Misidentification and misreporting of antibiotic resistance in Kluyvera bacteremia by blood culture molecular identification panels

The use of molecular identification panels has advanced the diagnosis for blood stream infections with fast turnaround time and high accuracy. Yet, this technology cannot completely replace conventional blood culture and standardized antibiotic susceptibility testing (AST) given its limitations and occasional false results. Here we present two cases of bacteremia caused by Kluyvera. Its identification and antibiotic resistance were at least partially mispresented by blood culture molecular identification panels on ePlex, Verigene, and Biofire. The detection of CTX-M resistance marker did not align with the susceptibility to the third generation cephalosporins among a wide range of antibiotics for this organism. Conventional extended-spectrum beta-lactamase (ESBL) testing was used to confirm the absence of ESBL. Caution should be taken when managing cases with CTX-M or ESBL detection in blood culture caused by uncommon pathogens. Conventional culture with microbial identification and standardized AST should continue to be the gold standard for routine patient care.

IMPORTANCE

This is the first report that highlights the limitations of blood culture molecular identification panels on identifying Kluyvera and its associated antibiotic resistance patterns. Both the false identification and overreporting of antibiotic resistance could mislead the treatment for bacteremia caused by this pathogen. Patient isolation could have been avoided due to the lack of extended-spectrum beta-lactamase (ESBL) activity of the organism. This report emphasizes the importance of confirming rapid identification and antibiotic resistance by molecular technologies with standardized methods. It also provides insight into the development of new diagnostic panels.

Rapid Nucleic Acid Diagnostic Technology for Pandemic Diseases

The recent global pandemic of coronavirus disease 2019 (COVID-19) has enormously promoted the development of diagnostic technology. To control the spread of pandemic diseases and achieve rapid screening of the population, ensuring that patients receive timely treatment, rapid diagnosis has become the top priority in the development of clinical technology. This review article aims to summarize the current rapid nucleic acid diagnostic technologies applied to pandemic disease diagnosis, from rapid extraction and rapid amplification to rapid detection. We also discuss future prospects in the development of rapid nucleic acid diagnostic technologies.

Laboratory evaluation of a rapid diagnostic test for dairy mastitis

Rapid diagnostic tests that differentiate between Gram positive, Gram negative and the absence of aerobic bacteria in milk samples from dairy cows with clinical mastitis can support antimicrobial treatment decisions and contribute to a more prudent use of antimicrobials in the dairy industry. The objective of this study was to evaluate the test characteristics of the novel rapid BACT mastitis test in discriminating causes of clinical mastitis under laboratory conditions. Test outcomes of 155 milk samples from clinical mastitis cases were incubated for 14-16 h in the BACT test and compared to results of bacteriological culture. The accuracy for detection of bacterial growth and Gram positive growth was 91 and 89%, respectively. The BACT test could provide an accurate and relatively fast decision tool for farmers to aid in antimicrobial treatment decisions in cases of clinical mastitis.

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.

Rapid Detection of Ceftazidime/Avibactam Susceptibility/Resistance in Enterobacterales by Rapid CAZ/AVI NP Test

We developed a novel culture-based test, the Rapid CAZ/AVI NP test, for rapid identification of ceftazidime/avibactam susceptibility/resistance in Enterobacterales. This test is based on glucose metabolization upon bacterial growth in the presence of a defined concentration of ceftazidime/avibactam (128/53 μg/mL). Bacterial growth is visually detectable by a red to yellow color change of red phenol, a pH indicator. A total of 101 well characterized enterobacterial isolates were used to evaluate the test performance. This test showed positive percent agreement of 100% and negative percent agreement of 98.5% with overall percent agreement of 99%, by comparison with the MIC gradient strip test (Etest) taken as the reference standard method. The Rapid CAZ/AVI NP test had only 1.5% major errors and 0% extremely major errors. This test is rapid (result within 2 hours 45 minutes), reliable, affordable, easily interpretable, and easy to implement in clinical microbiology laboratories without requiring any specific equipment.

Comparative analysis of a rapid diagnostic test and scoring tools for ESBL detection in Enterobacterales bloodstream infections for optimizing antimicrobial therapy

IMPORTANCE

Our study addresses a significant issue in the medical and scientific community-the delayed administration of appropriate antimicrobial treatments due to the time-consuming process of phenotypic susceptibility data collection in gram-negative bloodstream infections. Our research indicates that a multiplex PCR rapid diagnostic test (RDT) significantly outperformed two clinical scoring tools in predicting ceftriaxone susceptibility. Multiplex PCR also led to reduced instances of undertreatment with ceftriaxone and minimized overtreatment with carbapenems. Furthermore, multiplex PCR demonstrated high sensitivity and specificity in predicting ceftriaxone susceptibility. The results of our study underscore the potential RDTs to reduce the time to appropriate antimicrobial therapy, leading to improved patient outcomes and reduced healthcare costs.

Evaluation of the diagnostic utility of metagenomic next-generation sequencing testing for pathogen identification in infected hosts: a retrospective cohort study

Background

Metagenomic next-generation sequencing (mNGS) testing identifies thousands of potential pathogens in a single blood test, though data on its real-world diagnostic utility are lacking.

Objectives

Determine the diagnostic utility of mNGS testing in practice and factors associated with high clinical utility.

Design

Retrospective cohort study of mNGS tests ordered from June 2018 through May 2020 at a community teaching hospital.

Methods

Tests were included if ordered for diagnostic purposes in patients with probable or high clinical suspicion of infection. Exclusions included patient expiration, hospice care, or transfer outside of the institution. Utility criteria were established a priori by the research team. Two investigators independently reviewed each test and categorized it to either high or low diagnostic utility. Reviewer discordance was referred to a third investigator. The stepwise multiple regression method was used to identify clinical factors associated with high diagnostic utility.

Results

Among 96 individual tests from 82 unique patients, 80 tests met the inclusion criteria for analysis. At least one potential pathogen was identified in 58% of tests. Among 112 pathogens identified, there were 74 bacteria, 25 viruses, 12 fungi, and 1 protozoon. In all, 46 tests (57.5%) were determined to be of high diagnostic utility. Positive mNGS tests were identified in 36 (78.3%) and 11 (32.4%) of high and low diagnostic utility tests, respectively (p < 0.001). Antimicrobials were changed after receiving test results in 31 (67.4%) of high utility tests and 4 (11.8%) of low utility tests (p < 0.0001). In the multiple regression model, a positive test [odds ratio (OR) = 10.9; 95% confidence interval (CI), 3.2-44.4] and consultation with the company medical director (OR = 3.6; 95% CI, 1.1-13.7) remained significantly associated with high diagnostic utility.

Conclusion

mNGS testing resulted in high clinical utility in most cases. Positive mNGS tests were associated with high diagnostic utility. Consultation with the Karius® medical director is recommended to maximize utility.

The diagnostic accuracy of the GeneXpert ESBL-ampC prototype assay for rapid PCR-based detection of extended-spectrum beta-lactamase genes directly from urine

IMPORTANCE

Early identification of complicated urinary tract infections caused by ESBL-producing Enterobacterales has the potential to limit the use of carbapenems to those patients without alternative antibiotic options and avoid the empirical use of carbapenems in patients without ESBL-producing bacteria. The purpose for such a test will differ by setting and ESBL prevalence rates. Countries with low ESBL rates and cephalosporins as empiric treatment (e.g., The Netherlands) will need a rule-in test to decide to use carbapenems, while countries with high ESBL rates and empiric carbapenem treatment will need a rule-out test for ESBLs to de-escalate therapy early. Anyway, such as a test would-at least theoretically-improve patient care and reduce selective pressure for the emergence of carbapenem resistance.

