Randomized Trial of Rapid Multiplex Polymerase Chain Reaction-Based Blood Culture Identification and Susceptibility Testing

Clinical Impact of Rapid Species Identification From Positive Blood Cultures With Same-day Phenotypic Antimicrobial Susceptibility Testing on the Management and Outcome of Bloodstream Infections

BACKGROUND

Timely availability of microbiological results from positive blood cultures is essential to enable early pathogen-directed therapy. The Accelerate Pheno system (ADX) is a novel technology using fluorescence in situ hybridization for rapid species identification (ID) and morphokinetic bacterial analysis for phenotypic antimicrobial susceptibility testing (AST), with promising results. Yet the impact of this technology on clinical management and patient outcome remains unclear.

METHODS

We conducted a quasiexperimental before-and-after observational study and analyzed 3 groups with different diagnostic and therapeutic pathways following recent integration of ADX: conventional microbiological diagnostics with and without antimicrobial stewardship program (ASP) intervention, and rapid diagnostics (ADX in addition to conventional standard) with ASP intervention. Primary endpoints were time to adequate, to optimal and to step-down antimicrobial therapy. Secondary endpoints were antimicrobial consumption, in-hospital mortality, length of stay (LOS), and the incidence of Clostridioidesdifficile infection (CDI).

RESULTS

Two hundred four patients (conventional diagnostics, n = 64; conventional diagnostics + ASP, n = 68; rapid diagnostics + ASP; n = 72) were evaluated. The use of ADX significantly decreased time from Gram stain to ID (median, 23 vs 2.2 hours, P < .001) and AST (median, 23 vs 7.4 hours, P < .001), from Gram stain to optimal therapy (median, 11 vs 7 hours, P = .024) and to step-down antimicrobial therapy (median, 27.8 vs 12 hours, P = .019). However, groups did not differ in antimicrobial consumption, duration of antimicrobial therapy, mortality, LOS, or incidence of CDI.

CONCLUSIONS

Use of ADX significantly reduced time to ID and AST as well as time to optimal antimicrobial therapy but did not affect antimicrobial consumption and clinical outcome.

The state of antibiotic stewardship programs in 2021: The perspective of an experienced steward

Recognition of antibiotic stewardship programs (ASPs) as essential components of quality health care has dramatically increased in the past decade. The value of ASPs has been further reinforced during the coronavirus disease 2019 (COVID-19) pandemic because these programs were instrumental in monitoring antibiotic use, assessing emerging COVID-19 therapies, and coordinating implementation of monoclonal antibody infusions and vaccinations. ASPs are now required across hospital settings as a condition of participation for the Centers for Medicare and Medicaid Services and for accreditation by The Joint Commission. In the 2019 National Healthcare Safety Network annual survey, almost 89% of hospitals met the Seven Core Elements for ASPs defined by the Centers for Disease Control and Prevention. More than 61% of programs were co-led by physicians and pharmacists, evidence of the leadership role of both groups. ASPs employ many strategies to improve prescribing. Core interventions of preauthorization for targeted antibiotics, prospective audit and feedback, and development of local treatment guidelines have been supplemented with numerous emerging strategies. Diagnostic stewardship, optimizing duration of therapy, promoting appropriate conversion from intravenous to oral therapy, monitoring at transitions of care and hospital discharge, implementing stewardship initiatives in the outpatient setting, and increasing use of telemedicine are approaches being adopted across hospital settings. As a core function for medical facilities, ASP leaders must ensure that antibiotic use and ASP interventions promote optimal and equitable care. The urgency of success becomes progressively greater as complex patterns of antibiotic resistance continue to emerge, exacerbated by unpredictable factors such as a worldwide pandemic.

Optimizing the Use of Antibiotic Agents in the Pediatric Intensive Care Unit: A Narrative Review

Antibiotics are one of the most prescribed drug classes in the pediatric intensive care unit, yet the incidence of inappropriate antibiotic prescribing remains high in critically ill children. Optimizing the use of antibiotics in this population is imperative to guarantee adequate treatment, avoid toxicity and the occurrence of antibiotic resistance, both on a patient level and on a population level. Antibiotic stewardship encompasses all initiatives to promote responsible antibiotic usage and the PICU represents a major target environment for antibiotic stewardship programs. This narrative review provides a summary of the available knowledge on the optimal selection, duration, dosage, and route of administration of antibiotic treatment in critically ill children. Overall, more scientific evidence on how to optimize antibiotic treatment is warranted in this population. We also give our personal expert opinion on research priorities.

Expanding antimicrobial stewardship strategies for the NICU: Management of surgical site infections, perioperative prophylaxis, and culture negative sepsis

OBJECTIVE

To review antibiotic stewardship strategies for neonatal intensive care units (NICU) in the areas of management of surgical site infections, perioperative prophylaxis and culture negative late onset sepsis.

FINDING

Review of local microbiology, stratification of surgical procedures by risk of contamination of the surgical site, and adherence to evidence-based principles of perioperative antibiotic administration (targeted therapy, effective dosing, appropriate timing and limiting duration post-operatively) can help to minimize unnecessary antibiotic use for neonatal surgery. Creating a late onset sepsis case definition, appropriate collection and interpretation of blood cultures, and instituting antibiotic time-outs can minimize the overuse of antibiotics for culture negative sepsis.

CONCLUSION

Effective implementation of these antimicrobial stewardship strategies in the NICU can reduce unnecessary antimicrobial use and limit the emergence of resistant pathogens.

Evaluation of Microbiological Performance and the Potential Clinical Impact of the ePlex® Blood Culture Identification Panels for the Rapid Diagnosis of Bacteremia and Fungemia

Molecular rapid diagnostic assays associated with antimicrobial stewardship have proven effective for the early adaptation of empiric therapy in bloodstream infections. The ePlex^® BCID (GenMark Diagnostics) Panels allow identification of 56 bacteria and fungi and 10 resistance genes in 90 min directly from positive blood cultures. We prospectively evaluated 187 sepsis episodes at Grenoble University Hospital and retrospectively analyzed the cases to measure the potential clinical impact of the ePlex BCID results. Identification of all pathogens was obtained for 164/187 (88%) bloodstream infections with 100% detection of antimicrobial resistance genes (17 bla_CTX-M , 1 vanA, and 17 mecA genes). Only 15/209 (7%) strains were not covered by the panels. Sensitivity for detection of micro-organisms targeted by the RUO BCID-GP, BCID-GN, and BCID-FP Panels was respectively 84/84 (100%), 103/107 (96%), and 14/14 (100%). Interestingly, accurate identification of all pathogens was achieved in 15/17 (88%) polymicrobial samples. Retrospective analysis of medical records showed that a modification of antimicrobial treatment would have been done in 45% of the patients. Treatment modifications would have been an optimization of empiric therapy, a de-escalation or an escalation in respectively 16, 17, and 11% of the patients. Moreover, 11% of the samples were classified as contaminants or not clinically relevant and would have led to early de-escalation or withdrawal of any antibiotic. Detection of resistance genes in addition to identification alone increased escalation rate from 4 to 11% of the patients. Absence of the ePlex result was considered a lost opportunity for therapy modification in 28% of patients.

The Impact of Rapid Species Identification on Management of Bloodstream Infections: What's in a Name?

Bloodstream infections are a leading cause of morbidity and mortality. Molecular rapid diagnostic tests (mRDTs) are transforming care for patients with bloodstream infection by providing the opportunity to dramatically shorten times to effective therapy and speeding de-escalation of overly broad empiric therapy. However, because of the novelty of these tests which provide information regarding microbial identification and whether specific antibiotic-resistance mutations were detected, many front-line providers still delay final decisions until complete phenotypic susceptibility results are available several days later. Thus the benefits of mRDTs have been largely limited to circumstances where antimicrobial stewardship programs closely monitor these tests and intervene as soon as the results are available. We searched PubMed and Google Scholar for articles published from 1980 to 2019 using the terms antibiotic, antifungal, bacteremia, bloodstream infection, candidemia, candidiasis, children, coagulase negative staphylococcus, consultation, contamination, costs, echocardiogram, endocarditis, enterobacteriaceae, enterococcus, Gram-negative, guidelines, IDSA, immunocompromised, infectious disease or ID, lumbar puncture, meningitis, mortality, MRSA, MSSA, neonatal, outcomes, pediatric, pneumococcal, polymicrobial, Pseudomonas, rapid diagnostic testing, resistance, risk factors, sepsis, Staphylococcus aureus, stewardship, streptococcus, and treatment. With the data from this search, we aim to provide guidance to front-line providers regarding the interpretation and immediate actions to be taken in response to the identification of common bloodstream pathogens by mRDTs. In addition to antimicrobial therapy, additional diagnostic or therapeutic interventions are recommended for particular organisms and clinical settings to either determine the extent of infection or control its source. Pediatric perspectives are offered for those bloodstream pathogens for which management differs from that in adults.

