Impact of results of a rapid Staphylococcus aureus diagnostic test on prescribing of antibiotics for patients with clustered gram-positive cocci in blood cultures

Shortening identification times: comparative observational study of three early blood culture testing protocols

Background

While early appropriate antibiotic therapy is a proven means of limiting the progression of infections, especially bacteremia, empirical antibiotic therapy in sepsis is ineffective up to 30%. The aim of this study was to compare early blood culture testing protocols in terms of their ability to shorten the delay between blood sampling and appropriate antibiotic therapy.

Methods

In this french observational study, we compared three blood culture testing protocols. Positive blood cultures were tested using either GenMark ePlex panels (multiplex PCR period), a combination of MRSA/SA PCR, β-Lacta and oxidase tests (multitest period), or conventional identification and susceptibility tests only (reference period). Conventional identification and susceptibility tests were performed in parallel for all samples, as the gold standard.

Results

Among the 270 patients with positive blood cultures included, early and conventional results were in good agreement, especially for the multitest period. The delay between a blood culture positivity and initial results was 3.8 (2.9-6.9) h in the multiplex PCR period, 2.6 (1.3-4.5) h in the multitest period and 3.7 (1.8-8.2) h in the reference period (p<0.01). Antibiotic therapy was initiated or adjusted in 68 patients based on early analysis results. The proportion of patients receiving appropriate antibiotic therapy within 48 h of blood sampling was higher in the multiplex PCR and multitest periods, (respectively 90% and 88%) than in the reference period (71%).

Conclusion

These results suggest rapid bacterial identification and antibiotic resistance tests are feasible, efficient and can expedite appropriate antibiotic therapy.

Optimizing Treatment of Staphylococcus aureus Bloodstream Infections Following Rapid Molecular Diagnostic Testing and an Antimicrobial Stewardship Program Intervention

Pending antibiotic susceptibility results, vancomycin is often used for bloodstream infections (BSIs) to ensure treatment of methicillin-resistant Staphylococcus aureus (MRSA). As rapid discrimination of methicillin-susceptible S. aureus (MSSA) from MRSA in BSIs could decrease vancomycin use and allow early optimization of beta-lactam therapy, this study evaluated the impact of the use of rapid molecular testing for MSSA and MRSA coupled with an antimicrobial stewardship program (ASP) intervention. Between January and July 2020, the Cepheid Xpert MRSA/SA blood culture assay was performed on blood cultures with Gram-positive cocci in clusters that were identified as S. aureus using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The ASP team member then consulted with the treating physician. The time to optimal therapy (TTOT) and clinical outcomes, including length of hospital stay (LOS), were compared between the intervention (n = 29) and historical (n = 27) cohorts. TTOT was defined as the time from the first blood culture draw to the use of appropriately dosed antistaphylococcal beta-lactam monotherapy without vancomycin. Molecular testing significantly reduced the median time to MSSA and MRSA discrimination to 7.8 h, compared to 24.3 h with culture-based methods (P < 0.001). Compared to the control group, the median TTOT in the ASP intervention group was significantly shorter (P = 0.041) at 38.0 h (versus 50.1 h). Rapid discrimination between MRSA and MSSA using molecular testing, paired with an ASP intervention, significantly reduced the TTOT in patients with MSSA BSIs. IMPORTANCE Our research shows that time to optimal antibiotic treatment for serious bloodstream infections can be improved with rapid molecular sensitivity testing and feedback to prescribers. This can be implemented in laboratories without full microbiology services or training to improve patient outcomes by improving antimicrobial use.

Clinical Relevance of Xpert MRSA/SA in Guiding Therapeutic Decisions for Staphylococcal Infections: A Diagnostic Test Accuracy Analysis

Introduction

Rapid identification of the causal organism and antibiotic resistance is crucial for guiding targeted therapy in patients with suspected staphylococcal infection. A meta-analysis was carried out to evaluate the diagnostic relevance of Xpert™ MRSA/SA (Xpert) from clinical samples of various origins for limiting the use of unnecessary empirical methicillin-resistant Staphylococcus aureus (MRSA) therapy.

Methods

Five databases, including the Cochrane Library, Scopus, PubMed, Web of Science, and Embase, were comprehensively inspected from inception to October 12, 2021. The pooled summary estimates were evaluated using a bivariate random-effects model.

Results

Our inclusion criteria were met by 49 publications containing 68 datasets out of 735 citations. A total of 21 studies (n = 4996) examined the accuracy of Xpert in detecting methicillin-sensitive S. aureus (MSSA), while 47 studies (n = 45,430) examined the accuracy of Xpert in detecting MRSA. As compared to MRSA, Xpert’s diagnostic performance for MSSA detection was markedly higher [sensitivity: 0.97 (0.96–0.98), specificity: 0.97 (0.97–0.98), area under curve (AUC): 0.99 (0.99–1.0)]. Xpert’s pooled sensitivity and specificity differed marginally across sample types, including screening of colonization, lower respiratory tract (LRT), osteoarticular, and bloodstream samples. Notably, the Xpert pooled specificity was consistently ≥ 92% against microbiological culture across all sample types. The diagnostic efficiency heterogeneity was not explained by a meta-regression and subgroup analysis of research design, sample conditions, and sampling methods (P > 0.05).

Conclusion

Our findings suggest that Xpert could be used as the favoured screening test for the early detection of staphylococcal infection in a variety of sample types, with the goal of guiding therapeutic decisions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40121-022-00632-w.

