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

Diagnostic methods and protocols for rapid determination of methicillin resistance in Staphylococcus aureus bloodstream infections: a comparative analysis

PURPOSE

To evaluate diagnostic performance of four diagnostic methods for rapid determination of methicillin resistance in S. aureus positive blood cultures (BCs).

METHODS

Clinical and spiked BCs were subjected to the evaluation of the following methods and protocols: a. Eazyplex® MRSA Plus loop-mediated isothermal amplification (LAMP) assay directly from BC fluid; b. MALDI-TOF MS subtyping on BC pellet extracted with Rapid Sepsityper® protocol and on 4-h short-term subculture; c. Clearview™ Culture Colony PBP2a SA immunochromatography assay on BC pellet and on 4-h short-term subculture; d. EUCAST RAST cefoxitin screen test performed directly from BC and including reading times at 4-h, 6-h and 16-20-h.

RESULTS

Eazyplex® MRSA plus exhibited the best performance, showing 100% sensitivity, specificity, positive predictive value, and negative predictive value, followed by PBP2a SA Culture Colony Clearview assay and EUCAST RAST cefoxitin screen. MALDI-TOF MS subtyping showed the lowest diagnostic accuracy (59.8 and 65.7% directly from BC and from 4-h subculture, respectively). In detail, sensitivity and specificity ranged from 24.3% to 20.4% and from 88.9% to 98.3% for protocols performed from BC pellet and 4-h subculture, respectively.

CONCLUSIONS

The Eazyplex® MRSA Plus and the immunochromatographic Clearview™ PBP2a SA Culture Colony methods can provide reliable results within 1 h from the start of positive BC processing. MALDI TOF MS subtyping showed unacceptable specificity by performing analysis from BC pellets, while its sensitivity depends on the prevalence of PSM-positive MRSA strains. The EUCAST RAST, based on disc diffusion, showed excellent performance with a time-to-result of at least 4 h.

Case Commentary: The hidden side of oxacillin resistance in Staphylococcus aureus

Acquisition of PBP2a (encoded by the mec gene) is the key resistance mechanism to β-lactams in Staphylococcus aureus. The mec gene can be easily detected by PCR assays; however, these tools will miss mec-independent oxacillin resistance. This phenotype is mediated by mutations in cell wall metabolism genes that can be acquired during persistent infections under prolonged antibiotic exposure. The complex case presented by Hess et al. (Antimicrob Agents Chemother 67:e00437-23, 2023, https://doi.org/10.1128/aac.00437-23) highlights the diagnostic and therapeutic challenges in the management of mec-independent oxacillin resistance.

Impact of antimicrobial stewardship with the Xpert MRSA/SA BC assay at a tertiary hospital in Japan

INTRODUCTION

Genetic testing is gaining increasing importance as a part of antimicrobial stewardship (AS). Rapid identification and determination of methicillin susceptibility using the Xpert MRSA/SA BC assay can improve the management of Staphylococcus aureus bacteremia (SAB) and reduce inappropriate antibiotic use. However, few reports have described the effectiveness of this approach.

METHODS

The present study aimed to assess the influence of AS using the Xpert MRSA/SA BC assay. Cases were classified into the pre-intervention group (n = 98 patients), in which SAB was identified by traditional culture (November 2017 to November 2019), and the post-intervention group (n = 97 patients), in which the Xpert MRSA/SA BC assay was performed when necessary (December 2019 to December 2021).

RESULTS

Patient characteristics, prognosis, duration of antimicrobial use, and length of hospital stay were compared between the groups. The Xpert assay was performed in 66 patients in the post-intervention group (68.0%). The two groups showed no significant differences in severity and mortality. The rate of cases treated with anti-MRSA agents reduced following the intervention (65.3% vs. 40.4%, p = 0.008). The number of cases involving definitive therapy within 24 h was higher in the post-intervention group (9.2% vs. 24.7%, p = 0.007). The hospitalization rate at >60 days was lower in Xpert implementation cases among MRSA bacteremia cases (28.6% vs. 0%, p = 0.01).

CONCLUSIONS

Thus, the Xpert MRSA/SA BC assay has potential as an AS tool, especially for early definitive treatment to SAB and reduction of long-term hospitalization in MRSA bacteremia cases.

Studying Factors Affecting Success of Antimicrobial Resistance Interventions through the Lens of Experience: A Thematic Analysis

Antimicrobial resistance (AMR) affects the environment, and animal and human health. Institutions worldwide have applied various measures, some of which have reduced antimicrobial use and AMR. However, little is known about factors influencing the success of AMR interventions. To address this gap, we engaged health professionals, designers, and implementers of AMR interventions in an exploratory study to learn about their experience and factors that challenged or facilitated interventions and the context in which interventions were implemented. Based on participant input, our thematic analysis identified behaviour; institutional governance and management; and sharing and enhancing information as key factors influencing success. Important sub-themes included: correct behaviour reinforcement, financial resources, training, assessment, and awareness of AMR. Overall, interventions were located in high-income countries, the human sector, and were publicly funded and implemented. In these contexts, behaviour patterns strongly influenced success, yet are often underrated or overlooked when designing AMR interventions. Improving our understanding of what contributes to successful interventions would allow for better designs of policies that are tailored to specific contexts. Exploratory approaches can provide encouraging results in complex challenges, as made evident in our study. Remaining challenges include more engagement in this type of study by professionals and characterisation of themes that influence intervention outcomes by context.

Antimicrobial Resistance of Staphylococcus sp. Isolated from Cheeses

Simple Summary

As far as it is known, studies dealing with antimicrobial resistance in certain species of staphylococci, in particular, S. chromogenes and S. simulans, isolated from products made from unpasteurized milk are limited. In addition to that, little attention was paid to the resistance of staphylococcal isolates from regional sheep and goat cheeses. At this level, works are published that focus on the evaluation of resistance from only one sheep product, Bryndza. Other studies are only focused on the evaluation of resistance from raw sheep’s or goat’s milk. The study contributes to the knowledge of the possible spread of antimicrobial resistance from the farm to the final consumer in this area.

Abstract

S. aureus and some species of coagulase-negative staphylococci, including S. chromogenes and S. simulans, commonly cause intramammary infections. However, little attention was paid to the antimicrobial resistance of these species with respect to their occurrence in dairy products, for example, popular sheep and goat cheeses made from unpasteurized milk. The aim of this study was to investigate such sheep and goat cheeses for the occurrence and antimicrobial resistance of the relevant staphylococci species. The staphylococcal isolates were identified by polymerase chain reaction (130 isolates) and matrix assisted laser desorption/ionization time-of-flight mass spectrometry. The most common species of S. aureus (56 isolates) were identified, as well as S. chromogenes (16 isolates) and S. simulans (10 isolates). Antimicrobial resistance to penicillin, oxacilin, ceftaroline, teicoplanin, gentamicin, erythromycin, tetracycline and ofloxacin was subsequently determined in these species using the agar dilution method. The highest resistance was confirmed in all species, especially to penicillin (91%) and erythromycin (67%). The highest sensitivity was confirmed to ofloxacin (83%). Due to the high incidence of penicillin and oxacilin-resistant staphylococci, the mecA gene was detected by polymerase chain reaction, which was confirmed only in S. aureus isolates (19%). Our study shows that the tested strains (77%) were resistant to more than one antibiotic at a time.

