Multicenter Evaluation of the Accelerate PhenoTest BC Kit for Rapid Identification and Phenotypic Antimicrobial Susceptibility Testing Using Morphokinetic Cellular Analysis

Accurate and rapid antibiotic susceptibility testing using a machine learning-assisted nanomotion technology platform

Antimicrobial resistance (AMR) is a major public health threat, reducing treatment options for infected patients. AMR is promoted by a lack of access to rapid antibiotic susceptibility tests (ASTs). Accelerated ASTs can identify effective antibiotics for treatment in a timely and informed manner. We describe a rapid growth-independent phenotypic AST that uses a nanomotion technology platform to measure bacterial vibrations. Machine learning techniques are applied to analyze a large dataset encompassing 2762 individual nanomotion recordings from 1180 spiked positive blood culture samples covering 364 Escherichia coli and Klebsiella pneumoniae isolates exposed to cephalosporins and fluoroquinolones. The training performances of the different classification models achieve between 90.5 and 100% accuracy. Independent testing of the AST on 223 strains, including in clinical setting, correctly predict susceptibility and resistance with accuracies between 89.5% and 98.9%. The study shows the potential of this nanomotion platform for future bacterial phenotype delineation.

Rapid determination of antimicrobial susceptibility of Gram-negative bacteria from clinical blood cultures using a scattered light-integrated collection device

Background. A bloodstream infection (BSI) presents a complex and serious health problem, a problem that is being exacerbated by increasing antimicrobial resistance (AMR).Gap Statement. The current turnaround times (TATs) for most antimicrobial susceptibility testing (AST) methods offer results retrospective of treatment decisions, and this limits the impact AST can have on antibiotic prescribing and patient care. Progress must be made towards rapid BSI diagnosis and AST to improve antimicrobial stewardship and reduce preventable deaths from BSIs. To support the successful implementation of rapid AST (rAST) in hospital settings, a rAST method that is affordable, is sustainable and offers comprehensive AMR detection is needed.Aim. To evaluate a scattered light-integrated collection (SLIC) device against standard of care (SOC) to determine whether SLIC could accelerate the current TATs with actionable, accurate rAST results for Gram-negative BSIs.Methods. Positive blood cultures from a tertiary referral hospital were studied prospectively. Flagged positive Gram-negative blood cultures were confirmed by Gram staining and analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, Vitek 2, disc diffusion (ceftriaxone susceptibility only) and an SLIC device. Susceptibility to a panel of five antibiotics, as defined by European Committee on Antimicrobial Susceptibility Testing breakpoints, was examined using SLIC.Results. A total of 505 bacterial-antimicrobial combinations were analysed. A categorical agreement of 95.5 % (482/505) was achieved between SLIC and SOC. The 23 discrepancies that occurred were further investigated by the broth microdilution method, with 10 AST results in agreement with SLIC and 13 in agreement with SOC. The mean time for AST was 10.53±0.46 h and 1.94±0.02 h for Vitek 2 and SLIC, respectively. SLIC saved 23.96±1.47 h from positive blood culture to AST result.Conclusion. SLIC has the capacity to provide accurate AST 1 day earlier from flagged positive blood cultures than SOC. This significant time saving could accelerate time to optimal antimicrobial therapy, improving antimicrobial stewardship and management of BSIs.

The Application of Bacteriophage and Photoacoustic Flow Cytometry in Bacterial Identification

Infection with resistant bacteria has become an ever-increasing problem in modern medical practice. Bacteremia is a serious and potentially lethal condition that can lead to sepsis without early intervention. Currently, broad-spectrum antibiotics are prescribed until bacteria can be identified through blood cultures, a process that can take 2-3 days and is unable to provide quantitative information. Staphylococcus aureus (S. aureus) is a leading cause of bacteremia, and methicillin-resistant S. aureus (MRSA) accounts for more than a third of the cases. Other bacteria such as Clostridium difficile, Acinetobacter baumannii, and Carbapenem-resistant Enterobacteriaceae are becoming more prevalent and antibiotic-resistant. Rapid diagnostics for each of these superbugs has been a priority for health organizations around the world. Bacteriophages have evolved for millions of years to develop exquisite specificity in target binding using their host attachment proteins. Bacteriophages are viruses that infect bacteria. Bacteriophages use tail spikes, specialized attachment proteins, to bind specifically to their target bacterial cell surface proteins. We use bacteriophages and parts of bacteriophages as specific tags coupled with photoacoustic flow cytometry for the detection and quantification of bacteria. In photoacoustic flow cytometry, laser light is absorbed by particles under flow, and the ultrasound waves generated on the release of the energy are detected. Photoacoustics involves the detection of ultrasound waves resulting from laser irradiation. In photoacoustic flow cytometry, pulsed laser light is delivered to a sample flowing past a focused transducer, and particles that absorb laser light create a photoacoustic response. Bacteria can be tagged with dyed bacteriophage and processed through a photoacoustic flow cytometer where they are detected by the acoustic response. In this chapter, we describe the procedure and methods used to accomplish this. Often the limiting factor for the treatment of patients is the time spent waiting for results. It is our hope that the work presented in this chapter can be a foundation for future work and provide an ability to detect bacterial pathogens in blood cultures. Bacterial plate cultures and Gram staining are nineteenth-century technologies that have been the gold standards for decades, but current trends in resistant bacteria have necessitated a move toward more rapid and quantifiable diagnostic tools.

Antimicrobial Stewardship in the Hospital Setting: A Narrative Review

The increasing global threat of antibiotic resistance, which has resulted in countless fatalities due to untreatable infections, underscores the urgent need for a strategic action plan. The acknowledgment that humanity is perilously approaching the "End of the Miracle Drugs" due to the unjustifiable overuse and misuse of antibiotics has prompted a critical reassessment of their usage. In response, numerous relevant medical societies have initiated a concerted effort to combat resistance by implementing antibiotic stewardship programs within healthcare institutions, grounded in evidence-based guidelines and designed to guide antibiotic utilization. Crucial to this initiative is the establishment of multidisciplinary teams within each hospital, led by a dedicated Infectious Diseases physician. This team includes clinical pharmacists, clinical microbiologists, hospital epidemiologists, infection control experts, and specialized nurses who receive intensive training in the field. These teams have evidence-supported strategies aiming to mitigate resistance, such as conducting prospective audits and providing feedback, including the innovative 'Handshake Stewardship' approach, implementing formulary restrictions and preauthorization protocols, disseminating educational materials, promoting antibiotic de-escalation practices, employing rapid diagnostic techniques, and enhancing infection prevention and control measures. While initial outcomes have demonstrated success in reducing resistance rates, ongoing research is imperative to explore novel stewardship interventions.

A PCR-Reverse Dot Blot Hybridization Based Microfluidics Detection System for the Rapid Identification of 13 Fungal Pathogens Directly After Blood Cultures Over a Period of Time

Introduction

It is time-consuming to identify fungal pathogens from positive blood cultures using the standard culture-based method. And delayed diagnosis of bloodstream infection leads to significantly increased mortality.

Methods

We developed a PCR-reverse dot blot hybridization combined with microfluidic chip techniques to rapidly identify 13 fungal pathogens within 3-4 h using the sample of blood cultured over a period of time.

Results

We performed clinical validation using 43 blood culture-positive samples with a sensitivity of 96.7%, a specificity of 100%, and a concordance rate of 97.7%. Samples with different culture durations were evaluated using our approach, showing a detection rate of 85.2% at 16 h and 96.3% at 24 h; the platform could reach a detection limit of 103cfu/mL for the Candida spp. and 103 copies/mL for Aspergillus spp.

Discussion

The detection rate of the platform is much higher than the positive rates of concurrent blood cultures. This method bears substantial clinical application potential as it incorporates the microfluidic platform with low reagent consumption, automation, and low cost (about 10 dollars).

