Contemporary approaches to the rapid molecular diagnosis of sepsis

Platelet Metabolites as Candidate Biomarkers in Sepsis Diagnosis and Management Using the Proposed Explainable Artificial Intelligence Approach

Background: Sepsis is characterized by an atypical immune response to infection and is a dangerous health problem leading to significant mortality. Current diagnostic methods exhibit insufficient sensitivity and specificity and require the discovery of precise biomarkers for the early diagnosis and treatment of sepsis. Platelets, known for their hemostatic abilities, also play an important role in immunological responses. This study aims to develop a model integrating machine learning and explainable artificial intelligence (XAI) to identify novel platelet metabolomics markers of sepsis. Methods: A total of 39 participants, 25 diagnosed with sepsis and 14 control subjects, were included in the study. The profiles of platelet metabolites were analyzed using quantitative 1H-nuclear magnetic resonance (NMR) technology. Data were processed using the synthetic minority oversampling method (SMOTE)-Tomek to address the issue of class imbalance. In addition, missing data were filled using a technique based on random forests. Three machine learning models, namely extreme gradient boosting (XGBoost), light gradient boosting machine (LightGBM), and kernel tree boosting (KTBoost), were used for sepsis prediction. The models were validated using cross-validation. Clinical annotations of the optimal sepsis prediction model were analyzed using SHapley Additive exPlanations (SHAP), an XAI technique. Results: The results showed that the KTBoost model (0.900 accuracy and 0.943 AUC) achieved better performance than the other models in sepsis diagnosis. SHAP results revealed that metabolites such as carnitine, glutamate, and myo-inositol are important biomarkers in sepsis prediction and intuitively explained the prediction decisions of the model. Conclusion: Platelet metabolites identified by the KTBoost model and XAI have significant potential for the early diagnosis and monitoring of sepsis and improving patient outcomes.

Reliability of Droplet Digital PCR Alone and in Combination with Interleukin-6 and Procalcitonin for Prognosis of Bloodstream Infection

Purpose

Bloodstream infection(BSI) is linked with high mortality, underscoring the significance of prompt etiological diagnosis for timely and precise treatment. This study aims to investigate the diagnostic value of droplet digital polymerase chain reaction(ddPCR) in combination with conventional inflammatory markers [interleukin-6(IL-6) and procalcitonin(PCT)] concerning disease progression and treatment prognosis in BSI patients. Furthermore, the study aims to explore a more efficient clinical application strategy.

Patients and Methods

This prospective case seried study centers on 176 patients suspected of or confirmed with BSI. Blood samples were collected to extract nucleic acids for identifying pathogens (bacteria, fungi, and viruses) and determining copy loads via ddPCR.

Results

The sensitivity of ddPCR was markedly higher compared to the culture method (74.71% vs 31.03%). A positive correlation existed between bacterial load and levels of inflammatory markers [IL-6 (P=0.0182), PCT (P=0.0029), and CRP (P=0.0005)]. In suspected BSI cases, the combination of ddPCR and inflammatory markers could predict sepsis risk [ROC: Area under the curve(AUC)=0.6071, P=0.0383]. Within confirmed BSI patients, the ddPCR bacterial load of those with SOFA<7 was lower than that of the SOFA≥7 (P=0.0334). ddPCR (OR: 1.789, P=0.035) monitoring combined with PCT (OR: 1.787, P=0.035) holded predictive value for SOFA progression (AUC=0.7913, P=0.0003). Similarly, BSI survivors displayed a lower burden than non-survivors (P=0.0170). Additionally, ddPCR combinated with IL-6 provided a more accurate and expedited insight into clinical outcomes prediction for BSI confirmed patients (AUC=0.7352, P=0.0030). Serial monitoring of bacterial load by ddPCR effectively mirrored the clinical course of BSI in patients. Notably, patients with positive ddPCR virus infection exhibited significantly reduced lymphocyte counts (P=0.0003).

