Blood culture and metagenomic next-generation sequencing for detection of pathogenic organisms in patients with suspected bloodstream infection

A recent study published in scientific report We compared the detection of pathogenic organisms between blood cultures and metagenomic next-generation sequencing (mNGS) in patients with suspected bloodstream infections (BSIs).

Background

BSI can manifest as fungemia, viremia, and bacteremia, increasing hospital stay and costs. The incidence of BSI has increased over the past few years. Therefore, an increasing number of studies are focused on early identification of pathogens. mNGS has several advantages over traditional blood culture assays, including fast and broad-spectrum pathogen detection. Nevertheless, mNGS is not commonly used for BSI due to its high cost.

About research

In this study, researchers compared the consistency of pathogen detection between blood culture assays and mNGS. They retrospectively evaluated patients with suspected BSI admitted to the emergency department of Chinese hospitals between January 2020 and June 2022. Eligible patients aged 16 years or older had chills, a temperature of 38.5°C or higher, and had used antibiotics for more than 3 days. mNGS was performed on the sampling day.

Blood samples were collected from two anatomical sites and cultured for up to 7 days using standard microbiological procedures. For mNGS, DNA was isolated and a DNA library was created. Libraries that passed quality control were sequenced. Short, adapter, low-complexity, and low-quality reads were removed. The remaining reads were matched against microbial genome databases.

Unique reads had greater than 90% identity and greater than 80% alignment, with a suboptimal to optimal alignment score ratio of less than 0.8. Patient medical records were reviewed. The research team obtained data on demographics, comorbidities, laboratory tests, mechanical ventilation, central venous intubation, serial organ failure assessment (SOFA), and in-hospital mortality. Logistic regression was performed to identify risk factors for positive blood cultures or mNGS.

Investigation result

The study included 99 patients with suspected BSI. They were predominantly male and had an average age of 63 years. Inflammatory indices such as C-reactive protein (CRP), white blood cells (WBC), and procalcitonin (PCT) were elevated in patients. His 36.3% and his 56.5% of patients required mechanical ventilation and central venous intubation, respectively.

The median SOFA score was 6. In-hospital death occurred in 37 patients. There was a statistically significant difference between the number of patients who tested positive for blood culture assays and his mNGS. Sixty-five patients were positive for her mNGS, whereas blood culture assays were positive for her 12. mNGS detected virus in 22 patients and fungi or bacteria in the remaining patients.

In contrast, only fungi or bacteria were detected in blood cultures. The most common pathogens detected in blood cultures are: Hemolytic Staphylococcus, Klebsiella pneumoniae, and Enterococcus faecalis. Escherichia coli, Klebsiella pneumoniae, and salmonella enterica It was the most commonly identified pathogen in mNGS.

The detection rate was significantly higher with mNGS than with blood culture. Concordance between mNGS and blood cultures in fungal and bacterial detection was 12%. Logistic regression identified decreased WBC count, increased body mass index (BMI), and increased CRP as risk factors for pathogen detection in mNGS.

Age and increased CRP, rheumatic disease, and alcohol abuse were risk factors for fungal and bacterial detection in mNGS. Current smoking status and gender were identified as risk factors for positive blood cultures. The in-hospital mortality rates were 38.4% and 35.2% for mNGS-positive and -negative cases, respectively, and 38.4% and 37.2% for blood culture-positive and -negative cases.

Conclusion

Early diagnosis of BSI is very important. Blood cultures are currently the gold standard for detection, providing results within 3-5 days.In addition, multiplex real-time polymerase chain reaction (PCR) and metagenomics It is increasing. Of these, mNGS provides rapid results and may help improve patient management.

The positive blood culture rate was 13.1%, consistent with previous reports. mNGS and blood cultures identified fungi and bacteria, but only mNGS detected virus. The positive rate of mNGS was 3.31 times higher than that of blood culture. Mortality was 38.4%, higher than in previous studies.

There was no significant difference in mortality between culture- or mNGS-positive and -negative patients. This study found that mNGS had a higher positivity rate than conventional blood cultures, suggesting that the combined use of mNGS may maximize the detection rate of bloodstream pathogens.