Utilization of an immunochromatographic lateral flow assay for rapid detection of carbapenemase production in gram negative bacilli

BACKGROUND

Rapid detection of carbapenemase production in gram negative bacilli has important treatment considerations.

OBJECTIVE

We evaluated a lateral flow assay (LFA) for carbapenemase production compared with molecular detection of 5 (blaKPC, blaNDM, blaVIM, blaIMP, and blaOXA-48) carbapenemase genes.

METHODS

A total of 218 carbapenem nonsusceptible strains, including species of Enterobacterales, Pseudomonas aeruginosa isolated from clinical cultures were tested using the Cepheid Xpert Carba-R assay and the NG Biotech Carba-5 lateral flow immunoassay.

RESULTS

Overall agreement with LFA was 98.2% with accuracy for each target >99% compared with polymerase chain reaction. Results were available within 15 minutes compared with 1 hour for molecular detection.

CONCLUSION

The use of accurate, rapid diagnostics compliments antimicrobial stewardship programs.

Corrigendum: VIDIIA Hunter: a low-cost, smartphone connected, artificial intelligence-assisted COVID-19 rapid diagnostic platform approved for medical use in the UK

[This corrects the article DOI: 10.3389/fmolb.2023.1144001.].

Disposable Device for Bacterial Vaginosis Detection

Due to the increasing demand for clinical testing of infectious diseases at the point-of-care, the global market claims alternatives for rapid diagnosis tools such as disposable biosensors, avoiding the need for specialized laboratories and skilled personnel. Bacterial vaginosis (BV) is an infectious disease that commonly affects reproductive-age women and predisposes the infection of sexually transmitted diseases. Especially in asymptomatic cases, BV can lead to pelvic inflammatory conditions, postpartum endometritis, and preterm labor. Conventionally, BV diagnosis involves the microscopic analysis of vaginal swab samples; it thus requires highly trained personnel. In response, we report a novel microfluidic paper-based analytical device for BV diagnosis. Sialidase, a biomarker overexpressed in BV, was detected by exploiting an immunosensing mechanism previously discovered by our team. This technology employs a graphene oxide-coated surface as a quencher of fluorescence; the fluorescence of the immunoprobes that do not experiment immunoreactions (antibody-antigen) are deactivated by graphene oxide via non-radiative energy transfer, whereas those immunoprobes undergoing immunoreactions preserve their photoluminescence due to the distance and the low affinity between the immunocomplex and the graphene oxide-coated surface. Our paper-based test was typically carried out within 20 min, and the sample volume was 6 μL. Besides, it was tested with 14 vaginal swabs specimens to discriminate clinical samples of women with normal microbiota from those with BV. Our disposable device represents a new tool to prevent the consequences of BV.

Customized molecular diagnostics of bacterial bloodstream infections for carbapenem resistance: A convenient and affordable approach

The acute crisis of carbapenem resistance impedes the empirical use of carbapenems in medical emergencies, especially, bloodstream infections. Carbapenemase-producing carbapenem-resistant organisms (CP-CROs) attribute high case-fatality, necessitating rapid diagnostics to initiate early targeted antibiotics. Expensive diagnostics are the major driver of antibiotic misuse, neglecting evidence-based treatment in India. One in-house molecular diagnostics assay was customized for rapid detection of CP-CROs using positive blood-culture (BC) broths at a low-cost. The assay was validated using a known-set of isolates and evaluated on positive BC broths. DNA was extracted from positive BC broths using a modified alkali-wash/heat-lysis method. One end-point multiplex-PCR was customized targeting five carbapenemases (KPC, NDM, VIM, OXA-48-, and OXA-23-type) with 16S-rDNA as internal extraction control. Carbapenem resistance due to other carbapenemases, efflux-pump activity, and loss of porins was not under the scope of the assay. Promising analytical performances (sensitivity and specificity, >90%; kappa = 0.87), encouraged to assess diagnostic value, qualified the assay for the WHO minimal requirements (both≥95%) for a multiplex-PCR. Higher LR+ (>10) and lower LR- (<0.1) indicate a good diagnostic tool for ruling in or ruling out CRO bloodstream infections. Inclusion of OXA-23-type improved assay positivity. Multiple carbapenemases were detected in>30% of samples. Good concordance was found (kappa = 0.91) with twenty-six discrepant results. The results were available in 3 hours. The running cost of the assay was US$10 per sample. Fast and reliable detection of carbapenemase(s) allows clinicians and infection-control practitioners to execute early-directed therapy and containment measures. This convenient approach facilitates implementing the assay in resource-limited healthcare settings.

VIDIIA Hunter diagnostic platform: a low-cost, smartphone connected, artificial intelligence-assisted COVID-19 rapid diagnostics approved for medical use in the UK

Introduction: Accurate and rapid diagnostics paired with effective tracking and tracing systems are key to halting the spread of infectious diseases, limiting the emergence of new variants and to monitor vaccine efficacy. The current gold standard test (RT-qPCR) for COVID-19 is highly accurate and sensitive, but is time-consuming, and requires expensive specialised, lab-based equipment. Methods: Herein, we report on the development of a SARS-CoV-2 (COVID-19) rapid and inexpensive diagnostic platform that relies on a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay and a portable smart diagnostic device. Automated image acquisition and an Artificial Intelligence (AI) deep learning model embedded in the Virus Hunter 6 (VH6) device allow to remove any subjectivity in the interpretation of results. The VH6 device is also linked to a smartphone companion application that registers patients for swab collection and manages the entire process, thus ensuring tests are traced and data securely stored. Results: Our designed AI-implemented diagnostic platform recognises the nucleocapsid protein gene of SARS-CoV-2 with high analytical sensitivity and specificity. A total of 752 NHS patient samples, 367 confirmed positives for coronavirus disease (COVID-19) and 385 negatives, were used for the development and validation of the test and the AI-assisted platform. The smart diagnostic platform was then used to test 150 positive clinical samples covering a dynamic range of clinically meaningful viral loads and 250 negative samples. When compared to RT-qPCR, our AI-assisted diagnostics platform was shown to be reliable, highly specific (100%) and sensitive (98-100% depending on viral load) with a limit of detection of 1.4 copies of RNA per µL in 30 min. Using this data, our CE-IVD and MHRA approved test and associated diagnostic platform has been approved for medical use in the United Kingdom under the UK Health Security Agency's Medical Devices (Coronavirus Test Device Approvals, CTDA) Regulations 2022. Laboratory and in-silico data presented here also indicates that the VIDIIA diagnostic platform is able to detect the main variants of concern in the United Kingdom (September 2023). Discussion: This system could provide an efficient, time and cost-effective platform to diagnose SARS-CoV-2 and other infectious diseases in resource-limited settings.

Evaluation of NG-Test CARBA 5 version 2, Cepheid Xpert Carba-R, and carbapenem inactivation methods in comparison to whole-genome sequencing for the identification of carbapenemases in non-fermenting Gram-negative bacilli

NG-Test CARBA 5 (NG-Biotech) is a rapid in vitro multiplex immunoassay for the phenotypic detection and differentiation of the "big five" carbapenemase families (KPC, OXA-48-like, VIM, IMP, and NDM). Version 2 of this assay was evaluated alongside the Xpert Carba-R assay (Cepheid, Inc.), the modified carbapenem inactivation method (mCIM), and the CIMTris assay, with a collection of carbapenem-resistant non-fermenting Gram-negative bacilli comprising 138 Pseudomonas aeruginosa and 97 Acinetobacter baumannii isolates. Whole-genome sequencing (WGS) was used as the reference standard. For P. aeruginosa, NG-Test CARBA 5 produced an overall percentage agreement (OPA) with WGS of 97.1%, compared with 92.8% forXpert Carba-R and 90.6% for mCIM. For A. baumannii, as OXA-type carbapenemases (non-OXA-48) are not included, both the NG-Test CARBA 5 and Xpert Carba-R only had an OPA of 6.2%, while the CIMTris performed well with an OPA of 99.0%. The majority of A. baumannii isolates (95.9%) tested falsely positive for IMP on NG-Test CARBA 5; no IMP genes were found on WGS. No clear cause was found for this phenomenon; a cross-reacting protein antigen unique to A. baumannii is a possible culprit. NG-Test CARBA 5 performed well for carbapenemase detection in P. aeruginosa. However, results from A. baumannii isolates should be interpreted with caution.

