The role of breast milk in the colonization of neonatal gut and skin with coagulase-negative staphylococci

Molecular epidemiology and antibiotic resistance of staphylococci other than Staphylococcus aureus in children in Cape Town, South Africa

Introduction

Staphylococci other than Staphylococcus aureus (SOSA) have emerged as significant pathogens in healthcare settings, particularly among patients with indwelling devices and immunocompromised individuals. Staphylococcus epidermidis, Staphylococcus haemolyticus and Staphylococcus hominis are the most common commensal SOSA species and are implicated in infections such as endocarditis and bacteremia. SOSA infections in neonates and children have been reported globally. Recent increases in antibiotic resistance and virulence among SOSA strains in clinical settings have highlighted the need to describe the reservoirs of SOSA to enable monitoring of these emerging pathogens.

Methods

Stool samples were collected from 150 healthy children from Cape Town communities between 2017 and 2020. Staphylococci were isolated, identified using mass-spectrometry, and antimicrobial susceptibility testing and Illumina whole genome sequencing were performed.

Results

Among the participants, 50 (33.3%) were colonized by SOSA, with S. haemolyticus (n = 38; 25.3%) being the most common, followed by S. hominis (n = 5; 3.3%) and Mammalicoccus sciuri (n = 5; 3.3%). Out of the 77 initially isolated S. haemolyticus strains, 23 were identified as Staphylococcus borealis through whole genome sequencing. All S. haemolyticus isolates (n = 49) were methicillin resistant, with 65.3% (n = 32) harbouring mecA. In S. haemolyticus, SCCmec type VIII(4A) was detected in 42.0% of ST9 isolates while non-mecA methicillin resistant S. haemolyticus isolates were mostly ST49 (41.1%). Additionally, 16 (50.0%) S. haemolyticus strains contained non-typeable SCCmec elements.

Discussion

High rates of methicillin resistance were identified among colonizing SOSA in Cape Town, increasing the risk of transmission to clinical settings. This study also identified a new species, S. borealis, for the first time in Africa.

Effect of early directed implementation of family-integrated care measures on colonisation with Enterobacteriaceae in preterm neonates in NICU

BACKGROUND

Hospital-acquired strains (HASs) and multiresistant strains in neonatal intensive care unit often harbour virulence and resistance mechanisms, carrying the risk of invasive infections. We describe colonisation with Enterobacteriaceae in neonates receiving early directed versus routine family-integrated care (FIC) within the first month of life.

METHODS

A prospective cohort study included neonates with a gestational age below 34 weeks. During the first period, neonates were admitted to an open bay unit with transfer to the single-family room if available; feeding with the mother's own breast milk (MOBM) was introduced within 24 hours, and skin-to-skin contact (SSC) within 5 days of life (the routine care group). During the second period, following a wash-in of 2 months, care in a single-family room within 48 hours, the introduction of MOBM within two and SSC in 48 hours were applied (the intervention group). Enterobacteriaceae isolated from neonatal stool, breast milk and parental skin swabs were genotyped, Simpson's Index of Diversity (SID) calculated, and extended-spectrum beta-lactamases (ESBL) detected.

RESULTS

In 64 neonate-parents' groups, 176 Enterobacteriaceae, 87 in routine care and 89 in the intervention group were isolated; 26 vs 18 were HAS and one vs three ESBL positive, respectively. In the intervention group compared with the routine care group, SSC and MOBM feeding was started significantly earlier (p<0.001); during the first week of life, time spent in SSC was longer (median hours per day 4.8 (4-5.1) vs 1.9 (1.4-2.6), p<0.001) and the proportion of MOBM in enteral feeds was higher (median (IQR) 97.8% (95.1-100) vs 95.1% (87.2-97.4), p=0.011). Compared with the routine care group, the intervention group had higher SID and a reduction of HAS by 33.1% (95% CI 24.4% to 42.4%) in time series analysis.

CONCLUSIONS

Early implementation of FIC measures may hold the potential to increase diversity and reduce colonisation with HAS Enterobacteriaceae.

