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

Blood culture-free ultra-rapid antimicrobial susceptibility testing

Treatment assessment and patient outcome for sepsis depend predominantly on the timely administration of appropriate antibiotics1-3. However, the clinical protocols used to stratify and select patient-specific optimal therapy are extremely slow4. In particular, the major hurdle in performing rapid antimicrobial susceptibility testing (AST) remains in the lengthy blood culture procedure, which has long been considered unavoidable due to the limited number of pathogens present in the patient's blood. Here we describe an ultra-rapid AST method that bypasses the need for traditional blood culture, thereby demonstrating potential to reduce the turnaround time of reporting drug susceptibility profiles by more than 40-60 h compared with hospital AST workflows. Introducing a synthetic beta-2-glycoprotein I peptide, a broad range of microbial pathogens are selectively recovered from whole blood, subjected to species identification or instantly proliferated and phenotypically evaluated for various drug conditions using a low-inoculum AST chip. The platform was clinically evaluated by the enrolment of 190 hospitalized patients suspected of having infection, achieving 100% match in species identification. Among the eight positive cases, six clinical isolates were retrospectively tested for AST showing an overall categorical agreement of 94.90% with an average theoretical turnaround time of 13 ± 2.53 h starting from initial blood processing.

Evaluation of Vitek-2 and MicroScan ASTs directly from positive blood culture: A cost-effective 24-h reduction for Enterobacterales and staphylococci

The reduction of antimicrobial susceptibility testing (AST) time-to-result is a central need, especially in sepsis treatment. The current automated rapid ASTs are still too expensive for many laboratories. We aimed to evaluate three pre-treatment methods for a same-day inoculation on both automated AST platforms available in our laboratory. We tested 100 Enterobacterales or staphylococci positive bottles. We obtained good results with the different methods and instruments. In particular, Vitek-2 showed good performances with Enterobacterales AST when inoculated with bacterial pellet (96.6% categorical agreement - CA-, 93.3% essential agreement - EA). Also short-term incubation colonies for staphylococci AST had acceptable CA (94.2%), even if with 77.5% EA. MicroScan system for staphylococci AST with both short-term incubation and direct blood inoculation reached >95% CA, but 92.5% and 83.6% EA, respectively. On the other hand, Enterobacterales AST showed optimal performances only with bacterial pellet inoculation (97.6% CA). In fact, direct blood inoculation showed not acceptable parameters for several molecules. Both systems allow a 24-h reduction in time-to-result, by using the same instruments of routine activity after rapid and cheap pre-treatments.

Performance of Flow Cytometry-Based Rapid Assay in Detection of Carbapenemase-Producing Enterobacterales

Carbapenemase-producing Enterobacterales are increasingly being recognized in nosocomial infections. The performance of a flow cytometry-based rapid assay for their detection and differentiation was evaluated. This is a disruptive phenotypic technology, phenotypic and growth-independent, that searches for the lesions produced by drugs acting on cells after a short incubation time. Overall, 180 Gram-negative bacteria were studied, and results were compared with those obtained molecularly by PCR and phenotypically by 'KPC, MBL and OXA-48 Confirm Kit'. This phenotypic method was used as reference for comparison purposes. Susceptibility to carbapenems (imipenem, meropenem, and ertapenem) was determined by standard broth microdilution. Overall, 112 isolates (62.2%) were carbapenemase producers, 41 KPCs, 36 MβLs, and 31 OXA-48, and 4 strains were KPC + MβL co-producers. Sixty-eight isolates were carbapenemase-negative. The percentage of agreement, sensitivity, and specificity were calculated according to ISO 20776-2:2021. The FASTinov assay showed 97.7% agreement with the reference method for carbapenemase detection. Discrepant flow cytometry results were obtained in four isolates compared with both reference and PCR results. The sensitivity and specificity of this new technology were 95.3% and 98.5%, respectively, for KPCs, 97.6% and 99.3% for MβLs, and 96.9% and 98% for OXA-48 detection. In conclusion, we describe a rapid flow cytometry assay with high accuracy for carbapenemase detection and the differentiation of various carbapenemases, which should impact clinical microbiology laboratories and patient management.