MDRSA: A Web Based-Tool for Rapid Identification of Multidrug Resistant Staphylococcus aureus Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

As antibiotics resistance on superbugs has risen, more and more studies have focused on developing rapid antibiotics susceptibility tests (AST). Meanwhile, identification of multiple antibiotics resistance on Staphylococcus aureus provides instant information which can assist clinicians in administrating the appropriate prescriptions. In recent years, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a powerful tool in clinical microbiology laboratories for the rapid identification of bacterial species. Yet, lack of study devoted on providing efficient methods to deal with the MS shifting problem, not to mention to providing tools incorporating the MALDI-TOF MS for the clinical use which deliver the instant administration of antibiotics to the clinicians. In this study, we developed a web tool, MDRSA, for the rapid identification of oxacillin-, clindamycin-, and erythromycin-resistant Staphylococcus aureus. Specifically, the kernel density estimation (KDE) was adopted to deal with the peak shifting problem, which is critical to analyze mass spectra data, and machine learning methods, including decision trees, random forests, and support vector machines, which were used to construct the classifiers to identify the antibiotic resistance. The areas under the receiver operating the characteristic curve attained 0.8 on the internal (10-fold cross validation) and external (independent testing) validation. The promising results can provide more confidence to apply these prediction models in the real world. Briefly, this study provides a web-based tool to provide rapid predictions for the resistance of antibiotics on Staphylococcus aureus based on the MALDI-TOF MS data. The web tool is available at: http://fdblab.csie.ncu.edu.tw/mdrsa/.

Rapid versus standard antimicrobial susceptibility testing to guide treatment of bloodstream infection

BACKGROUND

Rapid antimicrobial susceptibility tests are expected to reduce the time to clinically important results of a blood culture. This might enable clinicians to better target therapy to a person's needs, and thereby, improve health outcomes (mortality, length of hospital stay), and reduce unnecessary prescribing of broad-spectrum antibiotics; thereby reducing antimicrobial resistance rates.

OBJECTIVES

To assess the effects of rapid susceptibility testing versus standard susceptibility testing for bloodstream infections (BSIs).

SEARCH METHODS

To identify studies with selected outcomes, we searched the Cochrane Infectious Diseases Group Specialised Register, CENTRAL, MEDLINE, LILACS, and two trials registries, between 1987 and October 2020. We used 'bloodstream infection' and 'antimicrobial susceptibility tests' as search terms. We had no language or publication status limitations.

SELECTION CRITERIA

Randomized controlled trials (RCTs) comparing rapid antimicrobial susceptibility testing (with a time-to-result of ≤ 8 hours) versus conventional antimicrobial susceptibility testing in people with a BSI caused by any bacteria, as identified by a positive blood culture.

DATA COLLECTION AND ANALYSIS

Two review authors independently screened references, full-text reports of potentially relevant studies, extracted data from the studies, and assessed risk of bias. Any disagreement was discussed and resolved with a third review author. For mortality, a dichotomous outcome, we extracted the number of events in each arm, and presented a risk ratio (RR) with 95% confidence interval (CI) to compare rapid susceptibility testing to conventional methods. We used Review Manager 5.4 to meta-analyse the data. For other outcomes, which are time-to-event outcomes (time-to-discharge from hospital, time-to-first appropriate antibiotic change), we conducted qualitative narrative synthesis, due to heterogeneity of outcome measures.  MAIN RESULTS: We included six trials, with 1638 participants. For rapid antimicrobial susceptibility testing compared to conventional methods, there was little or no difference in mortality between groups (RR 1.10, 95% CI 0.82 to 1.46; 6 RCTs, 1638 participants; low-certainty evidence). In subgroup analysis, for rapid genotypic or molecular antimicrobial susceptibility testing compared to conventional methods, there was little or no difference in mortality between groups (RR 1.02, 95% CI 0.69 to 1.49; 4 RCTs, 1074 participants; low-certainty evidence). For phenotypic rapid susceptibility testing compared to conventional methods, there was little or no difference in mortality between groups  (RR 1.37, 95% CI 0.80 to 2.35; 2 RCTs, 564 participants; low-certainty evidence). In qualitative analysis, rapid susceptibility testing may make little or no difference in time-to-discharge (4 RCTs, 1165 participants; low-certainty evidence). In qualitative analysis, rapid genotypic susceptibility testing compared to conventional testing may make little or no difference in time-to-appropriate antibiotic (3 RCTs, 929 participants; low-certainty evidence). In subgroup analysis, rapid phenotypic susceptibility testing compared to conventional testing may improve time-to-appropriate antibiotic (RR -17.29, CI -45.05 to 10.47; 2 RCTs, 564 participants; low-certainty evidence).  AUTHORS' CONCLUSIONS: The theoretical benefits of rapid susceptibility testing have not been demonstrated to directly improve mortality, time-to-discharge, or time-to-appropriate antibiotic in these randomized studies. Future large prospective studies should be designed to focus on the most clinically meaningful outcomes, and aim to optimize blood culture pathways.

Role of Rapid Diagnostics in Diagnosis and Management of Patients With Sepsis

Delayed administration of active anti-infective therapy is associated with increased rates of adverse events, mortality, and costs among sepsis patients. Inherent limitations of conventional culture identification methods and the lengthy turnaround time of antimicrobial susceptibility testing are significant barriers to the timely delivery of life-saving therapy, particularly among antibiotic-resistant infections. Culture-independent diagnostic techniques that detect pathogens and antimicrobial resistance genes within clinical samples present a tremendous benefit to timely diagnosis and management of patients. Improved outcomes for rapid intervention with rapid diagnostics have been documented and include decreased mortality rates, decreased health care delivery costs, and faster delivery of appropriate therapeutics.

Sepsis in the critically ill patient: current and emerging management strategies

Introduction: Sepsis, a dysregulated host response to infection, is a major cause of morbidity and mortality worldwide. Early identification and evidence-based treatment of sepsis are associated with improved outcomes.Areas covered: This narrative review was undertaken following a PubMed search for English language reports published before July 2020 using the terms 'sepsis,' 'septic shock,' 'fluids,' 'fluid therapy,' 'albumin,' 'corticosteroids,' 'vasopressor.' Emerging management strategies were identified following a search of the ClinicalTrails.gov database using the term 'sepsis.' Additional reports were identified by examining the reference lists of selected articles and based on personnel knowledge of the field of sepsis.Expert opinion: The core treatment of sepsis relies on source control, early antibiotics, and organ support. The main emerging strategies focus on immunomodulation, artificial intelligence, and on multi-omics approaches for a personalized therapy.

Rapid Detection of Methicillin-Resistant Staphylococcus aureus Directly from Blood for the Diagnosis of Bloodstream Infections: A Mini-Review

Staphylococcus aureus represents a major human pathogen able to cause a number of infections, especially bloodstream infections (BSI). Clinical use of methicillin has led to the emergence of methicillin-resistant S. aureus (MRSA) and MRSA-BSI have been reported to be associated with high morbidity and mortality. Clinical diagnosis of BSI is based on the results from blood culture that, although considered the gold standard method, is time-consuming. For this reason, rapid diagnostic tests to identify the presence of methicillin-susceptible S. aureus (MSSA) and MRSA isolates directly in blood cultures are being used with increasing frequency to rapidly commence targeted antimicrobial therapy, also in the light of antimicrobial stewardship efforts. Here, we review and report the most common rapid non-molecular and molecular methods currently available to detect the presence of MRSA directly from blood.

Molecular tracking of pathogens in central venous catheter

BACKGROUND

Central venous catheter-related bloodstream infection is an important adverse event in health care. Molecular methods are not yet substitutive of microbiological in the detection of the pathogens responsible for the infection, but they can help in the epidemiological characterization.

AIM

To detect bacteria by polymerase chain reaction, from material extracted from the tip of central catheters of patients suspected of infection at the intensive care unit.

METHODS

Catheters (n = 34) of patients suspected of central venous catheter-related infection were analyzed by polymerase chain reaction. The findings were compared with culture of catheter tip and blood cultures performed by the hospital.