From bottle to bedside: Implementation considerations and antimicrobial stewardship considerations for bloodstream infection rapid diagnostic testing

Antimicrobial stewardship (AMS) programs have been quick to adopt novel molecular rapid diagnostic technologies (mRDTs) for bloodstream infections (BSIs) to improve antimicrobial management. As such, most of the literature demonstrating the clinical and economic benefits of mRDTs for BSI is in the presence of active AMS intervention. Leveraging mRDTs to improve antimicrobial therapy for BSI is increasingly integral to AMS program activities. This narrative review discusses available and future mRDTs, the relationship between the clinical microbiology laboratory and AMS programs, and practical considerations for optimizing the use of these tools within a health system. Antimicrobial stewardship programs must work closely with their clinical microbiology laboratories to ensure that mRDTs are used to their fullest benefit while remaining cognizant of their limitations. As more mRDT instruments and panels become available and AMS programs continue to expand, future efforts must consider the expansion beyond traditional settings of large academic medical centers and how combinations of tools can further improve patient care.

Clinical impact of the accelerate PhenoTest® BC system on patients with gram-negative bacteremia and high risk of antimicrobial resistance: a prospective before-after implementation study

BACKGROUND

The Accelerate PhenoTest® BC system (AXDX) is a novel assay for rapid bacterial identification and antimicrobial susceptibility (AST). We report an evaluation of its impact on treatment of patients with Gram-negative bacteremia (GNB) with a high risk of antimicrobial resistance (AMR).

METHODS

A prospective single-center evaluation before and after implementation of AXDX in addition to standard-of-care (SOC) microbiology and antimicrobial stewardship program (ASP). Patients with GNB reported during laboratory working hours and prespecified risk factors for AMR were included. The primary outcome was an ASP-oriented beneficial antimicrobial change, defined as either an escalation of an inappropriate empiric treatment or de-escalation of a broad-spectrum treatment of a susceptible organism. Main secondary outcomes were time to an appropriate treatment, antimicrobial treatment duration, length of stay (LOS) and mortality.

RESULTS

Included were 46 and 57 patients in the pre- and post-intervention periods, respectively. The median time to an AST-oriented beneficial change was 29.2 h vs. 49.6 h, respectively (p < 0.0001). There were no significant differences in the time to appropriate treatment, LOS or mortality. Antimicrobial treatment duration was longer during the intervention period (10 vs. 8 days, p = 0.007). AXDX failed to correctly identify pathogens in all 6 cases of polymicrobial bacteremia. In two cases patient care was potentially compromised due to inappropriate de-escalation.

CONCLUSIONS

AXDX implementation resulted in a 20.4-hour shorter time to an ASP-oriented beneficial antimicrobial change. This should be weighed against the higher costs, the lack of other proven clinical benefits and the potential harm from mis-identification of polymicrobial bacteremias.

Recent updates in the development of molecular assays for the rapid identification and susceptibility testing of MRSA

INTRODUCTION

Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of healthcare- and community-associated infections. Nasal carriage of MRSA is a risk factor for subsequent MRSA infections. Increased morbidity and mortality are associated with MRSA infections and screening and diagnostic tests for MRSA play an important role in clinical management.

AREAS COVERED

A literature search was conducted in PubMed and supplemented by citation searching. In this article, we provide a comprehensive review of molecular-based methods for MRSA screening and diagnostic tests including individual nucleic acid detection assays, syndromic panels, and sequencing technologies with a focus on their analytical performance.

EXPERT OPINION

Molecular based-assays for the detection of MRSA have improved in terms of accuracy and availability. Rapid turnaround enables earlier contact isolation and decolonization for MRSA. The availability of syndromic panel tests that include MRSA as a target has expanded from positive blood cultures to pneumonia and osteoarticular infections. Sequencing technologies allow detailed characterizations of novel methicillin-resistance mechanisms that can be incorporated into future assays. Next generation sequencing is capable of diagnosing MRSA infections that cannot be identified by conventional methods and metagenomic next-generation sequencing (mNGS) assays will likely move closer to implementation as front-line diagnostics in the near future.

Reporting of Antimicrobial Resistance from Blood Cultures, an Antibacterial Resistance Leadership Group Survey Summary: Resistance Marker Reporting Practices from Positive Blood Cultures

BACKGROUND

We assessed how laboratories use and handle reporting of results of rapid diagnostics performed on positive blood culture broths, with a focus on antimicrobial resistance (AMR) markers.

METHODS

A survey assembled by the Antibacterial Resistance Leadership Group Diagnostics Committee was circulated from December 2020 to May 2021. The survey was sent to local hospitals, shared on the ClinMicroNet and Division C listservs, and included in a College of American Pathologists proficiency testing survey.

RESULTS

Ninety-six laboratories of various sizes across the United States (95%) and outside of the United States (5%) participated. Of the laboratories that had at least 1 rapid diagnostic in place (94%), significant heterogeneity in methods used and reporting practices was found across community (52%) and academic (40%) laboratories serving hospitals of various sizes. Respondents had implemented 1 to 6 different panels/platforms for a total of 31 permutations. Methods of reporting rapid organism identification and AMR results varied from listing all targets as "detected"/"not detected" (16-22%) without interpretive guidance, to interpreting results (23-42%), or providing therapeutic guidance comments to patient-facing healthcare teams (3-17%).

CONCLUSIONS

Current approaches to reporting molecular AMR test results from positive blood culture vary significantly across clinical laboratories. Providing interpretative comments with therapeutic guidance alongside results reported may assist clinicians who are not well-versed in genetic mechanisms of AMR. However, this is currently not being done in all clinical laboratories. Standardized strategies for AMR gene result reporting are needed.

Photoacoustic Flow Cytometry Using Functionalized Microspheres for Selective Detection of Bacteria

Photoacoustic flow cytometry is a method to detect rare analytes in fluids. We developed photoacoustic flow cytometry to detect pathological cells in body fluids, such as circulating tumor cells or bacteria in blood. In order to induce specific optical absorption in bacteria, we use modified bacteriophage that precisely target bacterial species or subspecies for rapid identification. In order to reduce detection variability and to halt the lytic lifescycle that results in lysis of the bacteria, we attached dyed latex microspheres to the tail fibers of bacteriophage that retained the bacterial recognition binding sites. We tested these microsphere complexes using Salmonella enterica (Salmonella) and Escherichia coli (E. coli) bacteria and found robust and specific detection of targeted bacteria. In our work we used LT2, a strain of Salmonella, against K12, a strain of E. coli. Using Det7, a bacteriophage that binds to LT2 and not to K12, we detected an average of 109.3±9.0 of LT2 versus 2.0±1.7 of K12 using red microspheres and 86.7±13.2 of LT2 versus 0.3±0.6 of K12 using blue microspheres. These results confirmed our ability to selectively detect bacterial species using photoacoustic flow cytometry.

Direct inoculation method for identification and antimicrobial susceptibility testing using matrix-assisted laser desorption ionization-time of flight mass spectrometry and both the Vitek 2 and MicroScan Walkaway 96 Plus systems

The aim of our study was to evaluate a protocol utilizing serum separator tubes (SST) to facilitate a faster, cost-effective, direct method for rapid sensitivity testing and identification of positive blood cultures. Spiked cultures were inoculated into either Becton Dickinson (BD) BACTEC^TM Aerobic Plus or Anaerobic/F bottles containing sterile human blood. Bottles were immediately processed when positive. A parallel study using patient isolates was used in which bacteria were pelleted by SST from positive blood cultures. For identification, a portion of the pellet was tested by matrix-assisted laser desorption/ionization as described by the manufacturer. MicroScan panels and Vitek 2 results were compared. Categorical agreement was used as comparison to standard subculture and/or polymerase chain reaction methods. No discordant identifications were observed, and 86% generated a successful identification when compared to subculture methods. For the Vitek 2, we observed a 99% essential agreement when compared to the subculture method. For the MicroScan Walkaway, we observed 94.9%, 97.4%, and 100% categorical agreement for MIC panels 53, 38, and MICroSTREP Plus 2, respectively. Turnaround times were reduced from 4 hours for identification and 11 hours for antimicrobial sensitivity testing. We conclude that the SST method results in timelier, actionable results for antimicrobial stewardship initiatives.

Differentiating methicillin resistant and susceptible Staphylococcus aureus from ocular infections using photoacoustic labeling

Introduction

Antibiotic resistance in bacterial species constitutes a growing problem in the clinical management of infections. Not only does it limit therapeutic options, but application of ineffective antibiotics allows resistant species to progress prior to prescribing more effective treatment to patients. Methicillin resistance in Staphylococcus aureus is a major problem in clinical infections as it is the most common hospital acquired infection.

