7.3 Upper Respiratory: Pharyngitis, Otitis, Sinusitis, Antigen/Molecular

7.3 Upper Respiratory: Pharyngitis, Otitis, Sinusitis, Antigen/Molecular

Quick Answer: Throat, nasopharynx, middle-ear, and sinus specimens carry dense indigenous flora. On M, pharyngitis culture pathogens are S. pyogenes, N. gonorrhoeae, and Arcanobacterium spp. Colony identification of C. diphtheriae and B. pertussis is SM-only—do not study tellurite or Bordet-Gengou as M-tested throat-culture ID. Antigen/molecular methods for group A streptococci and Bordetella pertussis are M content (II.E.4). Otitis media and sinusitis: H. influenzae, S. pneumoniae, M. catarrhalis. Negative RADTs need culture or NAAT backup, especially in children.

Official outline II.E Upper Respiratory (guideline 2025-09-25) is smaller than lower-tract bacteriology but is packed with “do not culture that on M” traps. Bacteriology is still 45–55% of the exam, so a GAS algorithm, a gonococcal pharynx, and the otitis trio are fair game. Specialist-only colony workups are not.

Specimen sources

Labeling matters. An external-ear swab grows S. aureus, diphtheroids, and Pseudomonas from canal flora and does not diagnose otitis media. A sinus “swab” of the naris is a nose culture. The outline’s sources are anatomic, not barcode names.

Indigenous flora colony and Gram-stain morphology

The pharynx is a mixed neighborhood. Expect viridans streptococci (alpha-hemolytic catalase-negative cocci in chains), saprophytic Neisseria (oxidase-positive Gram-negative diplococci, often yellow), Corynebacterium diphtheroids (club-shaped Gram-positive rods), coagulase-negative staphylococci, anaerobes in crypts, occasional Haemophilus, and yeast. S. pneumoniae and S. aureus can colonize without causing pharyngitis. That is why a throat culture is not worked like a sputum pathogen hunt and why “normal oropharyngeal flora” is a legitimate report.

A throat Gram stain is a poor standalone test for strep throat because mixed Gram-positive cocci are always there. Culture or antigen/molecular assays targeted at group A carbohydrate are the diagnostic tools. Ear and sinus fluids, by contrast, should be Gram stained: a predominant GNCB, lancet-shaped diplococcus, or GNDC in neutrophils is actionable.

Pharyngitis pathogens that M actually tests by culture

The outline’s culture list is three organisms wide. Learn those three in depth.

GAS workup. Plant a throat swab on sheep blood agar (some labs add a selective strep agar). Stab the agar so streptolysin O (oxygen-labile) can show subsurface hemolysis; streptolysin S (oxygen-stable) produces surface hemolysis. After 18–24 hours in 35–37 °C incubation (many labs use anaerobic or reduced-oxygen conditions to enhance hemolysis), pick catalase-negative beta-hemolytic colonies. PYR distinguishes S. pyogenes (positive) from group C/G S. dysgalactiae (negative). Latex grouping confirms group A. Bacitracin is a classic screen but is less specific than PYR plus grouping.

N. gonorrhoeae from the throat. This is not a routine strep plate add-on. It requires a clinical indication, chocolate or selective medium, increased CO2, and a complete identification (MALDI, biochemicals, or molecular) because commensal Neisseria are everywhere in the pharynx. Do not report “Gram-negative diplococci, probable GC” from a mixed throat Gram stain.

Arcanobacterium haemolyticum is the catalase-negative rod that mimics beta-hemolytic strep on blood agar, especially after 48 hours. Reverse CAMP (inhibition of staphylococcal beta-lysin) is the textbook reaction. It matters in teenagers with pharyngitis and rash when the GAS RADT is negative.

SM-only colony identification: C. diphtheriae and B. pertussis

The outline explicitly marks colony morphology and identification of Corynebacterium diphtheriae and Bordetella pertussis as SM ONLY. For M:

• Do not treat tellurite agar, Elek toxin testing, or methylene-blue Chinese-letter morphology as M-required throat-culture identification skills.
• Do not treat Bordet-Gengou, Regan-Lowe, or “mercury-drop” colonies as M-required culture ID.
• You may still recognize that these diseases exist and that public-health culture belongs in specialist laboratories.
• You must still know that antigen and molecular methods for S. pyogenes and Bordetella pertussis are on the M outline (II.E.4).