Human Milk Microbiota Profile Affected by Prematurity in Argentinian Lactating Women

To study (16S rRNA-sequencing) the impact of gestational and corrected ages on the microbiota profile of human milk (HM) of mothers that delivered full-term and pre-term children, HM samples were obtained and classified according to the gestational age as group T (full-term births ≥37 weeks), and group P (pre-term births <37 weeks). Group P was longitudinally followed, and the samples were collected at the full-term corrected gestational age: when the chronological age plus the gestational age were ≥37 weeks (PT group). The HM microbiota composition differed depending on the gestational age (T vs. P). Group T had lower levels of Staphylococcus and higher levels of Rothia and Streptococcus, as compared to group P. The alpha Simpson diversity value was higher in group T than in P, whereas no differences were found between groups T and PT, suggesting a microbial evolution of the composition of group P towards group T over chronological age. Full-term delivery was associated with a greater diversity of microbes in HM. The microbial composition of pre-term HM, at the corrected age, did not show significant differences, as compared to the samples obtained from the full-term group, suggesting that it would be appropriate to consider the corrected age in terms of the composition and the diversity of the milk in future studies.

Dynamics of oral microbiome acquisition in healthy infants: A pilot study

Objectives

The human oral microbiota is one of the most complex bacterial communities in the human body. However, how newborns initially acquire these bacteria remains largely unknown. In this study, we examined the dynamics of oral microbial communities in healthy infants and investigated the influence of the maternal oral microbiota on the acquisition of the infant's oral microbiota. We hypothesized that the infant oral microbial diversity increases with age.

Methods

One hundred and sixteen whole-salivary samples were collected from 32 healthy infants and their biological mothers during postpartum and 9- and 15-month well-infant visits. Bacterial genomic DNA was extracted and sequenced by Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) methods. The Shannon index was used to measure the microbial diversity of the infant-mother dyads (alpha diversity). The microbial diversity between the mother-infant dyads (beta-diversity) was calculated using the weighted non-phylogenetic Bray-Curtis distance in QIIME 1.9.1. Core microbiome analysis was performed using MicrobiomeAnalyst software. Linear discriminant analysis coupled with effect size analysis was used to identify differentially abundant features between mother and infant dyads.

Results

A total of 6,870,571 16S rRNA reads were generated from paired mother-infant saliva samples. Overall, oral microbial profiles significantly differed between the mother and infant groups (p < 0.001). The diversity of the salivary microbiomes in the infants increased in an age-dependent manner, whereas the core microbiome of the mothers remained relatively stable during the study period. Breastfeeding and gender did not affect the microbial diversity in infants. Moreover, infants had a greater relative abundance of Firmicutes and a lower abundance of Actinobacteria, Bacteroidetes, Fusobacteria, and Proteobacteria than their mothers. The SparCC correlation analysis demonstrated constant changes in infants' oral microbial community network (p < 0.05).

Conclusions

This study provides new evidence that the oral cavities of infants are colonized by a distinct group of bacterial species at birth. The acquisition and diversity of changes in oral microbial composition are dynamic during the first year of an infant's life. Before reaching the second birthday, the composition of the oral microbial community could be more similar to that of their biological mothers.

The Association between Infant Colic and the Multi-Omic Composition of Human Milk

Infant colic is a common condition with unclear biologic underpinnings and limited treatment options. We hypothesized that complex molecular networks within human milk (i.e., microbes, micro-ribonucleic acids (miRNAs), cytokines) would contribute to colic risk, while controlling for medical, social, and nutritional variables. This hypothesis was tested in a cohort of 182 breastfed infants, assessed with a modified Infant Colic Scale at 1 month. RNA sequencing was used to interrogate microbial and miRNA features. Luminex assays were used to measure growth factors and cytokines. Milk from mothers of infants with colic (n = 28) displayed higher levels of Staphylococcus (adj. p = 0.038, d = 0.30), miR-224-3p (adj. p = 0.023, d = 0.33), miR-125b-5p (adj. p = 0.028, d = 0.29), let-7a-5p (adj. p = 0.028, d = 0.27), and miR-205-5p (adj. p = 0.029, d = 0.26) compared to milk from non-colic mother-infant dyads (n = 154). Colic symptom severity was directly associated with milk hepatocyte growth factor levels (R = 0.21, p = 0.025). A regression model involving let-7a-5p, miR-29a-3p, and Lactobacillus accurately modeled colic risk (X² = 16.7, p = 0.001). Molecular factors within human milk may impact colic risk, and provide support for a dysbiotic/inflammatory model of colic pathophysiology.

