Nasal Swab and MRSA Screen

The nasal swab for methicillin resistant Staphylococcus aureus (MRSA) screening detects colonisation of the anterior nares, the main reservoir of Staphylococcus aureus in people.

Staphylococcus aureus is carried by 20 to 30% persistently and 30 to 50% intermittently. MRSA is present in 1 to 2% of the community and 5 to 10% or more of hospitalised patients, varying greatly by region.

Methods are culture on chromogenic agar (selective for MRSA, results in 18 to 48 hours), real time PCR for the mecA and mecC genes with the staphylococcal cassette chromosome junction and S. aureus specific gene (results in about 1 to 2 hours), and rapid antigen tests for PBP2a on isolates.

Screening may include groin, axilla, throat, perineum, wounds and catheter exit sites to increase yield by 10 to 40%.

Screening supports infection prevention (isolation of carriers, contact precautions, decolonisation), pre-operative prophylaxis (cardiac, orthopaedic and neurosurgical procedures) and targeted empirical therapy in colonised patients who develop infection.

MRSA colonisation raises the risk of subsequent infection about 10-fold (up to 30% within 1 year in hospitalised carriers). The negative predictive value of a nasal PCR for MRSA pneumonia is over 95 to 99%, making it a useful tool to stop unnecessary anti-MRSA antibiotics.

Indications. Admission screening of high risk patients (previous MRSA, recent hospitalisation or long term care, dialysis, intensive care, transfer from other facilities, wounds or devices, injecting drug use) as the local policy sets. Pre-operative screening before cardiothoracic, orthopaedic implant and neurosurgical procedures.

Contacts of a patient with MRSA on a ward or in an outbreak. Staff screening during outbreaks. Rule out of MRSA pneumonia in patients on empirical vancomycin or linezolid. Confirm decolonisation after treatment. Recurrent skin and soft tissue infection in a household.

Specimen. Nasal swab: a single moistened swab inserted about 1 to 2 cm into each anterior naris and rotated for 3 to 5 seconds against the nasal mucosa, using the same swab for both nostrils. Additional sites (groin or perineum, axilla, throat, wound, catheter exit site, sputum or tracheal aspirate) as locally required. Transport in Amies medium at room temperature or refrigerated for culture within 24 hours, and as the PCR system requires for molecular tests.

Reference values. Culture: no MRSA isolated. PCR: mecA (and mecC) with S. aureus marker not detected.

Interpretation.

• MRSA detected: colonisation (not infection), with infection control actions: contact precautions, single room or cohorting, hand hygiene, chlorhexidine bathing, and decolonisation (mupirocin nasal ointment for 5 days with chlorhexidine body wash) in selected patients such as before surgery.
• MRSA not detected on nasal swab: reduces but does not eliminate the likelihood of MRSA carriage, since nose only screening misses about 10 to 30% of carriers (who carry at other sites). Multisite swabs improve sensitivity.
• PCR positive for mecA only without S. aureus marker: coagulase negative staphylococci carrying mecA (false positive MRSA), and culture is needed. Cassette negative or mecC variants require assay design that detects them.
• Methicillin susceptible S. aureus (MSSA) detected: colonisation with susceptible strain, and screening and decolonisation of MSSA in surgical patients lowers surgical site infection in some cardiac and orthopaedic programmes.
• Nasal PCR negative in a patient with suspected MRSA pneumonia: MRSA pneumonia is very unlikely (negative predictive value 95 to 99%), and anti-MRSA antibiotics can be stopped safely, except in cavitary or necrotising disease or septic shock.
• Culture positive after decolonisation (screen at least 48 hours after the end of treatment, and repeat at 1 week to 1 month): persistent carriage.
• Panton-Valentine leukocidin positive community associated MRSA causes recurrent skin abscesses, necrotising pneumonia and severe disease in young healthy people, and is identified by gene testing in specialist laboratories.

Critical values and findings needing immediate action.

• MRSA in a blood culture, wound or sterile site (infection, not screening): intravenous vancomycin or an alternative (daptomycin, linezolid, ceftaroline) depending on site, with source control.
• MRSA carrier in intensive care, neonatal unit, burns or oncology ward: strict isolation, outbreak investigation if clustered, and notification to infection control.
• MRSA-positive patient with necrotising pneumonia, shock or toxin mediated disease: intensive care and addition of toxin suppressing antibiotic (clindamycin or linezolid) with immunoglobulin where indicated.
• Pre-operative MRSA-positive patient: decolonisation and adjustment of surgical prophylaxis to include vancomycin or teicoplanin.
• Staff colonised with MRSA linked to an outbreak: exclusion from work until decolonisation is documented.

Interferences and pitfalls.

• Colonisation is not infection, and positive screening should not trigger treatment of the patient for infection. It informs prophylaxis, isolation and empirical therapy.
• Nasal only screening has limited sensitivity, particularly in patients with extra-nasal carriage (groin, perineum, wounds), and sampling several sites is better.
• PCR can detect non-viable organisms and DNA for several days after decolonisation, and culture is preferred for confirmation of clearance. It can also give false positive results from mecA-carrying coagulase negative staphylococci.
• Chromogenic agar needs 24 to 48 hours and confirmation of presumptive colonies (coagulase, latex agglutination, cefoxitin disc diffusion), and some mecC strains are missed by PCR targeting mecA only.
• Mupirocin resistance (low- and high level) is increasing with widespread use, and decolonisation failure is more likely with resistant strains, extra-nasal carriage and reservoirs in the household.
• Screening tests do not replace hand hygiene, environmental cleaning and antimicrobial stewardship, which are the main controls.
• Universal decolonisation and screening policies differ between hospitals and countries. Adverse effects include resistance to mupirocin and chlorhexidine, allergy and cost.
• The timing of swabs relative to admission (within 24 hours) and repeat screening during a long stay (weekly in high risk units) are set by local policy.

Special groups.

• Neonates and children: neonatal units screen for outbreaks, and community acquired MRSA causes skin abscesses and pneumonia.
• Pregnancy: mupirocin and chlorhexidine are used for decolonisation in pregnancy, and MRSA colonisation in the vagina or rectum is a risk for neonatal infection.
• Dialysis, injecting drug users, prisoners, athletes and military recruits: increased colonisation and infection.
• Surgical patients: pre-operative screening and decolonisation with targeted prophylaxis reduce surgical site infection.
• Regions: MRSA prevalence varies from under 1% (Northern Europe) to over 50% of S. aureus isolates in some Asian, Middle Eastern and Latin American hospitals, with community associated lineages in Africa, and limited access to screening in low resource hospitals.

Follow up tests.

• Culture and susceptibility testing of the isolate (cefoxitin, mupirocin, vancomycin, linezolid).
• mecA or mecC and Panton-Valentine leukocidin PCR, spa typing or whole genome sequencing for outbreaks.
• Blood cultures when febrile, wound swab or pus culture.
• Multisite screening (groin, throat, axilla), repeat screening after decolonisation.
• Chlorhexidine susceptibility, household contact screening for recurrent infection, and environmental sampling in outbreaks.