Flow cytometry: Unravelling the real antimicrobial and antibiofilm efficacy of natural bioactive compounds

Flow cytometry (FCM) provides unique information on bacterial viability and physiology, allowing a real-time early warning antimicrobial and antibiofilm monitoring system for preventing the spread risk of foodborne disease. The present work used a combined culture-based and FCM approach to assess the in vitro efficacy of essential oils (EOs) from condiment plants commonly used in Mediterranean Europe (i.e., thyme EO, oregano EO, basil EO, and lemon EO) against planktonic and sessile cells of food-pathogenic Listeria monocytogenes 56 LY, and contaminant and alterative species Escherichia coli ATCC 25922 and Pseudomonas fluorescens ATCC 13525. Evaluation of the bacterial response to the increasing concentrations of natural compounds posed FCM as a crucial technique for the quantification of the live/dead, and viable but non-culturable (VBNC) cells when antimicrobial agents exert no real bactericidal action. Furthermore, the FCM results displayed higher numbers of viable bacteria expressed as Active Fluorescent Units (AFUs) with a greater level of repeatability compared with outcomes of the plate-count method. Overall, accurate counting of viable microbial cells is a critically important parameter in food microbiology, and flow cytometry provides an innovative approach with high-throughput potential for applications in the food industry as "flow microbiology".

Sedimentation field-flow fractionation for rapid phenotypic antimicrobial susceptibility testing: a pilot study

BACKGROUND

The increase in antibiotic resistance is a major public health issue. The development of rapid antimicrobial susceptibility testing (AST) methods is becoming a priority to ensure early and appropriate antibiotic therapy.

OBJECTIVES

To evaluate sedimentation field-flow fractionation (SdFFF) as a method for performing AST in less than 3 h.

METHODS

SdFFF is based on the detection of early biophysical changes in bacteria, using a chromatographic-type technology. One hundred clinical Escherichia coli strains were studied. A calibrated bacterial suspension was incubated for 2 h at 37°C in the absence (untreated) or presence (treated) of five antibiotics used at EUCAST breakpoint concentrations. Bacterial suspensions were then injected into the SdFFF machine. For each E. coli isolate, retention times and elution profiles of antibiotic-treated bacteria were compared with retention times and elution profiles of untreated bacteria. Algorithms comparing retention times and elution profiles were used to determine if the strain was susceptible or resistant. Performance evaluation was done according to CLSI and the ISO standard 20776-2:2021 with broth microdilution used as the reference method.

RESULTS

AST results from SdFFF were obtained in less than 3 h. SdFFF showed high categorical agreement (99.8%), sensitivity (99.5%) and specificity (100.0%) with broth microdilution. Results for each antimicrobial were also in agreement with the ISO 20776-2 recommendations, with sensitivity and specificity of ≥95.0%.

CONCLUSIONS

This study showed that SdFFF can be used as a rapid, accurate and reliable phenotypic AST method with a turnaround time of less than 3 h.

A multisite validation of a two hours antibiotic susceptibility flow cytometry assay directly from positive blood cultures

BACKGROUND

Rapid antimicrobial susceptibility testing (AST) is urgently needed to provide safer treatment to counteract antimicrobial resistance. This is critical in septic patients, because resistance increases empiric therapy uncertainty and the risk of a poor outcome. We validate a novel 2h flow cytometry AST assay directly from positive blood cultures (PBC) by using a room temperature stable FASTgramneg and FASTgrampos kits (FASTinov® Porto, Portugal) in three sites: FASTinov (site-1), Hospital Ramon y Cajal, Madrid, Spain (site-2) and Centro Hospitalar S. João, Porto, Portugal (site-3). A total of 670 PBC were included: 333 spiked (site-1) and 337 clinical PBC (151 site-2 and 186 site-3): 367 gram-negative and 303 gram-positive. Manufacturer instructions were followed for sample preparation, panel inoculation, incubation (1h/37ºC) and flow cytometry analysis using CytoFlex (Site-1 and -2) or DxFlex (site-3) both instruments from Beckman-Coulter, USA.