Conclusion

In a clinical context, qualitative ddPCR results and quantitative continuous monitoring can more precisely assess sepsis progression and treatment prognosis in BSI patients. Furthermore, ddPCR results offer quicker and more accurate reference points for clinical antibacterial and antiviral interventions.

Direct identification of pathogens via microbial cellular DNA in whole blood by MeltArray

Rapid identification of pathogens is critical for early and appropriate treatment of bloodstream infections. The various culture-independent assays that have been developed often have long turnaround times, low sensitivity and narrow pathogen coverage. Here, we propose a new multiplex PCR assay, MeltArray, which uses intact microbial cells as the source of genomic DNA (gDNA). The successive steps of the MeltArray assay, including selective lysis of human cells, microbial cell sedimentation, microbial cellular DNA extraction, target-specific pre-amplification and multiplex PCR detection, allowed the detection of 35 major bloodstream infectious pathogens in whole blood within 5.5 h. The limits of detection varied depending on the pathogen and ranged from 1 to 5 CFU/mL. Of 443 blood culture samples, including 373 positive blood culture samples and 70 negative blood culture samples, the MeltArray assay showed a sensitivity of 93.8% (350/373, 95% confidence interval [CI] = 90.7%-96.0%), specificity of 98.6% (69/70, 95% CI = 91.2%-99.9%), positive predictive value of 99.7% (95% CI = 98.1%-99.9%), and negative predictive value of 75.0% (95% CI = 64.7%-83.2%). The MeltArray detection results of 16 samples differed from MALDI-TOF and were confirmed by Sanger sequencing. Further testing of 110 whole blood samples from patients with suspected bloodstream infections using blood culture results revealed that the MeltArray assay had a clinical sensitivity of 100% (9/9, 95% CI = 62.8%-100.0%), clinical specificity of 74.5% (70/94, 95% CI = 64.2%-82.7%), positive predictive value of 27.3% (95% CI = 13.9%-45.8%), and negative predictive value of 100.0% (95% CI = 93.5%-100.0%). Compared with metagenomic next-generation sequencing, the MeltArray assay displayed a positive agreement of 85.7% (6/7, 95% CI = 42.0%-99.2%) and negative agreement of 100.0% (4/4, 95% CI = 39.6%-100.0%). We conclude that the MeltArray assay can be used as a rapid and reliable tool for direct identification of pathogens in bloodstream infections.

Direct antimicrobial susceptibility testing (AST) from positive blood cultures using Microscan system for early detection of bacterial resistance phenotypes

Antimicrobial Susceptibility Testing is mandatory for Bloodstream Infections management in order to establish appropriate antimicrobial therapy. Herein we evaluated new approach based on AST results directly from positive blood cultures, using Microscan WA to carry out rapid phenotypical profile of antibiotic resistance. Our investigations allow to reduce time versus traditional results.

A Mobile Device for Monitoring the Biological Purity of Air and Liquid Samples

A detector for identifying potential bacterial hazards in the air was designed and created in the Military Institute of Chemistry and Radiometry in the framework of the project FLORABO. The presence of fungi and bacteria in the air can affect the health of people in a given room. The need to control the amount of microorganisms, both in terms of quantity and quality, applies to both hospitals and offices. The device is based on the fluorescence spectroscopy analysis of the sample and then these results were compared to the resulting spectrogram database, which includes the standard curves obtained in the laboratory for selected bacteria. The measurements provide information about the presence, the type, and the approximate concentration of bacteria in the sample. The spectra were collected at different excitation wavelengths, and the waveforms are specific for each of the strains. It also takes under analysis the signal intensities of the different spectra (not only shape a maximum of the peak) so that the concentration of bacteria in the sample being tested can be determined. The device was tested in the laboratory with concentrations ranging from 10 to 10⁸ cells/mL. Additionally, the detector can distinguish between the vegetative forms of spores of the bacteria.

