Biology and Diagnosis of Skeletal Infection

OPBSInfectionRadiology

Must Know

• Surgical site infection (SSI) is the costliest of the five major healthcare associated infection types.
• One third of SSIs follow orthopaedic procedures.
• Staphylococci are the commonest SSI pathogens, followed by Enterobacteriaceae, streptococci and enterococci.
• Bacteria are the commonest cause of musculoskeletal infection.
• Bacteria are prokaryotes. They have a nucleoid, no nuclear envelope and no membrane-bound organelles.
• The cell wall is unique to prokaryotes and protects against osmotic stress.
• Gram positive organisms keep crystal violet after the alcohol rinse and look violet.
• Gram negative organisms keep only the safranin counterstain and look pink.

Antibiotic Resistance

Type	Meaning	Examples
Intrinsic (innate)	Inherent in the organism	Enzyme destruction of drug, altered wall permeability, altered structure, efflux changes, metabolic bypass
Extrinsic (acquired)	Gained by a previously sensitive organism	Chance mutation or uptake of resistance genes from another cell, often on plasmids

• Plasmids are small circles of double-stranded DNA carrying specialised genes such as resistance.
• A bacteriostatic drug can slow killing by a bactericidal drug (antagonism).
• A randomised trial found oral therapy noninferior to intravenous therapy in the first 6 weeks for complex bone and joint infection.

Biofilm

• Biofilm is a structured bacterial community with its own phenotype, formed on inert surfaces such as implants.
• Quorum sensing (cell to cell signalling) regulates the biofilm life cycle, motility, adhesion, virulence and metabolism.
• Biofilm bacteria resist antibiotics, host immunity and changes in pH, osmolarity and temperature better than planktonic cells.
• Four stages are initiation, maturation, maintenance and dispersion.
• In initiation bacteria adhere and form microcolonies, then secrete polysaccharide glycocalyx.
• Implants are coated quickly by plasma and matrix proteins (fibrinogen, laminin, fibronectin, collagen) that bacterial receptors bind.
• Pili and flagella aid adhesion, especially in gram negative organisms.
• Bacteria adhere more to stainless steel than titanium. Tantalum resists S aureus adherence.

More on adhesion forces

• Physical forces drawing organisms to the surface include van der Waals, hydrophobic and gravitational forces.
• Ionic, hydrogen and covalent bonding also contribute.
• Surface roughness, hydrophobicity, porosity and pore topology alter adhesion.
• Surface modification to stop attachment is an active research area.

Risk Factors and Prevention

• Spine SSI risks include longer operating time, BMI 30 or more, smoking and wound class II or higher.
• Nonmodifiable PJI risks with strong evidence include male sex, black race and TKA compared with THA.
• Modifiable risks include obesity, smoking, alcohol, diabetes, malnutrition (low albumin), anaemia and poor oral health.
• Optimise before elective arthroplasty to BMI under 40, HbA1c under 8 percent or fructosamine under 292 µmol/L.
• Stop disease-modifying and immunosuppressive drugs 2 to 4 weeks before surgery.
• CDC advises a full body wash with soap or antiseptic at least one day before surgery.
• Skin preparation should contain isopropyl alcohol. No single agent is proven best.
• Skin preparation removes at most about 80 percent of flora.
• If hair must go, use clippers or depilatory just before surgery. Shaving causes microtrauma.
• Bacteria cross woven reusable drapes within 30 minutes. Nonwoven disposable drapes are impermeable.
• Airborne bacteria within 30 cm of the wound correlate with infection.
• Closed doors give the fewest colony forming units. Swinging and open doors raise them.
• Laminar airflow cuts airborne particles by 80 percent, yet the International Consensus Meeting does not require it.
• WHO, CDC and the consensus group support dilute aqueous iodophor (betadine) irrigation before closure.

More on theatre and procedure data

• Orthopaedic SSI lengthens stay by a median 2 weeks, doubles readmission and more than triples cost.
• Arthroplasty risk factors from Tan et al include previous surgery, substance abuse, HIV and revision surgery.
• Skin flora include staphylococci, diphtheroids, Pseudomonas and Propionibacterium.
• Some studies favour 2 percent chlorhexidine cloths, others find no difference from povidone iodine.
• Single gown packs may reduce delay and traffic around the table.
• Personnel shed about 10 to the power 6 bacteria-laden skin scales a day.
• Phones and handheld devices often carry S aureus and should be disinfected.
• Laminar airflow used poorly can raise downwind contamination at the wound.
• Colony forming units per square foot per hour were 13.3 with closed, 19.4 with swinging and 24.8 with open doors.

Diagnosis

• ESR and CRP may rise in osteomyelitis or septic arthritis while white cell count stays near normal.
• AAOS supports combined ESR and CRP for PJI screening. D-dimer and IL-6 need validation.
• Aspiration is needed for definitive diagnosis of septic arthritis. Check cell count, Gram stain, culture and crystals.
• Native joint infection features are synovial WCC over 50,000/mm3 and over 75 percent polymorphs.
• A neutrophil differential over 90 percent strongly suggests infection.
• Synovial glucose falls below serum glucose in infection.
• Withhold antibiotics until cultures are taken where possible.
• IDSA advises transporting synovial fluid at room temperature, plus blood culture bottles when volume allows.
• PCR can detect Borrelia burgdorferi and Neisseria gonorrhoeae. Gonococcal cultures yield poorly, so culture the mucosal site too.