RESULTS

A proprietary software (bioFAST) was used to immediately generate a susceptibility report in less than 2 h. In parallel, samples were processed according to reference AST methods (disk diffusion and/or microdilution) and interpreted with EUCAST and CLSI criteria. Additionally, ten samples were spiked in all sites for inter-laboratory reproducibility. Sensitivity and specificity were >95% for all antimicrobials. Reproducibility was 96.8%/95.0% for FASTgramneg and 95.1%/95.1% for FASTgrampos regarding EUCAST/CLSI criteria, respectively.

CONCLUSION

FASTinov® kits consistently provide ultra-rapid AST in 2h with high accuracy and reproducibility on both Gram-negative and Gram-positive bacteria. This technology creates a new paradigm in bacterial infection management and holds the potential to significantly impact septic patient outcomes and antimicrobial stewardship.

An improved protocol for bacteria identification by MALDI-TOF MS directly from positive blood cultures

FASTinov® developed a rapid antimicrobial susceptibility test that includes the purification of a bacterial suspension directly from positive blood cultures (BC). In order to streamline laboratory workflow, the use of the bacterial suspension obtained through FASTinov® sample prep was tested for identification (ID) by matrix absorption laser deionization-time of flight mass spectrometry (MALDI-TOF MS) (Bruker) in 364 positive BC, and its accuracy assessed comparing with the MALDI-TOF MS ID of the next-day subcultured colonies. FASTinov sample prep was highly reliable for rapid ID directly from BC with proportion of agreement of 94.9% for Gram-positive and 96.3% for Gram-negative bacteria.

Rapid, Ultrasensitive, and Visual Detection of Pathogens Based on Cation Dye-Triggered Gold Nanoparticle Electrokinetic Agglutination Analysis

Rapid prescribing of the right antibiotic is the key to treat infectious diseases and decelerate the challenge of bacterial antibiotic resistance. Herein, by targeting the 16S rRNA of bacteria, we developed a cation dye-triggered electrokinetic gold nanoparticle (AuNP) agglutination (CD-TEAA) method, which is rapid, visual, ultrasensitive, culture-independent, and low in cost. The limit of detection (LOD) is as low as 1 CFU mL-1 Escherichia coli. The infection identifications of aseptic fluid samples (n = 11) and urine samples with a clinically suspected urinary tract infection (UTI, n = 78) were accomplished within 50 and 30 min for each sample, respectively. The antimicrobial susceptibility testing (AST) of UTI urine samples was achieved within 2.5 h. In ROC analysis of urine, the sensitivity and specificity were 100 and 96% for infection identification, and 100 and 98% for AST, respectively. Moreover, the overall cost of materials for each test is about US$0.69. Therefore, the CD-TEAA method is a superior approach to existing, time-consuming, and expensive methods, especially in less developed areas.

Rapid antimicrobial resistance detection methods for bloodstream infection in solid organ transplantation: Proposed clinical guidance, unmet needs, and future directions

Recent advances in antimicrobial resistance detection have spurred the development of multiple assays that can accurately detect the presence of bacterial resistance from positive blood cultures, resulting in faster institution of effective antimicrobial therapy. Despite these advances, there are limited data regarding the use of these assays in solid organ transplant (SOT) recipients and there is little guidance on how to select, implement, and interpret them in clinical practice. We describe a practical approach to the implementation and interpretation of these assays in SOT recipients using the best available data and expert opinion. These findings were part of a consensus conference sponsored by the American Society of Transplantation held on December 7, 2021 and represent the collaboration between experts in transplant infectious diseases, pharmacy, antimicrobial and diagnostic stewardship, and clinical microbiology. Areas of unmet need and recommendations for future investigation are also presented.

