Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome

BACKGROUND

Infant gut microbiota is highly malleable, but the long-term longitudinal impact of antibiotic exposure in early life, together with the mode of delivery on infant gut microbiota and resistome, is not extensively studied.

METHODS

Two hundred and eight samples from 45 infants collected from birth until 2 years of age over five time points (week 1, 4, 8, 24, year 2) were analysed. Based on shotgun metagenomics, the gut microbial composition and resistome profile were compared in the early life of infants divided into three groups: vaginal delivery/no-antibiotic in the first 4 days of life, C-section/no-antibiotic in the first 4 days of life, and C-section/antibiotic exposed in first 4 days of life. Gentamycin and benzylpenicillin were the most commonly administered antibiotics during this cohort's first week of life.

RESULTS

Newborn gut microbial composition differed in all three groups, with higher diversity and stable composition seen at 2 years of age, compared to week 1. An increase in microbial diversity from week 1 to week 4 only in the C-section/antibiotic-exposed group reflects the effect of antibiotic use in the first 4 days of life, with a gradual increase thereafter. Overall, a relative abundance of Actinobacteria and Bacteroides was significantly higher in vaginal delivery/no-antibiotic while Proteobacteria was higher in C-section/antibiotic-exposed infants. Strains from species belonging to Bifidobacterium and Bacteroidetes were generally persistent colonisers, with Bifidobacterium breve and Bifidobacterium bifidum species being the major persistent colonisers in all three groups. Bacteroides persistence was dominant in the vaginal delivery/no-antibiotic group, with species Bacteroides ovatus and Phocaeicola vulgatus found to be persistent colonisers in the no-antibiotic groups. Most strains carrying antibiotic-resistance genes belonged to phyla Proteobacteria and Firmicutes, with the C-section/antibiotic-exposed group presenting a higher frequency of antibiotic-resistance genes (ARGs).

CONCLUSION

These data show that antibiotic exposure has an immediate and persistent effect on the gut microbiome in early life. As such, the two antibiotics used in the study selected for strains (mainly Proteobacteria) which were multiple drug-resistant (MDR), presumably a reflection of their evolutionary lineage of historical exposures-leading to what can be an extensive and diverse resistome. Video Abstract.

Neonatal outcomes following introduction of routine probiotic supplementation to very preterm infants

AIM

To evaluate the combined outcome of death and/or severe grade necrotising enterocolitis (NEC) in very preterm infants admitted to Cork University Maternity Hospital, Ireland, before and after introduction of routine supplementation with Bifidobacterium bifidum and Lactobacillus acidophilus probiotics (Infloran®).

METHODS

A retrospective study of infants <32 weeks gestation and < 1500 g surviving beyond 72 h of life was performed. Two 6-year epochs; pre-probiotics (Epoch 1: 2008-2013) and with probiotics (Epoch 2: 2015-2020), were evaluated. The primary outcome was defined as death after 72 h or NEC Bell stage 2a or greater.

RESULTS

Seven-hundred-and-forty-four infants were included (Epoch 1: 391, Epoch 2: 353). The primary outcome occurred in 67 infants (Epoch 1: 37, Epoch 2: 30, p = 0.646). After adjustment, the difference was significant (OR [95% CI]: 0.53 [0.29 to 0.97], p = 0.038). Differences between epochs did not depend on gestational age group (<28 weeks; ≥28 weeks).

CONCLUSION

There was an associated reduction of the composite outcome of severe grade NEC and/or death, after adjustment for confounding variables, with introduction of routine administration of a B. bifidum and L. acidophilus probiotic at our institution.

Sudanese Toombak smokeless tobacco users harbour significantly altered long-term cortisol body production