COVID severity test (CoST sensor)-An electrochemical immunosensing approach to stratify disease severity

With the evolution of the COVID-19 pandemic, there is now a need for point-of-care devices for the quantification of disease biomarkers toward disease severity assessment. Disease progression has been determined as a multifactor phenomenon and can be treated based on the host immune response within each individual. CoST is an electrochemical immunosensor point-of-care device that can determine disease severity through multiplex measurement and quantification of spike protein, nucleocapsid protein, D-dimer, and IL-2R from 100 μL of plasma samples within a few minutes. The limit of detection was found to be 3 ng/mL and 21 ng/mL for S and N proteins whereas for D-dimer and IL-2R it was 0.0006 ng/mL and 0.242 ng/mL, respectively. Cross-reactivity of all the biomarkers was studied and it was found to be <20%. Inter and intra-assay variability of the CoST sensor was less than <15% confirming its ability to detect the target biomarker in body fluids. In addition, this platform has also been tested to quantify all four biomarkers in 40 patient samples and to predict the severity index. A significant difference was observed between healthy and COVID-19 samples with a p-value of 0.0002 for D-dimer and <0.0001 for other proteins confirming the ability of the COST sensor to be used as a point of care device to assess disease severity at clinical sites. This device platform can be modified to impact a wide range of disease indications where prognostic monitoring of the host response can be critical in modulating therapy.

The Effect of Rapid Point-of-Care Respiratory Pathogen Testing on Antibiotic Prescriptions in Acute Infections-A Systematic Review and Meta-analysis of Randomized Controlled Trials

Background

Rapid point-of-care testing for respiratory pathogens has gained increasing popularity, but its impact on antibiotic consumption is unclear. Thus, the aim of this systematic review and meta-analysis was to estimate the effect of rapid point-of-care testing on antibiotic prescriptions.

Methods

The search for this systematic review with meta-analysis was performed in February 2023. Randomized controlled trials investigating the impact of testing for respiratory pathogens in all-aged patients were included regardless of the comparator. The main outcome was the antibiotic prescription rate. Analyses were stratified by test type, test setting, and patient age. A random-effects Mantel-Haenszel model was used to calculate risk ratios with 95% confidence intervals. Risk of bias was assessed for included studies, and the quality of the evidence was rated according to GRADE.

Results

A total of 754 abstracts were screened, and 10 studies were included in the analysis. Risk of bias was high in 2, low in 4, and had some concerns in 4 studies. Four studies analyzed influenza and respiratory syncytial virus tests, and 6 studies analyzed multiplex (viral and/or bacterial) testing. The prescription rate was 48.2% (496/1029) in the influenza and respiratory syncytial virus test group and 48.7% (540/1109) in the control group (risk ratio [RR], 0.97; 95% CI, 0.92-1.02; moderate-quality evidence). The prescription rate in the multiplex testing group was 54.3% (1554/2859), and it was 57.3% (1336/2326) in the control group (RR, 1.00; 95% CI, 0.96-1.04; moderate-quality evidence). In an age-stratified analysis, the prescription rates showed no evidence of a difference (children: RR, 1.03; 95% CI, 0.81-1.30; adults: RR, 0.98; 95% CI, 0.96-1.01; very low- and moderate-quality evidence).

Conclusions

We found moderate-quality evidence that rapid point-of-care testing for respiratory pathogens does not decrease the antibiotic prescription rate.

Impact of Rapid Identification and Stewardship Intervention on Coagulase-Negative Staphylococcus Bloodstream Infection

We investigated the impact of rapid diagnostic testing with and without algorithm-based stewardship recommendations on antibiotic use for bloodstream infection with coagulase-negative staphylococci. A significant reduction in antibiotic days of therapy was achieved in the stewardship intervention group that was not seen with rapid diagnostic testing alone.

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.

Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections

Antimicrobial resistance is a major threat to human and animal health. There is an urgent need to ensure that antimicrobials are used appropriately to limit the emergence and impact of resistance. In the human and veterinary healthcare setting, traditional culture and antimicrobial sensitivity testing typically requires 48-72 h to identify appropriate antibiotics for treatment. In the meantime, broad-spectrum antimicrobials are often used, which may be ineffective or impact non-target commensal bacteria. Here, we present a rapid, culture-free, diagnostics pipeline, involving metagenomic nanopore sequencing directly from clinical urine and skin samples of dogs. We have planned this pipeline to be versatile and easily implementable in a clinical setting, with the potential for future adaptation to different sample types and animals. Using our approach, we can identify the bacterial pathogen present within 5 h, in some cases detecting species which are difficult to culture. For urine samples, we can predict antibiotic sensitivity with up to 95 % accuracy. Skin swabs usually have lower bacterial abundance and higher host DNA, confounding antibiotic sensitivity prediction; an additional host depletion step will likely be required during the processing of these, and other types of samples with high levels of host cell contamination. In summary, our pipeline represents an important step towards the design of individually tailored veterinary treatment plans on the same day as presentation, facilitating the effective use of antibiotics and promoting better antimicrobial stewardship.

Diagnosis of Multisystem Inflammatory Syndrome in Children by a Whole-Blood Transcriptional Signature

BACKGROUND

To identify a diagnostic blood transcriptomic signature that distinguishes multisystem inflammatory syndrome in children (MIS-C) from Kawasaki disease (KD), bacterial infections, and viral infections.

METHODS

Children presenting with MIS-C to participating hospitals in the United Kingdom and the European Union between April 2020 and April 2021 were prospectively recruited. Whole-blood RNA Sequencing was performed, contrasting the transcriptomes of children with MIS-C (n = 38) to those from children with KD (n = 136), definite bacterial (DB; n = 188) and viral infections (DV; n = 138). Genes significantly differentially expressed (SDE) between MIS-C and comparator groups were identified. Feature selection was used to identify genes that optimally distinguish MIS-C from other diseases, which were subsequently translated into RT-qPCR assays and evaluated in an independent validation set comprising MIS-C (n = 37), KD (n = 19), DB (n = 56), DV (n = 43), and COVID-19 (n = 39).

RESULTS

In the discovery set, 5696 genes were SDE between MIS-C and combined comparator disease groups. Five genes were identified as potential MIS-C diagnostic biomarkers (HSPBAP1, VPS37C, TGFB1, MX2, and TRBV11-2), achieving an AUC of 96.8% (95% CI: 94.6%-98.9%) in the discovery set, and were translated into RT-qPCR assays. The RT-qPCR 5-gene signature achieved an AUC of 93.2% (95% CI: 88.3%-97.7%) in the independent validation set when distinguishing MIS-C from KD, DB, and DV.

CONCLUSIONS

MIS-C can be distinguished from KD, DB, and DV groups using a 5-gene blood RNA expression signature. The small number of genes in the signature and good performance in both discovery and validation sets should enable the development of a diagnostic test for MIS-C.