If a question asks you to choose the correct M-level method for pertussis, pick a validated NAAT (or a DFA/antigen method if that is what the stem validates), not a description of picking colonies off Bordet-Gengou. If a question asks which pharyngitis organism is identified by PYR and group A latex, pick S. pyogenes.

Antigen and molecular methods (II.E.4)

Group A streptococcal RADT detects the group A carbohydrate in a minutes-long immunoassay. Specificity is high, so a positive RADT in a symptomatic patient is accepted for treatment without waiting for culture in many protocols. Sensitivity is imperfect (often cited in the 70–90% range depending on the kit and collection quality), so a negative RADT is backed up—especially in children, who have a higher risk of rheumatic fever. Backup is a throat culture on blood agar or a validated NAAT. Many laboratories have moved the backup from overnight culture to a molecular assay on the same swab. Adults with a negative RADT are sometimes not cultured because rheumatic fever risk is lower; follow the procedure in the stem rather than fighting a named guideline.

Poor collection (missing the tonsillar pillars, swabbing the tongue) causes false-negative antigen tests. Two swabs, or a validated dual-use swab, keep the backup legal when the RADT is negative.

Bordetella pertussis molecular/antigen testing is M content. Nasopharyngeal specimens, not throat swabs, are the correct source. PCR is the routine diagnostic method in most U.S. laboratories because culture is slow, fastidious, and specialist-level. Direct fluorescent antibody exists but is less sensitive than PCR. Serology is a public-health adjunct, not a rapid bench ID. Remember the split: molecular/antigen = M; colony ID = SM-only.

Molecular GAS assays are more sensitive than RADT and may detect nonviable nucleic acid. Correlate with symptoms so colonization is not treated as scarlet fever. The exam still wants you to know PYR, hemolysis, and grouping because culture backup and mixed plates have not disappeared.

Otitis media and sinusitis

The outline’s pathogens are the same three Gram-stain shapes you already use in CAP, recovered from middle ear or sinus rather than from sputum:

A tympanocentesis or sinus aspirate is a sterile-site-style specimen compared with a throat swab. Work up predominant growth. Mixed oral flora from a poorly collected “ear swab” of the canal is not the trio. S. pyogenes can cause otitis but is not the outline’s named set; do not replace Haemophilus with GAS when the question says otitis media.

Sinus surgical material may also grow anaerobes and Enterobacterales in chronic disease. For M, master the acute trio first.

Pathogenicity: M protein and streptolysin O

S. pyogenes virulence is the upper-respiratory pathogenicity story.

M protein is an antiphagocytic surface fibril encoded by emm. It inhibits complement deposition, defines serotypes, and is the link to acute rheumatic fever (molecular mimicry with cardiac myosin) and to some invasive-disease types. Antibody to M protein is type-specific. This is why untreated GAS pharyngitis in children is still a public-health problem and why laboratories back up negative RADTs.

Streptolysin O is an oxygen-labile, cholesterol-dependent cytolysin. It lyses leukocytes and is the antigen in ASO titers used for post-streptococcal sequelae (rheumatic fever, glomerulonephritis) when the acute culture window has passed. Because it is oxygen-labile, subsurface stabs on blood agar help you see hemolysis. Streptolysin S is oxygen-stable and explains the surface beta-hemolysis that makes the colony look like group A on a plate. Do not confuse streptolysin O (serology, subsurface) with streptolysin S (surface hemolysis).

Capsule (hyaluronic acid) makes some GAS mucoid; it is not the pneumococcal polysaccharide capsule. Pyrogenic exotoxins cause scarlet fever rash. Those facts support the same organism you already identified with PYR.

H. influenzae, pneumococcus, and M. catarrhalis use adhesion and, for the encapsulated pair, antiphagocytic capsules to invade middle-ear and sinus mucosa after a viral cold. M. catarrhalis BRO beta-lactamase explains why amoxicillin alone may fail. That is clinical correlation, not an AST chapter, but it is why the hockey-puck oxidase-positive GNDC is worth identifying to species from an ear fluid.

On exam day, sort questions by source first. A throat swab is GAS, GC, or Arcanobacterium—not a CAP workup. A negative RADT in a child still needs backup. A pertussis question on M is molecular or antigen from the nasopharynx, not colony morphology. An ear or sinus fluid with GNCB, GPDC, or GNDC is the Haemophilus–pneumococcus–Moraxella trio. Leave diphtheria and pertussis colony ID for SM.