Meconium microbiota predicts clinical early-onset neonatal sepsis in preterm neonates

Increased antibiotic resistance in preterm neonates under early antibiotic use

The standard use of antibiotics in newborns to empirically treat early-onset sepsis can adversely affect the neonatal gut microbiome, with potential long-term health impacts. Research into the escalating issue of antimicrobial resistance in preterm infants and antibiotic practices in neonatal intensive care units is limited. A deeper understanding of the effects of early antibiotic intervention on antibiotic resistance in preterm infants is crucial. This retrospective study employed metagenomic sequencing to evaluate antibiotic resistance genes (ARGs) in the meconium and subsequent stool samples of preterm infants enrolled in the Routine Early Antibiotic Use in Symptomatic Preterm Neonates study. Microbial metagenomics was conducted using a subset of fecal samples from 30 preterm infants for taxonomic profiling and ARG identification. All preterm infants exhibited ARGs, with 175 unique ARGs identified, predominantly associated with beta-lactam, tetracycline, and aminoglycoside resistance. Notably, 23% of ARGs was found in preterm infants without direct or intrapartum antibiotic exposure. Post-natal antibiotic exposure increases beta-lactam/tetracycline resistance while altering mechanisms that aid bacteria in withstanding antibiotic pressure. Microbial profiling revealed 774 bacterial species, with antibiotic-naive infants showing higher alpha diversity (P = 0.005) in their microbiota and resistome compared with treated infants, suggesting a more complex ecosystem. High ARG prevalence in preterm infants was observed irrespective of direct antibiotic exposure and intensifies with age. Prolonged membrane ruptures and maternal antibiotic use during gestation and delivery are linked to alterations in the preterm infant resistome and microbiome, which are pivotal in shaping the ARG profiles in the neonatal gut.This study is registered with ClinicalTrials.gov as NCT02784821.

IMPORTANCE

A high burden of antibiotic resistance in preterm infants poses significant challenges to neonatal health. The presence of antibiotic resistance genes, along with alterations in signaling, energy production, and metabolic mechanisms, complicates treatment strategies for preterm infants, heightening the risk of ineffective therapy and exacerbating outcomes for these vulnerable neonates. Despite not receiving direct antibiotic treatment, preterm infants exhibit a concerning prevalence of antibiotic-resistant bacteria. This underscores the complex interplay of broader influences, including maternal antibiotic exposure during and beyond pregnancy and gestational complications like prolonged membrane ruptures. Urgent action, including cautious antibiotic practices and enhanced antenatal care, is imperative to protect neonatal health and counter the escalating threat of antimicrobial resistance in this vulnerable population.

Dysbiosis of the initial stool microbiota increases the risk of developing necrotizing enterocolitis or feeding intolerance in newborns

Several perinatal factors influence the intestinal microbiome of newborns during the first days of life, whether during delivery or even in utero. These factors may increase the risk of developing necrotizing enterocolitis (NEC) by causing dysbiosis linked to a NEC-associated microbiota, which may also be associated with other gastrointestinal problems. The objective of our study was to evaluate the potential risks associated with microbial shifts in newborns with gastrointestinal symptoms and identify the intestinal microbiota of neonates at risk for NEC.During the study period, 310 preterm and term newborns' first passed meconium occurring within 72 h of birth were collected, and the microbiome was analyzed. We identified the risk factors in the NEC/FI group. Regarding microbiota, we compared the bacterial abundance between the NEC/FI group at the phylum and genus levels and explored the differences in the microbial composition of the 1st stool samples. A total of 14.8% (n = 46) of the infants were diagnosed with NEC or FI. In univariate analysis, the mean gestational age and birth weight were significantly lower in the NEC/FI group (p < 0.001). Prolonged rupture of membranes (PROM) > 18 h, chorioamnionitis, and histology were significantly higher in the NEC/FI group (p < 0.001). Multivariate analysis showed that gestational age (GA), prolonged membrane rupture (> 18 h), and early onset sepsis were consistently associated with an increased risk of NEC/FI. Infants diagnosed with NEC/FI exhibited a significantly lower abundance of Actinobacteria at the phylum level than the control group (p < 0.001). At the genus level, a significantly lower abundance of Streptococcus and Bifidobacterium which belong to the Actinobacteria phylum, was observed in the NEC/FI group (p < 0.001). Furthermore, the NEC/FI had significantly lower alpha diversities (Shannon Index,3.39 vs. 3.12; P = 0.044, respectively). Our study revealed that newborns with lower diversity and dysbiosis in their initial gut microbiota had an increased risk of developing NEC, with microbiota differences appearing to be associated with NEC/FI. Dysbiosis could potentially serve as a predictive marker for NEC- or GI-related symptoms.

