Daily Sepsis Research Analysis

BACKGROUND: Blood culture (BC) remains the cornerstone for diagnosis of bloodstream infections (BSI), but the long turn-around time (TAT) hampers timely selection of appropriate chemotherapy. Novel molecular approaches have been developed to provide faster results but are also affected by limitations. We developed a analytical workflow named LC-WGS (Whole-Genome Sequencing of Liquid Colony) for rapid whole-genome sequencing-based diagnosis of BSI, evaluating its accuracy performance over standard of care (SoC) diagnostic procedures. METHODS: A total of 85 prospectively collected positive BC were processed in parallel with SoC (subculturing, identification by MALDI-ToF, antimicrobial susceptibility testing by reference broth microdilution, usage of syndromic panels) and LC-WGS, which relied on automated purification of microbial cells (Qvella FAST system, Qvella Corp.), DNA purification, and real-time sequencing with the Oxford Nanopore MinION. A streamlined analysis pipeline was designed for pathogen identification (Kraken2), detection of resistance markers (KmerResistance, AMRFinderPlus), virulome profiling (abricate, VFDB), phylogenetic analysis (snippy, IQ-TREE), and pathogen subtyping (Meningotype). FINDINGS: Compared with SoC, LC-WGS returned accurate species-level identification for 98% (65/66) of monomicrobial and 88% (14/16) of polymicrobial BCs, with a TAT as short as ∼2·6 h. Accurate resistome profiling (allelic variants) was achieved for 94% (58/62) of the most clinically-relevant resistance profiles in ∼4·2 h. In silico serotying (Neisseria meningitidis), virulotyping (Escherichia coli, Klebsiella pneumoniae) and comparative phylogenomics for outbreak investigation (K. pneumoniae) proved also feasible. INTERPRETATION: In this proof-of-concept study, we proved that diagnosis of BSI can be significantly shortened using an optimised workflow based on real-time sequencing, providing rapid, actionable clinical microbiological data in support of timely selection of appropriate chemotherapy. LC-WGS proved also useful as molecular epidemiology tool for public health and infection control applications. FUNDING: This study was partially supported by an investigator-initiated grant from Qvella Corporation.

BACKGROUND: Microbial cultures for diagnosis of neonatal sepsis have low sensitivity and reporting delay. Advances in molecular microbiology have fostered new molecular assays that are rapid and may improve neonatal outcomes. OBJECTIVES: To assess the diagnostic accuracy of various molecular methods for the diagnosis of culture-positive bacterial and fungal sepsis in neonates and to explore heterogeneity among studies by analyzing subgroups classified by gestational age and type of sepsis onset and compare molecular tests with one another. SEARCH METHODS: We searched CENTRAL, MEDLINE, Embase and trial registries in August 2023. We checked reference lists of included studies and systematic reviews where subject matter related to the intervention or population examined in this review. SELECTION CRITERIA: We included studies that were prospective or retrospective, cohort or cross-sectional design, which evaluated molecular assays (index test) in neonates with suspected sepsis in comparison with microbial cultures (reference standard). DATA COLLECTION AND ANALYSIS: Two review authors independently screened studies, extracted data and assessed the methodological quality of the studies. We performed meta-analyses using the bivariate model and entered data into Review Manager. MAIN RESULTS: Seventy-four studies were eligible for inclusion, of which 68 studies provided data for meta-analysis. The total number of participants was 14,309 (1328 infants who were culture-positive and 12,981 infants who were culture-negative) from 68 studies that were included in the meta-analysis. The summary estimate of sensitivity was 0.91 (95% confidence interval (CI) 0.85 to 0.95) and of specificity was 0.88 (95% CI 0.83 to 0.92) (low-certainty evidence). We explored heterogeneity by subgroup analyses of type of test, gestational age, type of sepsis onset and prevalence of sepsis. We found insufficient explanations for the heterogeneity (low- to very low-certainty evidence). Sensitivity analyses including studies that analyzed blood samples, using good methodology and those that did not use multiple samples from the same participant revealed similar results (low-certainty evidence). AUTHORS' CONCLUSIONS: Molecular assays have the advantage of producing rapid results and have moderate diagnostic accuracy. Molecular assays may prevent overuse of antibiotics in neonates with suspected sepsis. The efficacy and cost-effectiveness of these molecular assays should be evaluated using randomized trials comparing molecular assays as an add-on test versus conventional methods without the add-on test in neonates with suspected sepsis.