Multiplex PCR Based Strategy for Detection of Fungal Pathogen DNA in Patients with Suspected Invasive Fungal Infections

A new and easy polymerase chain reaction (PCR) multiplex strategy, for the identification of the most common fungal species involved in invasive fungal infections (IFI) was developed in this work. Two panels with species-specific markers were designed, the Candida Panel for the identification of Candida species, and the Filamentous Fungi Panel for the identification of Aspergillus species and Rhizopusarrhizus. The method allowed the correct identification of all targeted pathogens using extracted DNA or by colony PCR, showed no cross-reactivity with nontargeted species and allowed identification of different species in mixed infections. Sensitivity reached 10 to 1 pg of DNA and was suitable for clinical samples from sterile sites, with a sensitivity of 89% and specificity of 100%. Overall, the study showed that the new method is suitable for the identification of the ten most important fungal species involved in IFI, not only from positive blood cultures but also from clinical samples from sterile sites. The method provides a unique characteristic, of seeing the peak in the specific region of the panel with the correct fluorescence dye, that aids the ruling out of unspecific amplifications. Furthermore, the panels can be further customized, selecting markers for different species and/or resistance genes.

Preliminary readings of antimicrobial susceptibility panels: A simple, fast and inexpensive way to detect bacterial resistance and enhance antibiotic treatment of bloodstream infections

Increasing incidence of resistant bacteria needs faster identification (ID) and antibiotic susceptibility testing (AST) in order to improve antimicrobial treatment of severe infections. We propose a preliminary reading of the AST MicroScan® panels coupled with mass spectrometry ID. A total of 157 bacterial clinical isolates were processed for routine ID and AST (in 22 cases, ID and AST were performed directly from positive blood culture bottles). For gram-negatives, data from the initial and final readings were recorded and compared [89.9% category agreement (CA), 6.9% very major errors (VME)]. In adition all the 32 ESBL producers were detected at 5.3-8.6 hours. For Staphylococcus aureus, all the 16 MRSA isolates were detected at 4.5 to 7.5 hours. Thus, we find our preliminary readings approach as a simple, inexpensive and reliable way to detect and identify the most prevalent resistant bacteria in our institution on the same day that ID/AST is performed.

Stewardship in sepsis

Sepsis is the major cause of mortality from any infectious disease worldwide. The goals of antimicrobial stewardship are to achieve optimum clinical outcomes and to ensure cost effectiveness and minimum unintended consequences, including toxic effects, selection of pathogenic organisms, and resistance. The combination of inadequate diagnostic criteria for sepsis with the extraordinary time pressure to provide broad-spectrum antimicrobial therapy is troubling from a stewardship perspective. Use of empirical therapy according to guidelines, de-escalation of therapy, switch from intravenous to oral therapy, therapeutic drug monitoring, use of a list of restricted antibiotics, and bedside consultation can lead to significant benefits for clinical outcomes, adverse events, and costs.

Development and first evaluation of a novel multiplex real-time PCR on whole blood samples for rapid pathogen identification in critically ill patients with sepsis

Molecular tests may enable early adjustment of antimicrobial therapy and be complementary to blood culture (BC) which has imperfect sensitivity in critically ill patients. We evaluated a novel multiplex real-time PCR assay to diagnose bloodstream pathogens directly in whole blood samples (BSI-PCR). BSI-PCR included 11 species- and four genus-specific PCRs, a molecular Gram-stain PCR, and two antibiotic resistance markers. We collected 5 mL blood from critically ill patients simultaneously with clinically indicated BC. Microbial DNA was isolated using the Polaris method followed by automated DNA extraction. Sensitivity and specificity were calculated using BC as reference. BSI-PCR was evaluated in 347 BC-positive samples (representing up to 50 instances of each pathogen covered by the test) and 200 BC-negative samples. Bacterial species-specific PCR sensitivities ranged from 65 to 100%. Sensitivity was 26% for the Gram-positive PCR, 32% for the Gram-negative PCR, and ranged 0 to 7% for yeast PCRs. Yeast detection was improved to 40% in a smaller set-up. There was no overall association between BSI-PCR sensitivity and time-to-positivity of BC (which was highly variable), yet Ct-values were lower for true-positive versus false-positive PCR results. False-positive results were observed in 84 (4%) of the 2200 species-specific PCRs in 200 culture-negative samples, and ranged from 0 to 6% for generic PCRs. Sensitivity of BSI-PCR was promising for individual bacterial pathogens, but still insufficient for yeasts and generic PCRs. Further development of BSI-PCR will focus on improving sensitivity by increasing input volumes and on subsequent implementation as a bedside test.