Temporal Investigation of the Maternal Origins of Fetal Gut Microbiota

In utero colonization or deposition of beneficial microorganisms and their by-products likely occurs through various mechanisms, such as hematogenous spread or ascension from the reproductive tract. With high-throughput sequencing techniques, the identification of microbial components in first-pass neonatal meconium has been achieved. While these components are low-biomass and often not abundant enough to culture, the presence of microbial DNA signatures may promote fetal immune tolerance or epigenetic regulation prior to birth. The aim of this study was to investigate the maternal source of the neonatal first-pass meconium microbiome. Maternal vaginal and anal samples collected from twenty-one maternal-infant dyad pairs were compared via principal component analysis to first-pass neonatal meconium microbial compositions. Results demonstrated the greatest degree of similarity between the maternal gut microbiome in the second and third trimesters and vaginal microbiome samples across pregnancy, suggesting that the maternal gut microbiota may translocate to the fetal gut during pregnancy. This study sheds light on the origin and timing of the potential transfer of maternal microbial species to offspring in utero.

Antibiotics, Analgesic Sedatives, and Antiseizure Medications Frequently Used in Critically Ill Neonates: A Narrative Review

Antibiotic, analgesic sedative, and antiseizure medications are among the most commonly used medications in preterm/sick neonates, who are at high risk of nosocomial infections, central nervous system complications, and are exposed to numerous painful/stressful procedures. These severe and potentially life-threatening complications may have serious short- and long-term consequences and should be prevented and/or promptly treated. The reported variability in the medications used in neonates indicates the lack of adequate neonatal studies regarding their effectiveness and safety. Important obstacles contributing to inadequate studies in preterm/sick infants include difficulties in obtaining parental consent, physicians' unwillingness to recruit preterm infants, the off-label use of many medications in neonates, and other scientific and ethical concerns. This review is an update on the use of antimicrobials (antifungals), analgesics (sedatives), and antiseizure medications in neonates, focusing on current evidence or knowledge gaps regarding their pharmacokinetics, indications, safety, dosage, and evidence-based guidelines for their optimal use in neonates. We also address the effects of early antibiotic use on the intestinal microbiome and its association with long-term immune-related diseases, obesity, and neurodevelopment (ND). Recommendations for empirical treatment and the emergence of pathogen resistance to antimicrobials and antifungals are also presented. Finally, future perspectives on the prevention, modification, or reversal of antibiotic resistance are discussed.

Gut microbiota and sepsis and sepsis-related death: a Mendelian randomization investigation

Background

It is unclear what the causal relationship is between the gut microbiota and sepsis. Therefore, we employed Mendelian randomization (MR) to determine whether a causal link exists between the two.

Methods

This study used publicly available genome-wide association studies (GWAS) summary data of gut microbiota, sepsis, sepsis (critical care), and sepsis (28-day death in critical care) to perform a two-sample MR analysis. To ensure the robustness of the results, we also conducted a sensitivity analysis.

