9.1 Skin, Soft Tissue, and Bone Pathogens

9.1 Skin, Soft Tissue, and Bone Pathogens

Quick Answer: Prefer deep tissue, biopsy, or closed-abscess aspirate over surface swabs. Skin: S. aureus, beta-hemolytic streptococci, P. aeruginosa. Soft tissue adds Enterobacteriaceae and anaerobes. Bone adds Kingella spp. C. perfringens gas gangrene shows double-zone hemolysis and stormy fermentation. Necrotizing fasciitis is group A streptococcus (type II) or mixed anaerobes such as Fournier gangrene (type I).

The M(ASCP) outline (II.G, guideline 2025-09-25) tests specimen sources (wound, abscess, biopsy), indigenous flora colony and Gram stain morphology, and identification of major pathogens by site. The exam item is usually a vignette: the right specimen, the right organism list, and a syndrome-level identification (gas gangrene, necrotizing fasciitis, hematogenous versus contiguous osteomyelitis).

Specimen sources: wound, abscess, biopsy

Skin, soft-tissue, and bone cultures are only as good as the material submitted. Deep tissue and biopsy are preferred over swabs. A swab dragged across a chronic ulcer, diabetic foot, or draining sinus recovers colonizing skin flora and cannot distinguish colonization from invasion. Surgical biopsy, operating-room debridement tissue, or a closed-space needle aspirate recovers organisms that are actually in tissue.

Practical hierarchy:

• Tissue biopsy or surgical debridement material is the highest-yield specimen for osteomyelitis, necrotizing infection, and chronic wounds.
• Needle aspirate of a closed abscess should go into anaerobic transport—not a dry swab dipped in pus.
• Bone biopsy obtained in the operating room or by interventional radiology is the osteomyelitis specimen of record. A sinus-tract swab is not a substitute for bone.
• Wound swabs are a last resort after the surface is cleansed, and only when tissue cannot be obtained.

Anaerobic transport is required for abscesses and for any suspected clostridial or mixed anaerobic infection. Dry swabs, delayed plating, and aerobic plates alone miss Bacteroides, Prevotella, Fusobacterium, anaerobic gram-positive cocci, and Clostridium. If the surgeon describes crepitus, foul odor, or necrotic fascia, set up an anaerobic plate and read the Gram stain immediately.

Always correlate the Gram stain with culture. Neutrophils plus a single morphotype that later matches the isolate is concordant infection. Neutrophils without organisms can still be infection (prior antibiotics, or fastidious Kingella). Squamous epithelial cells and mixed skin morphotypes on a swab predict mixed colonizing flora and a limited workup.

Indigenous flora: colony and Gram stain morphology

Intact skin is colonized. The laboratory must know what normal looks like so it does not over-work contaminants or under-call pathogens from sterile bone.

Soft-tissue flora resembles skin flora, with more anaerobes at oral, perineal, and gut-adjacent sites. Report mixed skin flora when a superficial specimen's Gram stain and culture agree. Do not fully identify every colony from a swab of a chronic ulcer. Do not treat a single colony of coagulase-negative staphylococcus from a swab as equivalent to S. aureus from an abscess aspirate.

Major pathogens by site

Skin: S. aureus, beta-hemolytic streptococci, P. aeruginosa

Staphylococcus aureus appears as gram-positive cocci in clusters. Colonies are creamy, often golden, and frequently beta-hemolytic on sheep blood agar. Catalase positive; tube coagulase or staphylococcal latex positive. It causes impetigo (including bullous impetigo), folliculitis, furuncles, carbuncles, abscesses, surgical-site infection, and cellulitis with pus. A quality abscess Gram stain of GPC in clusters that cultures as coagulase-positive staphylococci is the prototype concordant result.