Rapid Diagnostics of Joint Infections Using IS-Pro

Diagnosis of bone and joint infections (BJI) relies on microbiological culture which has a long turnaround time and is challenging for certain bacterial species. Rapid molecular methods may alleviate these obstacles. Here, we investigate the diagnostic performance of IS-pro, a broad-scope molecular technique that can detect and identify most bacteria to the species level. IS-pro additionally informs on the amount of human DNA present in a sample, as a measure of leukocyte levels. This test can be performed in 4 h with standard laboratory equipment. Residual material of 591 synovial fluid samples derived from native and prosthetic joints from patients suspected of joint infections that were sent for routine diagnostics was collected and subjected to the IS-pro test. Bacterial species identification as well as bacterial load and human DNA load outcomes of IS-pro were compared to those of culture. At sample level, percent positive agreement (PPA) between IS-pro and culture was 90.6% (95% CI 85.7- to 94%) and negative percent agreement (NPA) was 87.7% (95% CI 84.1 to 90.6%). At species level PPA was 80% (95% CI 74.3 to 84.7%). IS-pro yielded 83 extra bacterial detections over culture for which we found supporting evidence for true positivity in 40% of the extra detections. Missed detections by IS-pro were mostly related to common skin species in low abundance. Bacterial and human DNA signals measured by IS-pro were comparable to bacterial loads and leukocyte counts reported by routine diagnostics. We conclude that IS-pro showed an excellent performance for fast diagnostics of bacterial BJI.

Multicenter Evaluation of the BIOFIRE Blood Culture Identification 2 Panel for Detection of Bacteria, Yeasts, and Antimicrobial Resistance Genes in Positive Blood Culture Samples

Diagnostic tools that can rapidly identify and characterize microbes growing in blood cultures are important components of clinical microbiology practice because they help to provide timely information that can be used to optimize patient management. This publication describes the bioMérieux BIOFIRE Blood Culture Identification 2 (BCID2) Panel clinical study that was submitted to the U.S. Food & Drug Administration. Results obtained with the BIOFIRE BCID2 Panel were compared to standard-of-care (SoC) results, sequencing results, PCR results, and reference laboratory antimicrobial susceptibility testing results to evaluate the accuracy of its performance. Results for 1,093 retrospectively and prospectively collected positive blood culture samples were initially enrolled, and 1,074 samples met the study criteria and were included in the final analyses. The BIOFIRE BCID2 Panel demonstrated an overall sensitivity of 98.9% (1,712/1,731) and an overall specificity of 99.6% (33,592/33,711) for Gram-positive bacteria, Gram-negative bacteria and yeast targets which the panel is designed to detect. One hundred eighteen off-panel organisms, which the BIOFIRE BCID2 Panel is not designed to detect, were identified by SoC in 10.6% (114/1,074) of samples. The BIOFIRE BCID2 Panel also demonstrated an overall positive percent agreement (PPA) of 97.9% (325/332) and an overall negative percent agreement (NPA) of 99.9% (2,465/2,767) for antimicrobial resistance determinants which the panel is designed to detect. The presence or absence of resistance markers in Enterobacterales correlated closely with phenotypic susceptibility and resistance. We conclude that the BIOFIRE BCID2 Panel produced accurate results in this clinical trial.

Antiviral Prescribing Among Patients at an Ambulatory Cancer Center With Laboratory-Confirmed Influenza

Among 133 cancer outpatients diagnosed with influenza between 2016 and 2018, 110 (83%) were prescribed oseltamivir. Among 109 with a known symptom onset date, 53% presented for care and 31% were prescribed oseltamivir within 48 hours. Patient/provider education and rapid diagnostics are needed to improve early oseltamivir use among cancer patients with influenza.

Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics-Current State and Whole Genome Sequencing Implementation Perspectives

Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic).

Evaluation of the ID NOW among symptomatic individuals during the Omicron wave

Introduction. Starting in December, 2020, the ID NOW was implemented throughout the province of Alberta, Canada (population 4.4 million) in various settings.Gap statement. ID NOW's test performance with SARS-CoV-2 Omicron variant BA.1 is unknown.Aim. To assess the ID NOW performance among symptomatic individuals during the BA.1 Omicron wave and compare it to previous SARS-CoV-2 variant waves.Methodology. The ID NOW was assessed in two locations among symptomatic individuals: rural hospitals and community assessment centres (AC) during the period 5-18 January 2022. Starting 5 January, Omicron represented >95 % of variants detected in our population. For every individual tested, two swabs were collected: one for ID NOW testing and the other for either reverse-transcriptase polymerase chain reaction (RT-PCR) confirmation of negative ID NOW results or for variant testing of positive ID NOW results.Results. A total of 3041 paired samples were analysed (1139 RT-PCR positive). From this, 1873 samples were from 42 COVID-19 AC and 1168 from 69 rural hospitals. ID NOW sensitivity for symptomatic individuals presenting to community AC and rural hospitals was 96.0 % [95 % confidence interval (CI) 94.5-97.3 %, n=830 RT-PCR positive], and 91.6 % (95 % CI 87.9-94.4 %, n=309 RT-PCR positive), respectively. SARS-CoV-2 positivity rate was very high for both populations (44.3 % at AC, 26.5 % in hospital).Conclusions. Sensitivity of ID NOW SARS-CoV-2, compared to RT-PCR, is very high during the BA.1 Omicron wave, and is significantly higher when compared to previous SARS-CoV-2 variant waves.

Molecular Rapid Diagnostics Improve Time to Effective Therapy and Survival in Patients with Vancomycin-Resistant Enterococcus Bloodstream Infections

Delays in appropriate antibiotic therapy are a key determinant for deleterious outcomes among patients with vancomycin-resistant Enterococcus (VRE) bloodstream infections (BSIs). This was a multi-center pre/post-implementation study, assessing the impact of a molecular rapid diagnostic test (Verigene® GP-BC, Luminex Corporation, Northbrook, IL, USA) on outcomes of adult patients with VRE BSIs. The primary outcome was time to optimal therapy (TOT). Multivariable logistic and Cox proportional hazard regression models were used to determine the independent associations of post-implementation, TOT, early vs. delayed therapy, and mortality. A total of 104 patients with VRE BSIs were included: 50 and 54 in the pre- and post-implementation periods, respectively. The post- vs. pre-implementation group was associated with a 1.8-fold faster rate to optimized therapy (adjusted risk ratio, 1.841 [95% CI 1.234-2.746]), 6-fold higher likelihood to receive early effective therapy (<24 h, adjusted odds ratio, 6.031 [2.526-14.401]), and a 67% lower hazards for 30-day in-hospital mortality (adjusted hazard ratio, 0.322 [0.124-1.831]), after adjusting for age, sex, and severity scores. Inversely, delayed therapy was associated with a 10-fold higher risk of in-hospital mortality (aOR 10.488, [2.497-44.050]). Reduced TOT and in-hospital mortality were also observed in subgroups of immunosuppressed patients in post-implementation. These findings demonstrate that the addition of molecular rapid diagnostic tests (mRDT) to clinical microbiology and antimicrobial stewardship practices are associated with a clinically significant reduction in TOT, which is associated with lower mortality for patients with VRE BSIs, underscoring the importance of mRDTs in the management of VRE infections.

Impact of a Rapid Molecular Test for Klebsiella pneumoniae Carbapenemase and Ceftazidime-Avibactam Use on Outcomes After Bacteremia Caused by Carbapenem-Resistant Enterobacterales

BACKGROUND

Patients with bacteremia due to carbapenem-resistant Enterobacterales (CRE) experience delays until appropriate therapy and high mortality rates. Rapid molecular diagnostics for carbapenemases and new β-lactam/β-lactamase inhibitors may improve outcomes.