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.

High-impact RCTs without prospective informed consent: a systematic review

The prevalence of randomized controlled trials (RCTs) performed without fully informed prospective consent from subjects is unknown. We performed this study to estimate the prevalence of high-impact RCTs performed without informed consent from all subjects and examine whether such trials are becoming more prevalent. We performed a systematic review of English-language RCTs published from 2014 through 2018 identified in Scopus and sorted to identify the top 100 most highly cited RCTs each year. Text search of title and abstract included terms randomized controlled or clinical trial and spelling variants thereof, and excluded metaanalyses and systematic reviews. We independently identified the most highly cited RCTs based on predefined criteria and negotiated to agreement, then independently performed keyword searches, read, abstracted and coded information regarding informed consent from each paper and again negotiated to agreement. No quality indicators were assessed. We planned descriptive qualitative analysis and appropriate quantitative analysis to examine the prevalence and characteristics of trials enrolling subjects with other than fully informed prospective consent. We find that 44 (8.8%, binomial exact 95% CI 6.5% to 11.6%) of 500 high-impact RCTs did not secure informed consent from at least some subjects. The prevalence of such trials did not change over the 5 years (OR=1.09, z=0.78, p=0.44). A majority (66%) of the trials involved emergency situations, and 40 of 44 (90.9%) of the trials involved emergency interventions, pragmatic designs, were cluster randomized, or a combination of these factors. A qualitative analysis explores the methods of and justifications for waiving informed consent in our sample of RCTs.

Panels and Syndromic Testing in Clinical Microbiology

Syndromic panels have allowed clinical microbiology laboratories to rapidly identify bacteria, viruses, fungi, and parasites and are now fully integrated into the standard testing practices of many clinical laboratories. To maximize the benefit of syndromic testing, laboratories must implement strict measures to ensure that syndromic panels are being used responsibly. This article discusses commercially available syndromic panels, the benefits and limitations of testing, and how diagnostic and laboratory stewardship can be used to optimize testing and improve patient care while keeping costs at a minimum.

Update on Susceptibility Testing: Genotypic and Phenotypic Methods

Antimicrobial susceptibility testing (AST) is now, more than ever, a critical role of the microbiology laboratory. Several factors limit its application for patient care and antimicrobial resistance epidemiology, including time to results, requirements for pure cultures, and high starting concentration of bacteria. This review discusses the global status of AST and new phenotypic and genotypic methods in late-stage development or that are new to market.

Management of Gram-Negative Bloodstream Infections in the Era of Rapid Diagnostic Testing: Impact With and Without Antibiotic Stewardship

Background

Verigene Blood-Culture Gram-Negative is a rapid diagnostic test (RDT) that detects gram-negatives (GNs) and resistance within hours from gram stain. The majority of the data support the use of RDTs with antimicrobial stewardship (AMS) intervention in gram-positive bloodstream infection (BSI). Less is known about GN BSI.

Methods

This was a retrospective quasi-experimental (nonrandomized) study of adult patients with RDT-target GN BSI comparing patients pre-RDT/AMS vs post-RDT/pre-AMS vs post-RDT/AMS. Optimal therapy was defined as appropriate coverage with the narrowest spectrum, accounting for source and co-infecting organisms. Time to optimal therapy was analyzed using Kaplan-Meier and multivariable Cox proportional hazards regression.

Results

Eight-hundred thirty-two patients were included; 237 pre-RDT/AMS vs 308 post-RDT/pre-AMS vs 237 post-RDT/AMS, respectively. The proportion of patients on optimal antibiotic therapy increased with each intervention (66.5% vs 78.9% vs 83.2%; P < .0001). Time to optimal therapy (interquartile range) decreased with introduction of RDT: 47 (7.9–67.7) hours vs 24.9 (12.4–55.2) hours vs 26.5 (10.3–66.5) hours (P = .09). Using multivariable modeling, infectious diseases (ID) consult was an effect modifier. Within the ID consult stratum, controlling for source and ICU stay, compared with the pre-RDT/AMS group, both post-RDT/pre-AMS (adjusted hazard ratio [aHR], 1.34; 95% CI, 1.04–1.72) and post-RDT/AMS (aHR, 1.28; 95% CI, 1.01–1.64), improved time to optimal therapy. This effect was not seen in the stratum without ID consult.

Conclusions

With the introduction of RDT and AMS, both proportion and time to optimal antibiotic therapy improved, especially among those with an existing ID consult. This study highlights the beneficial role of RDTs in GN BSI.

Clinical impact of pharmacist-directed antimicrobial stewardship guidance following blood culture rapid diagnostic testing

BACKGROUND

Rapid diagnostic testing (RDT) has been shown to be associated with improved clinical outcomes.

AIM

To evaluate the clinical outcomes of using RDT paired with well-defined pharmacist-directed antimicrobial stewardship programme (ASP) guidance to achieve targeted treatment in patients with bacteraemia.

METHODS

In this quasi-study, a retrospective (pre-intervention) phase was compared with a prospective (post-intervention) phase. Adult patients with positive blood cultures identified using the BacT/ALERT system were included. Bacterial identification and susceptibility were provided by VITEK 2. During the post-intervention phase, Verigene ASP guidance was developed to optimize antibiotic selection. Pharmacists received the results from the microbiology laboratory, evaluated the appropriateness of current therapy (if any), and communicated the recommended antimicrobial therapy to the treating physician accordingly.

FINDINGS

The cohort consisted of 164 patients in the pre-intervention group and 148 patients in the post-intervention group. When comparing the post-intervention period with the pre-intervention period, the median time to culture identification was 22 vs 96 h (P<0.0001), median time to targeted antibiotics was 2 vs 22 h (P<0.0001), median time for antibiotic de-escalation was 12.2 vs 27 h (P<0.0001), and median time to escalation was 1.3 vs 24 h (P<0.003), respectively. In-hospital mortality and 30-day re-admission were significantly lower in the post-intervention group (P<0.003 and 0.034, respectively). Length of hospital stay was significantly shorter in the post-intervention group (6.5 vs 8 days; P=0.03).

CONCLUSION

Rapid identification of bacteraemia combined with a pharmacist's recommendation as an ASP initiative significantly improved time to optimal therapy, and may have decreased the risk of mortality and re-admission.

Impact of Rapid Antimicrobial Susceptibility Testing in Gram-Negative Rod Bacteremia: a Quasi-experimental Study

Clinical justification for rapid antimicrobial susceptibility testing (AST) in Gram-negative rod (GNR) bacteremia is compelling; however, evidence supporting its value is sparse. We investigated the impact of rapid AST on clinical and antimicrobial stewardship outcomes in real-world practice. We performed a before-and-after quasi-experimental study from February 2018 to July 2019 at a tertiary hospital of the 24-h/day, 7-day/week implementation of the direct Vitek 2 AST method from positive blood culture broth for GNR bacteremia with electronic isolate-specific de-escalation comments and daytime antibiotic stewardship program (ASP) intervention. The primary outcome was time to appropriate antibiotic escalation or de-escalation, and secondary outcomes included time to oral antibiotic stepdown, hospital length of stay (LOS), all-cause 30-day mortality, 7-day incidence of acute kidney injury (AKI), and 30-day incidence of Clostridioides difficile infection (CDI). A total of 671 GNR isolates were included from 643 adult patients. Among patients for whom antibiotic change occurred after rapid AST result, rapid AST was associated with a trend in decreased time to escalation or de-escalation (hazard ratio, 1.22; 95% confidence interval [CI], 0.99 to 1.51; P = 0.06), with median times of 52.3 versus 42.2 h. Secondary outcomes were similar in both groups and include median time to oral antibiotic stepdown, LOS, all-cause mortality, and incidence of AKI and CDI. Rapid AST led to improved stewardship measures but did not impact clinical patient outcomes. These results highlight that multiple variables in addition to the timing of the AST result contribute to clinical outcome and that further intervention may be required to clinically justify rapid AST implementation.