Imaging

Modality	Findings and use
Radiograph	First test. Rarely shows early osteomyelitis. Late bone destruction and sequestrum
Bone scan	Sensitive, not specific. Cold early, hot later
Leucocyte plus sulfur colloid marrow scan	Leucocyte activity without marrow activity means infection. Specificity over 90 percent
CT	Cortical destruction, intraosseous gas, involucrum. Punctate density with cortical loss suggests sequestrum
MRI	Marrow low T1, high T2. Abscess has sharp border and low signal rim. Penumbra sign in subacute osteomyelitis
Ultrasound	Effusion, guided hip aspiration, subperiosteal fluid
FDG-PET	No metal artefact. Reserve for suspected PJI with inconclusive tests such as dry tap

More on imaging signs

• Penumbra sign is a peripheral zone of slightly higher T1 signal than the central abscess cavity, ringed by low signal reactive bone.
• Chronic osteomyelitis on T2 shows cortical thickening, a sharp marrow interface and a well-defined soft tissue lesion.
• CT signs also include periosteal new bone, raised marrow attenuation, a narrowed canal and serpentine sinus tracts.
• PET/CT adds anatomical correlation and accuracy over PET alone.

Numbers to Remember

• Healthcare associated infection affects 1 in 31 inpatients.
• Spine SSI 2.3 percent in NSQIP. Arthroplasty infection 1 to 2.5 percent.
• About 30 percent of healthcare staff carry S aureus.
• Theatre staff rising from 8 to 16 raised SSI from 1.5 to 3.8 percent.
• TKA longer than 90 minutes doubled SSI and PJI compared with 60 minutes or less.
• Ideal skin preparation suppresses growth for at least 6 hours.

Exam Traps

• A bone scan can be cold early in infection.
• Leucocytes gather in marrow disturbed by implants, so a marrow scan is paired to separate marrow from infection.
• Shaving is not the recommended hair removal method.

Related pages. Periprosthetic Infections, Acute Osteomyelitis, Chronic Osteomyelitis, Septic Arthritis, Septic Arthritis in Children, Surgical Site Infection, Pyogenic Spinal Infection, General Orthopaedic Infections and Tuberculosis

Recent Review. Nucleic Acid Tests for Implant Infection

• Culture is negative in 7 to 50 percent of PJI and about 30 percent of fracture-related infection.
• Culture favours fast-growing planktonic organisms, misses biofilm and obligate polymicrobial species, and takes 3 to 10 days.
• The 16S rRNA gene is prokaryote specific. Conserved regions bind primers and hypervariable regions identify the bacterium.
• PCR needs template DNA, primers, free nucleotides and DNA polymerase, with DNA doubling each of 30 or more cycles.
• End-point PCR is qualitative, read as a gel band. Quantitative PCR monitors every cycle to measure target abundance.
• Fewer qPCR cycles to reach threshold fluorescence means more starting DNA in the sample.
• Sanger sequencing uses chain-terminating nucleotides and works only on a pure monoculture.
• 16S NGS sequences every variant of one amplicon. Metagenomic NGS uses random primers to read all DNA, including resistance genes.
• DNA from dead organisms or free DNA can give positive results without viable bacteria.
• Human mitochondrial ribosomes resemble bacterial ones, so bacterial primers may amplify mitochondrial DNA.

More on interpreting molecular results

• Reverse transcription of RNA to complementary DNA lets the same methods detect RNA, which reflects active transcription.
• RNA degrades easily, and RNA methods take days to weeks.
• NGS takes 4 days to 6 weeks and is prone to amplifying background contamination.
• Contamination can enter at collection, extraction, amplification, sequencing or data processing.
• Studies should report positive and negative extraction and PCR controls, primer sequences and read depth.
• A defined minimum read count separates true low-abundance organisms from contaminants.
• A 16S amplicon often cannot separate MSSA from MRSA, so a second targeted assay confirms the strain.
• Every 16S primer set carries bias toward some taxa.
• Treatment failure needing reoperation in implant infection exceeds 30 percent.