The Role of Coagulase-Negative Staphylococci Biofilms on Late-Onset Sepsis: Current Challenges and Emerging Diagnostics and Therapies

Infections are one of the most significant complications of neonates, especially those born preterm, with sepsis as one of the principal causes of mortality. Coagulase-negative staphylococci (CoNS), a group of staphylococcal species that naturally inhabit healthy human skin and mucosa, are the most common cause of late-onset sepsis, especially in preterms. One of the risk factors for the development of CoNS infections is the presence of implanted biomedical devices, which are frequently used for medications and/or nutrient delivery, as they serve as a scaffold for biofilm formation. The major concerns related to CoNS infections have to do with the increasing resistance to multiple antibiotics observed among this bacterial group and biofilm cells’ increased tolerance to antibiotics. As such, the treatment of CoNS biofilm-associated infections with antibiotics is increasingly challenging and considering that antibiotics remain the primary form of treatment, this issue will likely persist in upcoming years. For that reason, the development of innovative and efficient therapeutic measures is of utmost importance. This narrative review assesses the current challenges and emerging diagnostic tools and therapies for the treatment of CoNS biofilm-associated infections, with a special focus on late-onset sepsis.

Human milk microbial species are associated with infant head-circumference during early and late lactation in Guatemalan mother-infant dyads

Human milk contains abundant commensal bacteria that colonize and establish the infant's gut microbiome but the association between the milk microbiome and head circumference during infancy has not been explored. For this cross-sectional study, head-circumference-for-age-z-scores (HCAZ) of vaginally delivered breastfed infants were collected from 62 unrelated Mam-Mayan mothers living in eight remote rural communities in the Western Highlands of Guatemala during two stages of lactation, 'early' (6-46 days postpartum, n = 29) or 'late' (109-184 days postpartum, n = 33). At each stage of lactation, infants were divided into HCAZ ≥ -1 SD (early: n = 18; late: n = 14) and HCAZ < -1 SD (early: n = 11; late: n = 19). Milk microbiome communities were assessed using 16S ribosomal RNA gene sequencing and DESeq2 was used to compare the differential abundance (DA) of human milk microbiota with infant HCAZ subgroups at both stages of lactations. A total of 503 ESVs annotated 256 putative species across the 64 human milk samples. Alpha-diversity using Chao index uncovered a difference in microbial community richness between HCAZ ≥ -1 SD and HCAZ < -1 SD groups at late lactation (p = 0.045) but not at early lactation. In contrast, Canonical Analysis of Principal Coordinates identified significant differences between HCAZ ≥ -1 SD and HCAZ < -1 SD at both stages of lactation (p = 0.003); moreover, 26 milk microbial taxa differed in relative abundance (FDR < 0.05) between HCAZ ≥ -1 SD and HCAZ < -1 SD, with 13 differentially abundant at each lactation stage. Most species in the HCAZ ≥ -1 SD group were Streptococcus species from the Firmicutes phylum which are considered human colonizers associated with human milk whereas the HCAZ < -1 SD group at late lactation had more differentially abundant taxa associated with environmentally and 'potentially opportunistic' species belonging to the Actinobacteria genus. These findings suggest possible associations between brain growth of breastfed infants and the milk microbiome during lactation. Importantly, these data provide the first evidence of cross talk between the human milk microbiome and the infant brain that requires further investigation.

Human Milk Oligosaccharides and Bacterial Profile Modulate Infant Body Composition during Exclusive Breastfeeding

Human milk is a complex and variable ecosystem fundamental to the development of newborns. This study aimed to investigate relationships between human milk oligosaccharides (HMO) and human milk bacterial profiles and infant body composition. Human milk samples (n = 60) were collected at two months postpartum. Infant and maternal body composition was measured with bioimpedance spectroscopy. Human milk bacterial profiles were assessed using full-length 16S rRNA gene sequencing and 19 HMOs were quantitated using high-performance liquid chromatography. Relative abundance of human milk bacterial taxa were significantly associated with concentrations of several fucosylated and sialylated HMOs. Individual human milk bacteria and HMO intakes and concentrations were also significantly associated with infant anthropometry, fat-free mass, and adiposity. Furthermore, when data were stratified based on maternal secretor status, some of these relationships differed significantly among infants born to secretor vs non-secretor mothers. In conclusion, in this pilot study the human milk bacterial profile and HMO intakes and concentrations were significantly associated with infant body composition, with associations modified by secretor status. Future research designed to increase the understanding of the mechanisms by which HMO and human milk bacteria modulate infant body composition should include intakes in addition to concentrations.

