Oops, the microbes did it again: Gut dysbiosis precedes late-onset meningitis

Over the last two decades, the study of the microbiome has vastly expanded. What was once an underappreciated contributor to human health—outside of consideration as a source of pathogens and contamination—is now understood as an “organ” in its own right. Dysbiosis, an unhealthy shift in the microbiome, has been associated with disease states throughout the body. Moreover, we have come to realize that the microbiome, like other body systems, undergoes a characteristic developmental trajectory throughout infancy and childhood. Neonates and young infants have a unique microbiome, with bacterial communities that continue to develop until at least five years of age [1, 2]. The developing microbiome is also sensitive to dysbioses that have been linked to long-term sequelae, including immunological and metabolic disease [3–6].

The pre-term neonatal microbiome is particularly sensitive to microbiome-modulating factors. Pre-term infants are anatomically and immunologically underdeveloped [7, 8]. They are also more likely to be born via caesarean, which can disrupt normal colonization of the infant gut [9–11]. Further, hospitalized neonates are at increased risk of colonization with nosocomial pathogens [12, 13] and have substantially increased exposure to antibiotics. The resulting dysbiosis has been shown to contribute to the development of high-mortality infectious and inflammatory conditions, including necrotizing enterocolitis (NEC) [13–16], bloodstream infection (BSI) [14, 17, 18], and as recently described by Frerichs and Deianova et al., late-onset meningitis (LOM) [19].

Late-onset meningitis (LOM), that is, neonatal meningitis presenting between postnatal days 3 and 28 [20], is associated with both a high mortality rate and poor neurodevelopmental outcomes for survivors [20, 21]. Current diagnostic approaches are invasive: the gold standard consists of analysis and culture of cerebral spinal fluid (CSF). Lumbar punctures can be difficult to obtain and/or contraindicated. Further, culture-based approaches require days of incubation and may be falsely negative due to antibiotic administration prior to CSF collection.

Given such challenges, non-invasive, point-of-care diagnostics would represent a major advance, especially in resource-limited settings. Frerichs and Deianova et al. address this compelling need, as their findings suggest that LOM, similar to NEC and BSI, is preceded by a shift in the intestinal bacterial community characterized by intestinal pathogen outgrowth. Importantly, this dysbiosis can be detected prior to clinical symptoms of LOM—suggesting the possibility of identifying at-risk infants in time to intervene. Importantly, this work also suggests that many serious bacterial infections of infancy (NEC, BSI, and LOM) may have a similar mechanism of disease, or alternatively, that they exist on a sort of continuum. In this model (Figure 1), a dysregulation of the microbiome leads to an outgrowth of pathogenic taxa. These unwelcome blooms may directly contribute to the development of NEC, or given the immature nature of the gut epithelium, may translocate across the gut epithelium to the blood stream, causing BSI. Bacteremia pathogens have been identified in the infant gut prior to the onset of BSI [17, 18, 22]. In a subset of bacteremic neonates, the bacteria further translocate to the meninges, possibly via the highly vascularized choroid plexus, which is incompletely polarized in pre-term neonates [23], causing LOM.

Figure 1 |. Prospective model of the relationship between gut dysbiosis and serious bacterial infections in neonates.

Gut dysbiosis, characterized by an outgrowth of pathogenic taxa, contributes to the development of necrotizing enterocolitis (NEC), an inflammatory condition. The pathogenic taxa may also translocate the gut epithelium to the blood stream, initiating a bloodstream infection (BSI). In a subset of neonates, the pathogen further translocates from the blood stream to the meninges, causing late-onset meningitis (LOM) with or without BSI. Created with BioRender.com.

In this issue of JID, Frerichs and Deianova et al. detail their findings that LOM is preceded by intestinal pathogen outgrowth using a prospective longitudinal study of pre-term infants (< 30 weeks gestational age) across nine neonatal intensive care units in the Netherlands and Belgium. Fecal samples were collected from neonates during the first 28 days of life; the microbiota was assessed via 16S rRNA gene sequencing and the fecal volatile metabolome through both gas chromatography-ion mobility spectrometry (GC-IMS) and GC-time-of-flight mass spectrometry (GC-TOF-MS). Cases and controls were matched by center, gestational age, birth weight and postnatal age.

Of this 1,397-member cohort, 21 neonates were diagnosed with LOM, and 19 of these had preceding bacteremia. Microbiota analysis demonstrated an increased relative abundance of Pseudomonadota (formerly Proteobacteria) concomitant with decreases in the relative abundance of Bacillota (formerly Firmicutes) and Bacteroidota (formerly Bacteroidetes) in subjects that developed LOM relative to controls. Using a binned time-interval approach, the researchers were able to discriminate between cases and controls using both Random Forest and MaAsLin2 approaches. Indeed, the best performing Random Forest classification model based on the fecal microbiota was associated with the 1–3 day pre-diagnosis interval (AUC: 0.88) and was partially driven by a reduced relative abundance of Bacteroides and increased relative abundance of Escherichia/Shigella, as has previously been noted preceding both NEC and BSI [16, 18, 24].

Excitingly, fecal volatile profiles also appear to change prior to LOM diagnosis. GC-IMS analysis identified significant differences between cases and controls one day prior to diagnosis (Random Forest, AUC: 0.74) and GC-TOF-MS distinguished between cases and controls two days prior to diagnosis (Random Forest, AUC: 0.82). This aligns with similar findings from this group and others where multiple analytical techniques identified discriminatory changes in fecal VOCs within 3 days of diagnosis for both BSI and NEC [25–31].

This study builds on the growing literature linking pathogen outgrowth in the gastrointestinal tract and serious bacterial infections in infancy. As suggested by Frerichs and Deianova et al., the field would benefit from larger, longitudinal multi-omics studies to validate these findings. Optimally, these studies would account for within-patient variability, as study of the pre-term gut microbiome is complicated by its plastic nature [17, 32, 33]. However, the current study provides exciting support for the possibility of surveillance and early intervention with microbiota-directed therapeutics—perhaps antibiotics, probiotics, or some other strategy to protect the immature mucosal barrier. Given the suspected role of pathogen outgrowth in serious bacterial infections in neonates, and the negative association between Bifidobacterium and pathogenic taxa in the pre-term neonate gut [17, 32, 34], the possibility of probiotic administration presents a particularly intriguing approach that already has shown some promise in prevention of NEC [35].