METHODS

We conducted an observational study of patients with CRE bacteremia from 2016 to 2018 at 8 New York and New Jersey medical centers and assessed center-specific clinical microbiology practices. We compared time to receipt of active antimicrobial therapy and mortality between patients whose positive blood cultures underwent rapid molecular testing for the Klebsiella pneumoniae carbapenemase (KPC) gene (blaKPC) and patients whose cultures did not undergo this test. CRE isolates underwent antimicrobial susceptibility testing by broth microdilution and carbapenemase profiling by whole-genome sequencing. We also assessed outcomes when ceftazidime-avibactam and polymyxins were used as targeted therapies.

RESULTS

Of 137 patients with CRE bacteremia, 89 (65%) had a KPC-producing organism. Patients whose blood cultures underwent blaKPC PCR testing (n = 51) had shorter time until receipt of active therapy (median: 24 vs 50 hours; P = .009) compared with other patients (n = 86) and decreased 14-day (16% vs 37%; P = .007) and 30-day (24% vs 47%; P = .007) mortality. blaKPC PCR testing was associated with decreased 30-day mortality (adjusted odds ratio: .37; 95% CI: .16-.84) in an adjusted model. The 30-day mortality rate was 10% with ceftazidime-avibactam monotherapy and 31% with polymyxin monotherapy (P = .08).

CONCLUSIONS

In a KPC-endemic area, blaKPC PCR testing of positive blood cultures was associated with decreased time until appropriate therapy and decreased mortality for CRE bacteremia, and ceftazidime-avibactam is a reasonable first-line therapy for these infections.

Rapid and Simple Approaches for Diagnosis of Staphylococcus aureus in Bloodstream Infections

Staphylococcus aureus is an important causative pathogen of bloodstream infections. An amplification assay such as real-time PCR is a sensitive, specific technique to detect S. aureus. However, it needs well-trained personnel, and costs are high. A literature review focusing on rapid and simple methods for diagnosing S. aureus was performed. The following methods were included: (a) Hybrisep in situ hybridization test, (b) T2Dx system, (c) BinaxNow Staphylococcus aureus and PBP2a, (d) Gram staining, (e) PNA FISH and QuickFISH, (f) Accelerate Pheno^TM system, (g) MALDI-TOF MS, (h) BioFire FilmArray, (i) Xpert MRSA/SA. These rapid and simple methods can rapidly identify S. aureus in positive blood cultures or direct blood samples. Furthermore, BioFire FilmArray and Xpert MRSA/SA identify methicillin-resistant S. aureus (MRSA), and the Accelerate Pheno^TM system can also provide antimicrobial susceptibility testing (AST) results. The rapidity and simplicity of results generated by these methods have the potential to improve patient outcomes and aid in the prevention of the emergence and transmission of MRSA.

Ultrasensitive Detection of C-Reactive Protein by a Novel Nanoplasmonic Immunoturbidimetry Assay

Nanotechnology has attracted much attention, and may become the key to a whole new world in the fields of food, agriculture, building materials, machinery, medicine, and electrical engineering, because of its unique physical and chemical properties, including high surface area and outstanding electrical and optical properties. The bottom-up approach in nanofabrication involves the growth of particles, and we were inspired to propose a novel nanoplasmonic method to detect the formation of nanoparticles in real time. This innovative idea may contribute to the promotion of nanotechnology development. An increase in nanometer particle size leads to optical extinction or density (OD)-value changes in our nanosensor chip at a specific wavelength measured in a generic microplate reader. Moreover, in applying this method, an ultrasensitive nanoplasmonic immunoturbidimetry assay (NanoPITA) was carried out for the high-throughput quantification of hypersensitive C-reactive protein (CRP), a well-known biomarker of cardiovascular, inflammatory, and tumor diseases. The one-step detection of the CRP concentration was completed in 10 min with high fidelity, using the endpoint analysis method. The new NanoPITA method not only produced a linear range from 1 ng/mL to 500 ng/mL CRP with the detection limit reduced to 0.54 ng/mL, which was an improvement of over 1000 times, with respect to regular immunoturbidity measurement, but was also effective in blood detection. This attractive method, combined with surface plasmon resonance and immunoturbidimetry, may become a new technology platform in the application of biological detection.

Molecular point-of-care testing for lower respiratory tract pathogens improves safe antibiotic de-escalation in patients with pneumonia in the ICU: results of a randomised controlled trial

BACKGROUND

Effective treatment of pneumonia requires timely administration of appropriate antimicrobials but standard diagnostic tests take around 48 hours to generate results. Highly accurate, rapid molecular tests have been developed for identifying organisms in lower respiratory tract samples, however their impact on antibiotic use is unknown. The aim of this study was to assess the impact of syndromic molecular point-of-care testing compared to conventional diagnostic testing, on antibiotic use.

METHODS

In this pragmatic, randomised controlled trial, we enrolled critically ill adults with pneumonia. Patients were assigned (1:1) to molecular testing of samples at the point-of-care or routine clinical care. The primary outcome was the proportion of patients who received results-directed antimicrobial therapy.

RESULTS

200 patients were randomly assigned to point-of-care testing (n=100) or the control group (n=100). 85 patients had community acquired pneumonia (42 in the mPOCT group and 43 in the control group), 69 hospital acquired pneumonia (30 in mPOCT and 39 in control) and 46 ventilator associated pneumonia (28 in mPOCT and 18 in control). The median [IQR] time to results was 1.7 [1.6-1.9] hours for point-of-care testing and 66.7 [56.7-88.5] hours for standard diagnostics (difference of -65.0 hours, 95%CI -68.0 to -62.0; p<0.0001). 71 (71%) patients in the point-of-care testing arm had pathogens detected compared to 51 (51%) in the control arm (difference of 20%, 95%CI 7 to 33; p=0.004). 80 (80%) of patients in the point-of-care group received results-directed therapy, compared with 29 (29%) of 99 in the control group (difference of 51%, 95%CI 39-63; p<0.0001). Time to results-directed therapy was 2.3 [1.8-7.2] hours in the mPOCT group and 46.1 [23.0-51.5] hours in the control group (difference of -43.8 hours, 95% CI -48.9 to -38.6; p<0.0001). 42 (42%) patients in mPOCT group had antibiotics de-escalated compared with 8 (8%) of 98 in the control group (difference of 34%, 95%CI 23-45; p<0.0001). Time to de-escalation was 4.8 [2.4-13.0] hours in the mPOCT group compared with 46.5 [26.3-48.6] hours in the control group (difference of -41.4 hours, 95%CI -53 to -29.7; p<0.0001). There was no major difference in antibiotic duration or in clinical or safety outcomes between the two groups.

CONCLUSIONS

Use of molecular point-of-care testing in patients with pneumonia returned results more rapidly and identified more pathogens than conventional testing. This was associated with improvements in appropriate antimicrobial use and appeared safe.

Impact of Respiratory Viral Panel Results on Piperacillin-Tazobactam Use in a Medical Intensive Care Unit: A Single-Center Retrospective Study

PURPOSE

In critically ill patients with acute respiratory infection, antibiotic stewardship can be challenging given the acuity and complexities of such patients, and the associated high mortality. This study determined the impact of respiratory viral panel (RVP) testing on piperacillin-tazobactam (PT) use in patients admitted to a medical intensive care unit (MICU).

METHODS

This retrospective chart review used data from adults admitted to a MICU between January 1, 2017, and January 31, 2018, and with findings from at least one RVP available.