[Diagnosis and treatment of catheter-related bloodstream infection in hemodialysis: 10 years later]

Patients in hemodialysis on central venous catheter as vascular access are at risk of infections. Catheter-related bloodstream infection is one of the most serious catheter-complications in hemodialysis patients. Its clinical and microbiological diagnosis is challenging. The implementation of empiric antibiotic therapy is based on old recommendations proposing the combination of a molecule targeting methicillin-resistant Staphylococcus aureus and a betalactamin active on P. aeruginosa, and also adapting this probabilistic treatment by carrying out a microbiological register on a local scale, which is rarely done. In our hemodialysis center at Bordeaux University Hospital, an analysis of the microorganisms causing all catheter-related bloodstream infection over the period 2018-2020 enabled us to propose, in agreement with the infectious disease specialists, an adapted probabilistic antibiotic therapy protocol. This approach allowed us to observe a low incidence of meticillinoresistance of Staphylococcus. For catheters inserted more than 6 months ago, we observed no Staphylococcus, no multi-resistant Pseudomonas, and only 2% of Enterobacteria resistant to cephalosporins. A frequent updating of the microbiological epidemiology of catheter-related bloodstream infection, in partnership with the infectious diseases team in each hemodialysis center, allowing an adaptation of the probabilistic antibiotic therapy, and seems to have a good feasibility. This strategy might favor the preservation of microbial ecology on an individual and collective scale in maintenance hemodialysis patients.

Detection of Methicillin-Resistant Staphylococcus aureus Infections Using Molecular Methods

The application of molecular detection methods for bacterial pathogens has dramatically improved the outcomes of septic patients, including those with methicillin-resistant Staphylococcus aureus (MRSA) infections. Molecular methods can be applied to a variety of clinical specimens including nasal swabs, growth in blood culture bottles, and wounds. While data show that the overall accuracy of molecular tests for MRSA is high, results can be confounded by the presence of multiple staphylococcal species in a specimen, insertions and deletions of DNA in and around the Staphylococcal Cassette Chromosome mec (SCCmec) element, and point mutations in mecA. Herein, we explore the complexities of molecular approaches to MRSA detection and the instances where phenotypic methods should be pursued to resolve discrepancies between genotypic and phenotypic results.

Do rapid diagnostic methods improve antibiotic prescribing in paediatric bacteraemia?

AIM

Rapid blood culture pathogen identification facilitated by matrix-assisted laser desorption ionisation time-of-flight and GeneXpert has the potential to improve antibiotic prescribing. This study investigates the impact of these rapid diagnostics on the timeliness of effective and optimal antibiotic prescribing in paediatric patients with bacteraemia.

METHODS

A single centre retrospective cohort study was performed comparing paediatric bacteraemia cases pre- and post-rapid diagnostic implementation. Primary outcomes were the proportion of cases receiving, and median time to administration of effective and optimal antibiotics from blood culture collection. Secondary outcomes included hospital length of stay, intensive care unit admissions, and all-cause mortality.

RESULTS

A total of 255 bacteraemia cases were subject to final data analysis, 129 in the control cohort (pre-implementation of rapid diagnostics) and 126 in the rapid diagnostics cohort. The median time to effective (2.3 vs. 1.8 h, P = 0.20) and optimal therapy (44.4 vs. 39.1 h, P = 0.66) did not differ significantly between the cohorts. There was also no significant difference found in the number of cases reaching effective (120 vs. 116, P = 0.77) and optimal therapy (66 vs. 62, P = 0.76), length of stay (7 vs. 9 days), all-cause mortality (1.6 vs. 1.6%) and number of intensive care unit admissions (20 vs. 15).

CONCLUSION

The implementation of rapid diagnostics, when used in isolation, resulted in no improvement in antibiotic prescribing or patient clinical outcomes. To be effective, rapid diagnostics must be coupled with active real-time antimicrobial stewardship promotion, de-escalation or modification based on early laboratory results.

Identification of Staphylococci by Polymerase Chain Reaction Directly from a Positive Blood Culture and Effect on Patient Care

BACKGROUND

As one of the most common bloodstream infections worldwide, Staphylococcus aureus bacteremia places a major burden on health care. Implementation of a rapid, genetic-based diagnostic test may have important implications in the clinical management of patients with S. aureus bacteremia.

OBJECTIVES

The primary objective was to assess concordance between testing based on polymerase chain reaction (PCR) and the current gold standard, culture and sensitivity testing; the secondary objective was to assess the impact of this technology on patient care.

METHODS

A pre-post intervention retrospective chart review was used to document the hospital course of patients with a diagnosis of S. aureus bacteremia before and after implementation of the PCR-based diagnostic system. Laboratory results from all patient samples subjected to PCR-based analysis following implementation of this system were compared with culture and sensitivity data for the same samples to determine accuracy of the new system. In addition, time to optimal therapy for each patient was calculated as the interval between the initiation of empiric and terminal therapies. The appropriateness of antimicrobial treatment was characterized as guideline-concordant, nonconcordant with the guidelines, or nonconcordant yet still clinically appropriate.

RESULTS

In total, 98 and 99 patients met the inclusion criteria before and after implementation of the PCR-based diagnostic system, respectively. PCR-based results displayed 99.8% concordance (440/441 total samples) with results from culture and sensitivity testing. The time to optimal therapy was significantly shorter after implementation, by a mean of 22.8 h (p < 0.001). Overall, 97% of empiric and 99% of terminal antimicrobial regimens were either guideline-concordant or clinically appropriate for treatment of S. aureus bacteremia; 3% of empiric and 1% of terminal antimicrobial regimens were nonconcordant with clinical guidelines without any explanation based on other clinical considerations.