The Sudanese, in particular its male population, are known to utilise a smokeless tobacco product (Toombak) which is placed in the oral cavity and can be replaced several times a day. Toombak has been shown to harm human health and is highly addictive. The effect on body cortisol response over a retrospective period in users of this product has not been previously explored. In addition, psycho-dependency scores of Toombak users have not been analysed. In this study, 37 male subjects, age 18-45 years were recruited, of which 18 were non-users of Toombak and 19 were Toombak users. One hair sample was collected from each user and non-user of Toombak. Each hair sample (n=37) was placed in a pre-prepared long piece of foil with two labels on either side marked: 'scalp-side' and 'distant-side'. Cortisol was extracted by mincing 10 mg of 'scalp-side' hair, not exceeding 3 cm, with methanol addition, incubation, and sonication. Cortisol was measured using the enzyme-linked immunosorbent assay kit (Enzo Life Sciences, UK). The amount of hair cortisol in the samples was determined using spectrophotometry at wavelength 405 nm measured in pg/ml and visualised with a four parametric logistic curve. Toombak users were further asked to complete the Fagerstrom Test for Nicotine Dependence-Smokeless Tobacco questionnaire (FTND-ST) comprising of six questions. Scores of > 5 indicated a significant dependence, while a score of < 4 marked low to moderate dependence. The mean concentration of hair cortisol in Toombak users (9.7 pg/ml) was significantly lower (p=0.023) compared to non-users (19.4 pg/ml), with total concentrations ranging from 2.1 to 55.6 pg/ml. FTND-ST scores ranged from 4 to 9, with high levels of psycho-dependency (score > 5) and nicotine tolerance found in 85 % of Toombak users. Cortisol body release in Sudanese smokeless tobacco users was found to be significantly altered. While low cortisol levels do lead to anxiolytic effects, in the long-term, this can allow for increased susceptibility to low cortisol-associated diseases.

Altered oral microbiome in Sudanese Toombak smokeless tobacco users carries a newly emerging risk of squamous cell carcinoma development and progression

There are an estimated 6-10 million smokeless tobacco (Toombak) users in Sudan, the majority being males. Toombak is known to be a carcinogenic product that is likely to modify the oral microbiome spatiality into a high-risk potential for the development and progression of oral cancer, but previous studies are lacking in this field. Here, we endeavour for the first time the exploration of the oral microbiome in key mucosal areas of the oral cavity and assess the microbiome variations in premalignant and oral squamous cell carcinoma (OSCC) samples from both users and non-users of Toombak. 16S rRNA sequencing was performed on DNA obtained from pooled saliva, oral mucosa and supragingival plaque from 78 Sudanese users and non-users of Toombak, aged between 20 and 70 years. In 32 of the pooled saliva samples, the mycobiome (fungal) environment was analysed through ITS sequencing. Then, 46 formalin-fixed paraffin-embedded samples of premalignant and OSCC samples were collected, and their associated microbiomes sequenced. The oral Sudanese microbiome was found to be enriched in Streptococcaceae, but Staphylococcaceae were significantly more abundant amongst Toombak users. Genera enriched in the oral cavity of Toombak users included Corynebacterium_1 and Cardiobacterium while in non-users, Prevotella, Lactobacillus and Bifidobacterium were prominent. Aspergillus was the most abundant fungus in the mouths of Toombak users with a marked loss of Candida. The genus Corynebacterium_1 was abundant in the buccal, floor of the mouth and saliva microbiomes as well as in oral cancer samples from Toombak users indicating a possible role for this genus in the early stages of oral cancer development. An oral cancer microbiome that favours poor survival and metastasis in those who use Toombak also emerged that includes the genera Stenotrophomonas and Schlegelella. Those utilising Toombak carry an altered oral microbiome that may be an additional risk factor for this products carcinogenicity to the oral structures. These significant microbiome modulations are a newly emerging key driving factor in oral cancer development and progression in Toombak users while it is also shown that Toombak users carry an oral cancer microbiome that may increase the potential for a poorer prognosis.

Cross-sectional observational study protocol: missing microbes in infants born by caesarean section (MiMIC): antenatal antibiotics and mode of delivery

INTRODUCTION

The intestinal microbiome in early life plays a major role in infant health and development. Factors like antibiotic exposure, breast/formula feeding and mode of delivery are known to affect the microbiome. The increasing occurrence of caesarean section (C-section) deliveries and antibiotic exposure warrants further insight into the potential missing microbes in those infants. The study objective is to study the effect of maternal antibiotic administration during pregnancy and/or C-section mode of delivery on the development of the infant's intestinal microbiome until the age of 2 years.

METHODS AND ANALYSIS

A single site, cross-sectional observational study of C-section and vaginally delivered infants being either exposed to maternal antibiotic treatment or not during the third trimester of pregnancy. Throughout the nine visits, stool, urine, saliva, hair, breast milk and vaginal swabs will be collected from either mother and/or infant for microbiome and metabolomic analysis.

ETHICS AND DISSEMINATION

The protocol was approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. The trial has been registered at ClinicalTrials.gov.The findings from this study will be disseminated in peer-reviewed journals, during scientific conferences, and directly to the study participants. Sequencing data will be deposited in public databases.

TRIAL REGISTRATION NUMBER

NCT04134819.