FINDINGS

RVP testing was performed on samples from 90 patients admitted to the MICU. RVP was positive in 41% (37/90) of patients, and 53.3% (48/90) received PT during their MICU stay. PT was discontinued in 25.5% (23/90) of patients, 16.2% (6/37) with a positive RVP and 32.1% (17/53) with a negative RVP. Overall mortality was significantly lower in the positive RVP group versus the negative RVP group (odds ratio = 0.28; P = 0.001). In a multivariate Cox proportional hazards model (adjusted for acute kidney injury and culture positivity), the risk for PT discontinuation was significantly less in patients with a positive RVP compared to those with a negative RVP (primary outcome). Overall mortality rate and median length of stay were significantly lower in patients with a positive RVP compared to those in patients with a negative RVP (secondary outcomes). The 30-day hospital readmission rate and the risk for AKI were not significantly different between those with positive versus negative RVP.

IMPLICATIONS

Reasons for these observations are currently unclear, but deserve further exploration in future studies. It is hypothesized that the treating providers were concerned about the presence of concurrent bacterial infections along with the diagnosed viral infections given that the patients were critically ill. This suggests that RVP results did not impact PT-prescribing practices in the MICU, and thus that the routine use of RVP solely for guiding antimicrobial-stewardship practices may not be effective.

Limitations of Molecular and Antigen Test Performance for SARS-CoV-2 in Symptomatic and Asymptomatic COVID-19 Contacts

COVID-19 has brought unprecedented attention to the crucial role of diagnostics in pandemic control. We compared severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) test performance by sample type and modality in close contacts of SARS-CoV-2 cases. Close contacts of SARS-CoV-2-positive individuals were enrolled after informed consent. Clinician-collected nasopharyngeal (NP) swabs in viral transport media (VTM) were tested with a routine clinical reference nucleic acid test (NAT) and PerkinElmer real-time reverse transcription-PCR (RT-PCR) assay; positive samples were tested for infectivity using a VeroE6TMPRSS2 cell culture model. Self-collected passive drool was also tested using the PerkinElmer RT-PCR assay. For the first 4 months of study, midturbinate swabs were tested using the BD Veritor rapid antigen test. Between 17 November 2020 and 1 October 2021, 235 close contacts of SARS-CoV-2 cases were recruited, including 95 with symptoms (82% symptomatic for ≤5 days) and 140 asymptomatic individuals. Reference NATs were positive for 53 (22.6%) participants; 24/50 (48%) were culture positive. PerkinElmer testing of NP and saliva samples identified an additional 28 (11.9%) SARS-CoV-2 cases who tested negative by reference NAT. Antigen tests performed for 99 close contacts showed 83% positive percent agreement (PPA) with reference NAT among early symptomatic persons, but 18% PPA in others; antigen tests in 8 of 11 (72.7%) culture-positive participants were positive. Contacts of SARS-CoV-2 cases may be falsely negative early after contact, but more sensitive platforms may identify these cases. Repeat or serial SARS-CoV-2 testing with both antigen and molecular assays may be warranted for individuals with high pretest probability for infection.

Nanotechnology Approaches for Rapid Detection and Theranostics of Antimicrobial Resistant Bacterial Infections

As declared by WHO, antimicrobial resistance (AMR) is a high priority issue with a pressing need to develop impactful technologies to curb it. The rampant and inappropriate use of antibiotics due to the lack of adequate and timely diagnosis is a leading cause behind AMR evolution. Unfortunately, populations with poor economic status and those residing in densely populated areas are the most affected ones, frequently leading to emergence of AMR pathogens. Classical approaches for AMR diagnostics like phenotypic methods, biochemical assays, and molecular techniques are cumbersome and resource-intensive and involve a long turnaround time to yield confirmatory results. In contrast, recent emergence of nanotechnology-assisted approaches helps to overcome challenges in classical approaches and offer simpler, more sensitive, faster, and more affordable solutions for AMR diagnostics. Nanomaterial platforms (metallic, quantum-dot, carbon-based, upconversion, etc.), nanoparticle-based rapid point-of-care platforms, nano-biosensors (optical, mechanical, electrochemical), microfluidic-assisted devices, and importantly, nanotheranostic devices for diagnostics with treatment of AMR infections are examples of rapidly growing nanotechnology approaches used for AMR management. This review comprehensively summarizes the past 10 years of research progress on nanotechnology approaches for AMR diagnostics and for estimating antimicrobial susceptibility against commonly used antibiotics. This review also highlights several bottlenecks in nanotechnology approaches that need to be addressed prior to considering their translation to clinics.

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.

Clinical and Financial Impact of a Diagnostic Stewardship Program for Children with Suspected Central Nervous System Infection

OBJECTIVE

To investigate the optimal implementation and clinical and financial impacts of the FilmArray Meningitis Encephalitis Panel (MEP) multiplex polymerase chain reaction testing of cerebrospinal fluid (CSF) in children with suspected central nervous system infection.

STUDY DESIGN

A pre-post quasiexperimental cohort study to investigate the impact of implementing MEP using a rapid CSF diagnostic stewardship program was conducted at Children's Hospital Colorado (CHCO). MEP was implemented with electronic medical record indication selection to guide testing to children meeting approved use criteria: infants <2 months, immunocompromised, encephalitis, and ≥5 white blood cells/μL of CSF. Positive results were communicated with antimicrobial stewardship real-time decision support. All cases with CSF obtained by lumbar puncture sent to the CHCO microbiology laboratory meeting any of the 4 aforementioned criteria were included with preimplementation controls (2015-2016) compared with postimplementation cases (2017-2018). Primary outcome was time-to-optimal antimicrobials compared using log-rank test with Kaplan-Meier analysis.

RESULTS

Time-to-optimal antimicrobials decreased from 28 hours among 1124 preimplementation controls to 18 hours (P < .0001) among 1127 postimplementation cases (72% with MEP testing conducted). Postimplementation, time-to-positive CSF results was faster (4.8 vs 9.6 hours, P < .0001), intravenous antimicrobial duration was shorter (24 vs 36 hours, P = .004), with infectious neurologic diagnoses more frequently identified (15% vs 10%, P = .03). There were no differences in time-to-effective antimicrobials, hospital admissions, antimicrobial starts, or length of stay. Costs of microbiologic testing increased, but total hospital costs were unchanged.

CONCLUSIONS

Implementation of MEP with a rapid central nervous system diagnostic stewardship program improved antimicrobial use with faster results shortening empiric therapy. Routine MEP testing for high-yield indications enables antimicrobial optimization with unchanged overall costs.

Biomolecules capturing live bacteria from clinical samples

Rapid phenotypic antimicrobial susceptibility testing (AST) requires the enrichment of live bacteria from patient samples, which is particularly challenging in the context of life-threatening bloodstream infections (BSIs) due to low bacterial titers. Over two decades, an extensive array of pathogen-specific biomolecules has been identified to capture live bacteria. The prevailing biomolecules are immune proteins of the complement system, antibodies, aptamers, phage proteins, and antimicrobial peptides. These biomolecules differ by their binder generation technologies and exhibit highly variable specificities, ranging from bacterial strains to most pathogenic bacteria. Here, we summarize how these diverse biomolecules were identified, list examples of successfully reported capture assays, and provide an outlook on the use of nanobodies raised against conserved surface-accessible proteins as promising biomolecules for pathogen capture.

Biosensors and Point-of-Care Devices for Bacterial Detection: Rapid Diagnostics Informing Antibiotic Therapy

With an exponential rise in antimicrobial resistance and stagnant antibiotic development pipeline, there is, more than ever, a crucial need to optimize current infection therapy approaches. One of the most important stages in this process requires rapid and effective identification of pathogenic bacteria responsible for diseases. Current gold standard techniques of bacterial detection include culture methods, polymerase chain reactions, and immunoassays. However, their use is fraught with downsides with high turnaround time and low accuracy being the most prominent. This imposes great limitations on their eventual application as point-of-care devices. Over time, innovative detection techniques have been proposed and developed to curb these drawbacks. In this review, a systematic summary of a range of biosensing platforms is provided with a strong focus on technologies conferring high detection sensitivity and specificity. A thorough analysis is performed and the benefits and drawbacks of each type of biosensor are highlighted, the factors influencing their potential as point-of-care devices are discussed, and the authors' insights for their translation from proof-of-concept systems into commercial medical devices are provided.