FINDINGS

The prevalence of bacteria was Staphylococcus aureus (50%), Enterococcus faecalis (41.2%), Klebsiella pneumoniae (32.4), Pseudomonas aeruginosa (20.6%), Acinetobacter baumannii (38.2%), Escherichia coli (2.9%), and Enterobacter cloacae (0%). No blood culture showed bacterial growth, the culture of catheter tip revealed bacteria in 21 (61.8%) and the polymerase chain reaction had positivity in 31 (91.2%) of the catheters. The mean central venous catheter time was 11 days, and the jugular vein was the site of insertion.

CONCLUSION

The molecular method identified more bacteria than microbiological methods and revealed colonization of the catheters. The most commonly found bacteria are in the environment and in the microbiota of the skin, which suggests contamination by the hands of health professionals and points out the need for more efforts in preventive strategies.

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.

Fundamentals and implementation of Microbiological Diagnostic Stewardship Programs

Microbiological diagnostic stewardship programs promote coordinated measures aimed at optimizing the use of diagnostic techniques, thus favouring the adoption of adequate and cost-effective therapeutic, clinical and preventive decisions. The implementation of microbiological diagnostic stewardship relies upon the creation of multidisciplinary committees led by clinical microbiologists for the design of diagnostic algorithms, the adequacy of the laboratory computer system to monitor the relevance of the requested diagnostic tests, the implementation of a quality control system, the design and performance of studies of cost-effectiveness, the training of the petitioner and the technical and nursing staff and the continuous evaluation of the program. The incorporation of microbiological diagnostic stewardship in routine care reports tangible benefits for the patient while strengthening the pivotal role of the clinical microbiologist in the management of infectious diseases.

The implementation of rapid microbial identification via MALDI-ToF reduces mortality in gram-negative but not gram-positive bacteremia

Our goals were to study the effect of rapid microbial identification (RMI) of positive blood culture on patient's outcome and to identify specific microbiological characteristics related to clinical benefit of RMI. This was a retrospective-cohort study of hospitalized, adult patients with bacteremia. The outcome of patients with bacteremia episodes was compared before vs. after the initiation of RMI. RMI was done by matrix-assisted laser desorption/ionization time-of-flight testing of microcolonies. The study included 1460 and 2710 cases in the pre- and post-intervention periods, respectively. There were similar rates of gram-negative, gram-positive, anaerobes, and polymicrobial infections, but higher rate of contaminants in the intervention period (39.9 vs. 43.7%, p = 0.019). The median time-to-identification decreased from 47.5 to 21.3 h (p < 0.001). Post-intervention, the median LOS declined from 10.83 to 9.79 days (p = 0.016), the rate of ICU transfer declined from 13.8 to 11.6% (p = 0.054), and the mortality rate declined from 20.9 to 18.3% (p = 0.047). The improvement in outcome variables remained statistically significant in multivariate analysis when performed for all episodes and non-contaminants but not for contaminants. The mortality declined in gram-negative bacteremia (20% vs. 15.5%, p = 0.005 in multivariate analysis) but not in gram-positive bacteremia (18.1% vs. 18.5%). RMI reduces mortality from gram-negative but not gram-positive bacteremia.

Ideal and Actual Impact of Rapid Diagnostic Testing and Antibiotic Stewardship on Antibiotic Prescribing and Clinical Outcomes in Children With Positive Blood Cultures

BACKGROUND

Implementing matrix-assisted laser desorption ionization-time of flight and multiplex polymerase chain reaction has been associated with decreased mortality and hospital length of stay in adults, but the impact in pediatrics is less understood.

METHODS

This pre-post quasi-experimental study compared antibiotic prescribing for positive blood cultures in patients ≤21 years of age collected in 2012 (preintervention) and in 2015 (after matrix-assisted laser desorption ionization-time of flight/multiplex polymerase chain reaction). Time to effective and optimal antimicrobial therapy was evaluated using Cox proportional hazards regression. Time to ideal optimal therapy was estimated as the earliest potential initiation of optimal therapy. Antibiotic use and clinical outcomes were measured.

RESULTS

There were 242 and 192 positive monomicrobial blood cultures in 2012 and 2015, respectively. Postintervention, time to optimal therapy (73.8 vs. 48.8 hours; P < 0.001) and organism identification (55.6 vs. 29.5 hours; P < 0.001) were reduced, and patients were more likely to receive optimal therapy by 7 days (hazard ratio, 1.85; P < 0.001). In the ideal scenario in 2015, there was an 8.8-hour delay in initiating optimal therapy based on the time that sufficient microbiologic data were available. Postintervention, time to effective therapy (2.8 vs. 2.7 hours; P = 0.782) and clinical outcomes did not differ. Unnecessary antibiotic duration for probable contaminants (skin flora) (43.1 vs. 29.7 hours; P = 0.027), vancomycin for methicillin-sensitive Staphylococcus aureus (54.0 vs. 41.3 hours; P = 0.008) and nonpenicillin/ampicillin antibiotics for group A Streptococcus, group B Streptococcus and Enterococcus faecalis (87.2 vs. 33.4 hours; P < 0.001) were reduced postintervention.

CONCLUSIONS

Rapid diagnostics reduced time to optimal antimicrobial therapy and unnecessary antibiotic use without worse clinical outcomes.

Clinical utility of direct application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry and rapid disk diffusion test in presumptive antimicrobial therapy for bacteremia

OBJECTIVE

To study how and to what degree the rapid pathogen identification by MALDI-TOF MS coupled with rapid disk diffusion test improve the current clinical practice of patients with bacteremia in a tertiary teaching hospital with full-time ID consultation service.

PATIENTS AND METHODS

MALDI-TOF MS and 8H disk diffusion tests were directly applied to the positive blood cultures samples and the results were reflected on antimicrobial therapy (n = 119). The appropriateness of antimicrobial selection through these interventions was verified with conventional culture results in comparison with historical control (n = 129). The mortality of patients between the two periods was also compared.

RESULTS

The appropriateness of antimicrobial selection was higher (99.2%) in the intervention than in the control group (93.8%) (p 0.024), but there was no difference in 28-day mortality between the two periods (16.8%, 14.8%) (p 0.668). The duration of presumptive antimicrobial therapy with anti-MRSA agents and carbapenem antibiotics did not differ between the two periods indicating that the intervention was not effective in decreasing the unnecessary antibiotics. On the other hand, some bacteremic patients with pathogens whose drug susceptibilities were invariably sensitive to the standard class of antibiotics definitely benefitted from the intervention.

CONCLUSION

The intervention utilizing MALDI-TOF MS and the rapid disk diffusion test may not demonstrate overall improvement in bacteremia mortality in the institution with full-time infectious disease consultants. Its utility has yet to be evaluated in different setting hospitals.

Antibiotic Use in the Intensive Care Unit: Optimization and De-Escalation

Appropriate antimicrobial therapy is essential to ensuring positive patient outcomes. Inappropriate or suboptimal utilization of antibiotics can lead to increased length of stay, multidrug-resistant infections, and mortality. Critically ill intensive care patients, particularly those with severe sepsis and septic shock, are at risk of antibiotic failure and secondary infections associated with incorrect antibiotic use. Through the initiation of active empiric antibiotic therapy based upon local susceptibilities, daily evaluation of signs and symptoms of infection and narrowing of antibiotic therapy when feasible, providers can streamline the treatment of common intensive care unit (ICU) infections. Optimizing antibiotic dosing through prolonged infusions can be beneficial in intensive care populations with altered pharmacokinetics. Antimicrobial stewardship teams can assist ICU providers in managing and implementing these tactics. This review will discuss the current literature on antibiotic use in the ICU applying antimicrobial stewardship strategies. Based upon the most recent evidence, ICUs would benefit from employing empiric guidelines for antibiotic use, collecting appropriate specimens and implementing molecular diagnostics, optimizing the dosing of antibiotics, and reducing the duration of total therapy. These strategies for antibiotic use have the potential to enhance patient care while preventing adverse outcomes.