A simple, inexpensive, and rapid method to assess antibiotic effectiveness against exoelectrogenic bacteria

A sufficiently fast and simple antimicrobial susceptibility testing (AST) is urgently required to guide effective antibiotic usages and to surveil the antimicrobial resistance rate. Here, we establish a rapid, quantitative, and high-throughput phenotypic AST by measuring electrons transferred from the interiors of microbial cells to external electrodes. Because the transferred electrons are based on microbial metabolic activities and are inversely proportional to the concentration of potential antibiotics, the changes in electrical outputs can be readily used as a transducing signal to efficiently monitor bacterial growth and antibiotic susceptibility. The sensing is performed by directly measuring the total energy, or all the accumulated microbial electricity, generated by microbial fuel cells (MFCs) arranged in a large-capacity disposable, paper-based testbed. A common Gram-negative pathogenic bacterium Pseudomonas aeruginosa wild-type PAO1 and first-line antibiotic gentamicin (GEN) are used in our experiments. The minimum inhibitory concentration (MIC) values generated from our technique are validated by the gold standard broth microdilution (BMD). Our new approach provides quantitative, actionable MIC results within just 5 h because it measures electricity produced by bacterial metabolism instead of the days needed for growth-observation methods. Moreover, as the equipment needed is simple, common, and inexpensive, our test has immense potential to be adopted in the field or resource-limited hospitals and labs to provide insightful assessments for research and clinical practices.

Pharmacist-Driven Implementation of Fast Identification and Antimicrobial Susceptibility Testing Improves Outcomes for Patients with Gram-Negative Bacteremia and Candidemia

Bloodstream infections (BSI) are associated with increased morbidity and mortality, especially when caused by Gram-negative or fungal pathogens. The objective of this study was to assess the impact of fast identification-antimicrobial susceptibility testing (ID/AST) with the Accelerate Pheno system (AXDX) from May 2018 to December 2018 on antibiotic therapy and patient outcomes. A pre-post quasiexperimental study of 200 patients (100 pre-AXDX implementation and 100 post-AXDX implementation) was conducted.

Bloodstream infections (BSI) are associated with increased morbidity and mortality, especially when caused by Gram-negative or fungal pathogens. The objective of this study was to assess the impact of fast identification-antimicrobial susceptibility testing (ID/AST) with the Accelerate Pheno system (AXDX) from May 2018 to December 2018 on antibiotic therapy and patient outcomes. A pre-post quasiexperimental study of 200 patients (100 pre-AXDX implementation and 100 post-AXDX implementation) was conducted. The primary endpoints measured were time to first antibiotic intervention, time to most targeted antibiotic therapy, and 14-day hospital mortality. Secondary endpoints included hospital and intensive care unit (ICU) length of stay (LOS), antibiotic intensity score at 96 h, and 30-day readmission rates. Of 100 patients with Gram-negative bacteremia or candidemia in each cohort, 84 in the preimplementation group and 89 in the AXDX group met all inclusion criteria. The AXDX group had a decreased time to first antibiotic intervention (26.3 versus 8.0, P = 0.003), hours to most targeted therapy (14.4 versus 9, P = 0.03), hospital LOS (6 versus 8, P = 0.002), and average antibiotic intensity score at 96 h (16 versus 12, P = 0.002). Both groups had a comparable 14-day mortality (0% versus 3.6%, P = 0.11). In this analysis of patients with Gram-negative bacteremia or candidemia, fast ID/AST implementation was associated with decreased hospital LOS, decreased use of broad-spectrum antibiotics, shortened time to targeted therapy, and an improved utilization of antibiotics within the first 96 h of therapy.

Cluster randomized trial of an antibiotic time-out led by a team-based pharmacist

OBJECTIVE

Antibiotic time-outs (ATOs) have been advocated to improve antibiotic use without dedicated stewardship resources, but their utility is poorly defined. We sought to evaluate the effectiveness of an ATO led by a team-based pharmacist.

DESIGN

Cluster randomized controlled trial.

SETTING

Six medicine teams at an academic medical facility.

PATIENTS

Inpatients who received antibiotics and were cared for by a medicine team.

INTERVENTION

In phase A (2 months) pharmacist-led ATOs were implemented on 3 medicine teams (ATO-A) while 3 teams maintained usual care (UC-A). In phase B (2 months), ATOs were continued in the ATO group (ATO-B) and ATOs were initiated in the UC group (UC ATO-B). We targeted 2 ATO points: early (<72 hours after antibiotics were initiated) and late (after the early period but ≤5 days after antibiotic initiation).

RESULTS

In total, 290 ATOs were documented (181 early, 87 late, and 22 subsequent) among 538 admissions. The most common ATO recommendations were narrow therapy (148 of 290), no change (124 of 290), and change to oral (30 of 290). ATO initiation was lower in the UC ATO-B group than in either ATO group (21.8% UC ATO-B vs 69.2% ATO-A and -B). Overall antibiotic use was not different between the groups (P = .51), although intravenous (IV) levofloxacin use decreased in the UC group after ATO implementation (49 DOT/1,000 PD vs 20 DOT/1,000 PD; P = .022). The ratio of oral (PO) to intravenous (IV) DOT was lower in the UC group than in any of the ATO groups (P = .032). We detected no differences in mortality, length of stay, readmission, C. difficile infection, or antibiotic adverse events.

CONCLUSIONS

Implementation of a pharmacist-led ATO was feasible and well accepted but did not change overall antibiotic use. An ATO may promote increased use of oral antibiotics, but more effective strategies for self-stewardship are needed.

Role of Early De-escalation of Antimicrobial Therapy on Risk of Clostridioides difficile Infection Following Enterobacteriaceae Bloodstream Infections

BACKGROUND

There is a paucity of data on the effect of early de-escalation of antimicrobial therapy on rates of Clostridioides difficile infection (CDI). This retrospective cohort study evaluated impact of de-escalation from antipseudomonal β-lactam (APBL) therapy within 48 hours of Enterobacteriaceae bloodstream infections (BSIs) on 90-day risk of CDI.

METHODS

Adult patients hospitalized for >48 hours for treatment of Enterobacteriaceae BSI at Palmetto Health hospitals in Columbia, South Carolina, from 1 January 2011 through 30 June 2015 were identified. Multivariable Cox proportional hazards regression was used to examine time to CDI in patients who received >48 hours or ≤48 hours of APBL for empirical therapy of Enterobacteriaceae BSI after adjustment for the propensity to receive >48 hours of APBL.

RESULTS

Among 808 patients with Enterobacteriaceae BSI, 414 and 394 received >48 and ≤48 hours of APBL, respectively. Incidence of CDI was higher in patients who received >48 hours than those who received ≤48 hours of APBL (7.0% vs 1.8%; log-rank P = .002). After adjustment for propensity to receive >48 hours of APBL and other variables in the multivariable model, receipt of >48 hours of APBL (hazard ratio [HR], 3.56 [95% confidence interval {CI}, 1.48-9.92]; P = .004) and end-stage renal disease (HR, 4.27 [95% CI, 1.89-9.11]; P = .001) were independently associated with higher risk of CDI.

CONCLUSIONS

The empirical use of APBL for >48 hours was an independent risk factor for CDI. Early de-escalation of APBL using clinical risk assessment tools or rapid diagnostic testing may reduce the incidence of CDI in hospitalized adults with Enterobacteriaceae BSIs.

Implementation of antibiotic stewardship programmes in French ICUs in 2018: a nationwide cross-sectional survey

BACKGROUND

Antibiotic stewardship programmes have a pivotal role in ICUs, but the level of implementation of these programmes at the regional or national level is not well known.

OBJECTIVES

The aim of our study was to assess the level of implementation of antibiotic stewardship programmes in French ICUs.