What are the most relevant publications in Clinical Microbiology in the last two years?

This minireview describes some of the articles published in the last two years related to innovative technologies including CRISPR-Cas, surface-enhanced Raman spectroscopy, microfluidics, flow cytometry, Fourier transform infrared spectroscopy, and artificial intelligence and their application to microbiological diagnosis, molecular typing and antimicrobial susceptibility testing. In addition, some articles related to resistance to new antimicrobials (ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, and cefiderocol) are also described.

Current and Future Flow Cytometry Applications Contributing to Antimicrobial Resistance Control

Antimicrobial resistance is a global threat to human health and welfare, food safety, and environmental health. The rapid detection and quantification of antimicrobial resistance are important for both infectious disease control and public health threat assessment. Technologies such as flow cytometry can provide clinicians with the early information, they need for appropriate antibiotic treatment. At the same time, cytometry platforms facilitate the measurement of antibiotic-resistant bacteria in environments impacted by human activities, enabling assessment of their impact on watersheds and soils. This review focuses on the latest applications of flow cytometry for the detection of pathogens and antibiotic-resistant bacteria in both clinical and environmental samples. Novel antimicrobial susceptibility testing frameworks embedding flow cytometry assays can contribute to the implementation of global antimicrobial resistance surveillance systems that are needed for science-based decisions and actions.

Antimicrobial stewardship programs in the Intensive Care Unit in patients with infections caused by multidrug-resistant Gram-negative bacilli

Antimicrobial stewardship programs (ASPs) have been shown to be effective and safe, contributing to reducing and adjusting antimicrobial use in clinical practice. Such programs not only reduce antibiotic selection pressure and therefore the selection of multidrug-resistant strains, but also reduce the potential deleterious effects for individual patients and even improve the prognosis by adjusting the choice of drug and dosage, and lessening the risk of adverse effects and interactions. Gram-negative bacilli (GNB), particularly multidrug-resistant strains (MDR-GNB), represent the main infectious problem in the Intensive Care Unit (ICU), and are therefore a target for ASPs. The present review provides an update on the relationship between ASPs and MDR-GNB.

Rapid Antimicrobial Susceptibility Testing Based on a Bio-Inspired Chemiluminescence Sensor

Indiscriminate usage of antibiotics has caused accelerating growth and global expansion of antimicrobial resistance. Therefore, rapid antimicrobial susceptibility testing (AST) for guiding antibiotic prescription and preventing the spread of antimicrobial resistance is in urgent need. Phenotypic AST is the clinical gold standard method; however, no phenotypic AST has realized a colony-to-answer at about 1 h by utilizing the chemiluminescence sensor to detect the enzyme expressed by bacteria. Inspired by the bubble formation in the mixture of Escherichia coli and H₂O₂, we demonstrate a strategy based on the chemiluminescence sensor for rapid AST. Compared with the gold standard methods, the values of AUC are 0.960 for E. coli and 0.950 for Staphylococcus aureus, close to 1, indicating superb diagnostic performance as an AST method. The whole process from colonies to answer is 55 min for E. coli and 70 min for S. aureus. The chemiluminescence readout is based on the common equipment in the laboratory of the hospital, which is conducive to follow-up clinical promotion. Our sensor promises great potential in rapid AST, facilitating antimicrobial stewardship.

