A PCR method for the identification of methicillin-resistant Staphylococcus aureus (MRSA) from screening swabs

Differentiation between Staphylococcus aureus and coagulase-negative Staphylococcus species by real-time PCR including detection of methicillin resistants in comparison to conventional microbiology testing

BACKGROUND

Staphylococcus aureus has long been recognized as a major pathogen. Methicillin-resistant strains of S. aureus (MRSA) and methicillin-resistant strains of S. epidermidis (MRSE) are among the most prevalent multiresistant pathogens worldwide, frequently causing nosocomial and community-acquired infections.

METHODS

In the present pilot study, we tested a polymerase chain reaction (PCR) method to quickly differentiate Staphylococci and identify the mecA gene in a clinical setting.

RESULTS

Compared to the conventional microbiology testing the real-time PCR assay had a higher detection rate for both S. aureus and coagulase-negative Staphylococci (CoNS; 55 vs. 32 for S. aureus and 63 vs. 24 for CoNS). Hands-on time preparing DNA, carrying out the PCR, and evaluating results was less than 5 h.

CONCLUSIONS

The assay is largely automated, easy to adapt, and has been shown to be rapid and reliable. Fast detection and differentiation of S. aureus, CoNS, and the mecA gene by means of this real-time PCR protocol may help expedite therapeutic decision-making and enable earlier adequate antibiotic treatment.

Clinical utility of the Xpert MRSA assay for early detection of methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is responsible for many nosocomial and community-acquired infections, resulting in significant morbidity and mortality. A practical way to limit the spread of MRSA is early detection and proper treatment. However, screening culture for MRSA typically requires 2-3 days. The Xpert MRSA assay (Cepheid, Sunnyvale, CA, USA) is a real-time polymerase chain reaction-based assay developed for screening an MRSA-specific DNA sequence within the staphylococcal cassette chromosome in 2 h. Lower respiratory tract specimens, such as transtracheal aspirates (TTAs) and bronchoalveolar lavage fluid (BALF), are commonly obtained from intubated patients. Therefore, using the lower respiratory tract specimens with the Xpert MRSA assay may be a practical tool for patient care. We performed the Xpert MRSA assay on 108 TTA and 21 BALF specimens from 92 patients and compared the results to those obtained by culture. The two assays showed concordant results in 120 (93.0%) cases and discordant results in 9 (7.0%) cases, which were culture‑negative and Xpert MRSA-positive. Among the discordant cases, 5 patients developed culture-positive samples 2-15 days after the Xpert MRSA detected MRSA. We conclude that the Xpert MRSA assay is a rapid, sensitive and clinically useful test, particularly for the early detection of MRSA.

Transmission rates, screening methods and costs of MRSA--a systematic literature review related to the prevalence in Germany

Methicillin-resistant Staphylococcus aureus (MRSA) infections represent a serious challenge for health care institutions, which is inherent in the combination of prevalence, transmission rates and costs. Furthermore, performing an MRSA screening requires information on the complex system of effectiveness, accuracy and costs of different screening methods. The purpose of this study was to give an overview of parameters with decisive significance for the burden of MRSA and the selection of a specific MRSA screening strategy. A systematic literature search for peer-reviewed health economic studies associated with MRSA was performed (from 1995 to the present). Eighty-seven different studies met all inclusion and exclusion criteria. Primary outcomes included the prevalence of MRSA, MRSA transmission rates, performance characteristics of MRSA screening methods, costs for pre-emptive isolation precautions and costs per MRSA case. The prevalence rates reported for all inpatients (1.2-5.3 %) as well as for inpatients with risk factors or patients in risk areas (3.85-20.6 %) vary greatly. The range of cross-transmission rates per day reported for patients with MRSA in isolation is 0.00081-0.009 and for carriers not in isolation is 0.00137-0.140, respectively. For polymerase chain reaction (PCR) methods, the mean sensitivity and specificity were 91.09 and 95.79 %, respectively. Culture methods show an average sensitivity of 89.01 % and an average specificity of 93.21 %. The turn-around time for PCR methods averages 15 h, while for the culture method, it can only be estimated as 48-72 h. This review filtered important parameters and cost drivers, and covered them with literature-based averages. These findings serve as an ideal evidence base for further health economic considerations of the cost-effectiveness of different MRSA screening methods.

