Daily Sepsis Research Analysis
Rapid, clinically integrated metagenomics in the ICU demonstrated high diagnostic sensitivity, same-day turnaround, and measurable impact on antimicrobial and immunomodulatory decisions. Phage-informed mNGS improved specificity for distinguishing infection from colonization, while cardiac epigenomic profiling in murine sepsis revealed early chromatin accessibility changes and candidate transcriptional regulators of organ dysfunction.
Summary
Rapid, clinically integrated metagenomics in the ICU demonstrated high diagnostic sensitivity, same-day turnaround, and measurable impact on antimicrobial and immunomodulatory decisions. Phage-informed mNGS improved specificity for distinguishing infection from colonization, while cardiac epigenomic profiling in murine sepsis revealed early chromatin accessibility changes and candidate transcriptional regulators of organ dysfunction.
Research Themes
- Rapid pan-microbial diagnostics and clinical impact in ICU sepsis care
- Bacteriophage-informed metagenomics to distinguish infection from colonization
- Epigenomic mechanisms underpinning sepsis-induced organ dysfunction
Selected Articles
1. Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study.
A same-day pan-kingdom metagenomic service in ICU patients achieved high sensitivity (bacteria 97%, fungi 89%, viruses 89%) and identified additional pathogens in 30% of samples. Results altered antimicrobial therapy in 28% and contributed to immunomodulation in 20% of patients, demonstrating both patient-level and public health value.
Impact: This study operationalizes rapid pan-microbial metagenomics with demonstrated clinical decision impact, a key step beyond analytic validity alone. It sets a benchmark for integrating metagenomics into ICU sepsis workflows.
Clinical Implications: Incorporating rapid metagenomics into ICU diagnostics can enable earlier de-escalation/escalation of antimicrobials, support initiation of immunomodulators, and enhance infection control and surveillance. Multicentre evaluation should address outcomes, stewardship, and cost-effectiveness.
Key Findings
- 94% of 114 samples passed QC; 94% of QC-passed samples yielded same-day preliminary results.
- Sensitivity in lower respiratory tract samples after 24 h: bacteria 97% (95% CI 87–100), fungi 89% (65–99), viruses 89% (71–98), with only one bacterial false positive.
- Metagenomics identified 42 additional pathogens in 32 (30%) of 107 samples beyond routine diagnostics.
- Antimicrobial therapy changed in 28% of samples (21% de-escalated, 7% escalated); immunomodulation initiated in 20% of patients.
- Clinically significant pathogens for infection control/public health were found in 14% of patients.
Methodological Strengths
- Prospective, real-world service evaluation with predefined workflow and turnaround targets.
- Pan-kingdom detection (bacteria, fungi, DNA/RNA viruses) with comparison to routine diagnostics.
- Direct measurement of clinical decision impact (antimicrobial changes, immunomodulation) and public health relevance.
Limitations
- Single-centre design with modest sample size and potential selection bias.
- No randomized assessment of patient outcomes; exclusion of containment level 3 organisms.
- Resource and cost requirements not assessed.
Future Directions: Conduct multicentre trials to evaluate patient outcomes, antimicrobial stewardship metrics, and cost-effectiveness; standardize reporting thresholds; integrate with host-response biomarkers.