Methods

We developed a photoacoustic flow cytometer using engineered bacteriophage as probes for rapid determination of methicillin resistance in Staphylococcus aureus with thirteen clinical samples obtained from keratitis patients. This method irradiates cells under flow with 532 nm laser light and selectively generates acoustic waves in labeled bacterial cells, thus enabling detection and enumeration of them. Staphylococcus aureus isolates were classified from culture isolation as either methicillin resistant or susceptible using cefoxitin disk diffusion testing. The photoacoustic method enumerates bacterial cells before and after treatment with antibiotics. Decreasing counts of bacteria after treatment indicate susceptible strains. We quantified the bacterial cells in the treated and untreated samples.

Results

Using k-means clustering on the data, we achieved 100% concordance with the classification of Staphylococcus aureus resistance using culture.

Discussion

Photoacoustics can be used to differentiate methicillin resistant and susceptible strains of bacteria from ocular infections. This method may be generalized to other bacterial species using appropriate bacteriophages and testing for resistance using other antibiotics.

The Accelerate Pheno™ System-A New Tool in Microbiological Diagnostics of Bloodstream Infections: A Pilot Study from Poland

The aim of this study was to evaluate the usefulness of the Accelerate Pheno™ system (APS) (Accelerate Diagnostics, Denver, CO, USA) for rapid laboratory diagnosis of bloodstream infections. The study included 45 positive blood samples obtained from patients hospitalized in University Hospital No. 1 in Bydgoszcz, Poland. In 40 (88.9%) blood samples, the APS was capable of identification of at least one microorganism at the genus or species level and in 38 (84.4%) of them additionally assessed antimicrobial susceptibility. The time of identification and the time to result of antimicrobial susceptibility ranged from 1:32 to 1:42 and 5:02 to 5:36 h, respectively. Six positive blood samples revealed a poly-microbial culture. In these cases, only one out of two or three microorganisms was detected by the APS, and the system assessed antimicrobial susceptibility only for them. For 78.6% positive blood samples, agreement on identification compared to mass spectrometry was found. For all but one sample, a 96-100% compliance of the resistance category was achieved when comparing the antimicrobial susceptibility testing results to conventional methods. Using the APS, the total time to report was reduced from 13:34 to even 63:47 h compared to the standard microbiological laboratory workflow. The APS is a very useful system, especially for the rapid assessment of antimicrobial susceptibility of bacteria directly from positive blood samples, offering the greatest potential for microbiology laboratories operating around the clock.

A novel rRNA hybridization-based approach to rapid, accurate Candida identification directly from blood culture

Invasive fungal infections are increasingly common and carry high morbidity and mortality, yet fungal diagnostics lag behind bacterial diagnostics in rapidly identifying the causal pathogen. We previously devised a fluorescent hybridization-based assay to identify bacteria within hours directly from blood culture bottles without subculture, called phylogeny-informed rRNA-based strain identification (Phirst-ID). Here, we adapt this approach to unambiguously identify 11 common pathogenic Candida species, including C. auris, with 100% accuracy from laboratory culture (33 of 33 strains in a reference panel, plus 33 of 33 additional isolates tested in a validation panel). In a pilot study on 62 consecutive positive clinical blood cultures from two hospitals that showed yeast on Gram stain, Candida Phirst-ID matched the clinical laboratory result for 58 of 59 specimens represented in the 11-species reference panel, without misclassifying the 3 off-panel species. It also detected mixed Candida species in 2 of these 62 specimens, including the one discordant classification, that were not identified by standard clinical microbiology workflows; in each case the presence of both species was validated by both clinical and experimental data. Finally, in three specimens that grew both bacteria and yeast, we paired our prior bacterial probeset with this new Candida probeset to detect both pathogen types using Phirst-ID. This simple, robust assay can provide accurate Candida identification within hours directly from blood culture bottles, and the conceptual approach holds promise for pan-microbial identification in a single workflow.

LAY SUMMARY

Candida bloodstream infections cause considerable morbidity and mortality, yet slow diagnostics delay recognition, worsening patient outcomes. We develop and validate a novel molecular approach to accurately identify Candida species directly from blood culture one day faster than standard workflows.

Compound Raman microscopy for rapid diagnosis and antimicrobial susceptibility testing of pathogenic bacteria in urine

Rapid identification and antimicrobial susceptibility testing (AST) of bacteria are key interventions to curb the spread and emergence of antimicrobial resistance. The current gold standard identification and AST methods provide comprehensive diagnostic information but often take 3 to 5 days. Here, a compound Raman microscopy (CRM), which integrates Raman spectroscopy and stimulated Raman scattering microscopy in one system, is presented and demonstrated for rapid identification and AST of pathogens in urine. We generated an extensive bacterial Raman spectral dataset and applied deep learning to identify common clinical bacterial pathogens. In addition, we employed stimulated Raman scattering microscopy to quantify bacterial metabolic activity to determine their antimicrobial susceptibility. For proof-of-concept, we demonstrated an integrated assay to diagnose urinary tract infection pathogens, S. aureus and E. coli. Notably, the CRM system has the unique ability to provide Gram-staining classification and AST results within ~3 h directly from urine samples and shows great potential for clinical applications.

Evaluation of the Performance and Clinical Impact of a Rapid Phenotypic Susceptibility Testing Method Directly from Positive Blood Culture at a Pediatric Hospital

Bloodstream infection poses a significant medical emergency that necessitates timely administration of appropriate antibiotics. Standard laboratory workup for antimicrobial susceptibility testing (AST) involves subculture of organisms from positive blood bottles followed by testing using broth microdilution; however, this process can take several days. The Accelerate Pheno Blood Culture panel (Pheno) provides rapid phenotypic testing of selected Gram-negative organisms directly from positive blood cultures. This has the potential to shorten the AST process to several hours and impact time to antimicrobial optimization and subsequent clinical outcomes; however, these metrics have not been assessed in pediatric populations. We retrospectively compared two patient cohorts with blood cultures positive for on-panel Gram-negative organisms: 82 cases tested by conventional AST methods, and 80 cases postintervention at our pediatric hospital. Susceptibility testing from the Pheno yielded 91.5% categorical agreement with a broth microdilution-based reference method with 7.4% minor error, 1.1% major error, and 0.1% very major error rates. The median time from blood culture positivity to AST decreased from 20.0 h to 9.7 h (P < 0.001), leading to an overall decrease in time from blood culture positivity to change in therapy from 36.0 h to 25.0 h (P < 0.001). There was no observed change in length of stay or 30-day mortality. Median duration on meropenem decreased from 64.8 h to 31.6 h (P = 0.04). We conclude the Pheno had accurate performance and that implementation allowed for faster AST reporting, improved time to optimal therapy, and decreased duration on meropenem in children.

Burden of bacterial bloodstream infections and recent advances for diagnosis

Bloodstream infections (BSIs) and subsequent organ dysfunction (sepsis and septic shock) are conditions that rank among the top reasons for human mortality and have a great impact on healthcare systems. Their treatment mainly relies on the administration of broad-spectrum antimicrobials since the standard blood culture-based diagnostic methods remain time-consuming for the pathogen's identification. Consequently, the routine use of these antibiotics may lead to downstream antimicrobial resistance and failure in treatment outcomes. Recently, significant advances have been made in improving several methodologies for the identification of pathogens directly in whole blood especially regarding specificity and time to detection. Nevertheless, for the widespread implementation of these novel methods in healthcare facilities, further improvements are still needed concerning the sensitivity and cost-effectiveness to allow a faster and more appropriate antimicrobial therapy. This review is focused on the problem of BSIs and sepsis addressing several aspects like their origin, challenges, and causative agents. Also, it highlights current and emerging diagnostics technologies, discussing their strengths and weaknesses.

