Can the Xpert MRSA/SA BC assay be used as an antimicrobial stewardship tool? A prospective assay validation and descriptive impact assessment study in a South African setting

Background Positive blood cultures showing Gram positive cocci in clusters signifies either Staphylococcus aureus or the less-virulent coagulase-negative staphylococci. Rapid identification and methicillin susceptibility determination with the Xpert MRSA/SA BC assay can improve management of S. aureus bloodstream infection and reduce inappropriate antibiotic use. Methods We prospectively evaluated the Xpert MRSA/SA BC assay in comparison with culture, on samples referred to our laboratory in the Western Cape, South Africa. We interviewed attending clinicians upon culture result availability, to assess antibiotic choices and estimate potential impact of the assay. Results Of the 231 samples included, there was 100% concordance between the Xpert MRSA/SA BC assay and culture (methicillin-resistant S. aureus 15/15, methicillin-susceptible S. aureus 42/42, coagulase-negative staphylococci 170/170). Time to final result could be reduced by approximately 30 h with the assay. Of the 178 patients with adequate antibiotic history, optimisation of antistaphylococcal therapy could have occurred more than 1 day sooner in 68.9% with S. aureus bloodstream infection (31/45, 95% CI 53.2–81.4%). Six of the 11 patients with methicillin-resistant S. aureus bloodstream infection (54.5%) could have received anti-MRSA cover sooner. Fifty-four days of antibiotic therapy could have been spared, equating to 0.3 days (95% CI, 0.2–0.4) saved per patient, driven by broad-spectrum beta-lactams (32 days, in 18.0% of the cohort). Conclusion This assay has potential as an antimicrobial stewardship tool; costing and impact on clinical outcome in patients with S. aureus bloodstream infection should be assessed. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05857-7.


Background
Staphylococcus aureus is a common cause of bloodstream infection (BSI) [1], with a mortality rate of 20-40% [1]. In contrast, coagulase-negative staphylococci (CoNS) are generally regarded as skin commensals of low pathogenic potential, although they can be clinically significant in selected circumstances.
Differentiating between CoNS and S. aureus in positive blood culture broths showing Gram positive cocci in clusters (GPCC) on Gram stain, typically requires assessment of morphological and biochemical characteristics after overnight incubation. In addition, susceptibility testing is required to differentiate between methicillin-susceptible and methicillin-resistant S. aureus (MSSA and MRSA, respectively). These requirements can result in delayed initiation of appropriate therapy in patients with S. aureus BSI, with potentially adverse outcomes including secondary infectious complications [2], a higher mortality rate and prolonged hospital stay [1]. Conversely, inappropriate antibiotic administration unnecessarily exposes the patient to potential adverse effects of the medication, alters gastrointestinal flora, and also has ecological effects, including contributing to antibiotic selective pressure which drives resistance.
The Xpert MRSA/SA BC System (Cepheid, Sunnyvale, California) differentiates between MRSA, MSSA and CoNS from positive blood cultures within approximately 1 h, using a real-time, semi-automated, nucleic acid-based test which targets spa and the SCCmec-orfX junction (for S. aureus), and mecA (for methicillin resistance). Published studies, summarised in one paper [3], report sensitivities and specificities of 96.4-100% and 98.0-100% respectively, for the detection of MSSA, and values of 87.5-100% and 98.3-100% respectively, for detection of MRSA. Initial concerns regarding undercalling of MRSA with specific SCCmec variants, were resolved in 2013 [3].
We evaluated the Xpert MRSA/SA BC System (Xpert) and assessed the potential impact of implementation of this test as an antimicrobial stewardship tool in the patient population served by our laboratory in Cape Town, South Africa.

Study aims, design and setting
We aimed to assess the performance and role of the Xpert in facilitating more appropriate antibiotic use in patients with S. aureus bloodstream infection, and reducing inappropriate antibiotic therapy in those with S. aureus and with coagulase-negative staphylococci. We performed a prospective observational study to evaluate the Xpert against the reference method of culture-based techniques, and to describe the potential impact of implementation of this assay in our setting by combining clinical history with attending clinician survey.
The study took place from January to June 2016 at the National Health Laboratory Service (NHLS) Microbiology laboratory at Tygerberg Hospital in the Western Cape, South Africa. Tygerberg Hospital is a 1384-bedded referral hospital serving the northern and eastern subdistricts of the Cape Metro region, and the surrounding rural districts, including 4 regional hospitals and 17 district hospitals.
Blood culture bottles were submitted from facilities throughout this drainage area at the clinicians' discretion. The automated blood culture system in use is the BacT/Alert 3D Microbial Detection System (bioMérieux, Marcy L'Étoile, France) which includes anaerobic (FN Plus), aerobic (FA Plus) and paediatric bottles (PF Plus). These were kept at room temperature during transport, and were incubated as soon as possible after specimen receipt. After flagging positive, Gram stains are performed on an aliquot of the broth. All patients with positive blood cultures exclusively showing GPCC on Gram stain, were included. Blood culture specimens showing mixed morphology on Gram stain, and duplicate blood culture samples from the same patient, were excluded.
Paediatric patients were defined as patients below the age of 13 years.