BACKGROUND: Most clinical metagenomic studies do not provide rapid results, detect pathogens from all microbial kingdoms, or measure clinical impacts. We aimed to evaluate the feasibility, performance, and clinical impacts of a rapid pan-microbial respiratory metagenomic service for patients admitted to intensive care units (ICUs). METHODS: This was a single-centre observational study of a rapid metagenomics service that tests respiratory samples from ICU patients at Guy's and St Thomas' hospitals, London, UK, between Dec 5, 2023, and April 12, 2024. Testing used a previously published pan-microbial metagenomics workflow, which simultaneously detects bacteria, fungi, and DNA and RNA viruses; provides same-day preliminary results after 2 h; and provides final results after 24 h. Patients were included if they were aged 18 years or older, admitted to the ICU, had confirmed respiratory failure requiring supplemental oxygen or advanced airway support, and had at least one of the following: (1) clinical suspicion of lower respiratory tract infection based on clinical, biochemical, or radiological findings, (2) sepsis of unknown origin, and (3) concern from an intensive care physician regarding inflammatory pathology. Patients with a suspected or confirmed containment level three organism were excluded. The outcome was performance characteristics of the metagenomic test compared with routine diagnostic testing, detection of additional pathogens by metagenomics, change in antimicrobial prescribing within 24 h of testing, and initiation of immunomodulation. FINDINGS: We processed 114 samples (1-5 per day) from 74 patients (39 [53%] female and 35 [47%] male). 107 (94%) of 114 samples passed quality control, of which 101 (94%) provided same-day preliminary results. Bacteria were detected in 45 (43%) of 104 tested specimens, fungal organisms in 17 (16%) of 104 tested specimens, and viruses in 28 (34%) of 83 tested specimens. Sensitivity in lower respiratory tract samples after 24 h was 97% (95% CI 87-100) for bacteria, 89% (65-99) for fungi, and 89% (71-98) for viruses, with only one false positive for bacteria. Metagenomics identified 42 pathogens not detected by other tests in 32 (30%) of 107 samples. Antimicrobial therapy was changed after metagenomic results from 30 (28%) of 107 samples: 22 (21%) were de-escalated and eight (7%) were escalated. Metagenomics contributed to the initiation of immunomodulation in 15 (20%) of 74 patients for a range of inflammatory conditions. Pathogens with clinical significance to local infection control or national public health were found in ten (14%) of 74 patients, including three invasive Group A streptococci, two parvovirus B19, and one each of HIV-1, measles virus, Mycobacterium tuberculosis, Neisseria meningitidis, and Mycoplasma pneumoniae. INTERPRETATION: Respiratory metagenomics for ICU patients showed good performance and turnaround time, and diverse clinical and public health benefits. This ability to inform both personalised patient therapy and infectious disease surveillance needs evaluation in multicentre studies. FUNDING: None.
2. Bacteriophage combined with mNGS enhances the specificity of bacterial infection diagnosis.
Retrospective analysis of 299 samples showed that pathogen-specific bacteriophage signals in plasma and BALF correlate with true bacterial infections and can aid in distinguishing infection from colonization. For Acinetobacter baumannii, Myoviridae signals achieved 86.36% sensitivity and 52.94% specificity for infection versus colonization.
Impact: Incorporating phage reads into mNGS addresses a key limitation—low specificity for infection versus colonization—offering a mechanistically plausible and scalable enhancement to diagnostic pipelines.
Clinical Implications: Phage-informed mNGS may reduce unnecessary antibiotics by improving specificity, particularly for problematic pathogens like A. baumannii. Prospective validation and standardized thresholds are needed before routine adoption.
Key Findings
- Across 299 samples from 218 patients, pathogen-specific phage proportions increased in infections by A. baumannii, K. pneumoniae, P. aeruginosa, and S. aureus.
- In BALF with A. baumannii infection, Autographiviridae, Siphoviridae, and Myoviridae proportions were significantly higher than in colonization.
- Myoviridae yielded 86.36% sensitivity and 52.94% specificity for distinguishing A. baumannii infection from colonization.
- In sepsis, combining phage signals with mNGS improved identification of causative pathogens compared with mNGS alone.
Methodological Strengths
- Moderate sample size with dual matrices (plasma and BALF) and inclusion of cell-free DNA.
- Systematic phage annotation aligned with bacterial taxa and infection status.
- Direct comparison between infection and colonization groups.
Limitations
- Retrospective single-period analysis with potential misclassification of infection versus colonization.
- Specificity remains moderate; clinical outcome impact not assessed.
- Generalizability limited to a single region and time frame.
Future Directions: Prospective multicentre validation, establishment of quantitative phage thresholds, and assessment of impact on antimicrobial stewardship and outcomes.