Dynamic Changes in the Human Milk Metabolome Over 25 Weeks of Lactation

Human milk (HM) provides essential nutrition for ensuring optimal infant growth and development postpartum. Metabolomics offers insight into the dynamic composition of HM. Studies have reported the impact of lactation stage, maternal genotype, and gestational age on HM metabolome. However, the majority of the studies have considered changes within the first month of lactation or sampled with large intervals. This leaves a gap in the knowledge of progressing variation in HM composition beyond the first month of lactation. The objective of this study was to investigate whether the HM metabolome from mothers with term deliveries varies beyond 1 month of lactation, during the period in which HM is considered fully mature. Human milk samples (n = 101) from 59 mothers were collected at weeks 1–2, 3–5, 7–9, and 20–25 postpartum and analyzed using ¹H nuclear magnetic resonance spectroscopy. Several metabolites varied over lactation and exhibited dynamic changes between multiple time points. Higher levels of HM oligosaccharides, cis-aconitate, O-phosphocholine, O-acetylcarnitine, gluconate, and citric acid were observed in early lactation, whereas later in lactation, levels of lactose, 3-fucosyllactose, glutamine, glutamate, and short- and medium-chain fatty acids were increased. Notably, we demonstrate that the HM metabolome is dynamic during the period of maturity.

The human milk microbiome aligns with lactation stage and not birth mode

We analysed the human milk microbiome in a cohort of 80 lactating women and followed the dynamics in taxa over the course of lactation from birth to 6 months. Two hundred and thirty one milk samples were collected from full-term lactating women at 1, 4, 8 and 24 weeks following birth and analysed for microbiota composition using 16S rRNA sequencing. A significant decrease in milk microbiota diversity was observed throughout the first 6 months of lactation, with the greatest difference seen between week 8 and week 24. Nine genera predominated in milk over lactation from week 1 to week 24, comprising of Staphylococcus, Streptococcus, Pseudomonas, Acinetobacter, Bifidobacterium, Mesorhizobium, Brevundimonas, Flavobacterium, and Rhodococcus; however, fluctuations in these core genera were apparent over time. There was a significant effect of stage of lactation on the microbiome, while no effect of birth mode, infant sex and maternal BMI was observed throughout lactation. Streptococcus had the highest mean relative abundance at week 1 and 24 (17.3% and 24% respectively), whereas Pseudomonas predominated at week 4 (22%) and week 8 (19%). Bifidobacterium and Lactobacillus had the highest mean relative abundance at week 4 (5% and 1.4% respectively), and occurred at a relative abundance of ≤ 1% at all other time points. A decrease in milk microbiota diversity throughout lactation was also observed. This study concluded that lactation stage was the primary driving factor in milk microbiota compositional changes over lactation from birth to 6 months, while mode of delivery was not a factor driving compositional changes throughout human lactation.

First encounters of the microbial kind: perinatal factors direct infant gut microbiome establishment

The human gut microbiome harbors a diverse range of microbes that play a fundamental role in the health and well-being of their host. The early-life microbiome has a major influence on human development and long-term health. Perinatal factors such as maternal nutrition, antibiotic use, gestational age and mode of delivery influence the initial colonization, development, and function of the neonatal gut microbiome. The perturbed early-life gut microbiome predisposes infants to diseases in early and later life. Understanding how perinatal factors guide and shape the composition of the early-life microbiome is essential to improving infant health. The following review provides a synopsis of perinatal factors with the most decisive influences on initial microbial colonization of the infant gut.

Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures

Emerging evidence indicates maternal microbiota as one major reservoir for pioneering microbes in infants. However, the global distinct and identical features of mother-infant gut microbiota at various taxonomic resolutions and metabolic functions across cohorts and potential of infant microbial prediction based on their paired mother's gut microbiota remain unclear. Here, we analyzed 376 mother-infant dyads (468 mother and 1024 infant samples) of eight studies from six countries and observed higher diversity at species and strain levels in maternal gut microbiota but not their metabolic functions. A number of 290 species were shared in at least one mother-infant dyad, with 26 species (five at strain level) observed across cohorts. The profile of mother-infant shared species and strains was further influenced by delivery mode and feeding regimen. The mother-sourced species in infants exhibited similar strain heterogeneity but more metabolic functions compared to other-sourced species, suggesting the comparable stability and fitness of shared and non-shared species and the potential role of shared species in the early gut microbial community, respectively. Predictive models showed moderate performance accuracy for shared species and strains occurrences in infants. These generalized mother-infant shared species and strains may be considered as the primary targets for future work toward infant microbiome development and probiotics exploration.

