Metagenomics Approaches to Investigate the Neonatal Gut Microbiome

Unmasking the invisible enemy: A case report of metagenomics-guided diagnosis and treatment of neonatal septic meningitis caused by Corynebacterium aurimucosum in a preterm infant with neonatal lupus erythematosus

RATIONALE

Neonatal septic meningitis is a serious condition that can be caused by various pathogens, including Corynebacterium aurimucosum, a rare and opportunistic bacterium. We reports a case of infectious meningitis in a premature infant with neonatal lupus erythematosus caused by C aurimucosum. The purpose of this study is to explore the occurrence of meningitis caused by C aurimucosum in preterm infants with neonatal lupus erythematosus. We found that early diagnosis and treatment are crucial for this type of meningitis, especially for infants with impaired immunity or mothers receiving immunosuppressive therapy. This bacterium is rare in clinical practice, but it needs to be taken seriously.

PATIENT CONCERNS

The infant was born to a mother with systemic lupus erythematosus who had a history of long-term immunosuppressive therapy. The infant presented with preterm birth, purplish-red skin, fever, and widespread scarlet dermatitis. He also had positive anti-Ro/SSA and anti-La/SSB antibodies.

DIAGNOSIS

The infant was diagnosed with neonatal lupus erythematosus based on clinical and serological features. A lumbar puncture revealed septic meningitis with high levels of total nucleated cells, protein, and Pan's test in the CSF. The macrogenic examination identified C aurimucosum as the causative agent. The culture of the mother's vaginal secretion also revealed the same bacterium.

INTERVENTIONS

The infant was treated with anti-infective therapy with ceftriaxone, ampicillin, vancomycin, and meropenem. He also received prednisone and gammaglobulin infusion for neonatal lupus erythematosus.

OUTCOMES

The infant's temperature returned to normal, and his general condition and responsiveness improved. The CSF cytology and biochemistry normalized, and the culture was negative. The cranial MRI examination showed no abnormalities. The red rash disappeared, and the follow-ups after discharge revealed no complications.

LESSONS

This case highlights the importance of early diagnosis and treatment of neonatal septic meningitis caused by C aurimucosum, especially in infants with immunocompromised conditions or maternal history of immunosuppressive therapy. C aurimucosum should not be overlooked as a potential pathogen in neonatal septic meningitis.

The Nonbacterial Microbiome: Fungal and Viral Contributions to the Preterm Infant Gut in Health and Disease

The intestinal microbiome is frequently implicated in necrotizing enterocolitis (NEC) pathogenesis. While no particular organism has been associated with NEC development, a general reduction in bacterial diversity and increase in pathobiont abundance has been noted preceding disease onset. However, nearly all evaluations of the preterm infant microbiome focus exclusively on the bacterial constituents, completely ignoring any fungi, protozoa, archaea, and viruses present. The abundance, diversity, and function of these nonbacterial microbes within the preterm intestinal ecosystem are largely unknown. Here, we review findings on the role of fungi and viruses, including bacteriophages, in preterm intestinal development and neonatal intestinal inflammation, with potential roles in NEC pathogenesis yet to be determined. In addition, we highlight the importance of host and environmental influences, interkingdom interactions, and the role of human milk in shaping fungal and viral abundance, diversity, and function within the preterm intestinal ecosystem.

Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice

The study of microorganisms is a field of great interest due to their environmental (e.g., soil contamination) and biomedical (e.g., parasitic diseases, autism) importance. The advent of revolutionary next-generation sequencing techniques, and their application to the hypervariable regions of the 16S, 18S or 23S ribosomal subunits, have allowed the research of a large variety of organisms more in-depth, including bacteria, archaea, eukaryotes and fungi. Additionally, together with the development of analysis software, the creation of specific databases (e.g., SILVA or RDP) has boosted the enormous growth of these studies. As the cost of sequencing per sample has continuously decreased, new protocols have also emerged, such as shotgun sequencing, which allows the profiling of all taxonomic domains in a sample. The sequencing of hypervariable regions and shotgun sequencing are technologies that enable the taxonomic classification of microorganisms from the DNA present in microbial communities. However, they are not capable of measuring what is actively expressed. Conversely, we advocate that metatranscriptomics is a "new" technology that makes the identification of the mRNAs of a microbial community possible, quantifying gene expression levels and active biological pathways. Furthermore, it can be also used to characterise symbiotic interactions between the host and its microbiome. In this manuscript, we examine the three technologies above, and discuss the implementation of different software and databases, which greatly impact the obtaining of reliable results. Finally, we have developed two easy-to-use pipelines leveraging Nextflow technology. These aim to provide everything required for an average user to perform a metagenomic analysis of marker genes with QIMME2 and a metatranscriptomic study using Kraken2/Bracken.