METHODS

We conducted a nationwide cross-sectional survey from January to March 2018 using an online questionnaire sent as an E-mail link to ICU specialists (one questionnaire per ICU).

RESULTS

Overall, 113 out of 206 (55%) ICUs participated. Access to local epidemiology regarding bacterial resistance and antibiotic consumption data was reported in 84% and 65% of ICUs, respectively. Local guidelines for antibiotic use were available in 54% of ICUs. The duration of empirical antibiotic therapy was limited in 46% of cases, following the recommendation of an external expert in 33%. An antibiotic stewardship programme leader was reported at the hospital level by 94% of respondents, being an infectious disease physician in 80%. His/her role in the ICU was mostly to discuss specific cases (50%) and to provide advice on antibiotic prescriptions (26%). Regarding microbiological diagnosis, blood cultures were not processed at night or during weekends in 57%. Molecular biology and MS techniques were available in 62% and 59% of cases, respectively. Therapeutic drug monitoring of β-lactams was available in 46% of cases. Forty-three percent of respondents knew the expression 'antimicrobial/antibiotic stewardship'.

CONCLUSIONS

Antibiotic stewardship programmes are not optimally implemented in French ICUs. Improvement efforts and regular monitoring of the level of implementation are needed.

A highly multiplexed melt-curve assay for detecting the most prevalent carbapenemase, ESBL, and AmpC genes

Resistance to third-generation cephalosporins and carbapenems in Gram-negative bacteria is chiefly mediated by beta-lactamases including extended-spectrum beta-lactamase (ESBL), AmpC, and carbapenemase enzymes. Routine phenotypic detection methods do not provide timely results, and there is a lack of comprehensive molecular panels covering all important markers. An ESBL/carbapenemase high-resolution melt analysis (HRM) assay (SHV, TEM, CTX-M ESBL families, and NDM, IMP, KPC, VIM and OXA-48-like carbapenemases) and an AmpC HRM assay (16S rDNA control, FOX, MOX, ACC, EBC, CIT, and DHA) were designed and evaluated on 111 Gram-negative isolates with mixed resistance patterns. The sensitivity for carbapenemase, ESBL, and AmpC genes was 96.7% (95% confidence interval [CI]: 82.8-99.9%), 93.6% (95% CI: 85.7-97.9%), and 93.8% (95% CI: 82.8-98.7%), respectively, with a specificity of 100% (95% CI: 95.6-100%), 93.9% (95% CI: 79.8-99.3%), and 93.7% (95% CI: 84.5-98.2%). The HRM assays enable the simultaneous detection of the 14 most important ESBL, carbapenemase, and AmpC genes and could be used as a molecular surveillance tool or to hasten detection of antimicrobial resistance for treatment management.

New and novel rapid diagnostics that are impacting infection prevention and antimicrobial stewardship

PURPOSE OF REVIEW

The current review summarizes advances in rapid diagnostic testing that impacts infection prevention and antimicrobial stewardship programs.

RECENT FINDINGS

A variety of rapid diagnostic technologies to identify organisms in cultured blood are now available. When coupled with antimicrobial stewardship (ASP), these rapid technologies can optimize antimicrobial utilization and patient outcomes. Two rapid molecular panels that detect organisms related to pneumonia are available and may impact infection prevention surveillance definitions. Three molecular tests are available for the detection of meningitis and encephalitis pathogens. Still, the clinical impact of these broad, multiplexed panels need additional clarification. For Clostridioides difficile infections, ultrasensitive toxin A/B assays may provide enhanced sensitivity and specificity compared with enzyme immunoassay and molecular testing respectively. Finally, the adoption of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI TOF MS) for rapid organism identification is growing. Recent US Food and Drug Administration-clearance of a MALDI TOF MS platform for identification of Nocardia, Mycobacteria, and molds may expedite antimicrobial decisions for infections that traditionally required days to weeks for an identification.

SUMMARY

Tests with broad diagnostic scope and swift turnaround time are rapidly entering the market. Many impact infection prevention and ASP programs. Collaboration with the microbiology laboratory is crucial to ensure that new tests successfully optimize patient care.

Multicenter evaluation of a syndromic rapid multiplex PCR test for early adaptation of antimicrobial therapy in adult patients with pneumonia

Background

Improving timeliness of pathogen identification is crucial to allow early adaptation of antibiotic therapy and improve prognosis in patients with pneumonia. We evaluated the relevance of a new syndromic rapid multiplex PCR test (rm-PCR) on respiratory samples to guide empirical antimicrobial therapy in adult patients with community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), and ventilator-acquired pneumonia (VAP).

Methods

This retrospective multicenter study was conducted in four French university hospitals. Respiratory samples were obtained from patients with clinical and radiological signs of pneumonia and simultaneously tested using conventional microbiological methods and the rm-PCR. A committee composed of an intensivist, a microbiologist, and an infectious diseases specialist retrospectively assessed all medical files and agreed on the most appropriate antimicrobial therapy for each pneumonia episode, according to the results of rm-PCR and blinded to the culture results. The rm-PCR-guided antimicrobial regimen was compared to the empirical treatment routinely administered to the patient in standard care.

Results

We included 159 pneumonia episodes. Most patients were hospitalized in intensive care units (n = 129, 81%), and episodes were HAP (n = 68, 43%), CAP (n = 54, 34%), and VAP (n = 37, 23%). Conventional culture isolated ≥ 1 microorganism(s) at significant level in 95 (60%) patients. The syndromic rm-PCR detected at least one bacteria in 132 (83%) episodes. Based on the results of the rm-PCR, the multidisciplinary committee proposed a modification of the empirical therapy in 123 (77%) pneumonia episodes. The modification was a de-escalation in 63 (40%), an escalation in 35 (22%), and undetermined in 25 (16%) patients. In microbiologically documented episodes (n = 95), the rm-PCR increased appropriateness of the empirical therapy to 83 (87%), as compared to 73 (77%) in routine care.

Conclusions

Use of a syndromic rm-PCR test has the potential to reduce unnecessary antimicrobial exposure and increase the appropriateness of empirical antibiotic therapy in adult patients with pneumonia.

Updates on Rapid Diagnostic Tests in Infectious Diseases

In the last two decades there have been dramatic advances in development of rapid diagnostic tests. Turnaround time of the assays have significantly been shortened which led to reductions in time to appropriate antimicrobial therapy and improvement of patient clinical outcomes. Molecular-based assays generally have better sensitivity than conventional methods, but the cost is higher. The results need to be interpreted cautiously as detection of colonized organisms, pathogen detection in asymptomatic patients, and false negative/positive can occur. Indications and cost-effectiveness need to be considered for appropriate utilization of rapid diagnostic tests.

Rapid microbial identification and antimicrobial susceptibility testing to drive better patient care: an evolving scenario

Antimicrobial chemotherapy for septic patients begins with empirical therapy and can be subsequently revised when the results of microbiological testing become available. In recent years, a number of novel technologies for the microbiological diagnosis of sepsis have been developed that return results in a shorter timeframe compared with conventional diagnostic approaches. These novel technologies aid antimicrobial stewardship when treating septic patients by reducing the time to appropriate antimicrobial chemotherapy. Advantages and limitations of these technologies should be well understood upon their introduction in the diagnostic workflow. Increasingly popular DNA-based technologies primarily focus on the rapid identification of pathogens, but information on antimicrobial susceptibility is lacking or limited to a few clinically relevant resistance markers. Thus, DNA-based molecular techniques can complement conventional technologies but cannot replace them. On the other hand, a novel technology that provides both rapid identification of bacterial pathogens and a rapid phenotypic antibiogram with MIC values, and which starts from positive blood cultures, is a very promising approach for fast diagnosis of sepsis. To fully leverage the advantages offered by novel diagnostic technologies for sepsis requires a careful introduction into the laboratory workflow, following an evaluation by a health technology assessment approach. It may also require some reshaping of the workflow (e.g. to process the positive blood cultures on a 24/7 schedule) and of the laboratory organization (e.g. by creating a laboratory subsection for fast diagnosis of sepsis).