CONCLUSIONS

The study findings support the utility of using a direct-from-positive-blood-culture PCR-based diagnostic tool as the primary method of identifying S. aureus bacteremia in patients, as well as the acceptance of and acting upon the new assay's results by our local clinicians. PCR-based assays can help reduce the time to optimal terminal therapy for patients with bacteremia.

Rapid molecular testing for Staphylococcus aureus bacteraemia improves clinical management

Introduction. Staphylococcus aureus bacteraemia (SAB) causes significant morbidity and mortality. Standard diagnostic methods require 24-48 h to provide results, during which time management is guideline-based and may be suboptimal.Aim. Evaluate the impact of rapid molecular detection of S. aureus in positive blood culture bottle fluid on patient management.Methodology. Samples were tested prospectively at two clinical centres. Positive blood cultures with Gram-positive cocci in clusters on microscopy were tested with the Xpert MRSA/SA blood culture assay (Cepheid), as well as standard culture-based identification and antimicrobial sensitivity tests. Results were passed to clinical microbiologists in real time and used for patient management.Results. Of 264 blood cultures tested (184 and 80 from each centre), S. aureus was grown from 39 (14.8 %) with one identified as methicillin-resistant S. aureus; all Xpert results agreed with culture results. Median turnaround time from culture flagging positive to result reporting for Xpert was 1.7 h, compared to 25.7 h for species identification by culture. Xpert results allowed early changes to management in 40 (16.8 %) patients, with Xpert positive patients starting specific therapy for SAB and Xpert negative patients stopping or avoiding empiric antimicrobials for SAB.Conclusion. Rapid and accurate detection of S. aureus with the Xpert MRSA/SA BC assay in positive blood culture bottles allowed earlier targeted patient management. Negative Xpert results are suggestive of coagulase negative staphylococci, allowing de-escalation of antimicrobial therapy if clinically appropriate.

Training Student Pharmacists to Perform Point-of-Care Testing

Objective. To implement training in point-of-care testing (POCT) for student pharmacists and to assess students' comfort with performing and recommending POCT for Group A streptococcus (GAS), influenza, and human immunodeficiency virus (HIV) after completion of training. Methods. The POCT training was provided to students via a 3.5-hour module imbedded in an intensive, week-long course. The module included a lecture with active-learning exercises and time dedicated to practicing performing nasal and throat swabs. Student performance of swab procedures was evaluated via a rubric-based skills assessment graded by a faculty member. Student pharmacists completed a pre- and post-training Likert scale survey regarding their comfort with performing and recommending POCT, and initiating appropriate treatment. Student knowledge of POCT material was evaluated via a multiple-choice examination. Results. Most students performed proficiently on the POCT skills assessment on the first attempt (86% achieved proficiency in performing throat swabs and 88% in performing nasal swabs), and all students were proficient by the third attempt. Student comfort and interest in performing POCT and willingness to implement POCT in their future practice significantly increased from the pre- to the post-training survey. All students achieved competency as demonstrated by achieving a score of 80% or higher on the knowledge examination on the first or second attempt. Conclusion. Following a POCT training module, student pharmacists displayed increased willingness to perform and recommend POCT for GAS, influenza, and HIV. Expanding this training to other pharmacy schools and colleges could increase patient access to POCT.

Evaluation of performance of the GENECUBE assay for rapid molecular identification of Staphylococcus aureus and methicillin resistance in positive blood culture medium

Rapid identification of causative agents from positive blood culture media is a prerequisite for the timely targeted treatment of patients with sepsis. The GENECUBE (TOYOBO Co., Ltd.) is a novel, fully-automated gene analyzer that can purify DNAs and amplify target DNAs. In this study, we evaluated the ability of two newly developed GENECUBE assays to directly detect the nuc and mecA genes in blood culture medium; nuc is specific to Staphylococcus aureus, and mecA indicates methicillin resistance. We examined 263 positive blood culture samples taken at three hospitals from patients suspected of having staphylococcal bacteremia. The results were then compared with those obtained using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, antimicrobial susceptibility testing (Microscan system or Dry-plate EIKEN), and sequencing analysis. The GENECUBE assays had sensitivity and specificity of 100% in detecting both S. aureus and methicillin resistance in positive blood culture. The turnaround time of the examination was evaluated for 36 positive blood culture samples. The time between the initiation of incubation and completion of the GENECUBE examination was 23 h (interquartile range: IQR 21–37 h); the time between reporting of Gram stain examination and completion of the GENECUBE examination was 52 min (IQR 48–62 min). These findings show that the GENECUBE assays significantly reduce the assay time with no loss of sensitivity or specificity.