Performance of the Reveal Rapid Antibiotic Susceptibility Testing System on Gram-Negative Blood Cultures at a Large Urban Hospital

Timely and effective antibiotic treatment is vital for sepsis, with increasing incidence of antimicrobial-resistant bacteremia driving interest in rapid phenotypic susceptibility testing. To enable the widespread adoption needed to make an impact, antibiotic susceptibility testing (AST) systems need to be accurate, enable rapid intervention, have a broad antimicrobial menu and be easy to use and affordable. We evaluated the Specific Reveal (Specific Diagnostics, San Jose, CA) rapid AST system on positive blood cultures with Gram-negative organisms in a relatively resistant population in a large urban hospital to assess its potential for routine clinical use. One hundred four randomly selected positive blood cultures (Virtuo; bioMérieux) were Gram stained, diluted 1:1,000 in Pluronic water, inoculated into 96-well antibiotic plates, sealed with the Reveal sensor panel, and placed in the Reveal instrument for incubation and reading. The MIC and susceptible/intermediate/resistant category was determined and compared to results from Vitek 2 (bioMérieux) for the 17 antimicrobials available and to Sensititre (Thermo Fisher) for 24 antimicrobials. Performance was also assessed with contrived blood cultures with 33 highly resistant strains. Reveal was in 98.0% essential agreement (EA) and 96.3% categorical agreement (CA) with Sensititre, with just 1.3% very major error (VME) and 97.0%/96.2%/1.3% EA/CA/VME versus Vitek 2. Reveal results for contrived highly resistant strains were equivalent, with EA/CA/VME of 97.7%/95.2%/1.0% with CDC/FDA Antibiotic Resistance Isolate Bank references. Average time to result (TTR) for Reveal was 4.6 h. Sample preparation was relatively low skill and averaged 3 min. We conclude that the Reveal system enables accurate and rapid susceptibility testing of Gram-negative blood cultures.

Use of Antimicrobials for Bloodstream Infections in the Intensive Care Unit, a Clinically Oriented Review

Bloodstream infections (BSIs) in critically ill patients are associated with significant mortality. For patients with septic shock, antibiotics should be administered within the hour. Probabilistic treatment should be targeted to the most likely pathogens, considering the source and risk factors for bacterial resistance including local epidemiology. Source control is a critical component of the management. Sending blood cultures (BCs) and other specimens before antibiotic administration, without delaying them, is key to microbiological diagnosis and subsequent opportunities for antimicrobial stewardship. Molecular rapid diagnostic testing may provide faster identification of pathogens and specific resistance patterns from the initial positive BC. Results allow for antibiotic optimisation, targeting the causative pathogen with escalation or de-escalation as required. Through this clinically oriented narrative review, we provide expert commentary for empirical and targeted antibiotic choice, including a review of the evidence and recommendations for the treatments of extended-spectrum β-lactamase-producing, AmpC-hyperproducing and carbapenem-resistant Enterobacterales; carbapenem-resistant Acinetobacter baumannii; and Staphylococcus aureus. In order to improve clinical outcomes, dosing recommendations and pharmacokinetics/pharmacodynamics specific to ICU patients must be followed, alongside therapeutic drug monitoring.

Real time monitoring of Staphylococcus aureus biofilm sensitivity towards antibiotics with isothermal microcalorimetry

Biofilm-associated infections with Staphylococcus aureus are difficult to treat even after administration of antibiotics that according to the standard susceptibility assays are effective. Currently, the assays used in the clinical laboratories to determine the sensitivity of S. aureus towards antibiotics are not representing the behaviour of biofilm-associated S. aureus, since these assays are performed on planktonic bacteria. In research settings, microcalorimetry has been used for antibiotic susceptibility studies. Therefore, in this study we investigated if we can use isothermal microcalorimetry to monitor the response of biofilm towards antibiotic treatment in real-time. We developed a reproducible method to generate biofilm in an isothermal microcalorimeter setup. Using this system, the sensitivity of 5 methicillin-sensitive S. aureus (MSSA) and 5 methicillin-resistant S. aureus (MRSA) strains from different genetic lineages were determined towards: flucloxacillin, cefuroxime, cefotaxime, gentamicin, rifampicin, vancomycin, levofloxacin, clindamycin, erythromycin, linezolid, fusidic acid, co-trimoxazole, and doxycycline. In contrast to conventional assays, our calorimetry-based biofilm susceptibility assay showed that S. aureus biofilms, regardless MSSA or MRSA, can survive the exposure to the maximum serum concentration of all tested antibiotics. The only treatment with a single antibiotic showing a significant reduction in biofilm survival was rifampicin, yet in 20% of the strains, emerging antibiotic resistance was observed. Furthermore, the combination of rifampicin with flucloxacillin, vancomycin or levofloxacin was able to prevent S. aureus biofilm from becoming resistant to rifampicin. Isothermal microcalorimetry allows real-time monitoring of the sensitivity of S. aureus biofilms towards antibiotics in a fast and reliable way.

Multicenter Evaluation of the Acuitas ® AMR Gene Panel for Detection of an Extended Panel of Antimicrobial Resistance Genes among Bacterial Isolates

Background: The Acuitas® AMR Gene Panel is a qualitative, multiplex nucleic acid-based in vitro diagnostic test for detection and differentiation of 28 antimicrobial resistance (AMR) markers associated with not susceptible results (NS, i.e., intermediate or resistant) to one or more antimicrobial agents among cultured isolates of select Enterobacterales, Pseudomonas aeruginosa and Enterococcus faecalis. Methods: This study was conducted at four sites and included testing of 1,224 de-identified stocks created from 584 retrospectively collected isolates and 83 prospectively collected clinical isolates. The Acuitas results were compared with a combined reference standard including whole genome sequencing, organism identification and phenotypic antimicrobial susceptibility testing. Results: Positive percent agreement (PPA) for FDA-cleared AMR targets ranged from 94.4% for MCR-1 to 100% for armA, CTX-M-2, DHA, IMP, OXA-9, SHV, vanA and VEB. The negative percent agreement (NPA) for the majority of targets was ≥99%, except for AAC, AAD, CMY-41, P. aeruginosa gyrA mutant, Sul1, Sul2 and TEM targets (range: 96.5% to 98.5%). Three AMR markers did not meet FDA inclusion criteria (GES, SPM & MCR-2). For each organism, 1 to 22 AMR targets met the minimum reportable PPA/NPA and correlated with ≥80% positive predictive value with associated NS results for at least one agent (i.e., the probability of an organism carrying an AMR marker testing NS to the associated agent). Conclusion: We demonstrate that the Acuitas® AMR Gene Panel is an accurate method to detect a broad array of AMR markers among cultured isolates. The AMR markers were further associated with expected NS results for specific agent-organism combinations.

Recent Developments in Phenotypic and Molecular Diagnostic Methods for Antimicrobial Resistance Detection in Staphylococcus aureus: A Narrative Review

Staphylococcus aureus is an opportunistic pathogen responsible for a wide range of infections in humans, such as skin and soft tissue infections, pneumonia, food poisoning or sepsis. Historically, S. aureus was able to rapidly adapt to anti-staphylococcal antibiotics and become resistant to several classes of antibiotics. Today, methicillin-resistant S. aureus (MRSA) is a multidrug-resistant pathogen and is one of the most common bacteria responsible for hospital-acquired infections and outbreaks, in community settings as well. The rapid and accurate diagnosis of antimicrobial resistance in S. aureus is crucial to the early initiation of directed antibiotic therapy and to improve clinical outcomes for patients. In this narrative review, I provide an overview of recent phenotypic and molecular diagnostic methods for antimicrobial resistance detection in S. aureus, with a particular focus on MRSA detection. I consider methods for resistance detection in both clinical samples and isolated S. aureus cultures, along with a brief discussion of the advantages and the challenges of implementing such methods in routine diagnostics.

Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains

The spread of antimicrobial resistance (AMR) is a rapidly growing threat to humankind on both regional and global scales. As countries worldwide prepare to embrace a One Health approach to AMR management, which is one that recognizes the interconnectivity between human, animal, and environmental health, increasing attention is being paid to identifying and monitoring key contributing factors and critical control points. Presently, AMR sensing technologies have significantly progressed phenotypic antimicrobial susceptibility testing (AST) and genotypic antimicrobial resistance gene (ARG) detection in human healthcare. For effective AMR management, an evolution of innovative sensing technologies is needed for tackling the unique challenges of interconnected AMR across various and different health domains. This review comprehensively discusses the modern state-of-play for innovative commercial and emerging AMR sensing technologies, including sequencing, microfluidic, and miniaturized point-of-need platforms. With a unique view toward the future of One Health, we also provide our perspectives and outlook on the constantly changing landscape of AMR sensing technologies beyond the human health domain.