Impact of Rapid Susceptibility Testing System on the Management of Gram-Negative Bacteremia in a Network of Community Hospitals

BACKGROUND

Rapid initiation of optimal antimicrobial therapy is crucial for the management of Gram-negative (GN) bacteremia. We aimed to evaluate the impact of Accelerate PhenoTM (AxDx) system on change in therapy and length of stay among patients with GN bacteremia.

METHODS

We conducted a retrospective cohort study of adult patients hospitalized who had at least 1 blood culture with presence of Enterobacterales. We compared clinical outcomes among patients who had their blood cultures processed through standard methods alone vs AxDx.

RESULTS

We identified 255 bacteremia episodes among 243 unique patients. In the AxDx group, 31.1% of patients had deescalation of antibiotics within 48 h from blood culture collection compared to 20.0% of patients in the control group (P = 0.09). We found no impact of AxDx on the odds of deescalation at 48 h from blood culture collection [odds ratio (OR) 1.80 (95% CI 0.91-3.56), P = 0.09] or Gram stain report [OR 1.61 (95% CI 0.86-3.01), P = 0.14]. Escalation in therapy at 48 h from blood culture collection occurred in 16.8% and 16.9% of patients in the AxDx and control groups, respectively (P = 0.99). There was no impact on the odds of escalation at 48 h from blood culture collection [OR 0.99 (95% CI 0.47-2.11), P = 0.99] or Gram stain report [OR 1.26 (95% CI 0.57-2.80), P = 0.57]. No differences were seen in length of stay and mortality between the 2 groups.

CONCLUSIONS

The impact of rapid identification and susceptibility technologies may differ according to the setting in which they are implemented.

Membrane Technology for Rapid Point-of-Care Diagnostics for Parasitic Neglected Tropical Diseases

Parasitic neglected tropical diseases (NTDs) affect over one billion people worldwide, with individuals from communities in low-socioeconomic areas being most at risk and suffering the most. Disease management programs are hindered by the lack of infrastructure and resources for clinical sample collection, storage, and transport and a dearth of sensitive diagnostic methods that are inexpensive as well as accurate. Many diagnostic tests and tools have been developed for the parasitic NTDs, but the collection and storage of clinical samples for molecular and immunological diagnosis can be expensive due to storage, transport, and reagent costs, making these procedures untenable in most areas of endemicity. The application of membrane technology, which involves the use of specific membranes for either sample collection and storage or diagnostic procedures, can streamline this process, allowing for long-term sample storage at room temperature. Membrane technology can be used in serology-based diagnostic assays and for nucleic acid purification prior to molecular analysis. This facilitates the development of relatively simple and rapid procedures, although some of these methods, mainly due to costs, lack accessibility in low-socioeconomic regions of endemicity. New immunological procedures and nucleic acid storage, purification, and diagnostics protocols that are simple, rapid, accurate, and cost-effective must be developed as countries progress control efforts toward the elimination of the parasitic NTDs.

Impact of early antimicrobial stewardship intervention in patients with positive blood cultures: results from a randomized comparative study: Impact of stewardship on BSI outcomes

BACKGROUND

Antimicrobial stewardship intervention (ASI) appears necessary to realize the full benefits of rapid diagnostic technologies in clinical practice. This study aimed to compare clinical outcomes between early ASI paired with MALDI-TOF compared to MALDI-TOF with standard of care (SOC) reporting in patients with positive blood cultures.

METHODS

Adult patients with positive blood cultures and organism speciation via MALDI-TOF admitted between 2/2015 and 9/2015 were randomized to ASI or SOC in a 1:1 fashion. Patients admitted for at least 48 hours following positive culture were included in analyses. ASI was defined as a clinical assessment by a stewardship team member with non-binding treatment recommendations offered to the primary team. The primary outcome was time to definitive therapy. Secondary outcomes included post-culture length of stay (LOS), time to first change in antibiotics, and in-hospital mortality.

RESULTS

A total of 149 patients were included in analyses (76 in the ASI group and 73 in the SOC group). ASI and SOC arms did not differ according to age, sex, comorbidities, or severity of illness. Gram-positive organisms were common in both SOC and ASI arms (74.0 vs 61.8%, p=0.11). Time-to-definitive therapy was reduced, on average, by 30.3 hours in the ASI group (71.6 vs. 41.3 hours, p=0.01). Hospital LOS following the first positive blood culture was significantly shorter in the ASI group (8.7 vs. 11.2 days, p=0.049).

CONCLUSIONS

ASI combined with MALDI-TOF reduced the time to definitive therapy, time to first change in antibiotics, and was associated with a shorter post-culture LOS.

Assessing Differential Binding of Aggregation-Induced Emission-Based Luminogens to Host Interacting Surface Proteins of SARS-CoV-2 and Influenza Virus-An in silico Approach

Early detection of asymptomatic cases through mass screening is essential to constrain the coronavirus disease 2019 (COVID-19) transmission. However, the existing diagnostic strategies are either resource-intensive, time-consuming, or less sensitive, which limits their use in the development of rapid mass screening strategies. There is a clear pressing need for simple, fast, sensitive, and economical diagnostic strategy for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) screening even in resource-limited settings. In the current work, we assessed the in silico feasibility of directly labeling virus surface proteins using fluorogenic molecules with aggregation-induced emission (AIE) property. Here, we present the results for binding of two such AIE probes, phosphonic acid derivative of tetraphenyl ethylene (TPE-P) and sulfonic acid derivative of tetraphenyl ethylene (TPE-S), to SARS-CoV-2 spike protein based on in silico docking studies. Our results show that both TPE-P and TPE-S bind to angiotensin converting enzyme 2 (ACE2)-binding, and N-terminal domains of SARS-CoV-2 spike protein. Molecular dynamic simulations have revealed specific nature of these interactions. We also show that TPE-P and TPE-S bind to hemagglutinin protein of influenza virus, but the interaction strength was found to be different. This difference in interaction strength may affect the emission spectrum of aforementioned AIE probes. Together, these results form a basis for the development of AIE-based diagnostics for differential detection of SARS-CoV-2 and influenza viruses. We believe that these in silico predictions certainly aid in differentially labeling of the both viruses toward the development of rapid detection by AIE probes.

Prospective Evaluation of a Rapid Clinical Metagenomics Test for Bacterial Pneumonia

Background

The diagnosis of bacterial pathogens in lower respiratory tract infections (LRI) using conventional culture methods remains challenging and time-consuming.

Objectives

To evaluate the clinical performance of a rapid nanopore-sequencing based metagenomics test for diagnosis of bacterial pathogens in common LRIs through a large-scale prospective study.

Methods

We enrolled 292 hospitalized patients suspected to have LRIs between November 2018 and June 2019 in a single-center, prospective cohort study. Rapid clinical metagenomics test was performed on-site, and the results were compared with those of routine microbiology tests.