Clinical implications of preterm infant gut microbiome development

Perturbations to the infant gut microbiome during the first weeks to months of life affect growth, development and health. In particular, assembly of an altered intestinal microbiota during infant development results in an increased risk of immune and metabolic diseases that can persist into childhood and potentially into adulthood. Most research into gut microbiome development has focused on full-term babies, but health-related outcomes are also important for preterm babies. The systemic physiological immaturity of very preterm gestation babies (born earlier than 32 weeks gestation) results in numerous other microbiome-organ interactions, the mechanisms of which have yet to be fully elucidated or in some cases even considered. In this Perspective, we compare assembly of the intestinal microbiome in preterm and term infants. We focus in particular on the clinical implications of preterm infant gut microbiome composition and discuss the prospects for microbiome diagnostics and interventions to improve the health of preterm babies.

Probiotics, Prebiotics, and Synbiotics for the Prevention of Necrotizing Enterocolitis

Necrotizing enterocolitis (NEC) is a major cause of morbidity and mortality in preterm infants. The exact mechanism by which NEC develops is poorly understood however there is growing evidence to suggest that perturbations in the early-life gut microbiota composition increase the risk for NEC. Modulation of the gut microbiota with probiotics, prebiotics, or in combination (synbiotics) is an area which has attracted intense interest in recent years. In this narrative review, we present an overview of the role of the gut microbiota in the pathogenesis of NEC. We also examine the evidence currently available from randomized controlled trials, observational studies, systematic reviews, and meta-analysis examining the role of probiotics, prebiotics, and synbiotics in reducing the risk of or preventing NEC. Current clinical practice guidelines with recommendations on the routine administration of probiotics to preterm infants for NEC are also explored.

The ultra-structural, metabolomic and metagenomic characterisation of the sudanese smokeless tobacco 'Toombak'

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Toombak, a form of moist smokeless tobacco from Sudan is placed as a dip in the oral cavity most commonly used by males.

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The microbiome of Toombak predominantly consists of the phyla, Firmicutes and Actinobacteria while abundant species include Corynebacterium casei, Atopostipes suicloacalis and Oceanobacillus chironomi.

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High concentrations of iron, volatile aldehydes and tobacco specific nitrosamines were found in Toombak and can lead to toxicity.

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Toombak has a non-homogenous abrasive surface with a high sodium level in the ready to buy form that can damage the oral mucosa.

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New measures must be taken in Sudan to limit harmful compounds in Toombak.

Toombak is a smokeless tobacco produced from the Nicotiana rustica tobacco plant from Sudan. Pre-prepared and ready to buy Toombak samples were analysed using mass spectrometry (heavy metals), gas and liquid chromatography (metabolomics), 16S rRNA metagenomic sequencing (microbiome) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX) and pH analysis.

Chromium, cobalt, and copper were high in the pre-prepared form of Toombak while iron, tobacco specific nitrosamines (TSNAs), formaldehyde and acetaldehyde were high in both types. Firmicutes and Actinobacteria dominated Toombak. Samples of ready to buy Toombak showed inter-variational differences depending on place of purchase. We found Virgibacillus were increased in the pre-prepared form while Corynebacterium casei, Atopococus tabaci, Atopostipes suicloacalis, Oceanobacillus chironomi and Staphylococcus gallinarum were the most abundant species in the ready to buy forms. PICRUSt analysis highlighted increased activity of metal transport systems in the ready to buy samples as well as an antibiotic transport system. SEM-EDX highlighted large non-homogenous, irregular particles with increased sodium, while pH of samples was in the alkaline range.

The final composition of Toombak is affected by its method of preparation and the end product has the potential to impart many negative consequences on the health of its users. TSNA levels observed in Toombak were some of the highest in the world while the micro-environment of Toombak supports a distinct microbiota profile.

Vertical transfer of antibiotics and antibiotic resistant strains across the mother/baby axis

Antibiotic resistance is a health and socioeconomic crisis recognized as a serious threat affecting humans worldwide. Overuse of antibiotics enhances the spread of multidrug-resistant bacteria, causing drug-resistant infections which can be difficult to treat. This resistance, mostly of the acquired type, is thus a major clinical issue. Acquired resistance can occur by horizontal transfer of genes between bacteria (community settings), by vertical transmission that can occur between mother and her offspring at birth and during lactation, or spontaneously due to antibiotic exposure. While there have been multiple studies about the horizontal transfer of antibiotic-resistance genes, not many studies have been conducted to study their vertical transmission. Vertical transmission is of importance as the early bacterial colonization of infants has an impact on their health and immune programming throughout life. This review discusses some possible mechanisms of mother-to-infant transmission of antibiotics and antibiotic-resistant strains and addresses the knowledge gaps for further studies.