A new scheme for strain typing of methicillin-resistant Staphylococcus aureus on the basis of matrix-assisted laser desorption ionization time-of-flight mass spectrometry by using machine learning approach

Methicillin-resistant Staphylococcus aureus (MRSA), one of the most important clinical pathogens, conducts an increasing number of morbidity and mortality in the world. Rapid and accurate strain typing of bacteria would facilitate epidemiological investigation and infection control in near real time. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid and cost-effective tool for presumptive strain typing. To develop robust method for strain typing based on MALDI-TOF spectrum, machine learning (ML) is a promising algorithm for the construction of predictive model. In this study, a strategy of building templates of specific types was used to facilitate generating predictive models of methicillin-resistant Staphylococcus aureus (MRSA) strain typing through various ML methods. The strain types of the isolates were determined through multilocus sequence typing (MLST). The area under the receiver operating characteristic curve (AUC) and the predictive accuracy of the models were compared. ST5, ST59, and ST239 were the major MLST types, and ST45 was the minor type. For binary classification, the AUC values of various ML methods ranged from 0.76 to 0.99 for ST5, ST59, and ST239 types. In multiclass classification, the predictive accuracy of all generated models was more than 0.83. This study has demonstrated that ML methods can serve as a cost-effective and promising tool that provides preliminary strain typing information about major MRSA lineages on the basis of MALDI-TOF spectra.

Youngest survivor of perinatal infection by Eikenella corrodens : case analysis and literature review highlighting the merits of placental swab culture

Eikenella corrodens has been noted as a causative organism in both neonatal and perinatal sepsis. Positivity of blood cultures at birth among preterm infants may be influenced by the maternal use of peripartum antimicrobials and a normal C-reactive protein result within the first 24 hours need not always reflect the absence of fetal invasion by the highly pathogenic organisms. For these reasons, supportive and adjunctive approaches such as appropriately collected placental swabs for culture would be of value in optimizing the antimicrobial choice for sick preterm infants during the early neonatal period. Fetal infection by E. corrodens detected by placental swab culture influencing antimicrobial management of an extremely premature infant with sepsis is described. Management of the youngest premature survivor with the lowest birthweight among the reported cases in English language of neonatal E. corrodens infection is summarized and literature is reviewed. The value of placental swab, which is often underused, is highlighted in this review.

Recent advances in the microbiological diagnosis of bloodstream infections

Rapid identification (ID) and antimicrobial susceptibility testing (AST) of the causative agent(s) of bloodstream infections (BSIs) are essential for the prompt administration of an effective antimicrobial therapy, which can result in clinical and financial benefits. Immediately after blood sampling, empirical antimicrobial therapy, chosen on clinical and epidemiological data, is administered. When ID and AST results are available, the clinician decides whether to continue or streamline the antimicrobial therapy, based on the results of the in vitro antimicrobial susceptibility profile of the pathogen. The aim of the present study is to review and discuss the experimental data, advantages, and drawbacks of recently developed technological advances of culture-based and molecular methods for the diagnosis of BSI (including mass spectrometry, magnetic resonance, PCR-based methods, direct inoculation methods, and peptide nucleic acid fluorescence in situ hybridization), the understanding of which could provide new perspectives to improve and fasten the diagnosis and treatment of septic patients. Although blood culture remains the gold standard to diagnose BSIs, newly developed methods can significantly shorten the turnaround time of reliable microbial ID and AST, thus substantially improving the diagnostic yield.

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.

Interventions to improve antibiotic prescribing practices for hospital inpatients

BACKGROUND

Antibiotic resistance is a major public health problem. Infections caused by multidrug-resistant bacteria are associated with prolonged hospital stay and death compared with infections caused by susceptible bacteria. Appropriate antibiotic use in hospitals should ensure effective treatment of patients with infection and reduce unnecessary prescriptions. We updated this systematic review to evaluate the impact of interventions to improve antibiotic prescribing to hospital inpatients.

OBJECTIVES

To estimate the effectiveness and safety of interventions to improve antibiotic prescribing to hospital inpatients and to investigate the effect of two intervention functions: restriction and enablement.

SEARCH METHODS

We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (the Cochrane Library), MEDLINE, and Embase. We searched for additional studies using the bibliographies of included articles and personal files. The last search from which records were evaluated and any studies identified incorporated into the review was January 2015.

SELECTION CRITERIA

We included randomised controlled trials (RCTs) and non-randomised studies (NRS). We included three non-randomised study designs to measure behavioural and clinical outcomes and analyse variation in the effects: non- randomised trials (NRT), controlled before-after (CBA) studies and interrupted time series (ITS) studies. For this update we also included three additional NRS designs (case control, cohort, and qualitative studies) to identify unintended consequences. Interventions included any professional or structural interventions as defined by the Cochrane Effective Practice and Organisation of Care Group. We defined restriction as 'using rules to reduce the opportunity to engage in the target behaviour (or increase the target behaviour by reducing the opportunity to engage in competing behaviours)'. We defined enablement as 'increasing means/reducing barriers to increase capability or opportunity'. The main comparison was between intervention and no intervention.

DATA COLLECTION AND ANALYSIS

Two review authors extracted data and assessed study risk of bias. We performed meta-analysis and meta-regression of RCTs and meta-regression of ITS studies. We classified behaviour change functions for all interventions in the review, including those studies in the previously published versions. We analysed dichotomous data with a risk difference (RD). We assessed certainty of evidence with GRADE criteria.

MAIN RESULTS

This review includes 221 studies (58 RCTs, and 163 NRS). Most studies were from North America (96) or Europe (87). The remaining studies were from Asia (19), South America (8), Australia (8), and the East Asia (3). Although 62% of RCTs were at a high risk of bias, the results for the main review outcomes were similar when we restricted the analysis to studies at low risk of bias.More hospital inpatients were treated according to antibiotic prescribing policy with the intervention compared with no intervention based on 29 RCTs of predominantly enablement interventions (RD 15%, 95% confidence interval (CI) 14% to 16%; 23,394 participants; high-certainty evidence). This represents an increase from 43% to 58% .There were high levels of heterogeneity of effect size but the direction consistently favoured intervention.The duration of antibiotic treatment decreased by 1.95 days (95% CI 2.22 to 1.67; 14 RCTs; 3318 participants; high-certainty evidence) from 11.0 days. Information from non-randomised studies showed interventions to be associated with improvement in prescribing according to antibiotic policy in routine clinical practice, with 70% of interventions being hospital-wide compared with 31% for RCTs. The risk of death was similar between intervention and control groups (11% in both arms), indicating that antibiotic use can likely be reduced without adversely affecting mortality (RD 0%, 95% CI -1% to 0%; 28 RCTs; 15,827 participants; moderate-certainty evidence). Antibiotic stewardship interventions probably reduce length of stay by 1.12 days (95% CI 0.7 to 1.54 days; 15 RCTs; 3834 participants; moderate-certainty evidence). One RCT and six NRS raised concerns that restrictive interventions may lead to delay in treatment and negative professional culture because of breakdown in communication and trust between infection specialists and clinical teams (low-certainty evidence).Both enablement and restriction were independently associated with increased compliance with antibiotic policies, and enablement enhanced the effect of restrictive interventions (high-certainty evidence). Enabling interventions that included feedback were probably more effective than those that did not (moderate-certainty evidence).There was very low-certainty evidence about the effect of the interventions on reducing Clostridium difficile infections (median -48.6%, interquartile range -80.7% to -19.2%; 7 studies). This was also the case for resistant gram-negative bacteria (median -12.9%, interquartile range -35.3% to 25.2%; 11 studies) and resistant gram-positive bacteria (median -19.3%, interquartile range -50.1% to +23.1%; 9 studies). There was too much variance in microbial outcomes to reliably assess the effect of change in antibiotic use. Heterogeneity of intervention effect on prescribing outcomesWe analysed effect modifiers in 29 RCTs and 91 ITS studies. Enablement and restriction were independently associated with a larger effect size (high-certainty evidence). Feedback was included in 4 (17%) of 23 RCTs and 20 (47%) of 43 ITS studies of enabling interventions and was associated with greater intervention effect. Enablement was included in 13 (45%) of 29 ITS studies with restrictive interventions and enhanced intervention effect.