Results

171 bronchoalveolar lavage fluid (BAL) and 121 sputum samples were collected from patients with six kinds of LRIs. The turnaround time (from sample registration to result) for the rapid metagenomics test was 6.4 ± 1.4 hours, compared to 94.8 ± 34.9 hours for routine culture. Compared with culture and real-time PCR validation tests, rapid metagenomics achieved 96.6% sensitivity and 88.0% specificity and identified pathogens in 63 out of 161 (39.1%) culture-negative samples. Correlation between enriched anaerobes and lung abscess was observed by Gene Set Enrichment Analysis. Moreover, 38 anaerobic species failed in culture was identified by metagenomics sequencing. The hypothetical impact of metagenomics test proposed antibiotic de-escalation in 34 patients compared to 1 using routine culture.

Conclusions

Rapid clinical metagenomics test improved pathogen detection yield in the diagnosis of LRI. Empirical antimicrobial therapy could be de-escalated if rapid metagenomics test results were hypothetically applied to clinical management.

Development of a Novel Loop Mediated Isothermal Amplification Assay (LAMP) for the Rapid Detection of Epizootic Haemorrhagic Disease Virus

Epizootic haemorragic disease (EHD) is an important disease of white-tailed deer and can cause a bluetongue-like illness in cattle. A definitive diagnosis of EHD relies on molecular assays such as real-time RT-qPCR or conventional PCR. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a cost-effective, specific, and sensitive technique that provides an alternative to RT-qPCR. We designed two sets of specific primers targeting segment-9 of the EHD virus genome to enable the detection of western and eastern topotypes, and evaluated their performance in singleplex and multiplex formats using cell culture isolates (n = 43), field specimens (n = 20), and a proficiency panel (n = 10). The limit of detection of the eastern and western RT-LAMP assays was estimated as ~24.36 C_T and as ~29.37 C_T in relation to real-time RT-qPCR, respectively, indicating a greater sensitivity of the western topotype singleplex RT-LAMP. The sensitivity of the western topotype RT-LAMP assay, relative to the RT-qPCR assay, was 72.2%, indicating that it could be theoretically used to detect viraemic cervines and bovines. For the first time, an RT-LAMP assay was developed for the rapid detection of the EHD virus that could be used as either a field test or high throughput screening tool in established laboratories to control the spread of EHD.

A Piece of the Puzzle: The Role of Molecular Testing in Antimicrobial Stewardship

Molecular testing may have an important role in expediting the diagnosis of infectious diseases. Pediatric infectious diseases specialists need to be cognizant of the strengths and limitations of these existing and emerging technologies in order to ensure that they are used and interpreted appropriately.

Glycan-Based Flow-Through Device for the Detection of SARS-COV-2

The COVID-19 pandemic, and future pandemics, require diagnostic tools to track disease spread and guide the isolation of (a)symptomatic individuals. Lateral-flow diagnostics (LFDs) are rapid and of lower cost than molecular (genetic) tests, with current LFDs using antibodies as their recognition units. Herein, we develop a prototype flow-through device (related, but distinct to LFDs), utilizing N-acetyl neuraminic acid-functionalized, polymer-coated, gold nanoparticles as the detection/capture unit for SARS-COV-2, by targeting the sialic acid-binding site of the spike protein. The prototype device can give rapid results, with higher viral loads being faster than lower viral loads. The prototype's effectiveness is demonstrated using spike protein, lentiviral models, and a panel of heat-inactivated primary patient nasal swabs. The device was also shown to retain detection capability toward recombinant spike proteins from several variants (mutants) of concern. This study provides the proof of principle that glyco-lateral-flow devices could be developed to be used in the tracking monitoring of infectious agents, to complement, or as alternatives to antibody-based systems.

Culture independent detection systems for bloodstream infection

BACKGROUND

Sepsis and bloodstream infection are associated with significant morbidity and mortality, and early effective antimicrobial therapy has been demonstrated to improve patient outcomes. Traditional culture-based methods, however, have several limitations which hamper a prompt diagnosis in bloodstream infection, including long turnaround times and limited sensitivity. In the last years, advances have been made in the development of several technologies which allow the identification of pathogens and their resistance markers directly from whole blood, possibly representing promising alternatives to conventional culture methods.

OBJECTIVES

To review the currently commercially available emerging assays for the diagnosis of bloodstream infections directly from whole blood, including their performance and the available data about their impact on patients' outcome.

SOURCES

Peer-reviewed publications relevant to the topic have been searched through PubMed; manufacturers' websites have also been consulted as a data source.

CONTENT

We have reviewed available data about the following technologies: multiplex real-time PCR working directly from whole blood (Magicplex Sepsis Real-Time test, Seegene), PCR combined with T2 Magnetic Resonance (T2Candida and T2Bacteria panel, T2Biosystem), and metagenomics-based assays (including SepsiTest, Molzym; iDTECT Dx Blood, PathoQuest; Karius NGS plasma Test, Karius). Performance characteristics, advantages and pitfalls of each method are described, and available data about their impact on patients' clinical outcomes are discussed.

IMPLICATIONS

The potential of rapid diagnostic tests applied on whole blood in improving the management of patients with bloodstream infection and sepsis is high, both in terms of reducing turnaround times and improving the sensitivity of pathogen and antimicrobial resistance detection. However, overall, there is still a scarcity of data about the real-life performance of such tests, and well-designed studies are awaited for assessing the impact of these emerging technologies on patients' outcomes.

Rapid COVID-19 Molecular Diagnostic System Using Virus Enrichment Platform

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, is rapidly spreading and severely straining the capacities of public health communities and systems around the world. Therefore, accurate, rapid, and robust diagnostic tests for COVID-19 are crucial to prevent further spread of the infection, alleviate the burden on healthcare and diagnostic facilities, and ensure timely therapeutic intervention. To date, several detection methods based on nucleic acid amplification have been developed for the rapid and accurate detection of SARS-CoV-2. Despite the myriad of advancements in the detection methods for SARS-CoV-2, rapid sample preparation methods for RNA extraction from viruses have rarely been explored. Here, we report a rapid COVID-19 molecular diagnostic system that combines a self-powered sample preparation assay and loop-mediated isothermal amplification (LAMP) based naked-eye detection method for the rapid and sensitive detection of SARS-CoV-2. The self-powered sample preparation assay with a hydrophilic polyvinylidene fluoride filter and dimethyl pimelimidate can be operated by hand, without the use of any sophisticated instrumentation, similar to the reverse transcription (RT)-LAMP-based lateral flow assay for the naked-eye detection of SARS-CoV-2. The COVID-19 molecular diagnostic system enriches the virus population, extracts and amplifies the target RNA, and detects SARS-CoV-2 within 60 min. We validated the accuracy of the system by using 23 clinical nasopharyngeal specimens. We envision that this proposed system will enable simple, facile, efficient, and inexpensive diagnosis of COVID-19 at home and the clinic as a pre-screening platform to reduce the burden on the medical staff in this pandemic era.

A Portable RT-LAMP/CRISPR Machine for Rapid COVID-19 Screening

The COVID-19 pandemic has changed people’s lives and has brought society to a sudden standstill, with lockdowns and social distancing as the preferred preventative measures. To lift these measurements and reduce society’s burden, developing an easy-to-use, rapid, and portable system to detect SARS-CoV-2 is mandatory. To this end, we developed a portable and semi-automated device for SARS-CoV-2 detection based on reverse transcription loop-mediated isothermal amplification followed by a CRISPR/Cas12a reaction. The device contains a heater element mounted on a printed circuit board, a cooler fan, a proportional integral derivative controller to control the temperature, and designated areas for 0.2 mL Eppendorf^® PCR tubes. Our system has a limit of detection of 35 copies of the virus per microliter, which is significant and has the capability of being used in crisis centers, mobile laboratories, remote locations, or airports to diagnose individuals infected with SARS-CoV-2. We believe the current methodology that we have implemented in this article is beneficial for the early screening of infectious diseases, in which fast screening with high accuracy is necessary.