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Rapid detection of methicillin-resistant Staphylococcus aureus

Rapid detection of methicillin-resistant Staphylococcus aureus
Literature review current through: Jan 2024.
This topic last updated: Jan 31, 2022.

INTRODUCTION — Approaches to rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) include rapid culture methods and molecular techniques. Several studies have examined the role of rapid detection methods as a component of MRSA control strategies.

Molecular diagnostic methods can reduce the turnaround time for detection of MRSA colonization and detection of MRSA from positive blood cultures. Rapid MRSA detection tools can also reduce the risk of MRSA surgical site infection, by providing information to guide decisions regarding choice of perioperative antimicrobial prophylaxis and preoperative decolonization.

Laboratory tools for rapid detection will be discussed here; the microbiology of MRSA and clinical issues related to MRSA surveillance are discussed in detail separately. (See "Methicillin-resistant Staphylococcus aureus (MRSA): Microbiology" and "Methicillin-resistant Staphylococcus aureus (MRSA) in adults: Prevention and control".)

DEFINITION — By definition, all MRSA isolates carry the mecA gene or a related variant known as mecC. These genes confer resistance to almost all beta-lactam antibiotics, including cephalosporins and carbapenems.

ANATOMIC SAMPLING SITE(S) — For the purposes of MRSA infection control surveillance, the anterior nares are the most common site for MRSA carriage; other important sites include the throat, axilla, groin, and perineum [1-3]. Lower sensitivities have been observed for non-nasal sample sites (eg, throat, axilla), perhaps due to lower colonization rates or higher quantities of competing flora at these sites. Rectal swabs may contain polymerase chain reaction inhibitors and therefore are of limited utility when molecular methods are used [4].

LABORATORY TOOLS

Cefoxitin disk screen test — Apart from using molecular methods to detect the mecA/mecC genes directly, the most accurate phenotypic test for the presence of the mecA/mecC genes in S. aureus is the cefoxitin disk diffusion test. Cefoxitin is used because it is a more potent inducer of mecA/mecC expression than other agents such as oxacillin and the test results are relatively easy to interpret. The test involves incubating a lawn of the test isolate on Mueller Hinton agar +2% sodium chloride under standardized conditions with a cefoxitin disk (30 mcg). According to the Clinical and Laboratory Standards Institute (CLSI), a zone of growth inhibition around the cefoxitin disk of ≥22 mm rules out MRSA; a zone size <22 mm indicates that the mecA gene is present and the isolate should be reported as MRSA. The test requires overnight incubation [5]. The cefoxitin disk screen test diameter for those using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) is also <22 mm [6].

Rapid culture

Chromogenic agar — Rapid culture makes use of chromogenic agar, which contains media substrates that change color in the presence of S. aureus; selectivity for MRSA is achieved by incorporation of antibiotics into the agar. Use of such agar allows identification of MRSA from primary isolation plates within 24 to 48 hours, obviating the need for additional subcultures or biochemical tests [7].

Chromogenic media are used primarily for detection of MRSA from surveillance specimens (nasal swabs and swabs of the throat, groin, and rectum) [1]. Chromogenic media has also been evaluated for identification of MRSA in blood cultures with high sensitivity and specificity at 18 to 24 hours (97.6 and 100 percent, respectively) [8].

There are several commercially available chromogenic media [7]. The reported sensitivities of these media vary widely (50 to 100 percent) and depend on the duration of incubation and the "gold standard" comparator [7,9-16]. However, after 24 hours of incubation, the specificities of these media are consistently high (90 to 100 percent). Prolonging the incubation time to 48 hours improves sensitivity but reduces specificity [7].

Many laboratories use a combination of chromogenic agar (read at 24 hours) and conventional culture methods. This approach allows early detection of many MRSA-colonized patients at 24 hours, with the remainder detected within the conventional 48- to 72-hour timeframe [7].