Exclusively Breastfed Infant Microbiota Develops over Time and Is Associated with Human Milk Oligosaccharide Intakes

Temporal development of maternal and infant microbiomes during early life impacts short- and long-term infant health. This study aimed to characterize bacterial dynamics within maternal faecal, human milk (HM), infant oral, and infant faecal samples during the exclusive breastfeeding period and to document associations between human milk oligosaccharide (HMO) intakes and infant oral and faecal bacterial profiles. Maternal and infant samples (n = 10) were collected at 2−5, 30, 60, 90 and 120 days postpartum and the full-length 16S ribosomal RNA (rRNA) gene was sequenced. Nineteen HMOs were quantitated using high-performance liquid chromatography. Bacterial profiles were unique to each sample type and changed significantly over time, with a large degree of intra- and inter-individual variation in all sample types. Beta diversity was stable over time within infant faecal, maternal faecal and HM samples, however, the infant oral microbiota at day 2−5 significantly differed from all other time points (all p < 0.02). HMO concentrations and intakes significantly differed over time, and HMO intakes showed differential associations with taxa observed in infant oral and faecal samples. The direct clinical relevance of this, however, is unknown. Regardless, future studies should account for intakes of HMOs when modelling the impact of HM on infant growth, as it may have implications for infant microbiota development.

A systematic review of the factors influencing microbial colonization of the preterm infant gut

Prematurity coupled with the necessary clinical management of preterm (PT) infants introduces multiple factors that can interfere with microbial colonization. This study aimed to review the perinatal, physiological, pharmacological, dietary, and environmental factors associated with gut microbiota of PT infants. A total of 587 articles were retrieved from a search of multiple databases. Sixty studies were included in the review after removing duplicates and articles that did not meet the inclusion criteria. Review of this literature revealed that evidence converged on the effect of postnatal age, mode of delivery, use of antibiotics, and consumption of human milk in the composition of gut microbiota of PT infants. Less evidence was found for associations with race, sex, use of different fortifiers, macronutrients, and other medications. Future studies with rich metadata are needed to further explore the impact of the PT exposome on the development of the microbiota in this high-risk population.

Mother's Milk Microbiome Shaping Fecal and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Analysis

The child microbiome, including gut and skin communities, is shaped by a multitude of factors, and breastfeeding is one of the most essential. Food allergy (FA) and atopic dermatitis (AD) are among the most common diseases in pediatrics, with the prevalence of each up to 6% and 20%, respectively. Therefore, we aimed at finding differences between the fecal and skin microbiomes of FA and AD patients in the context of breastfeeding, by means of the Illumina sequencing of 16S rRNA gene fragment libraries amplified from the total DNA isolated from samples collected from allergic and healthy infants. We also analyzed milk samples from the mothers of the examined children and searched for patterns of incidence suggesting milk influence on an infant's allergy status. Here we show that a mother's milk influences her child's fecal and skin microbiomes and identify Acinetobacter as the taxon whose abundance is correlated with milk and child-derived samples. We demonstrate that breastfeeding makes allergic children's fecal and skin communities more similar to those of healthy infants than in the case of formula-feeding. We also identify signature taxa that might be important in maintaining health or allergy development.

Distinct Changes Occur in the Human Breast Milk Microbiome Between Early and Established Lactation in Breastfeeding Guatemalan Mothers