AUTHORS' CONCLUSIONS

We found high-certainty evidence that interventions are effective in increasing compliance with antibiotic policy and reducing duration of antibiotic treatment. Lower use of antibiotics probably does not increase mortality and likely reduces length of stay. Additional trials comparing antibiotic stewardship with no intervention are unlikely to change our conclusions. Enablement consistently increased the effect of interventions, including those with a restrictive component. Although feedback further increased intervention effect, it was used in only a minority of enabling interventions. Interventions were successful in safely reducing unnecessary antibiotic use in hospitals, despite the fact that the majority did not use the most effective behaviour change techniques. Consequently, effective dissemination of our findings could have considerable health service and policy impact. Future research should instead focus on targeting treatment and assessing other measures of patient safety, assess different stewardship interventions, and explore the barriers and facilitators to implementation. More research is required on unintended consequences of restrictive interventions.

Use of bacterial whole-genome sequencing to understand and improve the management of invasive Staphylococcus aureus infections

INTRODUCTION

Management of invasive Staphylococcus aureus infections is complex. Dramatic improvements in bacterial whole genome sequencing (WGS) offer new opportunities for personalising the treatment of S. aureus infections. Areas covered: We address recent achievements in S. aureus genomics, describe genetic determinants of antibiotic resistance and summarise studies that have defined molecular characteristics associated with risk and outcome of S. aureus invasive infections. Potential clinical use of WGS for resistance prediction, infection outcome stratification and management of persistent /relapsing infections is critically discussed. Expert commentary: WGS is not only providing invaluable information to track the emergence and spread of important S. aureus clones, but also allows rapid determination of resistance genotypes in the clinical environment. An evolving opportunity is to infer clinically important outcomes and optimal therapeutic approaches from widely available S. aureus genome data, with the goal of individualizing management of invasive S. aureus infections.

Antimicrobial susceptibility testing of Gram-positive and -negative bacterial isolates directly from spiked blood culture media with Raman spectroscopy

Patients suffering from bacterial bloodstream infections have an increased risk of developing systematic inflammatory response syndrome (SIRS), which can result in rapid deterioration of the patients' health. Diagnostic methods for bacterial identification and antimicrobial susceptibility tests are time-consuming. The aim of this study was to investigate whether Raman spectroscopy would be able to rapidly provide an antimicrobial susceptibility profile from bacteria isolated directly from positive blood cultures. First, bacterial strains (n = 133) were inoculated in tryptic soy broth and incubated in the presence or absence of antibiotics for 5 h. Antimicrobial susceptibility profiles were analyzed by Raman spectroscopy. Subsequently, a selection of strains was isolated from blood cultures and analyzed similarly. VITEK®2 technology and broth dilution were used as the reference methods. Raman spectra from 67 antibiotic-susceptible strains showed discriminatory spectra in the absence or at low concentrations of antibiotics as compared to high antibiotic concentrations. For 66 antibiotic-resistant strains, no antimicrobial effect was observed on the bacterial Raman spectra. Full concordance with VITEK®2 data and broth dilution was obtained for the antibiotic-susceptible strains, 68 % and 98 %, respectively, for the resistant strains. Discriminative antimicrobial susceptibility testing (AST) profiles were obtained for all bacterial strains isolated from blood cultures, resulting in full concordance with the VITEK®2 data. It can be concluded that Raman spectroscopy is able to detect the antimicrobial susceptibility of bacterial species isolated from a positive blood culture bottle within 5 h. Although Raman spectroscopy is cheap and rapid, further optimization is required, to fulfill a great promise for future AST profiling technology development.

Factors associated with 12 week case-fatality in Staphylococcus aureus bacteraemia: a prospective cohort study

Staphylococcus aureus bacteraemia (SAB) is a frequent and deadly disease. Given the lack of a randomized trial, optimal first-line antibiotic treatment is still debated. Our aim was to identify prognostic factors in SAB patients and to analyse the impact of first-line antibiotics. The VIRSTA prospective cohort study was conducted in eight tertiary care centres in France. Consecutive incident adults in whom a blood culture drawn in participating centres grew S. aureus between April 2009 and October 2011 were prospectively followed for 12 weeks. Factors associated with 12-week case-fatality were identified by multivariate logistic regression. We enrolled 2091 patients and analysed survival in 1972 (median age 67.8 years, interquartile range 55.5-78.9; females 692/1972, 35.1%). SAB was nosocomial or healthcare-related in 1372/1972 (69.6%) of cases and the primary focus was unknown in 414/1972 (21.0%) of cases. Week 12 case-fatality rate was 671/1972 (34.0%). The main independent prognostic factors on multivariate analysis were age (adjusted OR by 10-year increment 1.56; 95% CI 1.44-1.69), septic shock (OR 5.11; 95% CI 3.84-6.80), metastatic cancer (OR 4.28; 95% CI 2.88-6.38), and unknown primary focus (OR 2.62; 95% CI 2.02-3.41). In the 1538 patients with methicillin-sensitive S. aureus (MSSA) bacteraemia, first-line empiric antistaphylococcal penicillins (OR 0.40; 95% CI 0.17-0.95) and vancomycin (OR 0.37; 95% CI 0.17-0.83), alone or combined with an aminoglycoside, were associated with better outcome compared with other antibiotics. There are few modifiable prognostic factors for SAB. Initiating empiric antibiotics with antistaphylococcal penicillins or vancomycin may be associated with better outcome in MSSA bacteraemia.

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.

Identification of Staphylococcus spp. and detection of mecA by an oligonucleotide array

Phenotypic identification of coagulase-negative staphylococci (CoNS) is difficult and many staphylococcal species carry mecA. This study developed an array that was able to detect mecA and identify 30 staphylococcal species by targeting the internal transcribed spacer regions. A total of 129 target reference strains (30 species) and 434 clinical isolates of staphylococci were analyzed. Gene sequencing of 16S rRNA, gap or tuf genes was the reference method for species identification. All reference strains (100%) were correctly identified, while the identification rates of clinical isolates of S. aureus and CoNS were 98.9% and 98%, respectively. The sensitivity and specificity for mecA detection were 99% and 100%, respectively, in S. aureus isolates, and both values were 100% in isolates of CoNS. The assay takes 6 h from a purified culture isolate, and so far it has not been performed directly on patient samples.

