Diagnostic value of metagenomic next-generation sequencing in sepsis and bloodstream infection

Abstract

ObjectiveTo evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in sepsis and bloodstream infection (BSI).MethodsA retrospective analysis of patients diagnosed with sepsis and BSI at the First Affiliated Hospital of Zhengzhou University from January 2020 to February 2022 was conducted. All the patients underwent blood culture and were divided into mNGS group and non-mNGS group according to whether mNGS was performed or not. The mNGS group was further divided into early group (< 1 day), intermediate group (1–3 days), and late group (> 3 days) according to the time of mNGS inspection.ResultsIn 194 patients with sepsis and BSI, the positive rate of mNGS for identifying pathogens was significantly higher than that of blood culture (77.7% vs. 47.9%), and the detection period was shorter (1.41 ± 1.01 days vs. 4.82 ± 0.73 days); the difference was statistically significant (p < 0.05). The 28-day mortality rate of the mNGS group (n = 112) was significantly lower than that of the non-mNGS group (n = 82) (47.32% vs. 62.20%, p = 0.043). The total hospitalization time for the mNGS group was longer than that for the non-mNGS group (18 (9, 33) days vs. 13 (6, 23) days, p = 0.005). There was no significant difference in the ICU hospitalization time, mechanical ventilation time, vasoactive drug use time, and 90-day mortality between the two groups (p > 0.05). Sub-group analysis of patients in the mNGS group showed that the total hospitalization time and the ICU hospitalization time in the late group were longer than those in the early group (30 (18, 43) days vs. 10 (6, 26) days, 17 (6, 31) days vs. 6 (2, 10) days), and the ICU hospitalization time in the intermediate group was longer than that in the early group (6 (3, 15) days vs. 6 (2, 10) days); the differences were statistically significant (p < 0.05). The 28-day mortality rate of the early group was higher than that of the late group (70.21% vs. 30.00%), and the difference was statistically significant (p = 0.001).ConclusionsmNGS has the advantages of a short detection period and a high positive rate in the diagnosis of pathogens causing BSI and, eventually, sepsis. Routine blood culture combined with mNGS can significantly reduce the mortality of septic patients with BSI. Early detection using mNGS can shorten the total hospitalization time and the ICU hospitalization time of patients with sepsis and BSI.

Pathogen Diagnosis Value of Nanopore Sequencing in Severe Hospital-Acquired Pneumonia Patients

“…Previous studies had already demonstrated that the mNGS can improve the prognosis by guiding targeted antibiotic treatment with high sensitivity and specificity. 7 , 8 However, fewer clinical studies have verified the diagnostic accuracy and detection time of ONT sequencing. 13 And there was no clinical study exploring the consistency between ONT sequencing with the clinical diagnosis in patients with SHAP.…”

Comparative evaluation of 16S rRNA metagenomic sequencing in the diagnosis and understanding of bacterial endophthalmitis

“…Our findings also demonstrate that the pathogenesis for the syndrome can be determined even in cases with negative results from the bacterial culture. In fact, even if endophthalmitis is suspected clinically and the culture yields negative results, treatment for endophthalmitis is often continued until clinical findings improve 11–13 21. If the metagenome yields positive results in culture-negative cases, it can serve as a basis for continuing the use of antibiotics.…”

“…While WGS aims to analyse the genome of a single bacterium, 16S rRNA metagenomic analyses and shotgun metagenomics are used to comprehensively determine bacterial compositions in clinical specimens 7–10. Metagenomic analysis effectively detects pathogens responsible for systemic infectious diseases such as sepsis, pneumonia and urinary tract infection; in a short period of time and with high positivity rates 11–13. If pathogens are detected in the early stage of sepsis, proper selection of antibiotics for treatment can reduce the mortality rate 11–13.…”

2030: will we still need our microbiologist?

“…Examples include bacterial colony concentration, peptide nucleic acid fluorescence in situ hybridization (PNA FISH), and direct antimicrobial susceptibility testing (AST) from positive blood cultures [3]. Innovation extends even further with the adoption of emerging technologies that bypass the culture process entirely, such as polymerase chain reaction (PCR) on whole blood samples [4], T2 magnetic resonance technology [5], and next-generation sequencing (NGS) [6,7]. NGS, a large-scale DNA sequencing technology, still faces delays in producing results but amplicon-based sequencing has already improved its timeline, indicating the potential for similar advancements in whole genome sequencing techniques.…”