: seizures, myoclonus, ataxia, supranuclear gaze disturbances, hypothalamic dysfunction, dementia
- Pathognomonic: Oculomasticatory myorhythmia (pendular convergence movements of the eyes with contractions of masticatory muscles)
Common Gram negative organisms
Organism | Key Features & Clinical Notes |
Neisseria | N. meningitidis(“meningococcus”) has a polysaccharide capsule. Lives in nasopharynx and causes disease when entering bloodstream (meningitis, sepsis). Releases endotoxin causing hemorrhage (petechial rash), spiking fever, chills, myalgia. Can cause adrenal hemorrhage (Waterhouse-Friderichsen syndrome: adrenal insufficiency). Infants 6 months – 2 years, army recruits, dorm dwellers at risk. |
HACEK group | Grouping of gram-negative bacilli with enhanced ability to cause infective endocarditis (IE). Includes Haemophilus parainfluenzae, Haemophilus aphrophilus, Haemophilus paraphrophilus, Actinobacillus actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens, Kingellaspecies. Responsible for ~3% of native valve IE. Most common cause in persons who do not abuse IV drugs. |
Klebsiella pneumoniae | Causes nosocomial sepsis (second most common after E. coli), Foley catheter UTIs, pneumonia in aspiration-prone patients (alcoholic, intubated, debilitated). Pneumonia forms cavitations; sputum is classically currant jelly colored. |
Escherichia | Normally present in GI tract; virulent strains via DNA exchange can cause diarrhea (in developing world infants, immunocompromised, travelers). Three types: enterotoxigenic (ETEC), enteroinvasive (EIEC), enterohemorrhagic (EHEC). E. coli most common UTI cause, affects women/Pt with Foley catheters. Neonatal E. coli meningitis common. Most common gram-negative sepsis in hospitalized patients; nosocomial pneumonia. |
Salmonella | Three species: S. typhi(humans), S. cholerae-suis, S. enteritidis(animal GI tracts). Spread through contaminated food/water. S. typhi invades intestinal epithelium, then lymph/seed multiple organs. Typhoid fever: fever, diarrhea, headache, abdominal pain, inflamed organs (e.g., spleen). Light-skinned may show transient salmon-colored belly rash. |
Shigella | Fecal-oral transmission (contaminated water, poor hand hygiene), mainly in preschools/nursing homes. Bacteria attach to intestinal epithelium, invade, release Shiga toxin (inhibits protein synthesis, causes cell death). Results in inflammatory response, blood-and-pus diarrhea, abdominal pain. |
Haemophilus | Nonencapsulated (“untypable”) H. flu causes otitis media in children, upper respiratory infections in adults with chronic lung disease. Capsule limits invasiveness. Routine Hib vaccine has greatly reduced H. influenzae meningitis, acute epiglottitis, septic arthritis. |
Pseudomonas | Tends to infect sick/immunocompromised; very resistant to antibiotics. Appears blue-green, sweet grape smell. Causes problems in burns, IE in IV drug abusers, pneumonia (immunocompromised, cystic fibrosis), sepsis, otitis externa/media (esp. diabetic), UTI/pyelonephritis, osteomyelitis in IV drug abusers/children. |
Campylobacter | Campylobacter jejuni—one of three leading causes of gastroenteritis (others: Rotavirus, ETEC), mostly in children. Reservoir is animals; acquired by fecal-oral route/unpasteurized milk. Prodrome: fever, headache, bloody diarrhea, abdominal cramps. Associated with Guillain-Barre syndrome. |
Common Gram positive organisms
Organism | Key Features & Clinical Notes |
Streptococcus pneumoniae | Streptococcus pneumoniae has no Lancefield antigen, appears as lancet-shaped cocci in pairs (diplococci), and contains a polysaccharide capsule. These organisms are α-hemolytic. S. pneumoniaeis a common cause of pneumonia and meningitis in adults and of otitis media and conjunctivitis in children. The pneumococcal vaccine should be given to immunocompromised patients, older adults, those with HIV, and asplenic patients. |
Viridans streptococci (including milleri group) | Heterogeneous group of streptococci not defined by a single Lancefield antigen but share common features: gastrointestinal tract location (especially saliva), α-hemolytic. Cause: 1. Dental caries; 2. Subacute (slow-onset) bacterial endocarditis, especially post-dental procedures and on damaged/prosthetic valves (acute endocarditis usually staphylococcal); 3. Brain/abdominal abscesses. |
Streptococcus pyogenes | Lancefield group A strep, β-hemolytic. Multiple virulence factors produce disease by direct invasion, toxin release, or delayed antibody response. Can cause pharyngitis, skin infection, scarlet fever, toxic shock syndrome, rheumatic fever, and acute post-streptococcal glomerulonephritis. |
Streptococcus agalactiae | Lancefield group B Streptococcus(group B strep, or GBS), β-hemolytic. Lives in the vagina of 25% of women, associated with newborn infection during birth; neonatal meningitis, pneumonia, and sepsis most common. Pregnant women tested for GBS at 35-37 weeks and receive prophylactic penicillin if positive. GBS also causes sepsis in pregnant women, patients with medical co-morbidities, older adults. |
Streptococcus bovis | Group D Streptococcus; bacteremia highly associated with colon cancer. |
Enterococcus faecalis | Enterococcus faecalis and Enterococcus faecium are normal bowel inhabitants (grow well in bile) and commonly cause infections in hospitalized patients: UTI, biliary infections, endocarditis, wound infections, bacteremia/sepsis (IV catheters). May show resistance to VRE. |
Staphylococcus aureus | Present in nasal cavity of 30% of individuals, especially ill/hospital staff; spread by contact, reduced by handwashing. Most virulent staph species; survives long. Surface adhesion proteins (coagulase, protein A, lipase) contribute to virulence. Local skin infection may lead to furuncle/abscess, then invade organs via lymphatics/blood. Penicillin-resistant due to penicillinase. MRSA: resistant to beta-lactams, treat with vancomycin. MRSA may be >50% of cases. |
Staphylococcus epidermidis | Inhabits normal skin; frequent blood culture contaminant. Forms biofilm (polysaccharide scaffold), allowing adherence to synthetic materials (frequent on Foley catheters, IV lines, mechanical valves, stents, prosthetic joints). |
Clostridium difficile | Causes pseudomembranous enterocolitis, usually within a month after broad-spectrum antibiotic use (e.g. clindamycin, ampicillin), which reduces normal GI flora and allows overgrowth. Symptoms: abdominal cramps, diarrhea, fever due to toxin release. Diagnosis by toxin detection in stool. Treat with metronidazole (oral or IV) or vancomycin (oral only; IV vancomycin is ineffective for colitis). |
Actinomyces israelii | Gram-positive, beaded, filamentous anaerobe part of normal oral flora; causes actinomycosis. Erodes oral/GI mucosa, creates draining sinus tracts. Pus from abscesses contains yellow “sulfur” granules (microcolonies of A. israelii). Treat with penicillin G and abscess drainage. |