Measuring the impact of antimicrobial stewardship programs

Antimicrobial Stewardship Programs (ASPs) are being implemented worldwide to optimize antimicrobial therapy, and thereby improve patient safety and quality of care. Additionally, this should counteract resistance development. It is, however, vital that correct and timely diagnostics are performed in parallel, and that an institution runs a well-organized infection prevention program. Currently, there is no clear consensus on which interventions an ASP should comprise. Indeed this depends on the institution, the region, and the patient population that is served. Different interventions will lead to different effects. Therefore, adequate evaluations, both clinically and financially, are crucial. Here, we provide a general overview of, and perspective on different intervention strategies and methods to evaluate these ASP programs, covering before mentioned topics. This should lead to a more consistent approach in evaluating these programs, making it easier to compare different interventions and studies with each other and ultimately improve infection and patient management.

Novel pandemic influenza A (H1N1) and community-associated methicillin-resistant Staphylococcus aureus pneumonia

Postinfluenza bacterial pneumonia is a leading cause of influenza-associated death, and Staphylococcus aureus and Streptococcus pneumoniae have been important pathogens that have caused pneumonia since the influenza pandemic in 1919. Emergence of novel influenza A (H1N1) pdm09 and the concomitant global spread of community-associated methicillin-resistant S. aureus (CA-MRSA) have led to increasing prevalence of CA-MRSA pneumonia following influenza infection. Such an epidemiologic change poses a therapeutic challenge due to a high risk of inappropriate empiric antimicrobial therapy and poor clinical outcomes. Early diagnosis and initiation of appropriate antimicrobial therapy for post-influenza bacterial pneumonia have become even more important in the era of CA-MRSA. Therefore, novel molecular diagnostic techniques should be applied to more readily diagnose MRSA pneumonia.

Rapid Identification of Microorganisms by FilmArray Blood Culture Identification Panel Improves Clinical Management in Children

BACKGROUND

Blood cultures are a common investigation for children admitted to hospital. In routine practice, it takes at least 24 hours to identify an organism as a contaminant or clinically significant. FilmArray Blood Culture Identification Panel (FA-BCIP) is a multiplex polymerase chain reaction that can detect 24 pathogens within 1 hour. We assessed whether results from FA-BCIP lead to changes in clinical management in a tertiary referral paediatric hospital.

METHODS

We prospectively studied children having blood cultures taken at our tertiary children's hospital. Blood cultures were monitored and organisms identified using standard methods. FA-BCIP was performed when growth was initially detected in first positive blood cultures per episode, between January 1 and June 30, 2014. Assessment of whether the FA-BCIP result altered clinical management was made, specifically focused on antimicrobial stewardship and length of stay.

RESULTS

FA-BCIP was done on 117 positive blood cultures; 74 (63%) grew clinically significant organisms, 43 (37%) grew contaminants. FA-BCIP results were judged to alter clinical management in 63 of the 117 episodes (54%). Antimicrobials were started/altered in 23 (19%) episodes and de-escalated/withheld/stopped in 29 (25%) episodes. Ten children were discharged from hospital earlier, which saved a cumulative total of 14 bed days.

CONCLUSIONS

Rapid identification of microorganisms in pediatric blood cultures by FA-BCIP, led to changes in clinical management for half of the episodes. This improved antimicrobial stewardship and allowed early discharge from hospital for 10% of children. Future studies should focus on how best to use this technology in a cost-effective manner.

Effectiveness of Practices To Increase Timeliness of Providing Targeted Therapy for Inpatients with Bloodstream Infections: a Laboratory Medicine Best Practices Systematic Review and Meta-analysis

BACKGROUND

Bloodstream infection (BSI) is a major cause of morbidity and mortality throughout the world. Rapid identification of bloodstream pathogens is a laboratory practice that supports strategies for rapid transition to direct targeted therapy by providing for timely and effective patient care. In fact, the more rapidly that appropriate antimicrobials are prescribed, the lower the mortality for patients with sepsis. Rapid identification methods may have multiple positive impacts on patient outcomes, including reductions in mortality, morbidity, hospital lengths of stay, and antibiotic use. In addition, the strategy can reduce the cost of care for patients with BSIs.

OBJECTIVES

The purpose of this review is to evaluate the evidence for the effectiveness of three rapid diagnostic practices in decreasing the time to targeted therapy for hospitalized patients with BSIs. The review was performed by applying the Centers for Disease Control and Prevention's (CDC's) Laboratory Medicine Best Practices Initiative (LMBP) systematic review methods for quality improvement (QI) practices and translating the results into evidence-based guidance (R. H. Christenson et al., Clin Chem 57:816-825, 2011, http://dx.doi.org/10.1373/clinchem.2010.157131).

SEARCH STRATEGY

A comprehensive literature search was conducted to identify studies with measurable outcomes. A search of three electronic bibliographic databases (PubMed, Embase, and CINAHL), databases containing "gray" literature (unpublished academic, government, or industry evidence not governed by commercial publishing) (CIHI, NIHR, SIGN, and other databases), and the Cochrane database for English-language articles published between 1990 and 2011 was conducted in July 2011.

DATES OF SEARCH

The dates of our search were from 1990 to July 2011.

SELECTION CRITERIA

Animal studies and non-English publications were excluded. The search contained the following medical subject headings: bacteremia; bloodstream infection; time factors; health care costs; length of stay; morbidity; mortality; antimicrobial therapy; rapid molecular techniques, polymerase chain reaction (PCR); in situ hybridization, fluorescence; treatment outcome; drug therapy; patient care team; pharmacy service, hospital; hospital information systems; Gram stain; pharmacy service; and spectrometry, mass, matrix-assisted laser desorption-ionization. Phenotypic as well as the following key words were searched: targeted therapy; rapid identification; rapid; Gram positive; Gram negative; reduce(ed); cost(s); pneumoslide; PBP2; tube coagulase; matrix-assisted laser desorption/ionization time of flight; MALDI TOF; blood culture; EMR; electronic reporting; call to provider; collaboration; pharmacy; laboratory; bacteria; yeast; ICU; and others. In addition to the electronic search being performed, a request for unpublished quality improvement data was made to the clinical laboratory community.

MAIN RESULTS

Rapid molecular testing with direct communication significantly improves timeliness compared to standard testing. Rapid phenotypic techniques with direct communication likely improve the timeliness of targeted therapy. Studies show a significant and homogeneous reduction in mortality associated with rapid molecular testing combined with direct communication.

AUTHORS' CONCLUSIONS

No recommendation is made for or against the use of the three assessed practices of this review due to insufficient evidence. The overall strength of evidence is suggestive; the data suggest that each of these three practices has the potential to improve the time required to initiate targeted therapy and possibly improve other patient outcomes, such as mortality. The meta-analysis results suggest that the implementation of any of the three practices may be more effective at increasing timeliness to targeted therapy than routine microbiology techniques for identification of the microorganisms causing BSIs. Based on the included studies, results for all three practices appear applicable across multiple microorganisms, including methicillin-resistant Staphylococcus aureus (MRSA), methicillin-sensitive S. aureus (MSSA), Candida species, and Enterococcus species.

Impact of the multiplex polymerase chain reaction in culture-positive samples on appropriate antibiotic use in patients with staphylococcal bacteremia

Rapid identification of the microorganisms in patients with bacteremia may be useful in clinical practice. We evaluated the impact of the multiplex polymerase chain reaction (PCR) on appropriate antibiotic use for patients with gram-positive cocci cluster (GPCC) bacteremia. We divided the GPCC bacteremia cases into a pre-PCR group (2010-2011) and a post-PCR group (2012-2013). A total 664 cases were included in the pre-PCR group; and 570, in the post-PCR group. In methicillin-susceptible Staphylococcus aureus (MSSA) cases, optimal antibiotics were administered earlier in the post-PCR group (77.4h versus 42.6h, P=0.035). Although the proportions of glycopeptide exposure did not differ (54.7% versus 56.7%, P=0.799), the duration of exposure decreased (69.6h versus 30.7h, P=0.004). In methicillin-resistant S. aureus cases, the time to optimal antibiotics administration did not differ (45.4h versus 43.7h, P=0.275). Multiplex PCR test significantly improved the early initiation of optimal antibiotics in MSSA bacteremia and reduced the unnecessary glycopeptide exposure.