Human breast milk contains a diverse community of bacteria, but as breast milk microbiome studies have largely focused on mothers from high income countries where few women breastfeed to 6 months, the temporal changes in the breast milk microbiome that occur during later lactation stages have not been explored. For this cross-sectional study, microbiota from breast milk samples of Mam-Mayan mothers living in eight remote rural communities in the Western Highlands of Guatemala were analyzed. All mothers delivered vaginally and breastfed their infants for 6 months. Breast milk from 76 unrelated mothers was used to compare two lactation stages, either “early” (6–46 days post-partum, n = 33) or “late” (109–184 days post-partum, n = 43). Breast milk microbial communities were assessed using 16S ribosomal RNA gene sequencing and lactation stages were compared using DESeq2 differential abundance analysis. A total of 1,505 OTUs were identified, including 287 which could be annotated as putative species. Among several maternal factors, lactation stage explained microbiome variance and inertia in ordination with the most significance (p < 0.001). Differential abundance analysis identified 137 OTUs as significantly higher in either early or late lactation. These included a general shift from Staphylococcus and Streptococcus species in early lactation to Sphingobium and Pseudomonas species in late lactation. Species enriched in early lactation included putative commensal bacteria known to colonize the infant oral and intestinal tracts whereas species enriched in late lactation had a uniform functional trait associated with aromatic compound degradation. Differentially abundant species also included several species which have not previously been reported within breast milk, such as Janthinobacterium agaricidamnosum, Novosphingobium clariflavum, Ottowia beijingensis, and Flavobacterium cucumis. These discoveries describe temporal changes to the breast milk microbiome of healthy Guatemalan mothers from early to late lactation. Collectively, these findings illustrate how studying under-represented human populations might advance our understanding of factors that modulate the human milk microbiome in low and middle income countries (LMIC).

Human Milk-Based or Bovine Milk-Based Fortifiers Differentially Impact the Development of the Gut Microbiota of Preterm Infants

Background: Preterm infants are exposed to different dietary inputs during their hospitalization in the neonatal intensive care unit (NICU). These include human milk (HM), with a human milk-based (HMF) or a bovine milk-based (BMF) fortifier, or formula. Milk consumption and the type of fortification will cause changes in the gut microbiota structure of preterm infants. This study aimed to characterize the gut microbiota of PT infant according to the type of feeding and the type of HM fortification and its possible association with infant's growth. Methods: Ninety-seven infants born ≤33 wks of gestation or <1,500 g were followed during the hospitalization period in the NICU after birth until discharge. Clinical and dietary information was collected, including mode of delivery, pregnancy complications, mechanical ventilation, use of antibiotics, weight, and type and amount of milk consumed. To characterize the gut microbiota composition, weekly stool samples were collected from study participants. The V3-V4 region of the 16S rRNA bacterial gene was Sequenced using Illumina MiSeq technology. Results: After birth, black maternal race, corrected gestational age (GA) and exposure to pregnancy complications, had a significant effect on gut microbial diversity and the abundance of Enterococcus, Veillonella, Bifidobacterium, Enterobacter, and Bacteroides. Over the course of hospitalization, corrected GA and exposure to chorioamnionitis remained to have an effect on gut microbial composition. Two different enterotypes were found in the gut microbiota of preterm infants. One enriched in Escherichia-Shigella, and another enriched in uncharacterized Enterobacteriaceae, Klebsiella and Clostridium sensu stricto 1. Overall, HM and fortification with HMF were the most common feeding strategies. When consuming BMF, PT infants had higher growth rates than those consuming HMF. Milk and type of fortification were significantly associated with the abundance of Clostridium sensu stricto 1, Bifidobacterium and Lactobacillus. Conclusions: This observational study shows the significant association between milk consumption and the exposure to HMF or BMF fortification in the fecal microbiota composition of preterm infants. Additionally, these results show the effect of other perinatal factors in the establishment and development of PT infant's gut microbiota.

The Microbiota of the Human Mammary Ecosystem

Human milk contains a dynamic and complex site-specific microbiome, which is not assembled in an aleatory way, formed by organized microbial consortia and networks. Presence of some genera, such as Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium (formerly known as Propionibacterium), Lactobacillus, Lactococcus and Bifidobacterium, has been detected by both culture-dependent and culture-independent approaches. DNA from some gut-associated strict anaerobes has also been repeatedly found and some studies have revealed the presence of cells and/or nucleic acids from viruses, archaea, fungi and protozoa in human milk. Colostrum and milk microbes are transmitted to the infant and, therefore, they are among the first colonizers of the human gut. Still, the significance of human milk microbes in infant gut colonization remains an open question. Clinical studies trying to elucidate the question are confounded by the profound impact of non-microbial human milk components to intestinal microecology. Modifications in the microbiota of human milk may have biological consequences for infant colonization, metabolism, immune and neuroendocrine development, and for mammary health. However, the factors driving differences in the composition of the human milk microbiome remain poorly known. In addition to colostrum and milk, breast tissue in lactating and non-lactating women may also contain a microbiota, with implications in the pathogenesis of breast cancer and in some of the adverse outcomes associated with breast implants. This and other open issues, such as the origin of the human milk microbiome, and the current limitations and future prospects are addressed in this review.