Antimicrobial stewardship for acute-care hospitals: An Asian perspective

Inappropriate use of antibiotics is contributing to a serious antimicrobial resistance problem in Asian hospitals. Despite resource constraints in the region, all Asian hospitals should implement antimicrobial stewardship (AMS) programs to optimize antibiotic treatment, improve patient outcomes, and minimize antimicrobial resistance. This document describes a consensus statement from a panel of regional experts to help multidisciplinary AMS teams design programs that suit the needs and resources of their hospitals. In general, AMS teams must decide on appropriate interventions (eg, prospective audit and/or formulary restriction) for their hospital, focusing on the most misused antibiotics and problematic multidrug-resistant organisms. This focus is likely to include carbapenem use with the goal to reduce carbapenem-resistant gram-negative bacteria. Rather than initially trying to introduce a comprehensive, hospital-wide AMS program, it would be practical to begin by pilot testing a simple program based on 1 achievable core intervention for the hospital. AMS team members must work together to determine the most suitable AMS interventions to implement in their hospitals and how best to put them into practice. Continuous monitoring and feedback of outcomes to the AMS teams, hospital administration, and prescribers will enhance sustainability of the AMS programs.

Influence of GeneXpert MRSA/SA test implementation on clinical outcomes of Staphylococcus aureus bacteremia - a before-after retrospective study

Use of GeneXpert MRSA/SA in diagnostic algorithms of Staphylococcus aureus bacteremia may influence both patients' clinical outcomes and antibiotic stewardship. We evaluated these outcomes in a retrospective cohort before (1/6/2015-31/5/2016) and after (1/6/2016-31/8/2017) the introduction of the test in adult patients with Gram-positive cocci in clusters in blood cultures. We included 254 patients (125 preintervention, 129 postintervention). No significant difference in 30-day mortality or clinical success was demonstrated between periods. Appropriate antibiotic therapy rates were significantly higher in the postintervention group, and vancomycin use was significantly reduced (80.6% vs 53.6%, P < 0.01; 2.3±0.38 vs 2.98±1.02 defined daily doses/100 patient days, P = 0.026, respectively). Appropriate beta-lactam use was also significantly higher (56.7% postintervention vs 23.1% preintervention, P < 0.01). Use of GeneXpert MRSA/SA test has a positive effect on antibiotic stewardship measures, though it has no significant effect on clinical outcomes including mortality in this fatal infection.

Collaboration between an antimicrobial stewardship team and the microbiology laboratory can shorten time to directed antibiotic therapy for methicillin-susceptible staphylococcal bacteremia and to discontinuation of antibiotics for coagulase-negative staphylococcal contaminants

BACKGROUND

Rapid identification of Gram-positive cocci in clusters (GPCC) in positive blood cultures (pBC) may limit exposure to unnecessary or inappropriate antibiotics.

METHODS

Inpatients with pBC showing GPCC between October 2013 and December 2017 were included. In the baseline period (BL), final ID and susceptibility results were reported in the electronic medical record (EMR) within 48 h of telephoned Gram stain report. The laboratory introduced rapid phenotypic identification and direct susceptibility testing (INT1), later replaced by PCR (INT2). In the last Intervention (INT3), Antimicrobial Stewardship Response Team (ASRT) contacted providers with PCR results and recommendations.

RESULTS

Time to directed therapy (TDT) for MSSA and coagulase-negative Staphylococci (CoNS) decreased from BL to INT3 (48.5-17.9 h, 50.3-16.4 h, respectively). Time to ID from BL to INT3 for MSSA and CoNS also decreased (23.2-1.9 h, 44.7-2.8, respectively).

CONCLUSIONS

TDT can be improved by modification of reporting methods with utilization of an ASRT.

A review of novel technologies and techniques associated with identification of bloodstream infection etiologies and rapid antimicrobial genotypic and quantitative phenotypic determination

INTRODUCTION

The antimicrobial aspect of management of patients with blood stream infections (BSI) and sepsis is time critical. In an era of increasing antimicrobial resistance, rapid detection and identification of bacteria with antimicrobial susceptibility is crucial to direct therapy early in the course of illness. Molecular techniques offer a potential solution to this. Areas covered: In the present review the authors have discussed a number of novel solutions utilizing a variety of molecular techniques for pathogen detection, identification and antimicrobial susceptibility. The review is not designed to be an exhaustive literature review covering all diagnostic solutions ever developed, instead the authors have focused on what they have had experience using, evaluating or currently view as new and exciting with potential to revolutionize BSI diagnosis. The authors searched PubMed (Medline) and Google Scholar with terms: BSI, Bacteraemia, Candidaemia, Diagnostics, AST, Rapid, AMR, Novel and Blood Culture. The authors attended recent clinical microbiology technology congresses. Expert commentary: There are multiple exciting novel technologies at differing stages of development with potential to revolutionize diagnosis of BSI. More work is needed as well as a standardized assessment of different platforms in order to better understand the clinical and financial impacts these will have in clinical microbiology laboratories.

Carbapenem Resistance, Initial Antibiotic Therapy, and Mortality in Klebsiella pneumoniae Bacteremia: A Systematic Review and Meta-Analysis