Rapid identification of pathogens using molecular techniques

Real-time PCR is the traditional face of nucleic acid detection in the diagnostic microbiology laboratory and is now generally regarded as robust enough to be widely adopted. Methods based on nucleic acid detection of this type are bringing increased accuracy to diagnosis in areas where culture is difficult and/or expensive, and these methods are often effective partners to other rapid molecular diagnostic tools such as matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS). This change in practice has particularly affected the recognition of viruses and fastidious or antibiotic-exposed bacteria, but has been also shown to be effective in the recognition of troublesome or specialised phenotypes such as antiviral resistance and transmissible antibiotic resistance in the Enterobacteriaceae. Quantitation and high-intensity sequencing (of multiple whole genomes) has brought new opportunities as well as new challenges to the microbiology community. Diagnostic microbiologists currently training might be expected to deal less with the culture-based techniques of the last half-century than with the high-volume data and complex analyses of the next.

Eikenella corrodens Sepsis with Cerebrospinal Fluid Pleocytosis in a Very Low Birth Weight Neonate

We report a case of Eikenella corrodens sepsis associated with CSF pleocytosis in a very low birth weight neonate. A 1000-gram male neonate was born at 27-week gestation due to preterm labor. The patient presented with signs and symptoms of sepsis and was treated for suspected meningitis with intravenous ampicillin and gentamicin for 7 days, with cefotaxime added for three weeks. He had a normal brain MRI at discharge and normal development at 6 months of life. To our knowledge, this is the first case of E. corrodens sepsis and associated meningitis in a very low birth weight neonate.

Optimization of the score cutoff value for routine identification of Staphylococcus species by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry

Staphylococcus species are important pathogens. We evaluated 2 score cutoffs (2.0 and 1.7) and the replicate number (a single or a duplicate test) on the identification of staphylococci using the Bruker matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). A collection of 440 clinical isolates (11 species) and 144 reference strains (36 species) was evaluated. For clinical isolates using a cutoff of 2.0 and duplicate tests, the rates of species, genus, and unreliable identifications were 93.4%, 5.7%, and 0.9% respectively, while the respective values were 99.3%, 0.2%, and 0.5% when the cutoff was 1.7. The species identification rates were significantly higher (P<0.01) when a cutoff of 1.7 or a duplicate test was used. Similar results were obtained for reference strains. In conclusion, a cutoff of 1.7 and duplicate tests are recommended for identification of staphylococci using MALDI-TOF MS.

Diagnosis and treatment of bacteremia and endocarditis due to Staphylococcus aureus. A clinical guideline from the Spanish Society of Clinical Microbiology and Infectious Diseases (SEIMC)

Both bacteremia and infective endocarditis caused by Staphylococcus aureus are common and severe diseases. The prognosis may darken not infrequently, especially in the presence of intracardiac devices or methicillin-resistance. Indeed, the optimization of the antimicrobial therapy is a key step in the outcome of these infections. The high rates of treatment failure and the increasing interest in the influence of vancomycin susceptibility in the outcome of infections caused by both methicillin-susceptible and -resistant isolates has led to the research of novel therapeutic schemes. Specifically, the interest raised in recent years on the new antimicrobials with activity against methicillin-resistant staphylococci has been also extended to infections caused by susceptible strains, which still carry the most important burden of infection. Recent clinical and experimental research has focused in the activity of new combinations of antimicrobials, their indication and role still being debatable. Also, the impact of an appropriate empirical antimicrobial treatment has acquired relevance in recent years. Finally, it is noteworthy the impact of the implementation of a systematic bundle of measures for improving the outcome. The aim of this clinical guideline is to provide an ensemble of recommendations in order to improve the treatment and prognosis of bacteremia and infective endocarditis caused by S. aureus, in accordance to the latest evidence published.

The world's microbiology laboratories can be a global microbial sensor network

The microbes that infect us spread in global and local epidemics, and the resistance genes that block their treatment spread within and between them. All we can know about where they are to track and contain them comes from the only places that can see them, the world's microbiology laboratories, but most report each patient's microbe only to that patient's caregiver. Sensors, ranging from instruments to birdwatchers, are now being linked in electronic networks to monitor and interpret algorithmically in real-time ocean currents, atmospheric carbon, supply-chain inventory, bird migration, etc. To so link the world's microbiology laboratories as exquisite sensors in a truly lifesaving real-time network their data must be accessed and fully subtyped. Microbiology laboratories put individual reports into inaccessible paper or mutually incompatible electronic reporting systems, but those from more than 2,200 laboratories in more than 108 countries worldwide are now accessed and translated into compatible WHONET files. These increasingly web-based files could initiate a global microbial sensor network. Unused microbiology laboratory byproduct data, now from drug susceptibility and biochemical testing but increasingly from new technologies (genotyping, MALDI-TOF, etc.), can be reused to subtype microbes of each genus/species into sub-groupings that are discriminated and traced with greater sensitivity. Ongoing statistical delineation of subtypes from global sensor network data will improve detection of movement into any patient of a microbe or resistance gene from another patient, medical center or country. Growing data on clinical manifestations and global distributions of subtypes can automate comments for patient's reports, select microbes to genotype and alert responders.

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.

Comparison of the next-generation Xpert MRSA/SA BC assay and the GeneOhm StaphSR assay to routine culture for identification of Staphylococcus aureus and methicillin-resistant S. aureus in positive-blood-culture broths

A bloodstream infection with Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), is a serious condition that carries a high mortality rate and is also associated with significant hospital costs. The rapid and accurate identification and differentiation of methicillin-susceptible S. aureus (MSSA) and MRSA directly from positive blood cultures has demonstrated benefits in both patient outcome and cost-of-care metrics. We compare the next-generation Xpert MRSA/SA BC (Xpert) assay to the GeneOhm StaphSR (GeneOhm) assay for the identification and detection of S. aureus and methicillin resistance in prospectively collected blood culture broths containing Gram-positive cocci. All results were compared to routine bacterial culture as the gold standard. Across 8 collection and test sites, the Xpert assay demonstrated a sensitivity of 99.6% (range, 96.4% to 100%) and a specificity of 99.5% (range, 98.0% to 100%) for identifying S. aureus, as well as a sensitivity of 98.1% (range, 87.5% to 100%) and a specificity of 99.6% (range, 98.3% to 100%) for identifying MRSA. In comparison, the GeneOhm assay demonstrated a sensitivity of 99.2% (range, 95.2% to 100%) and a specificity of 96.5% (range, 89.2% to 100%) for identifying S. aureus, as well as a sensitivity of 94.3% (range, 87.5% to 100%) and a specificity of 97.8% (range, 96.1% to 100%) for identifying MRSA. Five of six cultures falsely reported as negative for MRSA by the GeneOhm assay were correctly identified as positive by the Xpert assay, while one culture falsely reported as negative for MRSA by the Xpert assay was correctly reported as positive by the GeneOhm assay.

Evaluation of VITEK mass spectrometry (MS), a matrix-assisted laser desorption ionization time-of-flight MS system for identification of anaerobic bacteria

Background

By conventional methods, the identification of anaerobic bacteria is more time consuming and requires more expertise than the identification of aerobic bacteria. Although the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems are relatively less studied, they have been reported to be a promising method for the identification of anaerobes. We evaluated the performance of the VITEK MS in vitro diagnostic (IVD; 1.1 database; bioMérieux, France) in the identification of anaerobes.