A good start in life is important-perinatal factors dictate early microbiota development and longer term maturation

Maternal health status is vital for the development of the offspring of humans, including physiological health and psychological functions. The complex and diverse microbial ecosystem residing within humans contributes critically to these intergenerational impacts. Perinatal factors, including maternal nutrition, antibiotic use and maternal stress, alter the maternal gut microbiota during pregnancy, which can be transmitted to the offspring. In addition, gestational age at birth and mode of delivery are indicated frequently to modulate the acquisition and development of gut microbiota in early life. The early-life gut microbiota engages in a range of host biological processes, particularly immunity, cognitive neurodevelopment and metabolism. The perturbed early-life gut microbiota increases the risk for disease in early and later life, highlighting the importance of understanding relationships of perinatal factors with early-life microbial composition and functions. In this review, we present an overview of the crucial perinatal factors and summarise updated knowledge of early-life microbiota, as well as how the perinatal factors shape gut microbiota in short and long terms. We further discuss the clinical consequences of perturbations of early-life gut microbiota and potential therapeutic interventions with probiotics/live biotherapeutics.

Effect of storage, temperature, and extraction kit on the phylogenetic composition detected in the human milk microbiota

Human milk is considered the optimum feeding regime for newborns and is a source of bacteria for the developing infant gastrointestinal tract. However, as with all low biomass samples, standardization across variabilities such as sample collection, storage, and extraction methods is needed to eliminate discrepancies in microbial composition across studies. The aim of this study was to investigate how different storage methods, temperatures, preservatives, and extraction kits influence the human milk microbiome, compared to fresh samples. Breast milk samples were processed via six different methods: fresh (Method 1), frozen at -80°C (Method 2), treated with RNAlater and stored at 4°C or -80°C (Methods 3 and 4), and treated with Milk Preservation Solution at room temperature (Methods 5 and 6). Methods 1-5 were extracted using PowerFoodTM Microbial DNA Isolation kit (Mobio), and Method 6 was extracted using Milk DNA Preservation and Isolation kit (Norgen BioTek). At genus level, the most abundant genera were shared across Methods 1-5. Samples frozen at -80°C had fewest significant changes while samples treated and extracted using Milk Preservation and Isolation kit had the most significant changes when compared to fresh samples. Diversity analysis indicated that variation in microbiota composition was related to the method and extraction kit used. This study highlighted that, when extraction from fresh milk samples is not an option, freezing at -80°C is the next best option to preserve the integrity of the milk microbiome. Furthermore, our results demonstrate that choice of extraction kit had a profound impact on the microbiota populations detected in milk.

The Sporobiota of the Human Gut

The human gut microbiome is a diverse and complex ecosystem that plays a critical role in health and disease. The composition of the gut microbiome has been well studied across all stages of life. In recent years, studies have investigated the production of endospores by specific members of the gut microbiome. An endospore is a tough, dormant structure formed by members of the Firmicutes phylum, which allows for greater resistance to otherwise inhospitable conditions. This innate resistance has consequences for human health and disease, as well as in biotechnology. In particular, the formation of endospores is strongly linked to antibiotic resistance and the spread of antibiotic resistance genes, also known as the resistome. The term sporobiota has been used to define the spore-forming cohort of a microbial community. In this review, we present an overview of the current knowledge of the sporobiota in the human gut. We discuss the development of the sporobiota in the infant gut and the perinatal factors that may have an effect on vertical transmission from mother to infant. Finally, we examine the sporobiota of critically important food sources for the developing infant, breast milk and powdered infant formula.

Breast Milk, a Source of Beneficial Microbes and Associated Benefits for Infant Health

Human breast milk is considered the optimum feeding regime for newborn infants due to its ability to provide complete nutrition and many bioactive health factors. Breast feeding is associated with improved infant health and immune development, less incidences of gastrointestinal disease and lower mortality rates than formula fed infants. As well as providing fundamental nutrients to the growing infant, breast milk is a source of commensal bacteria which further enhance infant health by preventing pathogen adhesion and promoting gut colonisation of beneficial microbes. While breast milk was initially considered a sterile fluid and microbes isolated were considered contaminants, it is now widely accepted that breast milk is home to its own unique microbiome. The origins of bacteria in breast milk have been subject to much debate, however, the possibility of an entero-mammary pathway allowing for transfer of microbes from maternal gut to the mammary gland is one potential pathway. Human milk derived strains can be regarded as potential probiotics; therefore, many studies have focused on isolating strains from milk for subsequent use in infant health and nutrition markets. This review aims to discuss mammary gland development in preparation for lactation as well as explore the microbial composition and origins of the human milk microbiota with a focus on probiotic development.