McClure EA, Werth P, Ross B, Gitajn IL. Application of nucleic acid-based strategies to detect infectious pathogens in orthopaedic implant-related infection. J Bone Joint Surg Am. 2023;105(7):556-68. PubMed

Recent Review. Adaptive Antimicrobial Resistance in PJI

• Hypermutability and small colony variants are permanent adaptations. Persister cells, transient resistance and phoenix colonies are transient.
• Hypermutable variants raise mutation rate 10 to 1,000 fold, triggered by antibiotic stress or defective mismatch repair genes.
• Small colony variants carry respiratory mutations limiting the Krebs cycle, relying on glycolysis and fermentation with low ATP.
• Aminoglycoside exposure reproducibly selects small colony variants. Hold blood agar plates beyond 72 hours to see them.
• Small colony variants live inside host cells and the osteocyte lacunar canalicular network, hidden from antibiotics and immunity.
• Persister cells are under 1 percent of a population and sit dormant in G0 despite available nutrients.
• Persisters regain normal metabolism and full antibiotic susceptibility once drug levels fall below the MIC.
• Toxin and antitoxin systems pair a stable toxin with a labile antitoxin. Stress degrades the antitoxin, inducing dormancy.
• Transient antimicrobial resistance relies on an inducible multidrug efflux pump that switches off once antibiotic pressure ends.
• Phoenix colonies, under 0.1 percent, regrow after high-dose aminoglycoside without new resistance genes or slowed metabolism.

More on clinical implications

• Up to 8 g of antibiotic may be added to one 40 g pack of PMMA in spacers.
• Calcium sulphate beads usually carry 2 to 3 g of antibiotic in 10 mL and kill biofilm 5 to 10 mm from a bead in the laboratory.
• Fresh blood supply at debridement or exchange can feed small colony variants back to wild-type growth.
• Small colony variants resist cell wall and protein synthesis inhibitors because of their low metabolism.
• Small colony variants push host immune cells to an anti-inflammatory state.
• Persister cell turnover in G0 may take 6 to 8 weeks or longer.
• Phoenix colony tolerance may come from more flexible mRNA translation around aminoglycoside action on the 30S subunit.
• Long antibiotic courses favour small colony variant selection.

Hamad C, Chowdhry M, Sindeldecker D, Bernthal NM, Stoodley P, McPherson EJ. Adaptive antimicrobial resistance, a description of microbial variants, and their relevance to periprosthetic joint infection. Bone Joint J. 2022;104-B(5):575-80. PubMed

Recent Review. Necrotising Fasciitis

• Incidence is 0.63 per 100,000 per year, limbs are involved in 40 percent, and 30 day mortality is 22 percent.
• Pain out of proportion to the visible skin is the cardinal early sign. Skin can look nearly normal at first.
• Streptococcal streptolysin S activates nociceptors, and the CGRP released blunts neutrophil recruitment and causes severe early pain.
• NSAIDs impair neutrophil migration and may promote group A streptococcal necrotising fasciitis. Stop them on suspicion.
• Type I. Polymicrobial aerobes and anaerobes, the commonest type, in older, diabetic or immunocompromised patients, with a slower course.
• Type II. Gram-positive monomicrobial, mainly invasive group A streptococci (less often S. aureus including MRSA), able to infect healthy people.
• Type III. Gram-negative monomicrobial, mostly Vibrio or Aeromonas after sea or fresh water exposure, with mortality near 66 percent.
• LRINEC is insensitive. A score of 8 or more detects only 41 percent of cases.
• Clindamycin or linezolid is added to a beta-lactam because beta-lactams do not stop ribosomal exotoxin production.
• Surgery delayed beyond 6 hours from presentation gives a more than fivefold rise in both death and amputation.

More on diagnosis and management

• Type IV is fungal, rare and missed without fungal culture media.
• Bacterial proteases, lipases and hyaluronidases dissect fascial planes, and platelet leucocyte plugs cause microvascular thrombosis.
• Comorbidity is present in 90 percent, most often smoking, diabetes, obesity, intravenous drug use and alcohol excess.
• Almost half are afebrile at presentation and only 27 percent are hypotensive.
• Gas on radiographs appears in only 25 percent, from coliforms or anaerobes such as Clostridium perfringens. Invasive group A streptococci do not produce crepitus.
• MRI may show T2 hyperintense deep fascia 3 mm or thicker across several compartments, but overcalls extent and delays surgery.
• Diagnosis is confirmed through a 3 cm incision showing necrotic fascia, grey dishwater fluid and a positive finger sweep test. A 20 percent negative exploration rate is acceptable.
• Deep tissue biopsies are cultured, not superficial swabs. Frozen section is unreliable.
• Excision covers the red (necrotic) and amber zones plus a 3 cm cuff of healthy green zone tissue.
• Review within 6 hours of surgery, with a planned relook at 12 to 24 hours.
• Group A streptococcal cases are barrier nursed, and staff inoculation injuries need penicillin prophylaxis.
• Intravenous immunoglobulin is considered in refractory type II disease and has no effect on Gram-negative infection.
• Streptococcal toxic shock syndrome raises mortality to about 67 percent.

White TO, Ablett AD, Neo C, Clement ND, Moran CG, Morgan MS, Duckworth AD. Necrotizing fasciitis. Bone Joint J. 2026;108-B(9):1078-86. PubMed

Source

Cooper AM, Goswami K, Parvizi J. Biology and Diagnosis of Skeletal Infection. In. Aaron RK, editor. Orthopaedic Basic Science. Foundations of Clinical Practice. 5th ed. Philadelphia, Wolters Kluwer, 2021.

Practise Type X questions on this topic

Reviewed by Professor Phong Tran, Head of Orthopaedic Surgery, Western Health. Last updated 17 October 2026.