Results

For sepsis susceptibility, inverse variance weighted (IVW) estimates revealed that Victivallales (OR = 0.86, 95% CI, 0.78-0.94, p = 0.0017) was protective against sepsis, while Lentisphaerae (OR = 0.89, 95% CI, 0.80-0.99), Gammaproteobacteria (OR = 1.37, 95% CI, 1.08-1.73), Clostridiaceae1 (OR = 1.21, 95% CI, 1.04-1.40), RuminococcaceaeUCG011 (OR = 1.10, 95% CI, 1.01-1.20), Dialister (OR = 0.85, 95% CI, 0.74-0.97), and Coprococcus2 (OR = 0.81, 95% CI, 0.69-0.94) presented a suggestive association with the development of sepsis (all p < 0.05). For sepsis (critical care), IVW estimates indicated that Lentisphaerae (OR = 0.70, 95% CI, 0.53-0.93), Victivallales (OR = 0.67, 95% CI, 0.50-0.91), Anaerostipes (OR = 0.49, 95% CI, 0.31-0.76), LachnospiraceaeUCG004 (OR = 0.51, 95% CI, 0.34-0.77), and Coprococcus1 (OR = 0.66, 95% CI, 0.44-0.99) showed a suggestive negative correlation with sepsis (critical care) (all p < 0.05). For sepsis (28-day death in critical care), IVW estimates suggested that four bacterial taxa had a normally significant negative correlation with the risk of sepsis-related death, including Victivallales (OR = 0.54, 95% CI, 0.30-0.95), Coprococcus2 (OR = 0.34, 95% CI, 0.14-0.83), Ruminiclostridium6 (OR = 0.43, 95% CI, 0.22-0.83), and Coprococcus1 (OR = 0.45, 95% CI, 0.21-0.97), while two bacterial taxa were normally significantly positively linked to the risk of sepsis-related death, namely, Mollicutes (OR = 2.03, 95% CI, 1.01-4.08) and Bacteroidales (OR = 2.65, 95% CI, 1.18-5.96) (all p < 0.05). The robustness of the above correlations was verified by additional sensitivity analyses.

Conclusion

This MR research found that several gut microbiota taxa were causally linked to the risk of sepsis, sepsis in critical care, and sepsis-related 28-day mortality in critical care.

Investigating prenatal and perinatal factors on meconium microbiota: a systematic review and cohort study

BACKGROUND

The first-pass meconium has been suggested as a proxy for the fetal gut microbiota because it is formed in utero. This systematic review and cohort study investigated how pre- and perinatal factors influence the composition of the meconium microbiota.

METHODS

We performed the systematic review using Covidence by searching PubMed, Scopus, and Web of Science databases with the search terms "meconium microbiome" and "meconium microbiota". In the cohort study, we performed 16 S rRNA gene sequencing on 393 meconium samples and analyzed the sequencing data using QIIME2.

RESULTS

Our systematic review identified 69 studies exploring prenatal factors, immediate perinatal factors, and microbial composition in relation to subsequent health of infants but gave only limited comparative evidence regarding factors related to the composition of the meconium microbiota. The cohort study pointed to a low-biomass microbiota consisting of the phyla Firmicutes, Proteobacteria and Actinobacteriota and the genera Staphylococcus, Escherichia-Shigella and Lactobacillus, and indicated that immediate perinatal factors affected the composition of the meconium microbiota more than did prenatal factors.

CONCLUSIONS

This finding supports the idea that the meconium microbiota mostly starts developing during delivery.

IMPACT

It is unclear when the first-pass meconium microbiota develops, and what are the sources of the colonization. In this systematic review, we found 69 studies exploring prenatal factors, immediate perinatal factors, and microbial composition relative to subsequent health of infants, but there was no consensus on the factors affecting the meconium microbiota development. In this cohort study, immediate perinatal factors markedly affected the meconium microbiota development while prenatal factors had little effect on it. As the meconium microbiota composition was influenced by immediate perinatal factors, the present study supports the idea that the initial gut microbiota develops mainly during delivery.

Effect of Feeding Fresh or Frozen Breast Milk on the Gut Microbiota of Premature Infants: A Prospective Observational Study

BACKGROUND

Breast milk is essential for premature infants. It contains a variety of functional and protective nutrients that help to create a suitable microenvironment for intestinal development and maturation. This prospective and observational study was planned to examine the effects of feeding premature infants with fresh or frozen breastmilk on their gut microbiota.

MATERIALS AND METHODS

The study was carried out with a total of 40 infants, with a gestational age of 28-326 weeks, fed fresh (n = 20) or frozen (n = 20) breastmilk. Stool samples were stored at -80°C until analysis. Infants were included in groups based on the feed type, which accounted for more than 70% of their 10-day feeding. The Mann-Whitney U, Chi-square, and t-tests were used to evaluate the demographic data. Stool samples were analyzed by sequencing the V3--V4 region of the 16S rRNA gene from the extracted DNA for microbiota analysis.