Maternal Vertical Transmission Affecting Early-life Microbiota Development

The association of the human microbiome with health outcomes has attracted much interest toward its therapeutic manipulation. The likelihood of modulating the human microbiome in early life is high and offers great potential to exert profound effects on human development since the early microbiota shows more flexibility compared to that of adults. The human microbiota, being similar to human genetics, can be transmitted from mother to infant, providing insights into early microbiota acquisition, subsequent development, and potential opportunities for intervention. Here, we review adaptations of the maternal microbiota during pregnancy, birth, and infancy, the acquisition and succession of early-life microbiota, and highlight recent efforts to elucidate mother-to-infant microbiota transmission. We further discuss how the mother-to-infant microbial transmission is shaped; and finally we address potential directions for future studies to promote our understanding within this field.

Mining Google Trends Data for Health Information: The Case of the Irish “CervicalCheck” Screening Programme Revelations

Background

In April 2018, the Irish cervical smear screening programme, “CervicalCheck”, came under intense scrutiny as the accuracy of hundreds of “negative” results were brought in question.

Aim

The goal of this brief report was to assess the impact of this real-life event on public information-seeking behaviour, using Google search anomalies as a proxy. Irish relative search volume data for several terms relating to cervical testing/cancer and human papillomavirus were extracted for a five-year period from February 2014 to January 2019 and analysed for the presence of anomalous spikes and shifts in the mean baseline.

Results

An unprecedented positive spike in searches relating to cervical testing/cancer was observed immediately after the CervicalCheck revelations, which remained anomalous for the month to follow (p < 0.05). This public interest preceded a mirroring increase in uptake of complimentary consultations offered by the Department of Health to the women concerned. Despite this service engagement and interest in cervical health, the relative search volumes for terms “human papillomavirus infection” and ”HPV vaccine” were just 78 and 51% of their maximum search volume for the five-year period.

Conclusions

Anomaly analysis revealed an unprecedented spike in information-seeking behaviour following the CervicalCheck revelations. However, this was not associated with a comparable elevation in HPV interest. This suggests that more public education and promotion of the HPV vaccine is warranted, in the context of vastly reduced uptake in recent years. Finally, Google Trends data represents a free an open source means by which to assess information-seeking behaviour of the public in relation to health and disease.

Parental opinion of consent in neonatal research

BACKGROUND

Neonatal research, particularly neonatal emergency research is a challenging area, notably in relation to obtaining valid prospective informed consent. The aim of this study is to determine parental perceptions of the consent process involved in performing research in newborn care, to explore methods used to obtain consent and their acceptability to parents.

METHODS

A parental questionnaire was developed that examined attitudes towards research and hypothetical research studies, in which the acceptability of various methods of consent was examined (informed, waived, deferred). These research scenarios were of varying time sensitivity and perceived risk level. The study setting was an Irish maternity hospital.

RESULTS

There were 600 responses to the questionnaire. In 93% of cases, parents felt that their involvement in the consent process was essential. In emergency situations, 52% felt full prospective informed consent was necessary; however, almost 28% of parents would feel pressure to consent. Most (75%) parents would prefer to be approached to discuss neonatal research studies antenatally, irrespective of study type and 40% of parents felt that neonates involved in research studies received overall better care. Acceptability of deferred consent was greater than waived, and was highest for the more emergency-based scenarios presented.

DISCUSSION

Parents feel that they should play a central role in research involving their children. There were differences in the acceptability of various consent methods with strongest agreement for informed consent and lowest agreement for waived consent. Parents were more willing to accede to deferred consent in the cardiopulmonary resuscitation scenario study. These findings provide useful insights to consent strategies in future newborn research studies.

Paediatrician's perspective of infant gut microbiome research: current status and challenges

Due to its innately intriguing nature and recent genomic technological advances, gut microbiome research has been at the epicentre of medical research for over a decade now. Despite the degree of publicisation, a comprehensive understanding and, therefore, acceptance of the area as a whole may be somewhat lacking within the broader medical community. This paper summarises the main analytical techniques and tools currently applied to compositional microbiome research. In addition, we outline five major lessons learnt from a decade of infant microbiome research, along with the current research gaps. Finally, we aim to provide an introduction and general guidelines relating to infant gut microbiome research for the practising paediatrician.