Performance and impact of a multiplex PCR in ICU patients with ventilator-associated pneumonia or ventilated hospital-acquired pneumonia

BACKGROUND

Early appropriate antibiotic therapy reduces morbidity and mortality of severe pneumonia. However, the emergence of bacterial resistance requires the earliest use of antibiotics with the narrowest possible spectrum. The Unyvero Hospitalized Pneumonia (HPN, Curetis) test is a multiplex PCR (M-PCR) system detecting 21 bacteria and 19 resistance genes on respiratory samples within 5 h. We assessed the performance and the potential impact of the M-PCR on the antibiotic therapy of ICU patients.

METHODS

In this prospective study, we performed a M-PCR on bronchoalveolar lavage (BAL) or plugged telescoping catheter (PTC) samples of patients with ventilated HAP or VAP with Gram-negative bacilli or clustered Gram-positive cocci. This study was conducted in 3 ICUs in a French academic hospital: the medical and infectious diseases ICU, the surgical ICU, and the cardio-surgical ICU. A multidisciplinary expert panel simulated the antibiotic changes they would have made if the M-PCR results had been available.

RESULTS

We analyzed 95 clinical samples of ventilated HAP or VAP (72 BAL and 23 PTC) from 85 patients (62 males, median age 64 years). The median turnaround time of the M-PCR was 4.6 h (IQR 4.4-5). A total of 90/112 bacteria were detected by the M-PCR system with a global sensitivity of 80% (95% CI, 73-88%) and specificity of 99% (95% CI 99-100). The sensitivity was better for Gram-negative bacteria (90%) than for Gram-positive cocci (62%) (p = 0.005). Moreover, 5/8 extended-spectrum beta-lactamases (CTX-M gene) and 4/4 carbapenemases genes (3 NDM, one oxa-48) were detected. The M-PCR could have led to the earlier initiation of an effective antibiotic in 20/95 patients (21%) and to early de-escalation in 37 patients (39%) but could also have led to one (1%) inadequate antimicrobial therapy. Among 17 empiric antibiotic treatments with carbapenems, 10 could have been de-escalated in the following hours according to the M-PCR results. The M-PCR also led to 2 unexpected diagnosis of severe legionellosis confirmed by culture methods.

CONCLUSIONS

Our results suggest that the use of a M-PCR system for respiratory samples of patients with VAP and ventilated HAP could improve empirical antimicrobial therapy and reduce the use of broad-spectrum antibiotics.

The clinical impact of implementing GenMark ePlex blood culture panels for around-the-clock blood culture identification; a prospective observational study

Background: Implementing rapid molecular blood culture diagnostics in the clinical management of sepsis is essential for early pathogen identification and resistance gene testing. The GenMark ePlex blood culture panels offer a broad microbial spectrum with minimal hands-on time and approximately 1.5 h to result. Therefore, ePlex can be utilized at times when the clinical microbiology laboratory is unavailable.Methods: From 23 October 2019 to 30 December 2019, consecutive non-duplicate positive blood cultures signalling microbial growth at the 24 h/7 days-a-week available clinical chemistry laboratory between 9 pm and 7 am were analysed with ePlex. All blood cultures were transported to the microbiology laboratory the following day for conventional identification and antibiotic susceptibility testing.Results: We used ePlex to test 91 blood cultures, of which 86 had confirmed microbial growth. Eighty-one were positive for ePlex target pathogens. The ePlex results were in complete agreement with conventional methods in 72/81 (88.9%) of cases and available within a median of 10.9 h earlier. Resistance gene targets (11 mecA and 1 CTX-M) were concordant with phenotypic susceptibility in all cases. In 18/86 (20.9%) of the patient cases, there was an opportunity to optimize antimicrobial therapy based on the ePlex result. The ePlex result affected clinical decision-making in 4/86 (4.7%) of the cases and reduced the average time to effective antimicrobial therapy by 8.9 h.Conclusions: Our implementation of ePlex is a feasible option to attain around-the-clock blood culture identification in many hospitals. It can significantly reduce time-to-pathogen identification and have an impact on clinical decision-making.

The diagnostic benefit of 16S rDNA PCR examination of infective endocarditis heart valves: a cohort study of 146 surgical cases confirmed by histopathology

Aims

Upon suspicion of infective endocarditis, the causative microorganism must be identified to optimize treatment. Blood cultures and culturing of removed valves are the mainstay of this diagnosis and should be complemented by growth-independent methods. We assessed the diagnostic benefit of examining removed endocarditis valves by broad-range bacterial PCR to detect causative bacteria in cases where culturing was not available, negative, or inconclusive because a skin commensal was detected, in patients from our clinical routine practice.

Methods and results

Patients from Heidelberg University Hospital with suspicion of endocarditis, followed by valve replacement and analysis by 16S rDNA PCR, between 2015 and 2018, were evaluated. 146 patients with definite infective endocarditis, confirmed by the valve macroscopics and/or histology, were included. Valve PCRs were compared to corresponding blood and valve culture results. Overall, valve PCR yielded an additional diagnostic benefit in 34 of 146 cases (23%) and was found to be more sensitive than valve culture. In 19 of 38 patients with both negative blood and valve cultures, valve PCR was the only method rendering a pathogen. In 23 patients with positive blood cultures detecting skin commensals, 4 patients showed discordant valve PCR results, detecting a more plausible pathogen, and in 11 of 23 cases, valve PCR confirmed commensals in blood culture as true pathogens. Only the remaining 8 patients had negative valve PCRs.

Conclusion

Valve PCR was found to be a valuable diagnostic tool in surgical endocarditis cases with negative blood cultures or positive blood cultures of unknown significance.

Trial registration

S-440/2017 on 28.08.2017 retrospectively registered.

Graphic abstract

Subdividing of all infective endocarditis patients in this study, showing that valve PCR yields valuable information for patients with skin commensals in blood cultures, which were either confirmed by the same detection in valve PCR or refuted by the detection of a different and typical pathogen in valve PCR. Additionally, benefit was determined in patients with negative or not available blood cultures and only positive detection in valve PCR. +: Positive; −: negative; n/a: not available results

Electronic supplementary material

The online version of this article (10.1007/s00392-020-01678-x) contains supplementary material, which is available to authorized users.

Clinical Impact of Accelerate PhenoTM Rapid Blood Culture Detection System in Bacteremic Patients

BACKGROUND

Accelerate Pheno blood culture detection system (AXDX) provides identification (ID) and antimicrobial susceptibility testing (AST) results within 8h of blood culture growth. Limited data exists regarding its clinical impact. Other rapid platforms coupled with antimicrobial stewardship program (ASP) real-time notification (RTN) have shown improved length of stay (LOS) in bacteremia.

METHODS

A single-center, quasi-experimental study of adult bacteremic inpatients before/after AXDX implementation was conducted comparing clinical outcomes from 1 historical and 2 intervention cohorts (AXDX and AXDX+RTN). Primary outcome was LOS.

RESULTS

Of 830 bacteremic episodes, 188 (77%) of 245 historical and 308 (155 AXDX, 153 AXDX+RTN; 65%) of 585 intervention episodes were included. Median LOS was shorter with AXDX (6.3d) and AXDX+RTN (6.7d) compared to historical (8.1d; P=0.001). Achievement of optimal therapy (AOT) was more frequent (93.6% and 95.4%) and median time to optimal therapy (TTOT) was faster (1.3d and 1.4d) in AXDX and AXDX+RTN compared to historical (84.6%, P≤0.001 and 2.4d; P≤0.001) respectively. Median antimicrobial days of therapy (DOT) was shorter in both intervention arms compared to historical (6d each vs 7d; P=0.011). Median LOS benefit was most pronounced in patients with coagulase negative Staphylococcus bacteremia (5.5d and 4.5d vs 7.2d; P=0.003) in AXDX, AXDX+RTN, and historical cohorts respectively.

CONCLUSIONS

LOS, AOT, TTOT, and total DOT significantly improved after AXDX implementation. Addition of RTN did not show further improvement over AXDX and an already active ASP. These results suggest AXDX can be integrated into healthcare systems with an active ASP even without the resources to include RTN.