RESULTS

Streptococcus and Enterobacteriales, the majority of which are considered human pathogens, in infants receiving frozen breastmilk (Streptococcus 69%, Enterobacteriales 79%) was higher than that in infants receiving fresh breastmilk (Streptococcus 16%, Enterobacteriales 49%). Further, the Lactobacillus and Bifidobacterium species were more abundant in infants who received fresh breastmilk (Lactobacillus 17%, Bifidobacterium 12%) than in infants who received frozen breastmilk (Lactobacillus 3%, Bifidobacterium 1%).

CONCLUSION

Thus, compared to frozen breast milk, fresh breastmilk has an effect on the diversity of preterm infants' gut microbiota.

Neonatal Paenibacilliosis: Paenibacillus Infection as a Novel Cause of Sepsis in Term Neonates With High Risk of Sequelae in Uganda

BACKGROUND

Paenibacillus thiaminolyticus may be an underdiagnosed cause of neonatal sepsis.

METHODS

We prospectively enrolled a cohort of 800 full-term neonates presenting with a clinical diagnosis of sepsis at 2 Ugandan hospitals. Quantitative polymerase chain reaction specific to P. thiaminolyticus and to the Paenibacillus genus were performed on the blood and cerebrospinal fluid (CSF) of 631 neonates who had both specimen types available. Neonates with Paenibacillus genus or species detected in either specimen type were considered to potentially have paenibacilliosis, (37/631, 6%). We described antenatal, perinatal, and neonatal characteristics, presenting signs, and 12-month developmental outcomes for neonates with paenibacilliosis versus clinical sepsis due to other causes.

RESULTS

Median age at presentation was 3 days (interquartile range 1, 7). Fever (92%), irritability (84%), and clinical signs of seizures (51%) were common. Eleven (30%) had an adverse outcome: 5 (14%) neonates died during the first year of life; 5 of 32 (16%) survivors developed postinfectious hydrocephalus (PIH) and 1 (3%) additional survivor had neurodevelopmental impairment without hydrocephalus.

CONCLUSIONS

Paenibacillus species was identified in 6% of neonates with signs of sepsis who presented to 2 Ugandan referral hospitals; 70% were P. thiaminolyticus. Improved diagnostics for neonatal sepsis are urgently needed. Optimal antibiotic treatment for this infection is unknown but ampicillin and vancomycin will be ineffective in many cases. These results highlight the need to consider local pathogen prevalence and the possibility of unusual pathogens when determining antibiotic choice for neonatal sepsis.

Early Gut Microbiota Profile in Healthy Neonates: Microbiome Analysis of the First-Pass Meconium Using Next-Generation Sequencing Technology

Gut microbiome development during early life has significant long-term effects on health later in life. The first-pass meconium is not sterile, and it is important to know the initial founder of the subsequent gut microbiome. However, there is limited data on the microbiota profile of the first-pass meconium in healthy neonates. To determine the early gut microbiota profile, we analyzed 39 samples of the first-pass meconium from healthy neonates using 16S rRNA sequencing. Our results showed a similar profile of the microbiota composition in the first-pass meconium samples. Pseudomonas was the most abundant genus in most samples. The evenness of the microbial communities in the first-pass meconium was extremely poor, and the average Shannon diversity index was 1.31. An analysis of the relationship between perinatal characteristics and the meconium microbiome revealed that primigravidae babies had a significantly higher Shannon diversity index (p = 0.041), and the Bacteroidales order was a biomarker for the first-pass meconium of these neonates. The Shannon diversity index was not affected by the mode of delivery, maternal intrapartum antibiotic treatment, prolonged rupture of membranes, or birth weight. Our study extends previous research with further characterization of the gut microbiome in very early life.

Impact of disinfectants on the intestinal bacterial symbionts and immunity of silkworm (Bombyx mori L.)