The microbiota of the mother at birth and its influence on the emerging infant oral microbiota from birth to 1 year of age: a cohort study

Background: The acquisition of microbial communities and the influence of delivery mode on the oral microbiota of the newborn infant remains poorly characterised. Methods: A cohort of pregnant women were enrolled in the study (n = 84). All infants were born full term, by Spontaneous vaginal delivery (SVD) or by Caesarean section (CS). At delivery a saliva sample along with a vaginal/skin sample from the mother. Saliva samples were the taken from the infant within one week of birth, and at week 4, week 8, 6 months and 1 year of age. We used high-throughput sequencing of V4-V5 region 16S rRNA amplicons to compare the microbiota of all samples. Results: The vaginal microbiota had a lower alpha diversity than the skin microbiota of the mother, while the infant oral microbiota diversity remained relatively stable from birth to 8 weeks of age. The oral microbiota of the neonate differed by birth modality up to 1 week of age (p < 0.05), but birth modality did not have any influence on the infant oral microbiota beyond this age. Conclusions: We conclude thatbirth mode does not have an effect on the infant oral microbiota beyond 4 weeks of age, and the oral microbiota of infants continues to develop until 1 year of age.

Advances in Infant Formula Science

Human milk contains a plethora of nutrients and bioactive components to help nourish the developing neonate and is considered the “gold standard” for early life nutrition—as befits the only food “designed” by evolution to feed human infants. Over the past decade, there is considerable evidence that highlights the “intelligence” contained in milk components that contribute to infant health beyond basic nutrition—in areas such as programming the developing microbiome and immune system and protecting against infection. Such discoveries have led to new opportunities for infant milk formula (IMF) manufacturers to refine nutritional content in order to simulate the functionality of breast milk. These include the addition of specialized protein fractions as well as fatty acid and complex carbohydrate components—all of which have mechanistic supporting evidence in terms of improving the health and nutrition of the infant. Moreover, IMF is the single most important dietary intervention whereby the human microbiome can be influenced at a crucial early stage of development. In this respect, it is expected that the complexity of IMF will continue to increase as we get a greater understanding of how it can modulate microbiota development (including the development of probiotics, prebiotics, and synbiotics) and influence long-term health. This review provides a scientific evaluation of key features of importance to infant nutrition, including differences in milk composition and emerging “humanized” ingredients.

Dose-interval study of a dual probiotic in preterm infants

OBJECTIVE

The objective of this study was to investigate the appropriate dosing interval of a probiotic (Infloran) given daily, biweekly and weekly in preterm infants <32 weeks' gestation.

METHODS

There were 8 infants in the daily group, 8 infants in the biweekly group and 10 infants in the weekly group, all born between 25 and 32 weeks' gestation. The control group consisted of 12 preterm infants who did not receive the probiotic. Infloran (250 mg/capsule), containing Bifidobacterium bifidum (1×10⁹ colony-forming unit (CFU)) and Lactobacillus acidophilus (1×10⁹ CFU), was administered in 2.5 mL of breast milk per kilogram weight of the infant (2×10⁹ CFU of bacteria in total), until 34 weeks postmenstrual age (PMA). Stool samples were collected at 31, 34, 41 and 44 weeks PMA and frozen at -20°C.

RESULTS

After administration of the probiotic at 31 weeks PMA, Bifidobacterium were significantly higher in the daily group (45%) in comparison with the biweekly (17%) and weekly (9%) groups. At 34 weeks PMA, Bifidobacterium were significantly higher again in the daily (60%) group in comparison with the biweekly (21%), weekly (23%) and control (15%) groups. At 41 weeks PMA a decrease in the relative abundances of Streptococcaceae and Enterococcaceae was found in all three probiotic groups, and by 44 weeks PMA significantly higher levels of Lactobacillus were found in the biweekly group (16.5%) in comparison with the weekly group (2.1%).

CONCLUSION

Our results indicate that a daily dose of Infloran is a suitable dosage for preterm infants in the neonatal intensive care unit, with significantly higher levels of Bifidobacterium found in the daily probiotic group up to 44 weeks PMA.