Development and Evaluation of a Loop-Mediated Isothermal Amplification Assay for Rapid and Specific Identification of Carbapenem-Resistant Acinetobacter baumannii Strains Harboring blaOXA-23, and the Epidemiological Survey of Clinical Isolates

Acinetobacter baumannii is an important nosocomial pathogen in hospital-acquired infections, and carbapenem resistance has been increasingly observed worldwide. Oxacillinase production by bla_OXA-23 is a predominant and prevalent carbapenem resistance mechanism of A. baumannii, especially in China. Rapid and specific detection of bla_OXA-23 may offer valuable insight for administration of directed antimicrobial therapy. In this study, we aimed to develop a loop-mediated isothermal amplification (LAMP)-based method for identifying carbapenem-resistant A. baumannii (CRAB) harboring the bla_OXA-23 gene. High-specificity primers for screening bla_OXA-23 were designed and synthesized, and the LAMP reactions were performed. Clinical A. baumannii strains isolated from the Former 307th Hospital of People's Liberation Army were used to determine the sensitivity and specificity of this method compared with those of phenotypic antimicrobial susceptibility testing and the traditional PCR method. Multilocus sequence typing (MLST) was performed to investigate the epidemiology of the A. baumannii bacterial population. Compared with antimicrobial susceptibility testing, the sensitivity and specificity of LAMP in detecting bla_OXA-23 were 88.4% and 97.7%, respectively. However, the LAMP method is much simpler and less time-consuming (within 60 minutes) than conventional PCR and phenotypic susceptibility testing. The 113 isolates could be clustered into 30 sequence types, and most strains (83/113) belonged to clonal complex (CC) 92, which is also the dominant CC in China. The LAMP-based method detected bla_OXA-23 in a simpler manner and could provide rapid results for identifying CRAB. Consequently, bla_OXA-23 may serve as a surrogate marker for the presence of CRAB in patients with serious infections in clinical practice.

Enhanced antimicrobial stewardship based on rapid phenotypic antimicrobial susceptibility testing for bacteraemia in patients with haematological malignancies: a randomized controlled trial

OBJECTIVES

Recently, rapid phenotypic antimicrobial susceptibility testing (AST) based on microscopic imaging analysis has been developed. The aim of this study was to determine whether implementation of antimicrobial stewardship programmes (ASP) based on rapid phenotypic AST can increase the proportion of patients with haematological malignancies who receive optimal targeted antibiotics during early periods of bacteraemia.

METHODS

This randomized controlled trial enrolled patients with haematological malignancies and at least one positive blood culture. Patients were randomly assigned 1:1 to conventional (n = 60) or rapid phenotypic (n = 56) AST. The primary outcome was the proportion of patients receiving optimal targeted antibiotics 72 hr after blood collection for culture.

RESULTS

The percentage receiving optimal targeted antibiotics at 72 hr was significantly higher in the rapid phenotypic AST group (45/56, 80.4%) than in conventional AST group (34/60, 56.7%) (relative risk (RR) 1.42, 95% confidence interval (CI) 1.09-1.83). The percentage receiving unnecessary broad-spectrum antibiotics at 72 hr was significantly lower (7/26, 12.5% vs 18/60, 30.0%; RR 0.42, 95% CI 0.19-0.92) and the mean time to optimal targeted antibiotic treatment was significantly shorter (38.1, standard deviation (SD) 38.2 vs 72.8, SD 93.0 hr; p < 0.001) in the rapid phenotypic AST group. The mean time from blood collection to the AST result was significantly shorter in the rapid phenotypic AST group (48.3, SD 17.6 vs 83.1, SD 22.2 hr).

DISCUSSION

ASP based on rapid phenotypic AST can rapidly optimize antibiotic treatment for bacteraemia in patients with haematological malignancy. Rapid phenotypic AST can improve antimicrobial stewardship in immunocompromised patients.

Incorporation of rapid diagnostic tests to improve time to antimicrobial therapy for gram-positive bacteremia and candidemia

Purpose

Even with rapid diagnostic technology to swiftly identify infectious organisms, prompt response is needed to translate results into appropriate actions. The purpose of this study was to determine if the introduction of real-time pharmacist response to positive rapid diagnostic test results would decrease time to antimicrobial therapy for gram-positive bacteremia and candidemia in a community hospital setting.

Methods

A quasi-experimental study was conducted in 2 community hospitals. The study comprised 2 cohorts of adult patients who tested positive for gram-positive bacteremia involving Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium, or Candida species. The preintervention cohort consisted of patients admitted from November 2017 through May 2018. The intervention cohort consisted of patients admitted from July 2018 through January 2019, after the intervention went live. The primary outcomes were time to optimal antimicrobial therapy and time to effective antimicrobial therapy.

Results

A total of 140 patients were included in the preintervention group, with 124 patients included in the intervention group. The mean (SD) time to effective therapy decreased from 13.9 (21.6) hours in the preintervention group to 8.6 (12.5) hours in the intervention group (hazard ratio [HR], 1.15; 95% confidence interval [CI], 0.89-1.48; P = 0.29). The mean (SD) time to optimal therapy significantly decreased from 53.7 (57.7) hours in the preintervention group to 38.4 (31.5) hours in the intervention group (HR, 1.73; 95% CI, 1.33-2.26; P &lt; 0.001).

Conclusion

The introduction of real-time pharmacist response to positive rapid diagnostic test results led to a significant decrease in time to optimal antimicrobial therapy but did not significantly affect time to effective therapy. The results showed that the allocation of limited resources of a community hospital to such a stewardship program is justifiable.

Use of Rapid Diagnostics To Manage Pediatric Bloodstream Infections? You Bet Your ASP!

Rapid diagnostic testing (RDT) can facilitate earlier optimization of the treatment of bloodstream infections, particularly in conjunction with an effective antimicrobial stewardship program (ASP). However, the effective implementation and workflow of RDTs are still a matter of debate, particularly in a pediatric setting. In this issue of the Journal of Clinical Microbiology, L. J. Juttukonda, S. Katz, J. Gillon, J. Schmitz, and R. Banerjee (J Clin Microbiol 58:e01400-19, 2020, https://doi.org/10.1128/JCM.01400-19) investigate the impact of a multiplex, molecular RDT on changes to antimicrobial therapy in an academic children's hospital. These data reveal several factors that clinical laboratories should consider prior to the implementation of RDTs for positive blood cultures.

Impact of a Rapid Blood Culture Diagnostic Test in a Children's Hospital Depends on Gram-Positive versus Gram-Negative Organism and Day versus Night Shift

Rapid diagnostic tests (RDTs) for bloodstream infections (BSIs) decrease the time to organism identification and resistance detection. RDTs are associated with early deescalation of therapy for Gram-positive BSIs. However, it is less clear how RDTs influence antibiotic management for Gram-negative BSIs and whether RDT results are acted on during off-hours. We performed a single-center, retrospective review of children with BSI and Verigene (VG) testing at a children's hospital. Of the 301 positive cultures included in the study (196 Gram-positive, 44 Gram-negative, 32 polymicrobial, and 29 non-VG targets), the VG result had potential to impact antibiotic selection in 171 cases; among these, antibiotic changes occurred in 119 (70%) cases. For Gram-negative cultures, the Verigene result correlated with unnecessary antibiotic escalation and exposure to broader-spectrum antibiotics than needed. In contrast, for Gram-positive cultures, the VG results correlated with appropriate antibiotic selection. VG results permitted early deescalation for methicillin-susceptible Staphylococcus aureus (MSSA) (19/24 [79%]) and avoidance of antibiotics for skin contaminants (30/85 [35%]). Antibiotic changes occurred more quickly during the day than at night (4.6 versus 11.7 h, respectively; P < 0.05), and antibiotic escalations occurred more quickly than did deescalations (4.1 versus 10.1 h, P < 0.01). In a pediatric institution with a low prevalence of Gram-negative resistance, the VG RDT facilitated antibiotic optimization for Gram-positive BSIs but led to unnecessary escalation of antibiotics for Gram-negative BSIs. The time to action was slower for RDT results reported at night than during the day. Laboratories should consider these factors when implementing blood culture RDTs.