Bioinspired Plasmonic Nanosensor for on-Site Antimicrobial Susceptibility Testing in Urine Samples

Delayed use of appropriate antibiotics for superbugs, particularly for extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pn), has caused extensive morbidity and mortality worldwide. Therefore, rapid and on-site antimicrobial susceptibility testing (AST) is urgently required. Unfortunately, currently, no phenotypic AST can realize a sample-to-answer result within 2 h directly from a clinical sample and without using laboratory equipment or customized devices. Inspired by observing that E. coli and K. pn can rapidly catalyze H₂O₂, we developed a plasmonic nanosensor that responds to the proliferation of bacteria for realizing rapid AST. The results can be determined with the naked eye, digitized using a smartphone, and validated using ultraviolet-visible spectrometry. Our assay achieved superb area under the curves of 0.9752 and 1 in a receiver operating characteristic analysis directly obtained from uncultured clinical urine samples infected by E. coli and K. pn, respectively. The entire process from sample collection to analysis takes 100 min for E. coli and 85 min for K. pn detection. Our platform provides a practical approach for performing on-site AST in clinics to improve the survival of patients. It releases the burden of superbugs and avoids the abuse of antibiotics.

Rapid Detection of Plasmid AmpC Beta-Lactamases by a Flow Cytometry Assay

Plasmidic AmpC (pAmpC) enzymes are responsible for the hydrolysis of extended-spectrum cephalosporins but they are not routinely investigated in many clinical laboratories. Phenotypic assays, currently the reference methods, are cumbersome and culture dependent. These methods compare the activity of cephalosporins with and without class C inhibitors and the results are provided in 24–48 h. Detection by molecular methods is quicker, but several genes should be investigated. A new assay for the rapid phenotypic detection of pAmpC enzymes of the Enterobacterales group-I (not usually AmpC producers) based on flow cytometry technology was developed and validated. The technology was evaluated in two sites: FASTinov, a spin-off of Porto University (Portugal) where the technology was developed, and the Microbiology Department of Ramón y Cajal University Hospital in Madrid (Spain). A total of 100 strains were phenotypically screened by disk diffusion for the pAmpC with the new 2 h assay. Molecular detection of the pAmpC genes was also performed on discrepant results. Forty-two percent of the strains were phenotypically classified as pAmpC producers using disk diffusion. The percentage of agreement of the flow cytometric assay was 93.0%, with 95.5% sensitivity and 91.1% specificity. Our proposed rapid assay based on flow cytometry technology can, in two hours, accurately detect pAmpC enzymes.

Real Life Clinical Impact of Antimicrobial Stewardship Actions on the Blood Culture Workflow from a Microbiology Laboratory

BACKGROUND

Accelerating the diagnosis of bacteremia is one of the biggest challenges in clinical microbiology departments. The fast establishment of a correct treatment is determinant on bacteremic patients' outcomes. Our objective was to evaluate the impact of antimicrobial therapy and clinical outcomes of a rapid blood culture workflow protocol in positive blood cultures with Gram-negative bacilli (GNB).

METHODS

A quasi-experimental before-after study was performed with two groups: (i) control group (conventional work-protocol) and (ii) intervention group (rapid workflow-protocol: rapid identification by Matrix-Assisted Laser Desorption/Ionization-Time-Of-Flight (MALDI-TOF) and antimicrobial susceptibility testing (AST) from bacterial pellet without overnight incubation). Patients were divided into different categories according to the type of intervention over treatment. Outcomes were compared between both groups.

RESULTS

A total of 313 patients with GNB-bacteremia were included: 125 patients in the control group and 188 in the intervention. The time from positive blood culture to intervention on antibiotic treatment decreased from 2.0 days in the control group to 1.0 in the intervention group (p < 0.001). On the maintenance of correct empirical treatment, the control group reported 2.0 median days until the clinical decision, while in the intervention group was 1.0 (p < 0.001). In the case of treatment de-escalation, a significant difference between both groups (4.0 vs. 2.0, p < 0.001) was found. A decreasing trend on the change from inappropriate treatments to appropriate ones was observed: 3.5 vs. 1.5; p = 0.12. No significant differences were found between both groups on 7-days mortality or on readmissions in the first 30-days.

CONCLUSIONS

Routine implementation of a rapid workflow protocol anticipates the report of antimicrobial susceptibility testing results in patients with GNB-bacteremia, decreasing the time to effective and optimal antibiotic therapy.