Methods

We used 274 anaerobic bacteria isolated from various clinical specimens. The results for the identification of the bacteria by VITEK MS were compared to those obtained by phenotypic methods and 16S rRNA gene sequencing.

Results

Among the 249 isolates included in the IVD database, the VITEK MS correctly identified 209 (83.9%) isolates to the species level and an additional 18 (7.2%) at the genus level. In particular, the VITEK MS correctly identified clinically relevant and frequently isolated anaerobic bacteria to the species level. The remaining 22 isolates (8.8%) were either not identified or misidentified. The VITEK MS could not identify the 25 isolates absent from the IVD database to the species level.

Conclusions

The VITEK MS showed reliable identifications for clinically relevant anaerobic bacteria.

Preparation of a blood culture pellet for rapid bacterial identification and antibiotic susceptibility testing

Bloodstream infections and sepsis are a major cause of morbidity and mortality. The successful outcome of patients suffering from bacteremia depends on a rapid identification of the infectious agent to guide optimal antibiotic treatment. The analysis of Gram stains from positive blood culture can be rapidly conducted and already significantly impact the antibiotic regimen. However, the accurate identification of the infectious agent is still required to establish the optimal targeted treatment. We present here a simple and fast bacterial pellet preparation from a positive blood culture that can be used as a sample for several essential downstream applications such as identification by MALDI-TOF MS, antibiotic susceptibility testing (AST) by disc diffusion assay or automated AST systems and by automated PCR-based diagnostic testing. The performance of these different identification and AST systems applied directly on the blood culture bacterial pellets is very similar to the performance normally obtained from isolated colonies grown on agar plates. Compared to conventional approaches, the rapid acquisition of a bacterial pellet significantly reduces the time to report both identification and AST. Thus, following blood culture positivity, identification by MALDI-TOF can be reported within less than 1 hr whereas results of AST by automated AST systems or disc diffusion assays within 8 to 18 hr, respectively. Similarly, the results of a rapid PCR-based assay can be communicated to the clinicians less than 2 hr following the report of a bacteremia. Together, these results demonstrate that the rapid preparation of a blood culture bacterial pellet has a significant impact on the identification and AST turnaround time and thus on the successful outcome of patients suffering from bloodstream infections.

Interventions to improve antibiotic prescribing practices for hospital inpatients

BACKGROUND

The first publication of this review in Issue 3, 2005 included studies up to November 2003. This update adds studies to December 2006 and focuses on application of a new method for meta-analysis of interrupted time series studies and application of new Cochrane Effective Practice and Organisation of Care (EPOC) Risk of Bias criteria to all studies in the review, including those studies in the previously published version. The aim of the review is to evaluate the impact of interventions from the perspective of antibiotic stewardship. The two objectives of antibiotic stewardship are first to ensure effective treatment for patients with bacterial infection and second support professionals and patients to reduce unnecessary use and minimize collateral damage.

OBJECTIVES

To estimate the effectiveness of professional interventions that, alone or in combination, are effective in antibiotic stewardship for hospital inpatients, to evaluate the impact of these interventions on reducing the incidence of antimicrobial-resistant pathogens or Clostridium difficile infection and their impact on clinical outcome.

SEARCH METHODS

We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE from 1980 to December 2006 and the EPOC specialized register in July 2007 and February 2009 and bibliographies of retrieved articles. The main comparison is between interventions that had a restrictive element and those that were purely persuasive. Restrictive interventions were implemented through restriction of the freedom of prescribers to select some antibiotics. Persuasive interventions used one or more of the following methods for changing professional behaviour: dissemination of educational resources, reminders, audit and feedback, or educational outreach. Restrictive interventions could contain persuasive elements.

SELECTION CRITERIA

We included randomized clinical trials (RCTs), controlled clinical trials (CCT), controlled before-after (CBA) and interrupted time series studies (ITS). Interventions included any professional or structural interventions as defined by EPOC. The intervention had to include a component that aimed to improve antibiotic prescribing to hospital inpatients, either by increasing effective treatment or by reducing unnecessary treatment. The results had to include interpretable data about the effect of the intervention on antibiotic prescribing or microbial outcomes or relevant clinical outcomes.

DATA COLLECTION AND ANALYSIS

Two authors extracted data and assessed quality. We performed meta-regression of ITS studies to compare the results of persuasive and restrictive interventions. Persuasive interventions advised physicians about how to prescribe or gave them feedback about how they prescribed. Restrictive interventions put a limit on how they prescribed; for example, physicians had to have approval from an infection specialist in order to prescribe an antibiotic. We standardized the results of some ITS studies so that they are on the same scale (percent change in outcome), thereby facilitating comparisons of different interventions. To do this, we used the change in level and change in slope to estimate the effect size with increasing time after the intervention (one month, six months, one year, etc) as the percent change in level at each time point. We did not extrapolate beyond the end of data collection after the intervention. The meta-regression was performed using standard weighted linear regression with the standard errors of the coefficients adjusted where necessary.

MAIN RESULTS

For this update we included 89 studies that reported 95 interventions. Of the 89 studies, 56 were ITSs (of which 4 were controlled ITSs), 25 were RCT (of which 5 were cluster-RCTs), 5 were CBAs and 3 were CCTs (of which 1 was a cluster-CCT).Most (80/95, 84%) of the interventions targeted the antibiotic prescribed (choice of antibiotic, timing of first dose and route of administration). The remaining 15 interventions aimed to change exposure of patients to antibiotics by targeting the decision to treat or the duration of treatment. Reliable data about impact on antibiotic prescribing data were available for 76 interventions (44 persuasive, 24 restrictive and 8 structural). For the persuasive interventions, the median change in antibiotic prescribing was 42.3% for the ITSs, 31.6% for the controlled ITSs, 17.7% for the CBAs, 3.5% for the cluster-RCTs and 24.7% for the RCTs. The restrictive interventions had a median effect size of 34.7% for the ITSs, 17.1% for the CBAs and 40.5% for the RCTs. The structural interventions had a median effect of 13.3% for the RCTs and 23.6% for the cluster-RCTs. Data about impact on microbial outcomes were available for 21 interventions but only 6 of these also had reliable data about impact on antibiotic prescribing.Meta-analysis of 52 ITS studies was used to compare restrictive versus purely persuasive interventions. Restrictive interventions had significantly greater impact on prescribing outcomes at one month (32%, 95% confidence interval (CI) 2% to 61%, P = 0.03) and on microbial outcomes at 6 months (53%, 95% CI 31% to 75%, P = 0.001) but there were no significant differences at 12 or 24 months. Interventions intended to decrease excessive prescribing were associated with reduction in Clostridium difficile infections and colonization or infection with aminoglycoside- or cephalosporin-resistant gram-negative bacteria, methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis. Meta-analysis of clinical outcomes showed that four interventions intended to increase effective prescribing for pneumonia were associated with significant reduction in mortality (risk ratio 0.89, 95% CI 0.82 to 0.97), whereas nine interventions intended to decrease excessive prescribing were not associated with significant increase in mortality (risk ratio 0.92, 95% CI 0.81 to 1.06).

AUTHORS' CONCLUSIONS

The results show that interventions to reduce excessive antibiotic prescribing to hospital inpatients can reduce antimicrobial resistance or hospital-acquired infections, and interventions to increase effective prescribing can improve clinical outcome. This update provides more evidence about unintended clinical consequences of interventions and about the effect of interventions to reduce exposure of patients to antibiotics. The meta-analysis supports the use of restrictive interventions when the need is urgent, but suggests that persuasive and restrictive interventions are equally effective after six months.