IMPORTANCE: The Centers for Medicare & Medicaid Services Severe Sepsis and Septic Shock Management Bundle (SEP-1) is supported by observational studies that report SEP-1 compliance is associated with lower mortality. Most studies, however, adjusted for limited confounders and provided little insight into why bundle-compliant care was not provided. OBJECTIVES: To identify the clinical factors that complicate the diagnosis and management of sepsis and assess their association with SEP-1 compliance and mortality. DESIGN, SETTING, AND PARTICIPANTS: This retrospective cohort study was conducted among 590 adults with sepsis in the emergency department of 4 academic hospitals from January 1, 2019, to December 31, 2022. Patients' medical records were reviewed between September 2022 and December 2023. MAIN OUTCOMES AND MEASURES: Study outcomes were (1) characteristics of patients who received SEP-1-compliant care vs characteristics of patients who received noncompliant care and (2) association between SEP-1 compliance and hospital mortality using multivariable models to adjust for successively more potential confounders (first demographics and comorbidities, then infection source, then severity of illness, and then clinical markers of complexity). RESULTS: Of 590 patients with sepsis (median age, 65 years [IQR, 53-77 years]; 329 men [55.8%]), 335 (56.8%) received SEP-1-compliant care, and 225 (43.2%) received noncompliant care. Compared with patients in the compliant group, patients in the noncompliant group were more likely to be 65 years or older (142 [55.7%] vs 158 [47.2%]; odds ratio [OR], 1.41 [95% CI, 1.01-1.95]), to have multiple comorbidities (Elixhauser score >20: 99 [38.8%] vs 99 [29.6%]; OR, 1.51 [95% CI, 1.07-2.13]), and to have a higher incidence of septic shock (107 [42.0%] vs 107 [31.9%]; OR, 1.54 [95% CI, 1.10-2.16]), kidney dysfunction (87 [34.1%] vs 80 [23.9%]; OR, 1.65 [95% CI, 1.15-2.37]), and thrombocytopenia (43 [16.9%] vs 37 [11.0%]; OR, 1.16 [95% CI, 1.02-2.62]) on presentation. Compared with patients in the compliant group, those in the noncompliant group also had more nonfebrile presentations (136 [53.3%] vs 121 [36.1%]; OR, 2.02 [95% CI, 1.45-2.82]), impaired mental status (92 [36.1%] vs 94 [28.1%]; OR, 1.45 [95% CI, 1.02-2.05]), need for bedside procedures (57 [22.4%] vs 41 [12.2%]; OR, 2.06 [95% CI, 1.33-3.21]), acute concurrent noninfectious illnesses (140 [54.9%] vs 151 [45.1%]; OR, 1.48 [95% CI, 1.07-2.06]), and noninfectious illness as the primary factor associated with their presentation (84 [32.9%] vs 71 [21.2%]; OR, 1.82 [95% CI, 1.08-3.08]). SEP-1 compliance was associated with lower crude mortality rates compared with noncompliance (40 [11.9%] vs 41 [16.1%]; unadjusted OR, 0.60 [95% CI, 0.37-0.98]), but there was no statistically significant difference between groups after successively adjusting for demographics and comorbidities (adjusted OR [AOR], 0.71 [95% CI, 0.42-1.18]), infection source (AOR, 0.71 [95% CI, 0.43-1.20]), severity of illness (AOR, 0.86 [95% CI, 0.50-1.49]), and clinical markers of complexity (AOR, 1.08 [95% CI, 0.61-1.91]). CONCLUSIONS AND RELEVANCE: In this cohort study of adults with sepsis, complex clinical presentations were more common among patients whose treatment was noncompliant with SEP-1. These nuances are poorly captured in most observational studies but confound the association between SEP-1 compliance and mortality.