Enrichment broth — A novel culture method (BacLite rapid MRSA test) allows a negative result to be reported in five hours, although this assay is not available in the United States [17]. This method uses a selective enrichment broth containing cefoxitin and magnetic microparticle extraction of S. aureus followed by detection of adenylate kinase (a nonspecific cell marker). A negative result can be reported after five hours; a positive result can typically be reported the following day. Excellent sensitivity and specificity of this assay for nasal swabs have been reported (94.6 percent and 96.9 percent, respectively), although false-positive reactions with coagulase-negative staphylococci (CoNS) can occur [17].

Molecular methods — Molecular assays utilize target DNA sequences that include regions of the SCCmec element (which is common in S. aureus as well as coagulase-negative staphylococci), together with additional nucleic sequences specific for S. aureus. Different assays use different combinations of targets. Notably, not all molecular assays detect the mecC variant present in some MRSA [18,19].

When used to detect MRSA colonization, the positive and negative predictive values of molecular methods depend upon the prevalence of MRSA in the population. The high sensitivity of these tests results in a high negative predictive value, particularly in low-prevalence settings. Therefore, negative results are useful for exclusion of MRSA in low prevalence settings. Positive results, however, may require confirmation by culture before a definitive diagnosis of MRSA colonization can be made. Conversely, in high-prevalence settings, assays with high specificity may be used to definitively identify MRSA carriers because the positive predictive value will be high.

Commercial assays — Several commercial and laboratory-developed methods have been described using techniques such as conventional polymerase chain reaction (PCR), multiplex PCR, real time PCR (RT-PCR), and gene-probe hybridization [20]. These techniques allow detection of MRSA within two to six hours. However, the relatively high cost of molecular methods often necessitates batching of specimens, lengthening the turnaround time [7]. Given the large number of SCCmec elements and variants, the performances of the different assays vary depending on the strains of MRSA and coagulase-negative staphylococci present in any given sample.

First-generation molecular assays target the SCCmec-orfX junction. This target is present in some methicillin-resistant coagulase-negative staphylococci (MRCoNS), so false positives can occur in the presence of MRCoNS. When these assays are used on specimens such as nasal swabs where MRCoNS are frequently present, specificity can be compromised. In addition, these assays do not directly detect the mecA gene. This means that occasional isolates with SCCmec but without mecA ("mecA dropouts") can falsely identify as MRSA. Finally, these assays do not detect MRSA strains carrying the mecC gene. The sensitivity and specificity of these earlier assays compared to conventional culture for MRSA detection in surveillance swabs ranged from 90 to 98 percent and 91 to 99 percent, respectively [21-24].

Second-generation assays, approved by the US Food and Drug Administration from 2008, typically target three genes: SCCmec-orfX junction, the mecA gene, and the staphylococcal protein A (spa) gene. The SCCmec-orfX identifies all staphylococci, the mecA gene identifies methicillin resistance, and the spa gene identifies S. aureus. All three targets must be positive for MRSA to be deemed present. These assays do not detect MRSA due to mecC. Third-generation assays contain the targets present in second-generation assays plus a mecC target.

The reported performance of molecular assays is shown in the table (table 1).

The EVIGENE MRSA kit detects mecA as well as two separate sequences specific for S. aureus using three specific DNA probes. It is available in parts of Europe but not in the United States [25]. Unlike molecular assays that use PCR, this assay does not involve an amplification step. This assay showed sensitivity and specificity rates in excess of 99 percent for detection of MRSA in blood [25].

A broad range of tests are under development; whole genome sequencing for MRSA detection may play an important role in the laboratory and at the point of care [26].

Laboratory developed — Several laboratory-developed assays using real-time PCR have been described. One widely studied method uses immune-mediated capture of S. aureus onto magnetic beads, followed by multiplex real-time PCR to detect mecA (within SCCmec) and the S. aureus-specific femA gene [27-29]. This assay was used in two studies evaluating the utility of molecular surveillance techniques for universal screening of surgical patients and as part of a strategy to reduce MRSA infections in intensive care units [28,29]. Compared with conventional culture, the sensitivity and specificity of this technique was 100 percent [30].

Blood cultures — Molecular assays can reduce the time to identification of MRSA in positive blood cultures with gram-positive cocci in clusters seen on Gram stain. Examples of performance characteristics of such assays are included in the table (table 1).