Systematic Evaluation of the Accelerate Pheno System for Susceptibility Testing of Gram-Negative Bacteria Isolated from Blood Cultures

Bacteremia is a major cause of morbidity and mortality. Rapid identification of pathogens for early targeted antimicrobial therapy is crucial for detecting emergence of antibiotic resistance and improving outcomes. However, there are limited data regarding the analytical performance of a rapid identification (ID) and antimicrobial susceptibility testing (AST) method like Accelerate Pheno blood culture detection system compared with the conventional methods routinely used in microbiology laboratories. We undertook a systematic quality improvement (QI) study to compare AST results obtained with Accelerate Pheno system rapid ID/AST system with a standard reference method in a university hospital microbiology laboratory. This was a single center, retrospective (5/10/19 to 8/1/19) and prospective (8/1/19 to 1/31/20) study that evaluated all blood cultures growing Gram-negative rods (GNR). We compared AST results obtained using the reference disk diffusion (DD) susceptibility method with those obtained by the Accelerate Pheno system. We calculated the error rates and categorical agreement between the Accelerate Pheno system and DD for each organism and specific drug tested. We evaluated 355 blood cultures growing GNR, of which 284 met the inclusion criteria. We grouped all Enterobacterales (n  =  263) for analysis (156 Escherichiacoli, 60 Klebsiella spp., 20 Proteus mirabilis, 17 Enterobacter spp., and 10 Serratiamarcescens). Twenty-one Pseudomonasaeruginosa isolates were analyzed separately. For Enterobacterales, categorical agreement (CA) was ≥90% for amikacin (AMK), aztreonam (ATM), cefepime (FEP), ceftriaxone (CRO), ertapenem (ETP), gentamicin (GEN), meropenem (MEM), and tobramycin (TOB); and very major error (VME) was <5% for ampicillin/sulbactam (SAM), GEN, MEM, TOB, CRO, and ceftazidime (CAZ). For ciprofloxacin (CIP), CA was 87% and VME was 8%. For P. aeruginosa, CA was ≥90% for AMK and TOB, and VME was ≥5% for AMK, CAZ, GEN, MEM, piperacillin-tazobactam (TZP), and TOB. Accelerate Pheno rapid ID/AST system for GNR isolated from blood culture (BCs) was reliable for some but not all agents in the panel. Based on the findings from this study, our laboratory reports Accelerate Pheno system AST results only for Enterobacterales, and we limit our reports to CRO, CAZ, TZP, CIP, ATM, and GEN.

IMPORTANCE This was an 8-month retrospective and prospective study looking at the analytical performance of the Accelerate Pheno system on clinical isolates obtained from patients seen in our tertiary care hospital. Most of the published literature on the analytical performance of Accelerate Pheno System has been from clinical trials with limited data from clinical microbiology laboratories postimplementation of the system. Here we compare the AST results on 355 blood cultures growing Gram-negative bacteria in Accelerate Pheno system with the CLSI reference disk diffusion (DD) method. The findings from this study highlight the “real-world” performance of the Accelerate Pheno system for Gram-negative bacteria from blood cultures. We provide data to show the reliable susceptibility testing results of Enterobacterales for most of the commonly used antimicrobial agents and significant limitation for susceptibility testing results of Pseudomonas aeruginosa on the Accelerate Pheno system.

Comparison of novel rapid diagnostic of blood culture identification and antimicrobial susceptibility testing by Accelerate Pheno system and BioFire FilmArray Blood Culture Identification and BioFire FilmArray Blood Culture Identification 2 panels

Background

Conventional turnaround time (TAT) for positive blood culture (PBC) identification (ID) and antimicrobial susceptibility testing (AST) is 2–3 days. We evaluated the TAT and ID/AST performance using clinical and seeded samples directly from PBC bottles with different commercial approaches: (1) Accelerate Pheno® system (Pheno) for ID/AST; (2) BioFire® FilmArray® Blood Culture Identification (BCID) Panel and/ or BCID2 for ID; (3) direct AST by VITEK® 2 (direct AST); and (4) overnight culture using VITEK® 2 colony AST.

Results

A total of 141 PBC samples were included in this evaluation. Using MALDI-TOF (Bruker MALDI Biotyper) as the reference method for ID, the overall monomicrobial ID sensitivity/specificity are as follows: Pheno 97.9/99.9%; BCID 100/100%; and BCID2 100/100%, respectively. For AST performance, broth microdilution (BMD) was used as the reference method. For gram-negatives, overall categorical and essential agreements (CA/EA) for each method were: Pheno 90.3/93.2%; direct AST 92.6/88.5%; colony AST 94.4/89.5%, respectively. For gram-positives, the overall CA/EAs were as follows: Pheno 97.2/98.89%; direct AST 97.2/100%; colony AST 97.2/100%, respectively. The BCID/BCID2 and direct AST TATs were around 9–20 h (1/9-19 h for ID with resistance markers/AST), with 15 min/sample hands-on time. In comparison, Pheno TATs were around 8–10 h (1.5/7 h for ID/AST) with 2 min/sample hands-on time, maintains a clinically relevant fast report of antibiotic minimal inhibitory concentration (MIC) and allows for less TAT and hands-on time.

Conclusion

In conclusion, to the best of our knowledge, this is the first study conducted as such in Asia; all studied approaches achieved satisfactory performance, factors such as TAT, panel of antibiotics choices and hands-on time should be considered for the selection of appropriate rapid ID and AST of PBC methods in different laboratory settings.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02403-y.

Machine learning for identifying resistance features of Klebsiella pneumoniae using whole-genome sequence single nucleotide polymorphisms

Introduction. Klebsiella pneumoniae, a gram-negative bacterium, is a common pathogen causing nosocomial infection. The drug-resistance rate of K. pneumoniae is increasing year by year, posing a severe threat to public health worldwide. K. pneumoniae has been listed as one of the pathogens causing the global crisis of antimicrobial resistance in nosocomial infections. We need to explore the drug resistance of K. pneumoniae for clinical diagnosis. Single nucleotide polymorphisms (SNPs) are of high density and have rich genetic information in whole-genome sequencing (WGS), which can affect the structure or expression of proteins. SNPs can be used to explore mutation sites associated with bacterial resistance.Hypothesis/Gap Statement. Machine learning methods can detect genetic features associated with the drug resistance of K. pneumoniae from whole-genome SNP data.Aims. This work used Fast Feature Selection (FFS) and Codon Mutation Detection (CMD) machine learning methods to detect genetic features related to drug resistance of K. pneumoniae from whole-genome SNP data.Methods. WGS data on resistance of K. pneumoniae strains to four antibiotics (tetracycline, gentamicin, imipenem, amikacin) were downloaded from the European Nucleotide Archive (ENA). Sequence alignments were performed with MUMmer 3 to complete SNP calling using K. pneumoniae HS11286 chromosome as the reference genome. The FFS algorithm was applied to feature selection of the SNP dataset. The training set was constructed based on mutation sites with mutation frequency >0.995. Based on the original SNP training set, 70% of SNPs were randomly selected from each dataset as the test set to verify the accuracy of the training results. Finally, the resistance genes were obtained by the CMD algorithm and Venny.Results. The number of strains resistant to tetracycline, gentamicin, imipenem and amikacin was 931, 1048, 789 and 203, respectively. Machine learning algorithms were applied to the SNP training set and test set, and 28 and 23 resistance genes were predicted, respectively. The 28 resistance genes in the training set included 22 genes in the test set, which verified the accuracy of gene prediction. Among them, some genes (KPHS_35310, KPHS_18220, KPHS_35880, etc.) corresponded to known resistance genes (Eef2, lpxK, MdtC, etc). Logistic regression classifiers were established based on the identified SNPs in the training set. The area under the curves (AUCs) of the four antibiotics was 0.939, 0.950, 0.912 and 0.935, showing a strong ability to predict bacterial resistance.Conclusion. Machine learning methods can effectively be used to predict resistance genes and associated SNPs. The FFS and CMD algorithms have wide applicability. They can be used for the drug-resistance analysis of any microorganism with genomic variation and phenotypic data. This work lays a foundation for resistance research in clinical applications.