INTRODUCTION: Metagenomic next-generation sequencing (mNGS) is an important tool for enhancing pathogen detection in infected patients. However, distinguishing between specimens that are infected or colonized is still a major challenge. OBJECTIVES: To explore the composition of bacteriophages in the blood and respiratory tract of the human body, the association between bacteriophage detection and bacterial infections, and whether bacteriophages can assist in differentiating infectious pathogens according to mNGS results. METHODS: Clinical samples from hospitalized patients were collected between January 2023 and February 2024. DNA and cell-free DNA were extracted from BALF and plasma retrospectively to identify the pathogens present, and bacteriophage annotations were conducted. RESULTS: A total of 299 samples, comprising 136 blood samples and 163 BALF samples, were obtained from 218 patients. Compared with the samples negative for bacteria, both blood and bronchoalveolar lavage fluid (BALF) samples infected with Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and S. aureus showed a corresponding increase in the proportions of phages related to these pathogens. In BALF samples with Acinetobacter baumannii infection, the proportions of Autographiviridae, Siphoviridae, and Myoviridae were significantly greater than those in the Acinetobacter baumannii colonization group. The sensitivity of Myoviridae for differentiating between infection and colonization was 86.36%, and the specificity was 52.94%. CONCLUSION: In sepsis, compared with conventional mNGS methods alone, the use of bacteriophages combined with mNGS was more effective in identifying causative pathogens and had higher specificity. These findings may provide new ideas and tools for improving clinical infection diagnosis.
3. Characterization of the Chromatin Accessibility in the Hearts of Mice With Lipopolysaccharide (LPS)-Induced Sepsis.
Integrating ATAC-seq with RNA-seq in an LPS-induced murine sepsis model, the study mapped extensive chromatin accessibility remodeling in hearts, especially at day 1 post-induction. Thousands of accessible regions changed (2389 increased, 5065 decreased), TF motifs (ERG, ETV2, Mef2c, JunB) were enriched, and 93 of 1311 genes with enhanced accessibility showed mRNA upregulation, implicating early epigenomic mechanisms in sepsis-induced cardiac dysfunction.
Impact: This work positions chromatin accessibility changes as an initiating mechanism for sepsis-induced cardiac dysfunction and highlights candidate transcriptional regulators, providing a mechanistic basis for biomarker and therapeutic target development.
Clinical Implications: Although preclinical, identifying early epigenomic changes and TF candidates may inform development of prognostic biomarkers for sepsis-induced cardiomyopathy and guide epigenetic therapies after validation in human tissues.
Key Findings
- ATAC-seq and RNA-seq integration revealed 2389 increased and 5065 decreased chromatin-accessible regions in sepsis mouse hearts.
- At day 1 post-induction, 877 genes were upregulated and 881 downregulated; 1311 genes showed enhanced accessibility, with 93 showing concordant mRNA upregulation.
- Transcription factor signatures (ERG, ETV2, Mef2c, JunB) were enriched in accessible regions associated with sepsis-induced cardiac dysfunction.
- Findings support chromatin accessibility alterations as an initial mechanism in SICD.
Methodological Strengths
- Multi-omics integration (ATAC-seq with RNA-seq) to link chromatin accessibility and transcriptional output.
- In vivo LPS-induced sepsis model focusing on an early critical timepoint (day 1).
- Genome-wide, unbiased mapping of accessible chromatin regions with TF motif enrichment analysis.
Limitations
- LPS-induced endotoxemia may not fully recapitulate human sepsis or polymicrobial models.
- Limited functional validation of candidate TFs and causal links.
- Sample sizes and biological replicates are not specified in the abstract.
Future Directions: Validate findings in human cardiac tissue and polymicrobial sepsis models; perturb TFs (e.g., ERG, ETV2, Mef2c, JunB) to test causality; evaluate therapeutic epigenetic modulation.
This study investigates the transcription and expression of genes associated with Sepsis-induced cardiac dysfunction (SICD) in a sepsis mouse model by examining chromatin accessibility. The assay for transposase-accessible chromatin by sequencing (ATAC-seq) was employed to investigate chromatin reshaping associated with SICD in the sepsis mouse model. ATAC-seq data were generated from the hearts of sepsis mice, and the relationship between chromatin accessibility and gene expression was analyzed in conjunction with RNA sequencing. RNA-seq results indicated that the most differentially expressed genes were present 1 day post-induction. We identified 2389 increased and 5065 decreased sepsis-associated chromatin-accessible regions in the heart tissues of sepsis mice. At 1 day post-induction, 877 genes were upregulated, and 881 were downregulated. Notably, an enhanced ATAC-seq signal was observed in approximately 1311 genes, with 93 showing upregulated mRNA levels. The signatures of numerous transcription factors, including ERG, ETV2, Mef2c, and JunB, were enriched in the SICD-associated accessible chromatin regions. This study demonstrates that alterations in chromatin accessibility may serve as an initial mechanism in sepsis-induced cardiac dysfunction.