The insect egg surface can serve as a vehicle for vertical symbiont transmission from the maternal parent to its offspring. Hypochlorite and formaldehyde are two common disinfectants used for insect egg surface sterilization. Here, we explored the intestinal microecology and immune response profile of the silkworm Bombyx mori strain Dazao after disinfectant exposure by using high-throughput sequencing technology and real-time PCR analysis. After egg surface sterilization, no significant difference (P > 0.05) in overall body weight was observed among the control, sodium hypochlorite, and formaldehyde groups. 16S rRNA metagenomic sequencing revealed that the main abundant intestinal bacteria were Enterococcus, Burkholderia, Phenylobacterium, Ralstonia, Chitinophaga, Bradyrhizobium, Herbaspirillum, and two unclassified Bacteroidetes species. Egg surface sterilization evidently altered the composition and abundance of intestinal microbiota but did not significantly change its alpha diversity. The dysbiosis of intestinal microbiota resulted in the perturbation of the immune response profile of the silkworm intestine. Our findings reveal that hypochlorite has a blocking effect on the symbiont transmission compared with formaldehyde. More importantly, egg surface sterilization exerts substantial effects on the ecophysiological traits of insects. The present study contributes to the scientific and reasonable application of disinfectants for insect egg surface sterilization during industrial silk production and laboratory-scale insect rearing.

First 1000 Days and Beyond After Birth: Gut Microbiota and Necrotizing Enterocolitis in Preterm Infants

Preterm birth remains a major maternal and infant health issue worldwide particularly with an increase in the global preterm birth rate, which requires more interventions to manage the consequences of preterm birth. In addition to traditional complications, recent studies have shown that the succession of gut microbiota of preterm infants is disordered due to the systemic physiological immaturity, which confers negative influences on the growth, development, and health of infants. In the present study, we briefly discussed the prevalence of preterm birth worldwide and then highlighted the signatures of gut microbiota in preterm infants within the first 1000 days of life after the birth categorized into birth, infancy, and childhood. Afterward, we focused on the potential association of clinical phenotypes typically associated with preterm birth (i.e., necrotizing enterocolitis) with gut microbiota, and the potential directions for future studies in this field are finally discussed.

Meconium Microbiome of Very Preterm Infants across Germany

Meconium constitutes infants' first bowel movements postnatally. The consistency and microbial load of meconium are different from infant and adult stool. While recent evidence suggests that meconium is sterile in utero, rapid colonization occurs after birth. The meconium microbiome has been associated with negative health outcomes, but its composition is not well described, especially in preterm infants. Here, we characterized the meconium microbiomes from 330 very preterm infants (gestational ages 28 to 32 weeks) from 15 hospitals in Germany and in fecal samples from a subset of their mothers (N = 217). Microbiome profiles were compiled using 16S rRNA gene sequencing with negative and positive controls. The meconium microbiome was dominated by Bifidobacterium, Staphylococcus, and Enterococcus spp. and was associated with gestational age at birth and age at sample collection. Bifidobacterial abundance was negatively correlated with potentially pathogenic genera. The amount of bacterial DNA in meconium samples varied greatly across samples and was associated with the time since birth but not with gestational age or hospital site. In samples with low bacterial load, human mitochondrial sequences were highly amplified using commonly used, bacterial-targeted 16S rRNA primers. Only half of the meconium samples contained sufficient bacterial material to study the microbiome using a standard approach. To facilitate future meconium studies, we present a five-level scoring system (“MecBac”) that predicts the success of 16S rRNA bacterial sequencing for meconium samples. These findings provide a foundational characterization of an understudied portion of the human microbiome and will aid the design of future meconium microbiome studies.

IMPORTANCE Meconium is present in the intestines of infants before and after birth and constitutes their first bowel movements postnatally. The consistency, composition and microbial load of meconium is largely different from infant and adult stool. While recent evidence suggests that meconium is sterile in utero, rapid colonization occurs after birth. The meconium microbiome has been associated with short-term and long-term negative health outcomes, but its composition is not yet well described, especially in preterm infants. We provide a characterization of the microbiome structure and composition of infant meconium and maternal feces from a large study cohort and propose a method to evaluate meconium samples for bacterial sequencing suitability. These findings provide a foundational characterization of an understudied portion of the human microbiome and will aid the design of future meconium microbiome studies.