Metagenomic Next-Generation Sequencing vs. Traditional Pathogen Detection in the Diagnosis of Infection After Allogeneic Hematopoietic Stem Cell Transplantation in Children

Abstract

Infection is a severe complication of allo-HSCT in children, however, the accurate detection of the infection is hard. In this study, we traced the records of 101 pediatric recipients with allo-HSCT to investigate the pathogens of infection, and collected 54 bronchoalveolar lavage fluid, 32 blood, and 15 cerebrospinal fluid samples. In these samples, 87 was with post-transplant infection and 14 without infection. Using the metagenomic next-generation sequencing (mNGS) and traditional pathogen detection, we compared their sensitivity and specificity to detect pathogens of infection. Our results showed that mNGS was more sensitive (89.7%) than conventional pathogen detection (21.8%), with a difference of 67.9% (P < 0.001), However, mNGS was less specific (78.5%) than traditional methods (92.9%), with a difference of 14.4% (P = 0.596). The sensitivity of mNGS for diagnosing pulmonary infections, bloodstream infections or viremia, and CNS infections post-transplant were 91.7, 85.7, and 90.9%, respectively. In contrast, the sensitivity of conventional testing for diagnosing pulmonary infections, bloodstream infections or viremia, and CNS infections post-transplant were 22.9, 21.4, and 18.2%, respectively. There were significant differences in the sensitivity of mNGS and conventional testing in BALF, blood, and CSF samples, with P values of 0.000, 0.000, and 0.002 respectively. Among the patients with pulmonary infection, 11 pathogens were both identified by mNGS and conventional testing, and 33 by mNGS only. The percentage with the mNGS-positive result was 44/48 (91.7%), including viruses (n = 12), bacteria (n = 17), fungi (n = 9) and mixed infections (n = 6). Among the patients diagnosed with fungal pneumonia (n = 9), the most prevalent pathogenic fungi were Pneumocystis jiroveci (n = 6), which were also detected in 4 patients with mixed infectious pneumonia. In the 28 blood specimens of patients with bloodstream infections or viremia, five patients were positive by both mNGS and conventional testing, 19 were positive by mNGS, and 1 was positive by traditional testing only. The percentage with the mNGS-positive results was 24/28 (85.7%), including viruses (n = 12), bacteria (n = 4), fungi (n = 3), and mixed infections (n = 5). Of the 15 CSF specimens enrolled, 11 patients were eventually diagnosed with CNS infections. Ten pathogens were identified by mNGS in the 11 patients, including viruses (n = 8), bacteria (n = 1), and fungi (n = 1). These results suggest that mNGS is more sensitive than conventional pathogen detection for diagnosing infections post HSCT in children which may help the clinic diagnosis. Pneumocystis jiroveci was the most frequent pathogen of pulmonary infections post-transplant, while viruses were the most common pathogens of CNS infections in allo-HSCT recipients.

Clinical Diagnosis Application of Metagenomic Next-Generation Sequencing of Plasma in Suspected Sepsis

“…First, BALF is obtained from the respiratory tract, which is typically contaminated with normal oral flora, commensal organisms, and colonizers, leading to a relatively lower purity than blood samples and more pathogens than blood samples. 34 The initial infection site of a bloodstream infection is a lung infection, but not all pathogens of lung infections will enter the blood to cause sepsis. A study indicated that BALF mNGS was more sensitive than blood mNGS for bacterial and fungal pulmonary infections, which was consistent with research about the conventional test that the yield of BALF culture was higher than that of blood culture.…”

Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing for Pathogen Detection in Patients with Suspected Infectious Diseases: A Retrospective Study from a Large Tertiary Hospital

“…Additionally, since respiratory tract was inhabited by a polymicrobial community, sputum, and BALF samples may be contaminated with oral normal flora, commensal organisms, and colonizers, leading to a relatively lower purity than other sample types. 32 Considering the costs, adverse effects, and resistance of antimicrobial therapies, possible pathogens should be comprehensively judged by professionals based on the patient’s clinical background and other laboratory examination results. Thus, it should be noted the types of samples when interpreting the results of mNGS.…”

Spectrum of bronchoalveolar bacterial microbiota following hematopoietic stem cell transplantation: age dependence and microbiota shifts

“…The new sequencing methods are recently applied for analysis of BAL microbiota. When comparing relative diagnostic efficiency of conventional bacterial cultures and novel metagenomic next-generation sequencing (mNGS) of BAL samples, a much higher sensitivity was revealed by analysis of different biological samples from pediatric HSCT patients by means of NGS approach, due to versatility of DNA reading technique and larger number of potentially pathogenic agents found by the multiple DNA sequencing [19]. The sensitivity of mNGS for diagnosing pulmonary infections post-transplant was 91.7 vs 22.9% by conventional testing.…”