Clinical Performance of the Novel GenMark Dx ePlex Blood Culture ID Gram-Positive Panel

Rapid identification from positive blood cultures is standard of care (SOC) in many clinical microbiology laboratories. The GenMark Dx ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel is a multiplex nucleic acid amplification assay based on competitive DNA hybridization and electrochemical detection using eSensor technology. This multicenter study compared the investigational-use-only (IUO) BCID-GP Panel to other methods of identification of 20 Gram-positive bacteria, four antimicrobial resistance genes, and both Pan Candida and Pan Gram-Negative targets that are unique to the BCID-GP Panel.

Rapid identification from positive blood cultures is standard of care (SOC) in many clinical microbiology laboratories. The GenMark Dx ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel is a multiplex nucleic acid amplification assay based on competitive DNA hybridization and electrochemical detection using eSensor technology. This multicenter study compared the investigational-use-only (IUO) BCID-GP Panel to other methods of identification of 20 Gram-positive bacteria, four antimicrobial resistance genes, and both Pan Candida and Pan Gram-Negative targets that are unique to the BCID-GP Panel. Ten microbiology laboratories throughout the United States collected residual, deidentified positive blood culture samples for analysis. Five laboratories tested both clinical and contrived samples with the BCID-GP Panel. Comparator identification methods included each laboratory’s SOC, which included matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and automated identification systems as well as targeted PCR/analytically validated real-time PCR (qPCR) with bidirectional sequencing. A total of 2,342 evaluable samples (1,777 clinical and 565 contrived) were tested with the BCID-GP Panel. The overall sample accuracy for on-panel organisms was 89% before resolution of discordant results. For pathogenic Gram-positive targets (Bacillus cereus group, Enterococcus spp., Enterococcus faecalis, Enterococcus faecium, Staphylococcus spp., Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus lugdunensis, Listeria spp., Listeria monocytogenes, Streptococcus spp., Streptococcus agalactiae, Streptococcus anginosus group, Streptococcus pneumoniae, and Streptococcus pyogenes), positive percent agreement (PPA) and negative percent agreement (NPA) ranged from 93.1% to 100% and 98.8% to 100%, respectively. For contamination rule-out targets (Bacillus subtilis group, Corynebacterium, Cutibacterium acnes, Lactobacillus, and Micrococcus), PPA and NPA ranged from 84.5% to 100% and 99.9% to 100%, respectively. Positive percent agreement and NPA for the Pan Candida and Pan Gram-Negative targets were 92.4% and 95.7% for the former and 99.9% and 99.6% for the latter. The PPAs for resistance markers were as follows: mecA, 97.2%; mecC, 100%; vanA, 96.8%; and vanB, 100%. Negative percent agreement ranged from 96.6% to 100%. In conclusion, the ePlex BCID-GP Panel compares favorably to SOC and targeted molecular methods for the identification of 20 Gram-positive pathogens and four antimicrobial resistance genes in positive blood culture bottles. This panel detects a broad range of pathogens and mixed infections with yeast and Gram-negative organisms from the same positive blood culture bottle.

Bloodstream infections in critically ill patients: an expert statement

Bloodstream infection (BSI) is defined by positive blood cultures in a patient with systemic signs of infection and may be either secondary to a documented source or primary—that is, without identified origin. Community-acquired BSIs in immunocompetent adults usually involve drug-susceptible bacteria, while healthcare-associated BSIs are frequently due to multidrug-resistant (MDR) strains. Early adequate antimicrobial therapy is a key to improve patient outcomes, especially in those with criteria for sepsis or septic shock, and should be based on guidelines and direct examination of available samples. Local epidemiology, suspected source, immune status, previous antimicrobial exposure, and documented colonization with MDR bacteria must be considered for the choice of first-line antimicrobials in healthcare-associated and hospital-acquired BSIs. Early genotypic or phenotypic tests are now available for bacterial identification and early detection of resistance mechanisms and may help, though their clinical impact warrants further investigations. Initial antimicrobial dosing should take into account the pharmacokinetic alterations commonly observed in ICU patients, with a loading dose in case of sepsis or septic shock. Initial antimicrobial combination attempting to increase the antimicrobial spectrum should be discussed when MDR bacteria are suspected and/or in the most severely ill patients. Source identification and control should be performed as soon as the hemodynamic status is stabilized. De-escalation from a broad-spectrum to a narrow-spectrum antimicrobial may reduce antibiotic selection pressure without negative impact on mortality. The duration of therapy is usually 5–8 days though longer durations may be discussed depending on the underlying illness and the source of infection. This narrative review covers the epidemiology, diagnostic workflow and therapeutic aspects of BSI in ICU patients and proposed up-to-date expert statements.

Appropriate Use and Future Directions of Molecular Diagnostic Testing

Purpose of Review

Major technologic advances in two main areas of molecular infectious disease diagnostics have resulted in accelerated adoption or ordering, outpacing implementation, and clinical utility studies. Physicians must understand the limitations to and appropriate utilization of these technologies in order to provide cost-effective and well-informed care for their patients.

Recent Findings

Rapid molecular testing and, to a lesser degree, clinical metagenomics are now being routinely used in clinical practice. While these tests allow for a breadth of interrogation not possible with conventional microbiology, they pose new challenges for diagnostic and antimicrobial stewardship programs. This review will summarize the most recent literature on these two categories of technologic advances and discuss the few studies that have looked at utilization and stewardship approaches. This review also highlights the future directions for both of these technologies.

Summary

The appropriate utilization of rapid molecular testing and clinical metagenomics has not been well established. More studies are needed to assess their prospective impacts on patient management and antimicrobial stewardship efforts as the future state of infectious disease diagnostics will see continued expansion of these technologic advances.

cAST: Capillary-Based Platform for Real-Time Phenotypic Antimicrobial Susceptibility Testing

Antimicrobial resistance is recognized as one of the greatest emerging threats to public health. Antimicrobial resistant (AMR) microorganisms affect nearly 2 million people a year in the United States alone and place an estimated $20 billion burden on the healthcare system. The rise of AMR microorganisms can be attributed to a combination of overprescription of antimicrobials and a lack of accessible diagnostic methods. Delayed diagnosis is one of the primary reasons for empiric therapy, and diagnostic methods that enable rapid and accurate results are highly desirable to facilitate evidence-based treatment. This is particularly true for clinical situations at the point-of-care where access to state-of-the-art diagnostic equipment is scarce. Here, we present a capillary-based antimicrobial susceptibility testing platform (cAST), a unique approach that offers accelerated assessment of antimicrobial susceptibility in a low-cost and simple testing format. cAST delivers an expedited time-to-readout by means of optical assessment of bacteria incubated in a small capillary form factor along with a resazurin dye. cAST was designed using a combination of off-the-shelf and custom 3D-printed parts, making it extremely suitable for use in resource-limited settings. We demonstrate that growth of bacteria in cAST is approximately 25% faster than in a conventional microplate, further validate the diagnostic performance with clinical isolates, and show that cAST can deliver accurate antimicrobial susceptibility test results within 4-8 h.

Proposal of a clinical score to stratify the risk of multidrug-resistant gram-negative rods bacteremia in cancer patients

Introduction

Multidrug-resistant gram-negative rods (MDR GNR) represent a growing threat for patients with cancer. Our objective was to determine the characteristics of and risk factors for MDR GNR bacteremia in patients with cancer and to develop a clinical score to predict MDR GNR bacteremia.

Material and Methods

Multicenter prospective study analyzing initial episodes of MDR GNR bacteremia. Risk factors were evaluated using a multiple logistic regression (forward-stepwise selection) analysis including variables with a p < 0.10 in univariate analysis.

Results

394 episodes of GNR bacteremia were included, with 168 (42.6 %) being MDR GNR. Five variables were identified as independent risk factors: recent antibiotic use (OR = 2.8, 95 % CI 1.7–4.6, p = 0.001), recent intensive care unit admission (OR = 2.9, 95 % CI 1.1–7.8, p = 0.027), hospitalization ≥ 7 days prior to the episode of bacteremia (OR = 3.5, 95 % CI 2–6.2, p = 0.005), severe mucositis (OR = 5.3, 95 % CI 1.8–15.6, p = 0.002), and recent or previous colonization/infection with MDR GNR (OR = 2.3, 95 % CI 1.2–4.3, p = 0.028). Using a cut-off value of two points, the score had a sensitivity of 66.07 % (95 % CI 58.4–73.2 %), a specificity of 77.8 % (95 % CI 71.4–82.7 %), a positive predictive value of 68 % (95 % CI 61.9–73.4 %), and a negative predictive value of 75.9 % (95 % CI 71.6–79.7 %). The overall performance of the score was satisfactory (AUROC 0.78; 95 % CI 0.73-0.82). In the cases with one or none of the risk factors identified, the negative likelihood ratio was 0.18 and the post-test probability of having MDR GNR was 11.68 %.