Diagnostic accuracy of culture-based and PCR-based detection tests for methicillin-resistant Staphylococcus aureus: a meta-analysis

A systematic review and meta-analysis were performed to determine and compare the sensitivity and specificity of PCR-based and culture-based diagnostic tests for methicillin-resistant Staphylococcus aureus (MRSA). Our analysis included 74 accuracy measurements from 29 publications. Nine tests were evaluated: the PCR-based Genotype MRSA Direct and IDI-MRSA, the chromogenic media CHROMagar, Chromogenic MRSA Medium, MRSA ID, MRSA Select and ORSAB, and the nonchromogenic culture media MSA-Cefoxitin and MSA-Oxacillin. For four chromogenic media, incubation periods of 18-24 and 48 h were evaluated. Considerable heterogeneity was detected in most analyses. A significantly higher sensitivity was found for the overall PCR pooled estimate (92.5; 95% CI 87.4-95.9) and the chromogenic media after 48 h of incubation (87.6; 95% CI 82.1-91.6) compared to the overall sensitivity of chromogenic media after 18-24 h (78.3; 95% CI 71.0-84.1). The specificity of chromogenic media after 18-24 h (98.6; 95% CI 97.7-99.1) was higher than the specificity of PCR (97.0; 95% CI 94.5-98.4) but declined after 48 h of incubation (94.7; 95% CI 91.6-96.8).The most sensitive chromogenic medium after 18-24 h of incubation was Chromogenic MRSA Medium (sensitivity: 89.3; 95% CI 72.8-96.3), whereas the most specific chromogenic medium after 18-24 h of incubation was MRSA Select (specificity: 99.4; 95% CI 98.6-99.7). After 48 h of incubation, MRSA Select had the highest sensitivity (93.2; 95% CI 83.5-97.0), whereas CHROMagar had the highest specificity (96.4; 95% CI 91.3-98.5). This meta-analysis showed statistically significant differences in diagnostic accuracy between several of the tests and the test methods evaluated. A reduction of the incubation time of chromogenic media (from 48 to 18-24 h) increases specificity but reduces sensitivity.

Clinical application of real-time PCR to screening critically ill and emergency-care surgical patients for methicillin-resistant Staphylococcus aureus: a quantitative analytical study

The clinical utility of real-time PCR screening assays for methicillin (methicillin)-resistant Staphylococcus aureus (MRSA) colonization is constrained by the predictive values of their results: as MRSA prevalence falls, the assay's positive predictive value (PPV) drops, and a rising proportion of positive PCR assays will not be confirmed by culture. We provide a quantitative analysis of universal PCR screening of critical care and emergency surgical patients using the BD GeneOhm MRSA PCR system, involving 3,294 assays over six months. A total of 248 PCR assays (7.7%) were positive; however, 88 failed to be confirmed by culture, giving a PPV of 65%. Multivariate analysis was performed to compare PCR-positive culture-positive (P+C+) and PCR-positive culture-negative (P+C-) assays. P+C- results were positively associated with a history of methicillin-sensitive Staphylococcus aureus infection or colonization (odds ratio [OR], 3.15; 95% confidence interval [CI], 1.32 to 7.54) and high PCR thresholds of signal intensity, indicative of a low concentration of target DNA (OR, 1.19 per cycle; 95% CI, 1.11 to 1.26). P+C- results were negatively associated with a history of MRSA infection or colonization (OR, 0.19; 95% CI, 0.09 to 0.42) and male sex (OR, 0.40; 95% CI, 0.20 to 0.81). P+C+ patients were significantly more likely to have subsequent positive MRSA culture assays and microbiological evidence of clinical MRSA infection. The risk of subsequent MRSA infection in P+C- patients was not significantly different from that in case-matched PCR-negative controls. We conclude that, given the low PPV and poor correlation between a PCR-positive assay and the clinical outcome, it would be prudent to await culture confirmation before altering infection control measures on the basis of a positive PCR result.

Direct detection of methicillin-resistant Staphylococcus aureus in clinical specimens by a nucleic acid-based hybridisation assay

The occurrence of methicillin-resistant Staphylococcus aureus (MRSA) is still increasing worldwide and is associated with significant morbidity, mortality and hospital costs. Screening for MRSA plays a key role in limiting further nosocomial spread of this organism. Control measures require a rapid and sensitive test for direct detection of MRSA carriage. This study evaluated an easy-to-use PCR-hybridisation assay for the direct detection of MRSA in clinical swab specimens. In total, 508 pairs of swabs from 242 patients at risk for MRSA carriage were analysed by the standard culture method and the PCR assay. One swab was used for PCR and culture, while the second was used for culture only. Of the 508 pairs tested, 37 were positive by culture and 35 were positive by PCR. Among the 471 culture-negative specimens, 465 were negative by PCR and six were PCR-positive. The PCR assay had a sensitivity of 94.59%, a specificity of 98.73%, a positive predictive value of 85.37%, and a negative predictive value of 99.57%. The PCR-hybridisation assay enabled reliable detection of MRSA carriage in c. 4 h, thereby allowing its effective use in an MRSA control strategy.