Probiotic Supplementation During the Perinatal and Infant Period: Effects on Gut Dysbiosis and Disease

The perinatal period is crucial to the establishment of lifelong gut microbiota. The abundance and composition of microbiota can be altered by several factors such as preterm delivery, formula feeding, infections, antibiotic treatment, and lifestyle during pregnancy. Gut dysbiosis affects the development of innate and adaptive immune responses and resistance to pathogens, promoting atopic diseases, food sensitization, and infections such as necrotizing enterocolitis (NEC). Recent studies have indicated that the gut microbiota imbalance can be restored after a single or multi-strain probiotic supplementation, especially mixtures of Lactobacillus and Bifidobacterium strains. Following the systematic search methodology, the current review addresses the importance of probiotics as a preventive or therapeutic tool for dysbiosis produced during the perinatal and infant period. We also discuss the safety of the use of probiotics in pregnant women, preterm neonates, or infants for the treatment of atopic diseases and infections.

A systematic comparison between infant formula compositions using the Bray-Curtis Similarity Index

BACKGROUND

Making an informed choice between the available infant formulas is challenging, as there is no unbiased tool allowing a systematic comparison between the very long lists of infant formula compositions.

AIM

The aim is to present the Bray-Curtis Similarity Index (BCSI) as a tool for systematic comparison between standard stage-1 infant formula (SS-1-IF) compositions.

METHODS

We obtained the nutrient levels from the packaging labels of 23 SS-1-IFs available in Al-Ahsa, Saudi Arabia, in April 2018. The international legislations that launched infant formula standards endorse targeting the minimum rather than the maximum proposed nutrients levels. Thus, we blindly compared between displayed nutrients levels on each of the 23-studied SS-1-IF and the minimum international proposed nutrient levels via using the BCSI.

RESULTS

The range of the total displayed components was 38-57. Except for docosahexaenoic acid, all displayed components were within the standard recommended range. The BCSI summarized all displayed nutrients in a single number. The BCSI of the studied SS-1-IF ranged from 0.4141 to 0.79730. We ranked the 23 studied SS-1-IFs based on the higher BCSI is the closer to the minimum proposed nutrient levels. A dendrogram segregated the SS-1-IFs into four clusters based on their BSCI and total numbers of all displayed components.

CONCLUSIONS

We think the BCSI is an appropriate tool for a systematic comparison between SS-1-IFs compositions and may help for choosing a SS-1-IF.

Genetic Relatedness of Staphylococcus haemolyticus in Gut and Skin of Preterm Neonates and Breast Milk of Their Mothers

BACKGROUND

Staphylococcus haemolyticus is a common colonizer and cause of late-onset sepsis (LOS) in preterm neonates. By describing genetic relatedness, we aimed to determine whether mother's breast milk (BM) is a source of S. haemolyticus colonizing neonatal gut and skin and/or causing LOS.

METHODS

S. haemolyticus was isolated from stool and skin swabs of 49 BM-fed preterm neonates admitted to neonatal intensive care unit, 20 healthy BM-fed term neonates and BM of mothers once a week and typed by multilocus variable number tandem repeat analysis and multilocus sequence typing. Virulence-related genes were determined by polymerase chain reaction.

RESULTS

Compared with term neonates, S. haemolyticus colonized more commonly gut (35% vs. 89.9%; P < 0.001) and skin (50% vs. 91.8%; P < 0.001) of preterm neonates and mothers' BM (15% vs. 38.8%). Isolates from preterm compared with term neonates and their mothers carried more commonly the mecA gene (83.5% vs. 5.4%; P < 0.001) and IS256 (52.4% vs. 2.7%; P < 0.001) and belonged to clonal complex 29 (89.1% vs. 63%; P = 0.014). Only 7 (14.3%) preterm and 3 (15%) term neonates were colonized in gut or on skin with multilocus variable number tandem repeat analysis types indistinguishable from those in BM. Most frequent multilocus variable number tandem repeat analysis types belonged to sequence type 3 or 42, comprised 71.1%-78.4% of isolates from preterm neonates/mothers and caused all 7 LOS episodes. LOS-causing strain colonized the gut of 4/7 and the skin of 5/7 neonates, but not BM, before onset of LOS.