Artificial Intelligence and Mapping a New Direction in Laboratory Medicine: A Review

BACKGROUND

Modern artificial intelligence (AI) and machine learning (ML) methods are now capable of completing tasks with performance characteristics that are comparable to those of expert human operators. As a result, many areas throughout healthcare are incorporating these technologies, including in vitro diagnostics and, more broadly, laboratory medicine. However, there are limited literature reviews of the landscape, likely future, and challenges of the application of AI/ML in laboratory medicine.

CONTENT

In this review, we begin with a brief introduction to AI and its subfield of ML. The ensuing sections describe ML systems that are currently in clinical laboratory practice or are being proposed for such use in recent literature, ML systems that use laboratory data outside the clinical laboratory, challenges to the adoption of ML, and future opportunities for ML in laboratory medicine.

SUMMARY

AI and ML have and will continue to influence the practice and scope of laboratory medicine dramatically. This has been made possible by advancements in modern computing and the widespread digitization of health information. These technologies are being rapidly developed and described, but in comparison, their implementation thus far has been modest. To spur the implementation of reliable and sophisticated ML-based technologies, we need to establish best practices further and improve our information system and communication infrastructure. The participation of the clinical laboratory community is essential to ensure that laboratory data are sufficiently available and incorporated conscientiously into robust, safe, and clinically effective ML-supported clinical diagnostics.

Identification of volatile compounds from bacteria by spectrometric methods in medicine diagnostic and other areas: current state and perspectives

Diagnosis of bacterial infections until today mostly relies on conventional microbiological methods. The resulting long turnaround times can lead to delayed initiation of adequate antibiotic therapy and prolonged periods of empiric antibiotic therapy (e.g., in intensive care medicine). Therewith, they contribute to the mortality of bacterial infections and the induction of multidrug resistances. The detection of species specific volatile organic compounds (VOCs) emitted by bacteria has been proposed as a possible diagnostic approach with the potential to serve as an innovative point-of-care diagnostic tool with very short turnaround times. A range of spectrometric methods are available which allow the detection and quantification of bacterial VOCs down to a range of part per trillion. This narrative review introduces the application of spectrometric analytical methods for the purpose of detecting VOCs of bacterial origin and their clinical use for diagnosing different infectious conditions over the last decade. KEY POINTS: • Detection of VOCs enables bacterial differentiation in various medical conditions. • Spectrometric methods may function as point-of-care diagnostics in near future.

Evaluation of FASTinov® ultra-rapid flow cytometry antimicrobial susceptibility testing directly from positive blood cultures

The ultra-rapid antimicrobial susceptibility test FASTinov® flow cytometry kit was directly evaluated on positive blood cultures (BC) at two sites: i) FASTinov® in Porto (Portugal) using spiked BC with well-characterized bacteria and ii) Ramon y Cajal University hospital in Madrid (Spain) using patients positive BC. Two kits were evaluated, FASTgramneg (Enterobacterales, Pseudomonas, Acinetobacter) and FASTgrampos (Staphylococcus, Enterococcus). A dedicated software for cytometric data analysis and interpretative reporting, both using CLSI and EUCAST criteria, were used. The FASTgramneg kit also provides information about the presence of resistant mechanisms, including ESBLs and carbapenemases. After 1-h incubation at 37°C bacteria were analysed by CytoFLEX® cytometer (Beckman, CA). Disk diffusion was performed as reference susceptibility method. Overall, 447 positive BC were included, 100 from hospitalized patients. Categorical agreement for FASTgramneg panel was 96.8% for EUCAST and 96.4% for CLSI. For FASTgrampos panel it was 98.6% when using both criteria. Using EUCAST criteria the percentage of errors for FASTgramneg panel was 2.1% minor errors (mE), 1.3% major errors (ME) and 0.6% very major errors (VME). Concerning CLSI, 2.9% mE, 0.9% ME and 0.4% VME were found. VMEs were mainly observed with amoxicillin-clavulanate, cefotaxime, ceftazidime and gentamicin. FASTgrampos panel showed 0.3% mE, 1.4% ME and 0.4% VME using EUCAST criteria (VME regarded gentamicin and Staphylococcus) while 0.4% mE, 1.4% ME and no VME when using CLSI criteria. FASTinov® flow cytometry kits represent a rapid alternative for direct antimicrobial susceptibility testing from positive BC, showing time-to-results <2-h, which can be used to personalized antibiotics and stewardship practices.

The EUCAST rapid disc diffusion method for antimicrobial susceptibility testing directly from positive blood culture bottles

Objectives

With increasing antimicrobial resistance, rapid antimicrobial susceptibility testing (RAST) becomes important, especially in patients with bloodstream infections. EUCAST decided to develop a standardized rapid method, based on EUCAST disc diffusion, to offer susceptibility reports within 4–8 h of a positive blood culture (BC).

Methods

BC bottles were spiked with clinical isolates (n = 332) of the seven most relevant sepsis pathogens with a variety of resistance mechanisms. RAST was performed directly from the bottle and zones read after 4, 6 and 8 h. Several variables were investigated, including the effect of using different BC bottles and of a 0–18 h delay between a positive signal and the performance of RAST.

Results

For five species, most inhibition zones could be read after 4 h. The proportion of results that could be interpreted increased from 75% at 4 h to 84% after 8 h. Categorical agreement against the reference method was good, with error rates of false susceptibility of 0.2%, 0.2% and 0.2% at 4, 6 and 8 h and false resistance of 1.2%, 0.2% and 0.1% at 4, 6 and 8 h, respectively.

Conclusions

With the EUCAST RAST method, reliable AST results can be delivered within 4–8 h of positivity of BC bottles for seven important bloodstream infection pathogens. To reduce the occurrence of errors and to absorb the variability caused by using a non-standardized inoculum, material from different manufacturers and workflow-related delays, we have introduced an area in which interpretation is not permitted, the Area of Technical Uncertainty.

Recognition of Diagnostic Gaps for Laboratory Diagnosis of Fungal Diseases: Expert Opinion from the Fungal Diagnostics Laboratories Consortium (FDLC)

Fungal infections are a rising threat to our immunocompromised patient population, as well as other nonimmunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics. To jointly address this diagnostic challenge, the Fungal Diagnostics Laboratory Consortium (FDLC) was recently created. The FDLC consists of 26 laboratories from the United States and Canada that routinely provide fungal diagnostic services for patient care. A survey of fungal diagnostic capacity among the 26 members of the FDLC was recently completed, identifying the following diagnostic gaps: lack of molecular detection of mucormycosis; lack of an optimal diagnostic algorithm incorporating fungal biomarkers and molecular tools for early and accurate diagnosis of Pneumocystis pneumonia, aspergillosis, candidemia, and endemic mycoses; lack of a standardized molecular approach to identify fungal pathogens directly in formalin-fixed paraffin-embedded tissues; lack of robust databases to enhance mold identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; suboptimal diagnostic approaches for mold blood cultures, tissue culture processing for Mucorales, and fungal respiratory cultures for cystic fibrosis patients; inadequate capacity for fungal point-of-care testing to detect and identify new, emerging or underrecognized, rare, or uncommon fungal pathogens; and performance of antifungal susceptibility testing. In this commentary, the FDLC delineates the most pressing unmet diagnostic needs and provides expert opinion on how to fulfill them. Most importantly, the FDLC provides a robust laboratory network to tackle these diagnostic gaps and ultimately to improve and enhance the clinical laboratory's capability to rapidly and accurately diagnose fungal infections.

New Microbiological Techniques for the Diagnosis of Bacterial Infections and Sepsis in ICU Including Point of Care

Purpose of Review

The aim of this article is to review current and emerging microbiological techniques that support the rapid diagnosis of bacterial infections in critically ill patients, including their performance, strengths and pitfalls, as well as available data evaluating their clinical impact.