BACKGROUND Mortality associated with infections caused by carbapenem-resistant Enterobacteriaceae (CRE) is higher than mortality due to carbapenem-sensitive pathogens. OBJECTIVE To examine the association between mortality from bacteremia caused by carbapenem-resistant (CRKP) and carbapenem-sensitive Klebsiella pneumoniae (CSKP) and to assess the impact of appropriate initial antibiotic therapy (IAT) on mortality. DESIGN Systematic review and meta-analysis METHODS We searched MEDLINE, EMBASE, CINAHL, and Wiley Cochrane databases through August 31, 2016, for observational studies reporting mortality among adult patients with CRKP and CSKP bacteremia. Search terms were related to Klebsiella, carbapenem-resistance, and infection. Studies including fewer than 10 patients per group were excluded. A random-effects model and meta-regression were used to assess the relationship between carbapenem-resistance, appropriateness of IAT, and mortality. RESULTS Mortality was higher in patients who had CRKP bacteremia than in patients with CSKP bacteremia (15 studies; 1,019 CRKP and 1,148 CSKP patients; unadjusted odds ratio [OR], 2.2; 95% confidence interval [CI], 1.8-2.6; I2=0). Mortality was lower in patients with appropriate IAT than in those without appropriate IAT (7 studies; 658 patients; unadjusted OR, 0.5; 95% CI, 0.3-0.8; I2=36%). CRKP patients (11 studies; 1,326 patients; 8-year period) were consistently less likely to receive appropriate IAT (unadjusted OR, 0.5; 95% CI, 0.3-0.7; I2=43%). Our meta-regression analysis identified a significant association between the difference in appropriate IAT and mortality (OR per 10% difference in IAT, 1.3; 95% CI, 1.0-1.6). CONCLUSIONS Appropriateness of IAT is an important contributor to the observed difference in mortality between patients with CRKP bacteremia and patients with CSKP bacteremia. Infect Control Hosp Epidemiol 2017;38:1319-1328.

Impact of a rapid molecular test for positive blood cultures from neonatal intensive care patients on clinical management: a retrospective audit

BACKGROUND

Both Staphylococcus aureus and coagulase negative Staphylococci are common causes of late-onset neonatal sepsis in the neonatal intensive care unit (NICU), usually relating to intravascular access device infections.

AIMS

This project aimed to review the impact on antimicrobial treatment and clinical outcome in the NICU setting, of the introduction of the Xpert MRSA/SA BC test (Cepheid, USA) for the identification of staphylococci in blood cultures.

METHODS

A retrospective audit was carried out of the pre- and post-intervention periods; the intervention was the introduction of the Xpert MRSA/SA BC test.

RESULTS

In total, 88 neonates had positive blood cultures with Staphylococcus spp., comprising 42 neonates in the pre-intervention and 46 in the post-intervention groups. The pre-intervention group had a higher birth weight (1.541 kg vs. 1.219 kg, p = 0.05) and higher platelet count (288 vs. 224 × 10⁹/L, p = 0.05). There was a trend towards a shorter duration of antimicrobial therapy in term infants and in the length of admission; however, this was not statistically significant (p = 0.2). All of the nine infants post-intervention with significant bacteraemia (S. aureus =3, CoNS =6) were changed to the optimal antimicrobial at the time the result was available.

CONCLUSIONS

This study shows that the introduction of the Xpert MRSA/SA BC test can lead to a reduction in the length of admission and duration of antimicrobials in term infants; however, the difference was not statistically significant. All nine infants with clinically significant bacteraemia were treated with the appropriate antimicrobial when the Xpert MRSA/SA BC test result was available.

Advances in Rapid Identification and Susceptibility Testing of Bacteria in the Clinical Microbiology Laboratory: Implications for Patient Care and Antimicrobial Stewardship Programs

Early availability of information on bacterial pathogens and their antimicrobial susceptibility is of key importance for the management of infectious diseases patients. Currently, using traditional approaches, it usually takes at least 48 hours for identification and susceptibility testing of bacterial pathogens. Therefore, the slowness of diagnostic procedures drives prolongation of empiric, potentially inappropriate, antibacterial therapies. Over the last couple of years, the improvement of available techniques (e.g. for susceptibility testing, DNA amplification assays), and introduction of novel technologies (e.g. MALDI-TOF) has fundamentally changed approaches towards pathogen identification and characterization. Importantly, these techniques offer increased diagnostic resolution while at the same time shorten the time-to-result, and are thus of obvious importance for antimicrobial stewardship. In this review, we will discuss recent advances in medical microbiology with special emphasis on the impact of novel techniques on antimicrobial stewardship programs.

Evolving Rapid Methicillin-resistant Staphylococcus aureus Detection: Cover All the Bases

The dissemination of methicillin-resistant (MR) Staphylococcus aureus (SA) in community and health-care settings is of great concern and associated with high mortality and morbidity. Rapid detection of MRSA with short turnaround time can minimize the time to initiate appropriate therapy and further promote infection control. Early detection of MRSA directly from clinical samples is complicated by the frequent association of MRSA with methicillin-susceptible SA (MSSA) and coagulase-negative Staphylococcus (CoNS) species. Infection associated with true MRSA or MSSA is differentiated from CoNS, requires target specific primers for the presence of SA and mec A or nuc or fem A gene for confirmation of MR. Recently, livestock-associated MRSA carrying mec C variant complicates the epidemiology of MRSA further. Several commercial rapid molecular kits are available with a different combination of these targets for the detection of MRSA or MSSA. The claimed sensitivity and specificity of the currently available commercial kits is varying, because of the different target combination used for detection of SA and MR.

