Sepsis: When Every Minute Counts

Sepsis is an acute life-threatening condition characterized by organ dysfunction due to a dysregulated immune response to pathogens. It along with other bloodstream infections (BSI) represents a major cause of morbidity and mortality, affecting over 13 million people worldwide and killing 20 to 50% of severely affected patients, as well as a source of immense economic burden. What is even more concerning is the observed increase in the incidence of sepsis and other bloodstream infections that has occurred in the past several decades, attributed partly to the failure of empiric antibiotic regimens as a result of growing antimicrobial resistance (AMR).

What can be done to improve outcomes in Sepsis?

To reduce sepsis-associated morbidity, mortality, and the economic burden the World Health Organization (WHO) and the Centers for Disease Control (CDC) recommends expeditious diagnosis and identification of the etiological pathogens as well as the rapid institution of proper targeted antimicrobial therapy. The urgency for the prescription of the correct antibiotic therapy is of paramount importance for improving outcomes in sepsis and other bloodstream infections, as every 1-hour delay in treatment results in a 3-7% increase in the odds of in-hospital death.

Overview of a Septic Patient and Current Diagnostic Approach

Septic patients will vary immensely depending on how severe their condition is. Sepsis is usually defined as a Systemic Inflammatory Response Syndrome(SIRS) as a result of an infection. The clinical presentation of a septic patient can involve varying degrees of fever, tachycardia, tachypnea, hypotension, leukocytosis, as well as symptoms and signs of organ hypoperfusion and dysfunction. The evaluation of sepsis relies on three groups of clinical and laboratory data, chiefly, general systemic manifestations, manifestations of organ dysfunction/failure, and lastly, and perhaps most importantly, microbiological documentation. The first two aspects of sepsis evaluation are relatively well managed with various scoring systems and laboratory panels, but the microbiological documentation remains a problematic front. Currently, it is recommended that at least two blood cultures with or without other potential sources of cultures be obtained before administering broad-spectrum antibiotics. Although seemingly straightforward there are downsides to this approach.

The flaws in the current microbiological diagnosis of Sepsis

The current technology used for the microbiological diagnosis of sepsis leaves much to be desired when it comes to expeditious pathogen identification. Identifying the etiological pathogens by currently available methods relies on obtaining correctly timed, sterile blood samples and their analysis with cultures, nucleic acid amplification tests (NAATs), and serologic assays. The downside to this approach is the fact that blood cultures are often contaminated and more importantly, these tests all take time, with a minimum requirement of 48 hours for commonly encountered pathogens and even up to a week for more fastidious organisms. Furthermore, identifying the spectrum of antibiotic resistance for the isolated pathogen takes even more time. Additionally, due to the hypothesis-based, targeted nature of these tests, they often fail to identify the underlying cause of a patient’s symptoms and the etiology of sepsis can remain unknown in up to 60% of cases. Thus, the current limitations to the identification of etiological pathogens have prevented the rapid institution of targeted, curative antimicrobial therapy and have made the situation worse by promoting poor antibiotic stewardship with the use of broad-spectrum antimicrobials that have contributed to the development of increased antimicrobial resistance. All of these factors combined have created an increased demand for new diagnostic tests and methodologies which would help alleviate the time required for the identification of an underlying pathogen and its spectrum of antibiotic resistance, and in addition, provide possible information about virulence genes, strain typing, and host immune response profiling.

The possible future of clinical microbiological diagnosis in Sepsis

One possible technique that could help solve the problem of microbiological diagnosis in sepsis is Metagenomic Next-Generation Sequencing(mNGS). The technology behind Metagenomic Next-Generation Sequencing offers numerous advantages.

  • Hypothesis-free, culture-independent approach to pathogen detection and identification of antimicrobial resistance encoding genes directly from clinical specimens all with an accelerated turnaround time.
  • mNGS allows for thousands to billions of DNA and/or RNA fragments to be simultaneously and independently sequenced, permitting the detection of any and all bacterial, fungal, and/or viral pathogens.
  • The “unbiased” or “agnostic” approach enables broad identification of both known and unexpected pathogens in critically ill patients.
  • mNGS can provide accurate determination or at least approximate estimation of the concentrations of organisms in the biologic sample through the counting of sequenced reads, which can be particularly useful in those cases of sepsis or other bloodstream infections that have more than one etiological pathogen implicated.
  • Metagenomic Next-Generation Sequencing has the ability to provide ancillary genomic information for evolutionary tracing, strain identification, and prediction of antibiotic resistance.

The combined benefits of rapid pathogen identification and determination of antimicrobial resistance make mNGS a potent and precise tool in the diagnosis of sepsis, bloodstream infections as well as other infectious diseases.

How can Metagenomic Next-Generation Sequencing improve outcomes in Sepsis?

Metagenomic Next-Generation Sequencing(mNGS) due to its rapid turnaround time can allow for the de-escalation of broad-spectrum antibiotic therapy and the institution of targeted therapy at the point of pathogen identification and then again when susceptibilities are obtained. The expeditious de-escalation and institution of targeted antibiotic therapy are arguably the single most important aspects that will reduce sepsis-related morbidity and mortality worldwide. As such, there is an immense potential for metagenomic sequencing diagnostics in the field of clinical microbiology that can improve the outcome not only in sepsis but potentially in every other infectious disease. However, to detect extremely low amount of microorganisms, human DNA interference is still the major bottleneck of sequencing technology in clinical microbiology. The presence of contaminating human DNA is common in the sequencing results for various microbes, making it necessary.

PaRTI-Seq® new approach in faster pathogen identification

Micronbrane Medical brings solution that helps to remove interference from the host sequence to shorten the analysis time. Devin® fractionation filter uses the patented Zwitterionic Interface Ultra Self Assemble Technology to remove up to 95% of white blood cells in just 5 minutes and thus enrich microorganisms in the filtered blood sample. Pre-processed blood sample has much less host DNA interference which makes it much easier to identify pathogens by the downstream sequencing test.

Coupled with PaRTI-Seq® (Pathogen Real-Time Identification by Sequencing) the whole process from receiving sample to report takes less than 24 hours. With PaRTI-Seq® and Devin®, the proper antibiotic therapy can be administered to patients in time.


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