CONCLUSIONS

S. haemolyticus colonizing gut and skin or causing LOS in preterm neonates rarely originate from BM but are mecA-positive strains adapted to hospital environment.

Genetic relatedness of Gram-negative bacteria colonizing gut and skin of neonates and mother's own milk

OBJECTIVE

We described colonization of mother's own milk with Gram-negative bacteria and its relationship with neonatal colonization.

STUDY DESIGN

Gram-negative bacteria isolated from weekly collected stool, skin and mother's own milk of hospitalized preterm (n = 49) and healthy term neonates (n = 20) were genotyped. Colonization-related factors were determined by logistic regression.

RESULTS

Gram-negative bacteria were isolated from mother's own milk of 22.4% (n = 11) and 15% (n = 3) of mothers of preterm and term neonates, respectively. According to pulsed-field gel electrophoresis genetically similar strains were present in mother's own milk and gut of 8.2% (n = 4) of mother-preterm neonate, but none of mother-term neonate pairs. In three of four late-onset sepsis caused by Gram-negative bacteria, colonization of gut, but not mother's own milk, with invasive species preceded late-onset sepsis.

CONCLUSIONS

Colonization of mother's own milk with Gram-negative bacteria is uncommon and transmission to neonatal gut may occur in less than one-tenth of neonate-mother pairs.

Higher intake of coagulase-negative staphylococci from maternal milk promotes gut colonization with mecA-negative Staphylococcus epidermidis in preterm neonates

OBJECTIVE

We aimed to determine factors associated with gut colonization of preterm neonates with coagulase-negative staphylococci (CoNS) from maternal milk (MM).

STUDY DESIGN

CoNS isolated from weekly collected stool and MM of hospitalized preterm (n = 49) and healthy term neonates (n = 20) were genotyped. Colonization-related factors were determined by Cox proportional hazards regression.

RESULT

Gut colonization with mecA-negative Staphylococcus epidermidis from MM was less prevalent (40.8% vs. 95%) and delayed (median age 15.5 vs. 2 days) in preterm compared with term neonates. Enhanced colonization was associated with higher intake of CoNS from MM (hazard ratio (95% confidence interval) 1.006 (1.00-1.01) for 10⁶ colony-forming units), lower proportion of mecA-positive predominant NICU strains in gut (0.09 (0.01-0.49) for 1%) and lower incidence of late-onset CoNS sepsis (5% vs. 34% in those without colonization).

CONCLUSION

Enteral feeding with larger proportion of unpasteurized MM and limiting spread of predominant strains may promote colonization with CoNS from MM.

Temporal development of the gut microbiome in early childhood from the TEDDY study

The development of the microbiome from infancy to childhood is dependent on a range of factors, with microbial-immune crosstalk during this time thought to be involved in the pathobiology of later life diseases1-9 such as persistent islet autoimmunity and type 1 diabetes10-12. However, to our knowledge, no studies have performed extensive characterization of the microbiome in early life in a large, multi-centre population. Here we analyse longitudinal stool samples from 903 children between 3 and 46 months of age by 16S rRNA gene sequencing (n = 12,005) and metagenomic sequencing (n = 10,867), as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We show that the developing gut microbiome undergoes three distinct phases of microbiome progression: a developmental phase (months 3-14), a transitional phase (months 15-30), and a stable phase (months 31-46). Receipt of breast milk, either exclusive or partial, was the most significant factor associated with the microbiome structure. Breastfeeding was associated with higher levels of Bifidobacterium species (B. breve and B. bifidum), and the cessation of breast milk resulted in faster maturation of the gut microbiome, as marked by the phylum Firmicutes. Birth mode was also significantly associated with the microbiome during the developmental phase, driven by higher levels of Bacteroides species (particularly B. fragilis) in infants delivered vaginally. Bacteroides was also associated with increased gut diversity and faster maturation, regardless of the birth mode. Environmental factors including geographical location and household exposures (such as siblings and furry pets) also represented important covariates. A nested case-control analysis revealed subtle associations between microbial taxonomy and the development of islet autoimmunity or type 1 diabetes. These data determine the structural and functional assembly of the microbiome in early life and provide a foundation for targeted mechanistic investigation into the consequences of microbial-immune crosstalk for long-term health.