Rapid molecular determination of methicillin resistance in staphylococcal bacteraemia improves early targeted antibiotic prescribing: a randomized clinical trial

Empiric therapy of methicillin-susceptible Staphylococcus aureus (MSSA) infections with vancomycin is associated with poorer outcome than targeted therapy with β-lactams. Our objective was to evaluate whether rapid determination of methicillin resistance shortens the time from Gram stain to targeted antimicrobial therapy in staphylococcal bacteraemia, thereby reducing vancomycin overuse. This was a single-centre open parallel RCT. Gram-positive cocci in clusters in positive blood culture underwent real-time PCR for rapid species and methicillin resistance determination parallel to conventional microbiology. Patients were randomized 1:1 so that clinicians would be informed of PCR results (intervention group) or not (control group). Eighty-nine patients (intervention 48, control 41) were analysed. MRSA was identified in seven patients, MSSA in 46, and CoNS in 36. PCR results were highly concordant (87/89) with standard microbiology. Median time (hours) from Gram stain to transmission of methicillin-susceptibility was 3.9 (2.8-4.3) vs. 25.4 (24.4-26-7) in intervention vs. control groups (p <0.001). Median time (hours) from Gram stain to targeted treatment was similar for 'all staphylococci' [6 (3.8-10) vs. 8 (1-36) p 0.13] but shorter in the intervention group when considering S. aureus only [5 (3-7) vs. 25.5 (3.8-54) p <0.001]. When standard susceptibility testing was complete, 41/48 (85.4%) patients in the intervention group were already receiving targeted therapy compared with 23/41 (56.1%) in the control group (p 0.004). There was no significant effect on clinical outcomes. Rapid determination of methicillin resistance in staphylococcal bacteraemia is accurate and reduces significantly the time to targeted antibiotic therapy in the subgroup of S. aureus, thereby avoiding unnecessary exposure to vancomycin.

Contemporary genomic approaches in the diagnosis and typing of Staphylococcus aureus

Staphylococcus aureus is a major human pathogen, causing disease in both community and healthcare settings. Over the past two decades, the epidemiology of S. aureus disease has changed dramatically, with the emergence and spread of community-associated methicillin-resistant S. aureus clones. This epidemiological shift, coupled with the association between delayed antimicrobial therapy and increased mortality in S. aureus bacteraemia, has greatly facilitated advances in the rapid molecular diagnosis of S. aureus. Rapid molecular testing for S. aureus can greatly reduce laboratory turnaround time, and in some circumstances, may lead to improved clinical outcomes. In addition, advances in DNA sequencing technology and bioinformatic analysis have shed new lights on the molecular epidemiology and transmission dynamics of S. aureus. In this context, we provide an overview of the key advances in the molecular diagnosis and typing of S. aureus, with a particular focus on the clinical impact and utility of genomic technologies.

Point-of-care testing for infectious diseases: opportunities, barriers, and considerations in community pharmacy

OBJECTIVES To identify opportunities to perform point-of-care (POC) testing and/or screening for infectious diseases in community pharmacies, provide an overview of such tests and how they are used in current practice, discuss how the Clinical Laboratory Improvement Amendments of 1988 (CLIA) affect pharmacists performing POC testing, and identify and discuss barriers and provide recommendations for those wanting to establish POC testing for infectious diseases services in community pharmacies. DATA SOURCES PubMed and Google Scholar were searched from November 2012 through May 2013 and encompassed the years 2000 and beyond for the narrative review section of this article using the search terms rapid diagnostic tests, POC testing and infectious diseases, pharmacy services, CLIA waiver, and collaborative drug therapy management. All state boards of pharmacy in the United States were contacted and their regulatory and legislative websites accessed in 2012 and January 2013 to review relevant pharmacy practice laws. DATA SYNTHESIS POC testing for infectious diseases represents a significant opportunity to expand services in community pharmacies. Pharmacist education and training are addressing knowledge deficits in good laboratory practices and test performance and interpretation. Federal regulations do not define the qualifications for those who perform CLIA-waived tests, yet few pharmacists perform such services. Fewer than 20% of states address POC testing in their statutes and regulations governing pharmacy. CONCLUSION POC testing for infectious diseases could benefit patients and society and represents an opportunity to expand pharmacy services in community pharmacies. Existing barriers to the implementation of such services in community pharmacies, including deficits in pharmacist training and education along with state regulatory and legislative variance and vagueness in statutes governing pharmacy, are not insurmountable.

Blood culture-based diagnosis of bacteraemia: state of the art

Blood culture remains the best approach to identify the incriminating microorganisms when a bloodstream infection is suspected, and to guarantee that the antimicrobial treatment is adequate. Major improvements have been made in the last years to increase the sensitivity and specificity and to reduce the time to identification of microorganisms recovered from blood cultures. Among other factors, the introduction in clinical microbiology laboratories of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry technology revolutionized the identification of microorganisms whereas the introduction of nucleic-acid-based methods, such as DNA hybridization or rapid PCR-based test, significantly reduce the time to results. Together with traditional antimicrobial susceptibility testing, new rapid methods for the detection of resistance mechanisms respond to major epidemiological concerns such as methicillin-resistant Staphylococcus aureus, extended-spectrum β-lactamase or carbapenemases. This review presents and discusses the recent developments in microbial diagnosis of bloodstream infections based on blood cultures.

Invasive Staphylococcus aureus Infections in Children in Tropical Northern Australia

BACKGROUND

Despite a high burden of staphylococcal skin disease in children and high incidence of Staphylococcus aureus bacteremia in adult Indigenous populations in northern Australia, there are few studies describing incidence or clinical information of invasive S aureus (ISA) infections in children.

METHODS

We conducted a retrospective review for all cases of S aureus bacteremia and sterile site infections, for children under 15 years, in northern Australia over a 4-year period (2007-2010). Cases were categorized as neonatal (<28 days) and pediatric (≥28 days).