Recent Findings

Bacterial infections and sepsis are responsible for significant morbidity and mortality in patients admitted to the intensive care unit and their management is further complicated by the increase in the global burden of antimicrobial resistance. In this setting, new diagnostic methods able to overcome the limits of traditional microbiology in terms of turn-around time and accuracy are highly warranted. We discuss the following broad themes: optimisation of existing culture-based methodologies, rapid antigen detection, nucleic acid detection (including multiplex PCR assays and microarrays), sepsis biomarkers, novel methods of pathogen detection (e.g. T2 magnetic resonance) and susceptibility testing (e.g. morphokinetic cellular analysis) and the application of direct metagenomics on clinical samples. The assessment of the host response through new “omics” technologies might also aid in early diagnosis of infections, as well as define non-infectious inflammatory states.

Summary

Despite being a promising field, there is still scarce evidence about the real-life impact of these assays on patient management. A common finding of available studies is that the performance of rapid diagnostic strategies highly depends on whether they are integrated within active antimicrobial stewardship programs. Assessing the impact of these emerging diagnostic methods through patient-centred clinical outcomes is a complex challenge for which large and well-designed studies are awaited.

Improving outcomes and antibiotic stewardship (IOAS) for patients with Gram-positive bloodstream infections through use of rapid testing: a quasi-experimental multicentre study of the Accelerate PhenoTest™ BC Kit

BACKGROUND

Data from the Improving Outcomes and Antibiotic Stewardship for Patients with Bloodstream Infections: Accelerate PhenoTest™ BC Kit (AXDX) Registry Study were analysed to determine the impact of rapid organism identification and antimicrobial susceptibility testing (AST) for Gram-positive bacteraemia.

PATIENTS AND METHODS

This multicentre, quasi-experimental study evaluated clinical and antimicrobial stewardship metrics following the implementation of AXDX. Data from hospitalized patients with bacteraemia were compared between groups, one that underwent testing on AXDX (post-AXDX) and one that underwent traditional identification and AST (pre-AXDX). An analysis of patients with Gram-positive bacteraemia was performed. The primary outcome was time to optimal therapy (TTOT). Secondary outcomes included time to first antibiotic modification (overall and Gram-positive), duration of unnecessary MRSA coverage, incidence of adverse events, length of stay and mortality.

RESULTS

A total of 219 (109 pre-AXDX, 110 post-AXDX) patients with Gram-positive bacteraemia were included. Median TTOT was 36.3 h (IQR, 16.9-56.7) in the pre-AXDX group and 20.4 h (IQR, 7.5-36.7) in the post-AXDX group (P = 0.01). Compared with pre-AXDX, median time to first antibiotic modification (29.1 versus 15.9 h; P = 0.002), time to first Gram-positive antibiotic modification (33.2 versus 17.2 h; P = 0.003) and median duration of unnecessary MRSA coverage (58.4 versus 29.7 h; P = 0.04) were reduced post-AXDX. A trend towards decreased acute kidney injury (24% versus 13%; P = 0.06) was observed in the post-AXDX group. Groups did not differ in other secondary outcomes.

CONCLUSIONS

Implementation of AXDX testing for patients with Gram-positive bacteraemia shortened the TTOT and reduced unnecessary antibiotic exposure due to faster antibiotic modifications.

Recent advances in rapid antimicrobial susceptibility testing systems

INTRODUCTION

Until recently antimicrobial susceptibility testing (AST) methods based on the demonstration of phenotypic susceptibility in 16-24 h remained largely unchanged.

AREAS COVERED

Advances in rapid phenotypic and molecular-based AST systems.

EXPERT OPINION

AST has changed over the past decade, with many rapid phenotypic and molecular methods developed to demonstrate phenotypic or genotypic resistance, or biochemical markers of resistance such as β-lactamases associated with carbapenem resistance. Most methods still require isolation of bacteria from specimens before both legacy and newer methods can be used. Bacterial identification by MALDI-TOF mass spectroscopy is now widely used and is often key to the interpretation of rapid AST results. Several PCR arrays are available to detect the most frequent pathogens associated with bloodstream infections and their major antimicrobial resistance genes. Many advances in whole-genome sequencing of bacteria and fungi isolated by culture as well as directly from clinical specimens have been made but are not yet widely available. High cost and limited throughput are the major obstacles to uptake of rapid methods, but targeted use, continued development and decreasing costs are expected to result in more extensive use of these increasingly useful methods.

The Genotype-to-Phenotype Dilemma: How Should Laboratories Approach Discordant Susceptibility Results?

Traditional culture-based methods for identification and antimicrobial susceptibility testing (AST) of bacteria take 2 to 3 days on average. Syndromic molecular diagnostic panels have revolutionized clinical microbiology laboratories as they can simultaneously identify an organism and detect some of the most significant antimicrobial resistance (AMR) genes directly from positive blood culture broth or from various specimen types (e.g., whole blood, cerebrospinal fluid, and respiratory specimens). The presence or absence of an AMR marker associated with a particular organism can be used to predict the phenotypic AST results to more rapidly guide therapy. Numerous studies have shown that genotypic susceptibility predictions by syndromic panels can improve patient outcomes. However, an important limitation of AMR marker detection to predict phenotype is the potential discrepancies that may arise upon performing phenotypic AST of the recovered organism in culture. The focus of this minireview is to address how clinical laboratories should interpret rapid molecular results from commercial platforms in relation to phenotypic AST. Stepwise approaches and solutions are provided to resolve discordant results between genotypic and phenotypic susceptibility results.

Comparison of novel approaches for expedited pathogen identification and antimicrobial susceptibility testing against routine blood culture diagnostics

Blood stream infections pose a major challenge for clinicians as the immediate application of an appropriate antibiotic treatment is the vital factor to safe the patients' lives. This preliminary study compares three different systems promising fast pathogen identification and susceptibility testing in comparison to conventional blood culture (BC): (i) the rapid antimicrobial susceptibility testing protocol according to EUCAST in combination with the Sepsityper^® kit (sRAST), (ii) the direct inoculation method on the VITEK^®2 system (dVIT) and (iii) testing with the Accelerate Pheno^® system (AccPh). All methods were assessed in terms of accuracy, time to result and usability. Twenty‐three BC samples obtained from patients suffering from proven sepsis were analysed in detail. Pathogen identification was successful in 95·6, 91·3 and 91·3% in sRAST, dVIT and AccPh, respectively. Categorical agreement in antimicrobial susceptibility testing was 89·5, 96 and 96·6%, respectively. Time to result from sample entry to reporting ranged from an average of 4·6 h for sRAST and 6·9 h for AccPh to 10·6 h for dVIT. These results imply a significant shortening of reporting times at considerably high agreement rates for these new diagnostic approaches.

Rapid Antimicrobial Susceptibility Testing on Clinical Urine Samples by Video-Based Object Scattering Intensity Detection

To combat the ongoing public health threat of antibiotic-resistant infections, a technology that can quickly identify infecting bacterial pathogens and concurrently perform antimicrobial susceptibility testing (AST) in point-of-care settings is needed. Here, we develop a technology for point-of-care AST with a low-magnification solution scattering imaging system and a real-time video-based object scattering intensity detection method. The low magnification (1-2×) optics provides sufficient volume for direct imaging of bacteria in urine samples, avoiding the time-consuming process of culture-based bacterial isolation and enrichment. Scattering intensity from moving bacteria and particles in the sample is obtained by subtracting both spatial and temporal background from a short video. The time profile of scattering intensity is correlated with the bacterial growth rate and bacterial response to antibiotic exposure. Compared to the image-based bacterial tracking and counting method we previously developed, this simple image processing algorithm accommodates a wider range of bacterial concentrations, simplifies sample preparation, and greatly reduces the computational cost of signal processing. Furthermore, development of this simplified processing algorithm eases implementation of multiplexed detection and allows real-time signal readout, which are essential for point-of-care AST applications. To establish the method, 130 clinical urine samples were tested, and the results demonstrated an accuracy of ∼92% within 60-90 min for UTI diagnosis. Rapid AST of 55 positive clinical samples revealed 98% categorical agreement with both the clinical culture results and the on-site parallel AST validation results. This technology provides opportunities for prompt infection diagnosis and accurate antibiotic prescriptions in point-of-care settings.