The targets used in these assays tend to be the same as those used in assays intended for use on nasal swabs. Molecular assays that have not been validated for use on blood cultures may have unacceptable sensitivity due to potential PCR inhibitors present in blood culture media.

Respiratory cultures — Rapid methods have also been applied to tracheal aspirate and bronchoalveolar lavage/wash specimens to help diagnose lower respiratory tract infection, including suspected ventilator-associated pneumonia [31-34]. Performance characteristics of their application are included in the table. These off-label use reports have observed high negative predictive values for MRSA [31-33] or, in the report of Paonessa et al, a low likelihood ratio for MRSA, indicating treatment for MRSA can be withheld. A study has evaluated a version of the GeneXpert assay designed for endotracheal aspirates [35]. This assay performed well in detecting S. aureus but there were too few MRSA cases to allow analysis. In a setting with high rates of lower respiratory tract infections due to S. aureus, these assays would be useful in assisting in treatment decisions.

CLINICAL APPROACH — Selection of a rapid detection technique depends upon whether the assay is intended for active surveillance or rapid identification of MRSA from blood cultures or respiratory samples. If used for active surveillance, the choice of technique depends in part on MRSA prevalence in the population screened; it is prudent to avoid molecular assays with low specificity. If used for rapid identification of MRSA from blood cultures, an assay validated for this purpose should be selected. Selection of rapid detection technique also depends on the hospital's logistical needs and capacity to batch specimens, the technical expertise of laboratory staff, and financial resources.

The clinical utility of direct MRSA detection in blood cultures should be carefully evaluated before routine testing is adopted. Rapid testing can result in a decreased time to optimization of antibiotic therapy [36]. In a study, where 51 percent of blood isolates were MRSA, combining nucleic acid microarray testing with direct physician notification reduced the time to infectious disease consult and targeted treatment and was associated with lower in-hospital and 30-day mortality [37]. The benefits and cost effectiveness of routine testing depend on the local prevalence of MRSA and local approaches to empiric treatment.

In settings where empiric treatment commonly includes vancomycin, the likely value will be in reducing unnecessary use of this agent. Shorter durations of vancomycin or linezolid occurred when rapid detection was used for ventilated patients with suspected MRSA pneumonia [34].

SOCIETY GUIDELINE LINKS — Links to society and government-sponsored guidelines from selected countries and regions around the world are provided separately. (See "Society guideline links: Management of Staphylococcus aureus infection".)

SUMMARY

Cefoxitin disk diffusion testing is an accurate phenotypic method for determining whether a Staphylococcus aureus isolate is methicillin-resistant S. aureus (MRSA). A zone size <22 mm indicates that the mecA gene is present, and the isolate should be reported as MRSA. (See 'Cefoxitin disk screen test' above.)

Rapid culture methods that utilize chromogenic agar allow detection of MRSA from active surveillance specimens at 24 hours with high specificity but lower sensitivity than conventional culture. (See 'Chromogenic agar' above.)

For the purposes of MRSA infection control surveillance, the anterior nares are the most common site for MRSA carriage; other important sites include the throat, axilla, groin, and perineum. (See 'Anatomic sampling site(s)' above.)

In general, molecular methods can detect MRSA with high sensitivity within several hours. Most techniques can reliably detect MRSA from active surveillance specimens. Several commercial assays have been developed for evaluation of positive blood cultures and show high sensitivity and specificity; only assays validated for this purpose should be used. (See 'Laboratory tools' above.)

The clinical utility of any testing algorithm for direct detection of MRSA in blood cultures needs to be carefully evaluated based on the local prevalence of MRSA, empiric treatment practices, and laboratory testing logistics. (See 'Clinical approach' above.)

Some molecular methods may have poor specificity for MRSA when used on specimens containing mixtures of S. aureus and methicillin-resistant coagulase-negative staphylococci. These assays have limited utility in definitively identifying MRSA carriage in low-prevalence settings. (See 'Molecular methods' above.)

Clinical issues related to MRSA surveillance are discussed in detail separately. (See "Methicillin-resistant Staphylococcus aureus (MRSA): Microbiology" and "Methicillin-resistant Staphylococcus aureus (MRSA) in adults: Prevention and control".)

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