Classification and management of suspected sepsis
Patients with positive blood cultures (indicating suspected sepsis) were defined as having communityacquired (CA) infection if the culture was collected < 72 h after admission, and hospital acquired (HA) infection thereafter; admission within the preceding 6 weeks was also considered a criterion for HA infection [4] .
Empiric management of CA infections was based on local guidelines, with ceftriaxone or amoxicillinclavulanate used for most infections; cloxacillin was recommended where S. aureus was likely. During the study period, standard-of-care was to administer a carbapenem +/− vancomycin (for suspected MRSA) for presumed hospital-acquired sepsis.
Regional hospital guidelines in our drainage area advise a targeted approach of a semi-synthetic betalactamase stable penicillin (cloxacillin) for MSSA BSI, with vancomycin advised for MRSA BSI.

Laboratory processing
Consecutive samples were processed in parallel using culture-based methods and Xpert, during weekdays between 8 am and 4 pm. The investigator performing the Xpert was blinded to the culture results.
Culture-based methods entailed inoculation and overnight incubation of basic enriched agar media; Kirby-Bauer disk diffusion testing of an aliquot of broth against a standard anti-staphylococcal antibiotic panel; and identification using DNAse and Mannitol Salt Agar (MSA) plates. A rapid latex agglutination test was performed using the Pastorex Staph Plus kit (Bio-Rad, Hercules, California) for indeterminate identification results. VITEK 2 Gram positive ID confirmation (bioMérieux, Marcy L'Étoile, France) was used at the discretion of the clinical microbiologist, and methicillin susceptibility was determined by cefoxitin disk diffusion testing using the Clinical and Laboratory Standards Institute (CLSI) guidelines [5].
Batched Xpert testing was performed on blood culture bottles, which were stored at 35°C following culturebased processing. The Xpert MRSA/SA BC G3 version 5 (Cepheid, Sunnyvale, California) was performed as per manufacturer's instructions. Briefly, 50 μl of blood culture broth was added to the vial containing the elution reagent and vortexed for 10 s. The contents of the vial were transferred to the test cartridge and loaded into the module. Xpert testing was performed as soon as possible after positivity; there was a maximum delay of 80 h for bottles flagging positive over a weekend. The results of the Xpert assay were not made available to the clinicians.
The results of these methods were interpreted as summarised in Table 1.

Impact assessment and definitions
As per standard practice, clinicians were contacted with the Gram stain result if the available clinical information or previous results suggested S. aureus sepsis, or if the patient was admitted in an Intensive Care Unit (ICU). In all other cases, clinicians were contacted with the culture result, whether S. aureus or CoNS.
Basic clinical and demographic information were obtained, including an antibiotic history. We surveyed the attending clinicians to assess whether knowledge of the culture and susceptibility result on the day the bottle flagged positive would have impacted antibiotic choice. This was categorised as: Modification: a change from an ineffective to a more effective agent, or the addition of a semisynthetic penicillin (MSSA) or glycopeptide (MRSA); De-escalation: a change in antibiotic to a narrowerspectrum, targeted antistaphylococcal agent, or cessation of some or all antibiotics; No change: no change to the empiric antibiotic regimen, or no antibiotics prescribed if the patient was not receiving antibiotics.
We regarded cephalosporins (with the exception of ceftazidime), beta-lactam-beta-lactamase inhibitors, carbapenems and vancomycin as being active against MSSA. Penicillin, ampicillin, amoxicillin, and ceftazidime were the beta-lactam agents regarded as being ineffective against MSSA.
CoNS were considered significant only if reported as the likely cause for the patient's clinical condition, as judged by the attending clinician.
Days of antibiotic therapy saved were also evaluated during clinician interview, based on the empiric antibiotic regimen commenced and on clinician opinion as to whether an earlier result would have impacted antibiotic choice or duration (i.e. if the Xpert had been utilised as soon as the bottle flagged positive, leading to a "final" result being available shortly after Gram stain availability).

Statistical analysis
Microsoft Excel, VassarStats (www.vassarstats.net) and EpiCalc 2000 v1.02 (Brixton Books, South London, UK) were used, with an α-level of 0.05 chosen. Continuous numerical variables were summarised using means and standard deviations for normally distributed variables, or medians and interquartile ranges (IQR) for variables not following a normal distribution. Binary categorical variables were summarised using proportions and 95% confidence intervals (CI). Comparison of selected independent proportions were evaluated using the z-test.

