How is a potentially contaminated sample treated?

Management of Potentially Contaminated Samples

A potentially contaminated sample should not be treated as clinically significant unless multiple positive cultures from separate sites confirm true infection, particularly when typical skin flora organisms are isolated from a single culture. 1

Immediate Assessment Steps

When contamination is suspected, the priority is distinguishing true infection from artifact:

• Obtain repeat blood cultures immediately before starting antimicrobials, drawing at least two sets from separate peripheral venipuncture sites, with each set including 20-30 mL of blood per culture 1
• Evaluate the organism isolated: Growth of typical skin flora (coagulase-negative staphylococci, Bacillus spp., Micrococcus spp., Propionibacterium spp., or other Gram-positive bacilli) in only one of multiple culture sets strongly indicates contamination 1
• Review collection technique: Samples drawn from existing intravascular devices rather than fresh venipuncture, poor skin antisepsis, or compromised skin integrity significantly increase contamination risk 1

Diagnostic Criteria for True Infection vs. Contamination

The key differentiating factors include:

• Multiple positive cultures with the same organism from different sites strongly suggest true bacteremia, while a single positive culture with a common contaminant organism suggests contamination 1
• For catheter-related concerns, discordant results between catheter and peripheral cultures may indicate contamination, though quantitative cultures or differential time to positivity can help clarify 1
• Clinical context matters: The presence of fever, chills, hypotension, or other signs of infection alongside positive cultures increases likelihood of true bacteremia 2

Treatment Decision Algorithm

Your management approach should follow this pathway:

If Contamination is Confirmed:

• Avoid unnecessary antimicrobial therapy and document contamination clearly in the medical record 1
• No treatment is indicated for confirmed contaminants 1

If True Bacteremia Cannot be Ruled Out:

• Consider empiric antimicrobial therapy for high-risk patients (neutropenic, immunocompromised, critically ill) or those with clinical signs of infection 1
• Initiate empiric antibiotics promptly in neutropenic patients, especially if a short-term central venous catheter is present 2
• Remove the catheter if it is the suspected source and the patient has a short-term CVC or an infected long-term catheter 2

For Microbiome/Research Samples:

• Sequence negative controls alongside samples to identify contamination points and establish baseline detection levels 3
• Compare suspected contaminated samples against negative controls: If samples contain no more microbial DNA than negative controls, they should not be considered positive 3
• Document all controls and contamination prevention measures used during collection and processing 3

Common Pitfalls to Avoid

Critical errors in contamination assessment include:

• Never rely on absence of visible PCR bands on agarose gel electrophoresis to confirm absence of contamination, as this method has low sensitivity 3
• Do not perform cultures during active antibiotic treatment unless the presumption is that the current antibiotic is ineffective; stop antibiotics for at least 48 hours before obtaining cultures 3
• Avoid using cotton-tipped swabs for culture collection as they may reduce culture yield 3
• Do not assume sterility equals DNA-free: Autoclaved equipment may still contain cell-free DNA that can contaminate low-biomass samples 3

Prevention of Future Contamination

To minimize recurrence:

• Implement standardized collection protocols with proper skin antisepsis using alcohol, tincture of iodine, or alcoholic chlorhexidine with adequate contact and drying time 1
• Use dedicated phlebotomy teams when available, as this reduces contamination rates 1
• For research samples, include at least one control sample for every four samples to accurately quantify contamination 3
• Decontaminate equipment with 80% ethanol followed by DNA-degrading solutions (sodium hypochlorite, UV-C exposure, or commercial DNA removal solutions) rather than just sterilization 3