Combining Functional Genomics and Whole-Genome Sequencing to Detect Antibiotic Resistance Genes in Bacterial Strains Co-Occurring Simultaneously in a Brazilian Hospital

(1) Background: The rise of multi-antibiotic resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. (2) Methods: We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 34 strains of Gram-negative and Gram-positive bacteria, providing the first genomic description of Morganella morganii and Ralstonia mannitolilytica clinical isolates from South America. (3) Results: We identified a high abundance of beta-lactamase genes in resistant organisms, including seven extended-spectrum beta-lactamases (OXA-1, OXA-10, CTX-M-1, KPC, TEM, HYDRO, BLP) shared between organisms from different species. Additionally, we identified several ARG-carrying plasmids indicating the potential for a fast transmission of resistance mechanism between bacterial strains. Furthermore, we uncovered two pairs of (near) identical plasmids exhibiting multi-drug resistance. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (Escherichia coli, Klebsiella pneumoniae, and M. morganii), we identified six beta-lactamase genes out of 15 predicted in silico as those mainly responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms. (4) Conclusions: Systematic studies similar to the one presented here should help to prevent outbreaks of novel multidrug-resistant bacteria in healthcare facilities.

Clinical evaluation of the acuitas® AMR gene panel for rapid detection of bacteria and genotypic antibiotic resistance determinants

Urinary tract infections are leading causes of hospital admissions. Accurate and timely diagnosis is important due to increasing morbidity and mortality from antimicrobial resistance. We evaluated a polymerase chain reaction test (Acuitas AMR Gene Panel with the Acuitas Lighthouse Software) for detection of 5 common uropathogens (Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Enterococcus faecalis) and antibiotic resistance genes directly from urine for prediction of phenotypic resistance. Overall percent agreement was 97% for semiquantitative detection of uropathogens versus urine culture using a cut-off of 10⁴ colony forming units per mL urine. Overall accuracy was 91% to 93% for genotypic prediction of common antibiotic resistance harbored by E. coli, K. pneumoniae, and P. mirabilis.

Core Recommendations for Antifungal Stewardship: A Statement of the Mycoses Study Group Education and Research Consortium

In recent years, the global public health community has increasingly recognized the importance of antimicrobial stewardship (AMS) in the fight to improve outcomes, decrease costs, and curb increases in antimicrobial resistance around the world. However, the subject of antifungal stewardship (AFS) has received less attention. While the principles of AMS guidelines likely apply to stewarding of antifungal agents, there are additional considerations unique to AFS and the complex field of fungal infections that require specific recommendations. In this article, we review the literature on AMS best practices and discuss AFS through the lens of the global core elements of AMS. We offer recommendations for best practices in AFS based on a synthesis of this evidence by an interdisciplinary expert panel of members of the Mycoses Study Group Education and Research Consortium. We also discuss research directions in this rapidly evolving field. AFS is an emerging and important component of AMS, yet requires special considerations in certain areas such as expertise, education, interventions to optimize utilization, therapeutic drug monitoring, and data analysis and reporting.

Optimizing Pharmacokinetics-Pharmacodynamics of Antimicrobial Management in Patients with Sepsis: A Review

Critically ill patients with sepsis or septic shock are at an increased risk of death. Early and aggressive interventions are essential for improving clinical outcomes. There are a number of therapeutic and practical challenges in the management of antimicrobials in patients with sepsis. These include the timely selection and administration of appropriate antimicrobials, significant physiological alterations that can influence antimicrobial pharmacokinetics, and significant interpatient variability of antimicrobial concentrations using standard dosing approaches. Understanding the impact of these factors on the probability of attaining pharmacokinetic-pharmacodynamic target goals is essential to guide optimal therapy. Using rapid diagnostic technology could facilitate timely selection of antimicrobials, and therapeutic drug monitoring would provide a more individualized dosing approach. Using an interdisciplinary sepsis team would also be beneficial in coordinating efforts to overcome the challenges encountered during this critical period to ensure optimal care.

Rapid Antimicrobial Susceptibility Testing Methods for Blood Cultures and Their Clinical Impact

Antimicrobial susceptibility testing (AST) of bacteria isolated in blood cultures is critical for optimal management of patients with sepsis. This review describes new and emerging phenotypic and genotypic AST methods and summarizes the evidence that implementation of these methods can impact clinical outcomes of patients with bloodstream infections.

Enlarging the Toolbox Against Antimicrobial Resistance: Aptamers and CRISPR-Cas

In the post-genomic era, molecular treatments and diagnostics have been envisioned as powerful techniques to tackle the antimicrobial resistance (AMR) crisis. Among the molecular approaches, aptamers and CRISPR-Cas have gained support due to their practicality, sensibility, and flexibility to interact with a variety of extra- and intracellular targets. Those characteristics enabled the development of quick and onsite diagnostic tools as well as alternative treatments for pan-resistant bacterial infections. Even with such potential, more studies are necessary to pave the way for their successful use against AMR. In this review, we highlight those two robust techniques and encourage researchers to refine them toward AMR. Also, we describe how aptamers and CRISPR-Cas can work together with the current diagnostic and treatment toolbox.

Implementation of a Rapid Phenotypic Susceptibility Platform for Gram-Negative Bloodstream Infections with Paired Antimicrobial Stewardship Intervention: Is the Juice Worth the Squeeze?

BACKGROUND

Implementation of the Accelerate Pheno TM Gram-negative platform (RDT) paired with antimicrobial stewardship program (ASP) intervention projects to improve time to institutional-preferred antimicrobial therapy (IPT) for Gram-negative bacilli (GNB) bloodstream infections (BSI). However, few data describe the impact of discrepant RDT results from standard of care (SOC) methods on antimicrobial prescribing.

METHODS

A single-center, pre-/post-intervention study of consecutive, non-duplicate blood cultures for adult inpatients with GNB BSI following combined RDT + ASP intervention was performed. The primary outcome was time to IPT. An a priori definition of IPT was utilized to limit bias and allow for an assessment of the impact of discrepant RDT results with the SOC reference standard.

RESULTS

Five hundred fourteen patients (PRE 264; POST 250) were included. Median time to antimicrobial susceptibility testing (AST) results decreased 29.4 hours (p < 0.001) post-intervention, and median time to IPT was reduced by 21.2 hours (p <0.001). Utilization (days of therapy [DOTs]/1000 days present) of broad-spectrum agents decreased (PRE 655.2 vs. POST 585.8; p = 0.043) and narrow-spectrum beta-lactams increased (69.1 vs 141.7; p <0.001). Discrepant results occurred in 69/250 (28%) post-intervention episodes, resulting in incorrect ASP recommendations in 10/69 (14%). No differences in clinical outcomes were observed.

CONCLUSIONS

While implementation of a phenotypic RDT + ASP can improve time to IPT, close coordination with Clinical Microbiology and continued ASP follow up are needed to optimize therapy. Although uncommon, the potential for erroneous ASP recommendations to de-escalate to inactive therapy following RDT results warrants further investigation.

The Evolving Landscape of Fungal Diagnostics, Current and Emerging Microbiological Approaches

Invasive fungal infections are increasingly recognized in immunocompromised hosts. Current diagnostic techniques are limited by low sensitivity and prolonged turnaround times. We review emerging diagnostic technologies and platforms for diagnosing the clinically invasive disease caused by Candida, Aspergillus, and Mucorales.

American Society of Transplantation and Cellular Therapy Series, 1: Enterobacterales Infection Prevention and Management after Hematopoietic Cell Transplantation

The Practice Guidelines Committee of the American Society of Transplantation and Cellular Therapy partnered with its Transplant Infectious Disease Special Interest Group to update its 2009 compendium-style infectious diseases guidelines for hematopoietic cell transplantation (HCT). A completely fresh approach was taken, with the goal of better serving clinical providers by publishing each stand-alone topic in the infectious diseases series in a concise format of frequently asked questions (FAQs), tables, and figures [1]. Adult and pediatric infectious diseases and HCT content experts developed and then answered FAQs, and then finalized topics with harmonized recommendations that were made by assigning a strength of recommendation ranging from A to E paired with a level of supporting evidence graded I to III. The first topic in the series focuses on potentially life-threatening infections in HCT caused by Enterobacterales, relevant infection risk factors, and practical considerations regarding prevention and treatment of these infections in the setting of emerging multidrug resistance.