RESULTS

Forty-four cases (9 neonatal, 35 pediatric) were identified. The annual incidence of ISA was 27.9 cases per 100 000 population. Among pediatric cases, the annual incidence was significantly higher in the Indigenous (46.6) compared with the non-Indigenous (4.4) population (IRR: 10.6 [95% confidence interval, 3.8-41.4]). Pediatric infections were predominantly community-associated (86%). Clinical infection sites included osteoarticular (66%), pleuropulmonary (29%), and endocarditis (9%), and multifocal disease was common (20%). Eighty-three percent of pediatric cases presented with sepsis; 34% resulted in intensive care admission. Neonatal cases were all born prematurely; 89% were late-onset infections. Overall, 27% of infections were due to methicillin-resistant S aureus (MRSA). Compared with methicillin-sensitive S aureus (MSSA), there was no difference in severity or presentation in pediatric MRSA cases, but a higher proportion of MRSA cases were readmitted.

CONCLUSIONS

The annual incidence of ISA infection in this study is among the highest described, largely due to a disproportionate burden in Indigenous children. Infections are frequently severe and infection with MRSA is common. Children presenting with suspected ISA in this region should be treated empirically for MRSA.

Improved sensitivity for molecular detection of bacterial and Candida infections in blood

The rapid identification of bacteria and fungi directly from the blood of patients with suspected bloodstream infections aids in diagnosis and guides treatment decisions. The development of an automated, rapid, and sensitive molecular technology capable of detecting the diverse agents of such infections at low titers has been challenging, due in part to the high background of genomic DNA in blood. PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) allows for the rapid and accurate identification of microorganisms but with a sensitivity of about 50% compared to that of culture when using 1-ml whole-blood specimens. Here, we describe a new integrated specimen preparation technology that substantially improves the sensitivity of PCR/ESI-MS analysis. An efficient lysis method and automated DNA purification system were designed for processing 5 ml of whole blood. In addition, PCR amplification formulations were optimized to tolerate high levels of human DNA. An analysis of 331 specimens collected from patients with suspected bloodstream infections resulted in 35 PCR/ESI-MS-positive specimens (10.6%) compared to 18 positive by culture (5.4%). PCR/ESI-MS was 83% sensitive and 94% specific compared to culture. Replicate PCR/ESI-MS testing from a second aliquot of the PCR/ESI-MS-positive/culture-negative specimens corroborated the initial findings in most cases, resulting in increased sensitivity (91%) and specificity (99%) when confirmed detections were considered true positives. The integrated solution described here has the potential to provide rapid detection and identification of organisms responsible for bloodstream infections.

Nonculture techniques for the detection of bacteremia and fungemia

ABSTRACT: 

Bacteremia and fungemia account for a substantial proportion of all cases of severe sepsis. Antibiotic resistance is a contributing factor in many hospital-acquired infection deaths. Traditional phenotypic methods for the identification of bacteria and yeasts from positive blood cultures and determining antimicrobial susceptibility require 48–72 h, delaying optimal therapy and negatively impacting patient outcomes. Molecular methods, including nonamplified DNA probe panels and peptide nucleic acid probes, and nucleic acid amplification methods such as PCR, proteomic methods (matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry) and direct biochemical tests provide more rapid identification of bacteria and fungi, and in some cases antimicrobial resistance markers, from positive blood cultures, as well as directly from whole blood. These methods vary in the breadth of organisms that they detect, and equally important, their ease of use. This article examines the principles, performance and practicality of the various rapid, nonculture techniques for the detection of bacteremia and fungemia.

Clinical consequences of using PNA-FISH in Staphylococcal bacteraemia

To optimize patient treatment and rational use of antimicrobials, it is important to provide fast information on findings in blood-cultures (BCs). The purpose of this study was to evaluate the impact of using peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) on positive BCs containing Gram-positive cocci in clusters to differentiate between Staphylococcus aureus (SA) and coagulase negative staphylococci (CoNS) on the prescribed antimicrobial therapy and on the number of contacts between microbiologist and clinician. All cases of positive BCs in our laboratory with SA or CoNS in the year 2011 were identified and the charts were reviewed retrospectively. The group of patients with BCs tested with PNA-FISH was compared to the group of patients with untested BCs. A total of 200 patients with SA and 725 patients with CoNS were included. The mean number of contacts was 0.82 when PNA-FISH showed CoNS and 1.39 when PNA-FISH was not done (p < 0.0001). More patients were recommended appropriate antimicrobial therapy for SA bacteraemia in the PNA-FISH group (98.0%) than in the non-PNA-FISH group (89.4 %) (p = 0.025). The percentage treated with dicloxacillin was 29.6 in the PNA-FISH group, and 8.2 in the non-PNA-FISH group (p = 0.0003). The use of PNA-FISH on BCs in this study was associated with more appropriate and narrow spectrum antimicrobial therapy for patients with SA in an area with low prevalence of methicillin-resistant SA, and a lower number of contacts between clinical microbiologist and clinician about BCs with CoNS as contaminants.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry and PCR-based rapid diagnosis of Staphylococcus aureus bacteraemia