Towards precision medicine in sepsis: a position paper from the European Society of Clinical Microbiology and Infectious Diseases

BACKGROUND

Our current understanding of the pathophysiology and management of sepsis is associated with a lack of progress in clinical trials, which partly reflects insufficient appreciation of the heterogeneity of this syndrome. Consequently, more patient-specific approaches to treatment should be explored.

AIMS

To summarize the current evidence on precision medicine in sepsis, with an emphasis on translation from theory to clinical practice. A secondary objective is to develop a framework enclosing recommendations on management and priorities for further research.

SOURCES

A global search strategy was performed in the MEDLINE database through the PubMed search engine (last search December 2017). No restrictions of study design, time, or language were imposed.

CONTENT

The focus of this Position Paper is on the interplay between therapies, pathogens, and the host. Regarding the pathogen, microbiologic diagnostic approaches (such as blood cultures (BCs) and rapid diagnostic tests (RDTs)) are discussed, as well as targeted antibiotic treatment. Other topics include the disruption of host immune system and the use of biomarkers in sepsis management, patient stratification, and future clinical trial design. Lastly, personalized antibiotic treatment and stewardship are addressed (Fig. 1).

IMPLICATIONS

A road map provides recommendations and future perspectives. RDTs and identifying drug-response phenotypes are clear challenges. The next step will be the implementation of precision medicine to sepsis management, based on theranostic methodology. This highly individualized approach will be essential for the design of novel clinical trials and improvement of care pathways.

Clinical uptake of antimicrobial stewardship recommendations following Nanosphere Verigene Blood Culture Gram-negative reporting

We performed a retrospective chart review of patients to determine if the Verigene Gram-negative blood culture (BC-GN) results would lead to earlier deescalation of empiric therapy for inpatients with GN bacteremia with Citrobacter spp., Enterobacter spp., Klebsiella spp., and Escherichia coli to appropriate targeted coverage. A total of 899 records were reviewed from April 2014 to February 2016 from three institutions within the Baylor Scott & White Health network. The cases were reviewed for initial antibiotic coverage, timing of Verigene results, change in antibiotic coverage, and how these changes related to the timing of Verigene results. The lab reported the BC-GN results and final conventional susceptibility results within 2.5 ± 1.3 and 73.6 ± 40.0 hours from the Gram stain, respectively. Overall, 29.1% of patients were transitioned from empiric to targeted therapy at 12.2 ± 13.5 hours in response to BC-GN results, which was significantly earlier (P < 0.001) than results by conventional methods. After accounting for patients already on targeted therapy, polymicrobial infections, and patients deceased or lost to follow-up, we identified antibiotic stewardship opportunities in ∼28% of GN infections. Further subanalysis demonstrated site-specific differences in the uptake of stewardship recommendations, whereby 32.4%, 50.5%, and 15.0% of cases at different hospitals demonstrated the expected change in antibiotics. These results suggest that Verigene had the expected impact in a third of the cases and the results reporting algorithm minimized the real-time involvement of the pharmacist while maintaining optimal patient management. However, this impact varied substantially by clinical site and was tempered by variable initial antibiotic coverage and clinician response.