Results
Our laboratory processed 2822 positive blood culture bottles between January and June 2016. Of these, 1158 (41.0, 95% CI 39.2-42.9%) demonstrated only GPCC on Gram stain and Information on the suspected source of sepsis was obtained in 46 patients with S. aureus BSI. The most commonly identified suspected source of sepsis (in isolation or as part of two potential sources) was skin or skin structure infection (n = 16, 34.8%), followed by suspected respiratory tract infection (n = 11, 23.9%). Source was undetermined at the time of clinician interview in 8 patients with S. aureus BSI (17.4%).
Characteristics of the included patients can be found in Supplementary Table 2.

Impact on antibiotic administration
Adequate antibiotic history was obtained in 181 patients, including 34 with MSSA and 11 with MRSA BSI. Three patients were unclassified due to discordance between culture result, clinical history and antibiotic therapy; these were excluded from the analysis (additional notes in Supplementary Table 3). Empiric antibiotic therapy choices for the remaining 178 patients (including one with significant CoNS BSI resulting from a central line infection) are outlined in Fig. 1.
The antibiotic changes over time are summarised in Fig. 2 (whole cohort) and Table 3 (subgroup with S. aureus BSI). The impact of the Xpert could be discerned by proxy if culture result availability approximated availability of the Gram  Table 4.

MRSA
Most patients with MRSA BSI did not receive an MRSAactive agent until release of the final culture result (

Days of therapy potentially saved
In the 178 patients with known antibiotic history, at least 32 days of exposure to a broad spectrum betalactam (beta-lactam-beta-lactamase inhibitor combination, extended-spectrum cephalosporin or carbapenem) could have been spared with earlier knowledge of the final result, equating to a reduction in broad spectrum beta-lactam use in 18.0% of the patients in this study (32/178, 95% CI 12.8-24.6%). A further 5 days of vancomycin use could have been avoided, and 17 days of antibiotic therapy could have been spared for the other agents (Supplementary Table 5). This equates to a reduction of 0.3 antibiotic days per patient (95% CI, 0.2-0.4).
In total, at least 54 days of antibiotic therapy could have been spared in the 178 patients with GPCC on blood culture in this study.

Evaluation
The Xpert MRSA/SA BC system reliably differentiated S. aureus from CoNS. The assay showed a high sensitivity and specificity, was easy to use and is potentially Fig. 1 Empiric antibiotics in patients with GPCC on blood culture and adequate antibiotic history. MSSA: methicillin-sensitive Staphylococcus aureus; GPCC: Gram positive cocci in clusters. a Ceftriaxone/cefotaxime were included as MSSA-active beta-lactam agents when used empirically implementable in a South African setting, where Xpert modules are widely available as part of the national programme for diagnosis of tuberculosis.
Methicillin resistance was detected with 100% accuracy in S. aureus; the small MRSA sample size precludes firm conclusions. Methicillin resistance in S. aureus is chiefly mediated by mecA at present, although mecC-mediated resistance has been reported in 0.004% of human isolates [6]. The assay also performed well for MSSA BSI, showing 100% concordance with culture-based testing. The error rate of 1.7% is similar to previous reports [3,7] and is acceptable. Although this assay has not been rigorously tested for the detection of methicillin resistance in CoNS to date, the negative predictive value of 95.8% in this context may be useful in selected cases of potentially significant CoNS bloodstream infection.
We recommend conventional culture to be performed at least limitedly in parallel, for mixed cultures, as a backup in case of an unsuccessful Xpert result and for further antimicrobial susceptibility testing or surveillance. Genotype-phenotype mismatch, with the Xpert assay incorrectly reporting a susceptible methicillin result due to insertions in the SCCmec-orfX junction region, has been reported in 3 S. aureus isolates from the United States [8], and misclassification of S. aureus as CoNS in 2 isolates from Australia [9]. Studies investigating the prevalence of mutations that may affect the targets of this assay in a South African setting are needed to define the role of this assay more accurately.