Beta-hemolytic streptococci, especially Streptococcus pyogenes (group A), appear as gram-positive cocci in chains with wide-zone beta hemolysis. Group A is PYR positive and bacitracin susceptible (presumptive). It causes nonbullous impetigo, erysipelas, cellulitis, and necrotizing fasciitis. Groups C and G (S. dysgalactiae) produce similar SST disease. Group B streptococcus appears in neonates and in diabetic soft-tissue and bone infection.

Pseudomonas aeruginosa is a gram-negative rod, oxidase positive, a non-lactose fermenter on MacConkey, often with blue-green pyocyanin and a grape or tortilla odor. Do not sniff plates to identify it. Classic skin associations are hot-tub folliculitis, burn wounds, macerated ulcers, and osteomyelitis after a puncture through a sneaker sole.

Soft tissue: add Enterobacteriaceae and anaerobes

Soft-tissue infection that is surgical, diabetic, decubitus, perineal, or intra-abdominal is often polymicrobial. S. aureus and beta-hemolytic streptococci still dominate monomicrobial cellulitis, but Enterobacteriaceae (E. coli, Klebsiella, Proteus, Enterobacter: oxidase-negative GNR that grow on MacConkey) and anaerobes appear in deep, foul, necrotic, or gut-adjacent wounds. A mixed Gram stain of GNR, GPC, and GPR from quality tissue is a true mixed infection, not contamination.

Bone: S. aureus, beta-hemolytic streptococci, Kingella spp.

S. aureus is the leading isolate in hematogenous osteomyelitis at all ages. Beta-hemolytic streptococci (GAS; GBS in neonates and some diabetics) also seed bone.

Kingella spp., principally K. kingae, are the outline's distinctive bone organisms. They are fastidious gram-negative coccobacilli, often beta-hemolytic on blood agar, grow on chocolate, usually fail MacConkey, oxidase positive, catalase negative, and CO2-enhanced. They are a leading cause of osteomyelitis and septic arthritis in children about 6–36 months old. Culture of joint fluid or bone can be negative; molecular methods recover Kingella when culture does not. Do not discard a tiny GNCB from a toddler's osteoarticular specimen as contaminant Haemophilus-like flora.

Syndromes that change the workup

Gas gangrene (clostridial myonecrosis). Clostridium perfringens is a boxcar-shaped gram-positive rod; spores are usually absent on tissue Gram stain. On blood agar it shows double-zone hemolysis (inner complete theta-toxin zone, outer incomplete alpha-toxin zone). In litmus milk it produces stormy fermentation. Lecithinase (Nagler) is positive. Crepitus after trauma or surgery is a critical-value clinical correlate—call the result; do not wait for a complete anaerobic identification panel.

Necrotizing fasciitis. Type II is typically group A Streptococcus (sometimes with S. aureus), often on an extremity after minor trauma, with a relatively monomicrobial Gram stain of GPC in chains. Type I is polymicrobial mixed anaerobes and Enterobacteriaceae. Fournier gangrene of the perineum or scrotum is the prototype mixed anaerobic necrotizing infection. The Gram stain is the first fork: pure chains versus mixed fecal/oral flora.

Osteomyelitis: hematogenous versus contiguous. Hematogenous disease is usually one organism, typically S. aureus (or Kingella in young children). Contiguous disease follows trauma, surgery, diabetic foot, or pressure ulcer and is often polymicrobial: staphylococci, streptococci, Enterobacteriaceae, anaerobes, and sometimes P. aeruginosa. Surface swabs of a draining sinus over osteomyelitis do not reliably predict the bone isolate.

On the exam

Lock the outline lists. Skin = S. aureus, beta-hemolytic streptococci, P. aeruginosa. Soft tissue adds Enterobacteriaceae and anaerobes. Bone adds Kingella. Then use the Gram stain and transport story: crepitus plus double-zone hemolysis is C. perfringens; mixed perineal necrotizing infection is Fournier/type I; a toddler bone/joint GNCB is Kingella; a swab of an ulcer is not a bone culture.