Effective empirical treatment is of paramount importance to improve the outcome of patients with Staphylococcus aureus bacteraemia. We aimed to evaluate a PCR-based rapid diagnosis of methicillin resistance (GeneXpert MRSA) after early detection of S. aureus bacteraemia using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Patients with a first episode of S. aureus bacteraemia identified using MALDI-TOF MS were randomized in a prospective interventional open study between October 2010 and August 2012. In the control group, antibiotic susceptibility testing was performed after MALDI-TOF MS identification on blood culture pellets. In the intervention group, a GeneXpert MRSA was performed after S. aureus identification. The primary outcome was the performance of GeneXpert MRSA directly on blood cultures. We then assessed the impact of early diagnosis of methicillin resistance on the empirical treatment. In all, 197 episodes of S. aureus bacteraemia were included in the study, of which 106 were included in the intervention group. Median time from MALDI-TOF MS identification to GeneXpert MRSA result was 97 min (range 25-250). Detection of methicillin resistance using GeneXpert MRSA had a sensitivity of 99% and a specificity of 100%. There was less unnecessary coverage of MRSA in the intervention group (17.1% versus 29.2%, p 0.09). GeneXpert MRSA was highly reliable in diagnosing methicillin resistance when performed directly on positive blood cultures. This could help to avoid unnecessary prescriptions of anti-MRSA agents and promote the introduction of earlier adequate coverage in unsuspected cases.

Rapid Identification of microbes in positive blood cultures by use of the vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system

Sepsis is a major cause of death worldwide among nonhospitalized people and hospitalized patients. A wide range of pathogens are involved, and the correct identification and correct antimicrobial therapy are critical to ensure optimal clinical outcomes. With the recent introduction of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), rapid identification of bacteria and fungi is now possible. The purpose of this study was to develop a rapid technique for identifying organisms in positive blood cultures using the Vitek MS system (bioMérieux). This technique is a lysis centrifugation method which involves a four-step washing and centrifugation procedure. A total of 253 positive monomicrobial blood cultures (Bactec Plus aerobic, anaerobic, and pediatric bottles) were tested using the Vitek MS system (KnowledgeBase version 2.0), with 92.1% and 88.1% of organisms overall being identified to the genus level and the species level, respectively. Of 161 Gram-positive bacterial isolates, 95.7% and 90.1% were identified to the genus level and the species level, respectively; of 92 Gram-negative bacterial isolates, 84.7% and 83.7% were identified to the genus level and the species level, respectively. The results obtained using this method demonstrate that the Vitek MS system can be used for rapid and effective identification of bacteria from positive blood cultures within 30 to 45 min after the positive signal has been provided by the Bactec FX blood culture system (Becton, Dickinson). This will lead to faster administration of the appropriate antimicrobial therapy and increase the chances for optimal clinical outcomes for patients.

Impact of a computerized alert system for bacteremia notification on the appropriate antibiotic treatment of Staphylococcus aureus bloodstream infections

A computerized alert system (CAS) has been introduced to notify bacteremia in real time. We evaluated the impact of the CAS on the administration of appropriate antibiotics in patients with Staphylococcus aureus bloodstream infections (BSIs). We retrospectively reviewed the medical records of patients with S. aureus BSI for each 1-year control and intervention periods, before and after the implementation of the CAS. The proportions of appropriate antibiotic treatment were compared between the control and intervention periods. The 30-day mortality of S. aureus bacteremia was also assessed in the study population. A total of 313 patients were included in the study. Appropriate antibiotics were initiated 7 h earlier in the intervention period (mean time, 13.5 h vs. 20.0 h; p = 0.136). The administration of appropriate antibiotics within the 24 h after blood acquisition was similar between the two periods, but this significantly increased from 3.3% in the control period to 10.6% in the intervention during the 24-36 h interval (p = 0.012). In the subgroup analysis, similar trends were observed in patients with methicillin-resistant isolates (6.7% vs. 18.2%; p = 0.032) and hospital-onset infection (3.5% vs. 17.1 %; p = 0.004). The independent risk factors for 30-day mortality of S. aureus bacteremia were age, a high Pitt bacteremia score, an increased Charlson's weighted index of comorbidity, and hospital-onset infection, although the appropriateness of antibiotic therapy within 36 h and the CAS were not identified as predictors. The CAS increased the proportion of appropriate antimicrobial therapy during the 24-36 h interval after bacteremia onset in patients with S. aureus BSIs.

Methicillin-resistant Staphylococcus aureus diagnostics: state of the art

INTRODUCTION

Methicillin-resistant Staphylococcus aureus (MRSA) is among the most common causes of community- and healthcare-acquired infections, accounting for > 80,000 invasive infections in the United States in 2010 according to the Center for Disease Control and Prevention's Active Bacterial Core Surveillance data. Control and treatment of MRSA depend on reliable identification, which is challenging. This article reviews the current status of detection and identification of MRSA.

AREAS COVERED

Publications since 2001, guidelines from the Clinical Laboratory Standards Institute and the European Committee on Antimicrobial Susceptibility Testing, common microbiology laboratory practices for identification and characterization of MRSA in human samples, and recent publications that assessed patient care outcomes of various detection and intervention strategies were surveyed for this review.

EXPERT OPINION

Given the predilection of Staphylococcus aureus to modify its genetic characteristics, thereby enabling the species to stay one step ahead of laboratory detection systems, phenotypic methods for detection of antibiotic resistance mechanisms, especially those directed against the beta-lactam family, will continue to be required, in some situations, for the foreseeable future. Molecular methods are now the gold standard for surveillance, yielding higher sensitivity than the slower, culture-based methods. The newer molecular surveillance methods for detecting methicillin-resistant S. aureus (MRSA) colonization and for rapid and accurate identification of S. aureus from growth in culture systems have revolutionized patient care, enabling rapid interventions that lead to better individual patient outcomes, such as fewer postsurgical site infections, and better overall institutional infection control (fewer healthcare-associated MRSA infections).