Conclusions

With the growing incidence of MDR GNR as etiologic agents of bacteremia in cancer patients, the development of this score could be a potential tool for clinicians.

Clinical microbiology

The clinical microbiology laboratory relies on traditional diagnostic methods such as culturing, Gram stains, and biochemical testing. Receipt of a high-quality specimen with an appropriate test order is integral to accurate testing. Recent technological advancements have led to decreased time to results and improved diagnostic accuracy. Examples of advancements discussed in this chapter include automation of bacterial culture processing and incubation, as well as introduction of mass spectrometry for the proteomic identification of microorganisms. In addition, molecular testing is increasingly common in the clinical laboratory. Commercially available multiplex molecular assays simultaneously test for a broad array of syndromic-related pathogens, providing rapid and sensitive diagnostic results. Molecular advancements have also transformed point-of-care (POC) microbiology testing, and molecular POC assays may largely supplant traditional rapid antigen testing in the future. Integration of new technologies with traditional testing methods has led to improved quality and value in the clinical microbiology laboratory.

After reviewing this chapter, the reader will be able to:•

List key considerations for specimen collection for microbiology testing.

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Discuss the advantages and limitations of automation in the clinical microbiology laboratory.

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Describe the evolution of microorganism identification methods.

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Discuss the benefits and limitations of molecular microbiology point-of-care testing.

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Summarize currently available multiplex molecular microbiology testing options.

Practical Guidance for Clinical Microbiology Laboratories: A Comprehensive Update on the Problem of Blood Culture Contamination and a Discussion of Methods for Addressing the Problem

In this review, we present a comprehensive discussion of matters related to the problem of blood culture contamination. Issues addressed include the scope and magnitude of the problem, the bacteria most often recognized as contaminants, the impact of blood culture contamination on clinical microbiology laboratory function, the economic and clinical ramifications of contamination, and, perhaps most importantly, a systematic discussion of solutions to the problem. We conclude by providing a series of unanswered questions that pertain to this important issue.

A rapid, adaptative DNA biosensor based on molecular beacon-concatenated dual signal amplification strategies for ultrasensitive detection of p53 gene and cancer cells

The cancer diagnosis with single level of biomarkers suffers from limitation of insufficient accuracy. Hence, developing sensitive, rapid and adaptative analytical strategies for double-level biomarkers are essential for improving the accuracy of clinical cancer diagnosis at early stage. Herein, a DNA biosensor was established based on the catalytic hairpin assembly-mediated Y-junction nicking enzyme assisted signal amplification (CHA-YNEASA) circuits, where the two circuits were concatenated by molecular beacon (MB). In absence of target, both the CHA and YNEASA circuits were effectively hindered because of MB's outstanding ability to control signal background. In presence of target, the initiated CHA circuits made enzyme recognition sequences in close proximity to the assisted sequences to open MB, leading to further trigger the YNEASA circuits. Due to the unique design of dual signal amplification strategies, CHA-YNEASA circuits significantly shorten the reaction time, and improve signal-to-background ratio as well as facilitate the analysis process. It was demonstrated that a high sensitivity with limit of detection (LOD) of 0.9 pM for p53 gene detection was obtained just within 23 min by the proposed DNA biosensor. Moreover, mismatched p53 gene at nucleic acid level was effectively discriminated and strong anti-interference capability was achieved. Noticeably, the DNA biosensor was adaptative for designing a cytosensor at cell level using hairpin DNA, containing MUC1 aptamer and initiation strand of CHA-YNEASA circuits, as switch based on modularity principle. The cytosensor is able to measure MUC1 positive breast cancer cells (MCF-7) with the LOD as low as 100 cells/mL. Excellent specificity for MUC1 negative cells, and good anti-interference capability in 10% fetal bovine serum (FBS) were observed by the cytosensor. Therefore, the proposed DNA biosensor is a sensitive, rapid, adaptative platform for detection of double-level biomarkers, offering novel strategy applied for clinical cancer diagnosis.

Collaborative Antimicrobial Stewardship: Working with Microbiology

There have been tremendous advances in methodologies available for detection and identification of organisms causing infections. Providers can now obtain identification results and antimicrobial susceptibility results in a shorter period of time. However, declining health care resources highlight the importance of selecting the right test at the right time to maximize diagnostic benefits. Therefore, the role of the antimicrobial stewardship team in the clinical microbiology laboratory has expanded to include diagnostic stewardship and provision of guidance on test selection for diagnosis and management of infection. This review focuses on the experience of our group in collaborative stewardship, emphasizing successes and challenges.

The Impact of Integrating Rapid PCR-Based Blood Culture Identification Panel to an Established Antimicrobial Stewardship Program in the United Arab of Emirates

BACKGROUND

Studies have shown improvement in the outcome of blood stream infections (BSI) due to the use of Rapid PCR-Based Blood Culture Identification Panel (BCID) in Antimicrobial stewardship programs (ASP). There is currently no data on the use of BCID with ASP in the United Arab Emirates (UAE).

METHOD

Pre-post quasiexperimental study included hospitalized patients with BSI, their positive blood cultures on BCID were studied in 2 groups: conventional culture with ASP (AS), and BCID with ASP (BCID). The primary outcomes were time to first appropriate antimicrobial therapy, infection related length of stay (LOS), ICU admission, 14 days bacteremia recurrence and in-hospital mortality. Secondary outcomes were 30 days reinfection rate, hospital cost and ASP interventions.

RESULTS

Out of total 477 positive blood cultures, 206 (AS and BCID) with real BSI were included. The time needed for organism identification was shorter in the BCID group than in the AS group (1.3 h vs. 51 h; P = 0.0002). BCID had a shorter time to appropriate antimicrobial therapy than AS (17.8 h vs.45 h; P = 0.0004). No statistical difference was observed in mortality rate, 14 days bacteremia recurrence, ICU admission, hospital cost, LOS or ASP interventions.

CONCLUSION

Implementing BCID to ASP significantly decreased the time needed to identify the organism and time to appropriate antimicrobial therapy. Similarly, LOS and hospital cost were reduced, however, the reduction was not statistically significant.

Carbapenem-Resistant Klebsiella pneumoniae: Microbiology Key Points for Clinical Practice

Carbapenemase–producing Klebsiella pneumoniae strains (Cp-Kpn) represent a challenge for clinical practitioners due to their increasing prevalence in hospital settings and antibiotic resistance. Clinical practitioners are often overwhelmed by the extensive list of publications regarding Cp-Kpn infections, treatment, characteristics, identification, and diagnosis. In this perspective article, we provide key points for clinical practitioners to consider for improved patient management including identification of risk factors and strategies for treatment. Additionally, we also discuss genetic underpinnings of antibiotic resistance, implementation of an antimicrobial stewardship program (ASP), and use of automated systems for detection of Cp-Kpn. Collectively, implementation of such key points would enhance clinical practices through providing practical knowledge to health professionals worldwide.

Molecular Diagnostic Advances in Transplant Infectious Diseases

PURPOSE OF REVIEW

The infectious complications of transplantation can have devastating consequences for patients. Early and accurate diagnosis is essential to good outcomes. This review describes recent advances in pathogen-directed diagnostic testing and discusses the role of new methods for transplant infectious diseases.

RECENT FINDINGS

Several molecular assays have been introduced into clinical practice in recent years. When the results of rapid testing are linked to patient-specific interventions, improved outcomes can be realized. Syndromic testing along with metagenomic next-generation sequencing (mNGS) represents novel approaches to infection diagnosis. However, the optimal use of these tests for transplant patients along with an overall assessment of cost-effectiveness demands further study. Molecular diagnostics are revolutionizing transplant care. Clinicians need to be aware of the current diagnostic landscape and have a working knowledge of the nuances related to test performance, result interpretation, and cost.