Rapid diagnostics for methicillin-resistant Staphylococcus aureus: current status

Methicillin-resistant Staphylococcus aureus (MRSA) is a significant cause of healthcare- and community-associated infections, and its prevalence continues to increase. These infections are associated with morbidity and excessive mortality compared with infections caused by methicillin-susceptible S. aureus (MSSA). Numerous studies have cited the increased healthcare costs associated with MRSA infections. Infection control guidelines that combine active surveillance with aggressive patient management, such as patient isolation, decontamination, and other strategies, have been shown to reduce transmission and subsequent infections. The availability of rapid molecular diagnostics has strengthened infection control programs by providing results in hours rather than days, as the time required for culture-based methods. This review summarizes the current status of rapid diagnostic methods available for MRSA detection from nasal surveillance specimens, and assays available for rapid identification of MRSA from positive blood cultures containing Gram-positive cocci in clusters. Both amplification- and probe-based assays are highlighted and discussed in detail. Future technological advances are likely to see real-time assays that combine multiple gene targets for assessment of microbial identification, virulence detection, and mechanisms of resistance beyond mecA.

Development of a real-time Staphylococcus aureus and MRSA (SAM-) PCR for routine blood culture

The notification of "Gram-positive cocci, possibly staphylococcus" in a blood culture drawn from a seriously ill patient is responsible for a large amount of vancomycin prescribing in institutions where methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of bacteraemia. A duplex real-time TaqMan polymerase chain reaction targeting the species-specific nuc gene, and the mecA gene encoding methicillin-resistance, was developed as a tool for rapid identification and detection of S. aureus and methicillin-resistance, and optimised for immediate as-needs testing. Three different DNA extraction methods achieved varying DNA quality, with PCR inhibition the main problem. Serial blood cultures (n=120) identified as possible staphylococci on Gram stain from our clinical laboratory were examined. There was one false negative result for a methicillin-resistant Staphylococcus epidermidis, which was positive on repeat testing, and one false negative result due to DNA extraction failure for MRSA from peritoneal dialysate inoculated into blood culture medium. Sensitivity and specificity of 97% and 100%, respectively, were obtained for mecA; and sensitivity and specificity of 98% and 100%, respectively, for nuc. Detection of slow-growing coagulase-negative staphylococci as co-infecting strains may be reduced. The assay quickly and reliably identified S. aureus in mixed infection, and identified methicillin resistance in both S. epidermidis and S. aureus strains.

Improved and rapid detection of methicillin-resistant Staphylococcus aureus nasal carriage using selective broth and multiplex PCR

To improve efficiency in detecting nasal methicillin-resistant Staphylococcus aureus (MRSA), we evaluated a multiplex PCR using pre-enrichment of the specimen in selective broths, and compared it with detection performed by routine tests in hospital laboratories. Nasal swab specimens from 311 patients were inoculated onto mannitol-salt agar (MSA) at the hospital laboratories and in two Mueller-Hinton broths with 7% NaCl containing oxacillin at concentrations of 2 and 4 micro g/ml. Isolates on MSA were identified as MRSA by classical laboratory tests (coagulase and oxacillin disk diffusion tests). Oxacillin broth cultures were subcultured on blood agar and MRSA isolates were identified by coagulase and susceptibility tests, including agar dilution and the oxacillin-screening method (gold standard method). Simultaneously, multiplex-PCR was performed from the selective broths to detect S. aureus species-specific and mecA gene segments (OxMPCR method). Thirty-two S. aureus isolates were recovered: 29 (90.6%) were MRSA strains and 3 (9.4%) were oxacillin-susceptible isolates. Twenty-eight (96.5%) MRSA isolates were detected by OxMPCR, while 17 (58.6%) were identified by routine tests (P=0.002). This new method for detection of MRSA nasal carriers showed higher sensitivity and led to faster reporting--i.e., within 24 h--of results.

Bayesian inference of hospital-acquired infectious diseases and control measures given imperfect surveillance data

This paper describes a stochastic epidemic model developed to infer transmission rates of asymptomatic communicable pathogens within a hospital ward. Inference is complicated by partial observation of the epidemic process and dependencies within the data. The epidemic process of nosocomial communicable pathogens can be partially observed by routine swabs testing for the presence of the pathogen. False-negative swab results must be accounted for and make it difficult to ascertain the number of patients who were colonized. Reversible jump Markov chain Monte Carlo methods are used within a Bayesian framework to make inferences about the colonization rates and unknown colonization times. The methods are applied to routinely collected data concerning methicillin-resistant Staphylococcus Aureus in an intensive care unit to estimate the effectiveness of isolation on reducing transmission of the bacterium.

Improving the treatment of musculoskeletal infections with molecular diagnostics

Molecular diagnostic strategies have been implemented to enhance the treatment of musculoskeletal infections. Once primarily a research tool, molecular-based assays, have become accepted clinical tests for the genomic detection of certain pathogens involved in bone and joint infections. Currently, culture remains the gold standard for identifying most organisms causing infection. However, molecular assays are beneficial in clinical cases in which standard culture-based tests are unreliable or untimely. We will review current clinical utility of this emerging technology and roles for assays in the future.