Potential impact of implementation
To our knowledge, this is the largest study assessing the potential impact of this assay to date. The median time saving to final result with use of this assay was approximately 30 h if the Xpert assay was performed immediately after microscopy, in line with previous estimates of a time saving of 24-48 h [2,10]. This crude estimate can be influenced by factors such as workflow. Antibiotic therapy was optimised on availability of final result in 68.9% with S. aureus BSI. This impact was most clearly demonstrated in patients with MRSA BSI, where more than 50% received anti-MRSA therapy only in response to the final culture result. A more modest impact could be seen for patients with MSSA BSI (approximately 21%); however, it must be noted that this is a conservative estimate as all beta-lactam agents were considered to have activity against MSSA in this analysis, although they may not be  equally suitable for the treatment of MSSA BSI and some are associated with a higher odds of death [11]. More rapid administration of appropriate therapy can significantly impact mortality. In one study, the mean mortality rate was 59% for patients with MRSA BSI who were initially started on a semisynthetic penicillin, as opposed to 23-36% for patients initially started on vancomycin [12]. The mean mortality rate was as low as 12% in patients empirically placed on a semisynthetic penicillin, who cultured MSSA [12]. Future studies should specifically assess the clinical impact of Xpert on more appropriate S. aureus therapy.
We estimated a reduction in broad spectrum betalactam antibiotic use in 18.0% of the cohort where antibiotic history was available, with 54 days of antibiotic therapy saved. This translates to a modest reduction in antibiotic days of therapy of 0.3 days per patient. When combined with the benefits shown in optimising therapy for S. aureus BSI infection, this may still be regarded as advantageous, particularly when considered with the consequences of unnecessary antibiotic prescription.
We initially expected this assay to be of most use in reducing antibiotic therapy in patients with CoNS, as has been reported previously [13], but this finding was not replicated. The vast majority of CoNS bloodstream isolates were regarded as being not clinically significant in this cohort, in keeping with the high rate of blood culture contamination in our setting [14]. Clinicians thus disregarded this "contaminated" result and continued the empiric antibiotic regimen that had been commenced based on the initial clinical assessment. Decisions regarding antibiotics are also governed by other factors not measured in this study, such as the clinical response to antibiotic therapy and additional test results. Although availability of relevant rapid diagnostic tests such as the Xpert is a core element to antimicrobial stewardship programmes in healthcare facilities in low-middle income countries [15], good quality microbiological sampling is also crucial and results in more appropriate use of laboratory resources. Ongoing educational interventions to optimise blood culture sampling (and reduce blood culture contamination) is a relatively cost-effective and easily implementable measure that can be instituted before turning to more costly solutions, and it is important that this remains a focus of antimicrobial stewardship programmes in resource-limited settings.
The potential benefits described must be weighed against the expense of the assay, including additional labour, infrastructure and consumable costs. The total cost of the test may be prohibitive in a resourceconstrained setting such as our own.
Limitations to this study include that the S. aureus BSI rate was only 25.1% of all blood cultures with Gram positive cocci in clusters, and that methicillin resistance was detected in 26.3% of all S. aureus-containing blood cultures (similar to a contemporaneous study in our setting (27.1%) [16]); this resulted in modest absolute numbers of MSSA and MRSA BSI. This may confer a more moderate impact of test performance than would be seen in higher prevalence settings. CA-MRSA is also not common in our setting currently [17]. Secondly, complete clinical records were not available for all patients, prohibiting case-by-case assessment of whether antibiotic changes occurred as a result of the microbiological results or the evolving clinical picture. Furthermore, clinician recall bias may have influenced these results. Thirdly, other patient comorbidities, such as renal failure and severity of illness, may have contributed to the choice of agents used and the decision to modify antibiotic therapy; this could not be easily assessed. Fourthly, we sampled a proportion of those eligible for inclusion; although we compared these populations for all the key variables that would be available in a routine diagnostic laboratory setting (thereby limiting selection bias), other variables, such as source of sepsis, were not taken into account. Additionally, significant CoNS BSI may have been underestimated in this study, as clinicians in our setting infrequently adhere to recommendations for multiple blood cultures to be submitted in the investigation of sepsis. Finally, most beta-lactam agents were considered to have anti-MSSA activity for the purposes of this study, which may result in an underestimate of the clinical benefit of the assay for MSSA BSI.

Conclusion
The Xpert MRSA/SA BC assay performed well in differentiating S. aureus from CoNS on positive blood cultures with Gram positive cocci in clusters and in detecting methicillin resistance in S. aureus, and the assay may be an effective antimicrobial stewardship tool. Further studies may need to be performed in areas with differing blood culture contamination and MRSA rates. We demonstrated potential benefit in reducing time to appropriate therapy in the majority of patients with S. aureus bloodstream infection. Antibiotic modification based on the clinical response may have played a role in amplifying or attenuating the benefit observed in this study. We showed a modest reduction in antibiotics prescribed; studies limited to a more homogenous population may show a greater benefit. Additional studies assessing potential impact should focus on individual patient clinical status and outcomes, and should take into account source control, cost reduction in terms of antibiotic administration and hospital stay, and comprehensive costing.
Additional file 1: Table S1. Diagnostic accuracy of the Xpert MRSA/SA BC assay on positive blood cultures containing Gram positive cocci in