Diagnosis and Surveillance of Neonatal Infections by Metagenomic Next-Generation Sequencing

Abstract

Microbial infections cause significant morbidity and mortality in neonates. Metagenomic next-generation sequencing is a hypothesis-free and culture-free test that enables broad identification of pathogens and antimicrobial resistance genes directly from clinical samples within 24 h. In this study, we used mNGS for etiological diagnosis and monitoring the efficacy of antibiotic treatment in a cohort of neonatal patients with severe infections. The median age was 19.5 (3-52) days, median gestational age was 37.96 (31-40⁺³) weeks, and the median birth weight was 3,261 (1,300-4,300) g. The types of infectious diseases included pneumonia, sepsis, and meningitis. mNGS reported microbial findings in all cases, which led to changes in antibiotic treatment. These included cases of Mycobacterium tuberculosis, Legionella pneumophila, and Bacillus cereus. Eight of ten infants recovered after antibiotic adjustment and showed normal development during follow-up. On the other hand, neurological retardation was seen in two infants with meningitis. mNGS enabled etiological diagnosis and guided antibiotic therapy when all conventional methods failed to discover the culprit. It has the potential to cut down the overall cost and burden of disease management in neonatal infections.

Keywords: Bacillus cereus; Legionella pneumophila; Mycobacterium tuberculosis; metagenomic next-generation sequencing; neonatal infections.

Figure 1

Chest computed tomography image of patient 1 showing many miliary nodules (arrowheads) can be seen in both lungs.

Figure 2

The treatment course in Mycobacterium tuberculosis case. CRP, C-reactive protein; NICU, neonatal intensive care unit; and NIPPV, non-invasive positive pressure ventilation.

Figure 3

Diagnosis of L. pneumophila infection by means of Unbiased Next-Generation Sequencing (mNGS) and 16s ribosomal RNA (rRNA) sequencing. The relative abundance of L. pneumophila from the patient’s bronchoalveolar lavage fluid (BALF) by mNGS and 16s rRNA sequencing (A). Sequence reads mapped to L. pneumophila by mNGS data (B).

Figure 4

The treatment course in Legionella pneumophila case. CRP, C-reactive protein; NICU, neonatal intensive care unit; L. pneumophila, Legionella pneumophila.

Figure 5

The treatment course in Bacillus cereus case. CRP, C-reactive protein; CSF, cerebral spinal fluid; NICU, neonatal intensive care unit; B. cereus, Bacillus cereus; and NCPAP, nasal continuous positive airway pressure.