Blood culture vs. metagenomic next-generation sequencing for the detection of pathogenic microbes in patients with suspected bloodstream infections

By Tarun Sai LomteJun 13 2023Reviewed by Danielle Ellis, B.Sc.

A recent study published in Scientific Reports compared the detection of pathogenic microbes between blood culture and metagenomic next-generation sequencing (mNGS) in patients suspected of bloodstream infections (BSIs).

Background

BSI can manifest as fungemia, viremia, and bacteremia, increasing hospitalization duration and costs. BSI incidence has increased over the past years. As such, research focus on the early identification of pathogens has been increasing. mNGS offers several advantages over a conventional blood culture assay, such as high speed and a wide range of pathogen detection. Nevertheless, mNGS is not commonly used for BSIs due to its high costs.

About the study

In the present study, researchers compared the pathogen detection consistency of blood culture assay and mNGS. They retrospectively evaluated patients with suspected BSIs admitted to the emergency department of a Chinese hospital between January 2020 and June 2022. Eligible patients aged 16 or older had chills and body temperature above 38.5 °C, with antibiotic usage longer than three days. mNGS was performed on the day of sampling.

Blood samples were collected from two anatomical sites and cultured for up to seven days using standard microbiological procedures. For mNGS, DNA was isolated, and DNA libraries were prepared. Quality control-passed libraries were sequenced. Short, adapter, low-complexity, and low-quality reads were removed. The remaining reads were aligned to microbial genome databases.

Unique reads had > 90% identity and > 80% alignment, with the ratio of sub-optimal to optimal alignment score lower than 0.8. Patients’ medical records were reviewed. The team obtained data on demographics, comorbidities, laboratory tests, mechanical ventilation, central venous intubation, sequential organ failure assessment (SOFA), and in-hospital death. Logistic regression was performed to identify risk factors for a positive blood culture or mNGS.

Findings

The study included 99 patients suspected of BSIs. They were predominantly males and aged 63 on average. Inflammatory indicators, such as C-reactive protein (CRP), white blood cells (WBCs), and procalcitonin (PCT), were elevated in patients. Mechanical ventilation and central venous intubation were required for 36.3% and 56.5% of patients, respectively.

The median SOFA score was six. In-hospital death occurred in 37 patients. There was a statistically significant difference in the number of patients positive on a blood culture assay and mNGS. Sixty-five patients were positive on mNGS compared to 12 on blood culture assays. mNGS detected a virus in 22 patients and fungi or bacteria in the remaining patients.

By contrast, blood cultures only detected fungi or bacteria. The most common pathogens detected through blood cultures were Staphylococcus haemolyticus, Klebsiella pneumoniae, and Enterococcus faecalis. Escherichia coli, K pneumoniae, and Salmonella enterica were the most commonly identified pathogens in mNGS.

The detection rate was significantly higher with mNGS than with blood culture; the concordance in detecting fungi and bacteria was 12% between mNGS and blood culture. Logistic regression identified lower WBC count, body mass index (BMI), and elevated CRP as risk factors for pathogen detection in mNGS.

Increased age and CRP, rheumatic diseases, and alcohol abuse were the risk factors for detecting fungi or bacteria in mNGS. Current smoking status and gender were identified as the risk factors for positive blood cultures. In-hospital mortality rates were 38.4% and 35.2% in mNGS-positive and -negative cases and 38.4% and 37.2% in blood culture-positive and -negative cases, respectively.

Conclusions

Early diagnosis of BSIs is crucial; blood cultures are currently the gold standard for detection, producing results within three to five days. Besides, other techniques based on multiplex real-time polymerase chain reaction (PCR) and metagenomics have been increasing. Of these, mNGS offers rapid results and could help improve patient management.

The rate of positive blood cultures was 13.1%, consistent with previous reports. While mNGS and blood cultures identified fungi and bacteria, only mNGS detected viruses. The positive rate of mNGS was 3.31-fold higher than that of blood cultures. The mortality rate was 38.4%, higher than in prior studies.

There were no significant differences in mortality rates between culture- or mNGS-positive and negative patients. The study revealed higher positivity rates with mNGS than with conventional blood cultures, and their combined use could maximize the detection rate of bloodstream pathogens.