Quantification of Human Milk Phospholipids: the Effect of Gestational and Lactational Age on Phospholipid Composition

Human milk (HM) provides infants with macro- and micronutrients needed for growth and development. Milk phospholipids are important sources of bioactive components, such as long-chain polyunsaturated fatty acids (LC-PUFA) and choline, crucial for neural and visual development. Milk from mothers who have delivered prematurely (<37 weeks) might not meet the nutritional requirements for optimal development and growth. Using liquid chromatography tandem-mass spectrometry, 31 phospholipid (PL) species were quantified for colostrum (<5 days postpartum), transitional (≥5 days and ≤2 weeks) and mature milk (>2 weeks and ≤15 weeks) samples from mothers who had delivered preterm (n = 57) and term infants (n = 22), respectively. Both gestational age and age postpartum affected the PL composition of HM. Significantly higher concentrations (p < 0.05) of phosphatidylcholine (PC), sphingomyelin (SM) and total PL were found in preterm milk throughout lactation, as well as significantly higher concentrations (p < 0.002) of several phosphatidylethanolamine (PE), PC and SM species. Multivariate analysis revealed that PLs containing LC-PUFA contributed highly to the differences in the PL composition of preterm and term colostrum. Differences related to gestation decreased as the milk matured. Thus, gestational age may impact the PL content of colostrum, however this effect of gestation might subside in mature milk.

Comparison of the salivary and dentinal microbiome of children with severe-early childhood caries to the salivary microbiome of caries-free children

BACKGROUND

The main objectives of this study were to describe and compare the microbiota of 1) deep dentinal lesions of deciduous teeth of children affected with severe early childhood caries (S-ECC) and 2) the unstimulated saliva of these children and 3) the unstimulated saliva of caries-free children, and to compare microbiota compositional differences and diversity of taxa in these sampled sites.

METHODS

Children with S-ECC and without S-ECC were recruited. The saliva of all children with and without S-ECC was sampled along with the deep dentinal microbiota from children affected by S-ECC. The salivary microbiota of children affected by S-ECC (n = 68) was compared to that of caries-free children (n = 70), by Illumina MiSeq sequencing of 16S rRNA amplicons. Finally, the caries microbiota of deep dentinal lesions of those children with S-ECC was investigated.

RESULTS

Using two beta diversity metrics (Bray Curtis dissimilarity and UniFrac distance), the caries microbiota was found to be distinct from that of either of the saliva groups (caries-free & caries-active) when bacterial abundance was taken into account. However, when the comparison was made by measuring only presence and absence of bacterial taxa, all three microbiota types separated. While the alpha diversity of the caries microbiota was lowest, the diversity difference between the caries samples and saliva samples was statistically significant (p < 0.001). The major phyla of the caries active dentinal microbiota were Firmicutes (median abundance value 33.5%) and Bacteroidetes (23.2%), with Neisseria (10.3%) being the most abundant genus, followed by Prevotella (10%). The caries-active salivary microbiota was dominated by Proteobacteria (median abundance value 38.2%) and Bacteroidetes (27.8%) with the most abundant genus being Neisseria (16.3%), followed by Porphyromonas (9.5%). Caries microbiota samples were characterized by high relative abundance of Streptococcus mutans, Prevotella spp., Bifidobacterium and Scardovia spp.

CONCLUSIONS

Distinct differences between the caries microbiota and saliva microbiota were identified, with separation of both salivary groups (caries-active and caries-free) whereby rare taxa were highlighted. While the caries microbiota was less diverse than the salivary microbiota, the presence of these rare taxa could be the difference between health and disease in these children.

Respiratory adaptation in term infants following elective caesarean section

OBJECTIVE

To determine respiratory rate (RR), tidal volume (TV) and end-tidal carbon dioxide (EtCO₂) values in full-term infants immediately after caesarean section, and to assess whether infants that develop transient tachypnoea of the newborn (TTN) follow the same physiological patterns.

DESIGN AND PATIENTS

A Respironics NM3 Monitor (Philips, Netherlands) continuously measured RR, TV and EtCO₂ for 7 min in infants >37 weeks' gestation following elective caesarean section (ECS). Monitoring was repeated at 2 hours of age for 2 min. Gestation, birth weight, Apgar scores and admissions to neonatal unit were documented.

SETTING

The operative delivery theatre of Cork University Maternity Hospital, Ireland.

RESULTS

There were 95 term infants born by ECS included. Median (IQR) gestation was 39 weeks (38.2-39.1) and median (IQR) birth weight 3420 g (3155-3740). Median age at initiation of monitoring was 26.5 s (range: 20-39). Data were analysed for the first 7 min of life. Mean breaths per minute (bpm) increased over the first 7 min of life (44.31-61.62). TV and EtCO₂ values were correlated and increased from 1 min until maximum mean values were recorded at 3 min after delivery (5.18 mL/kg-6.44 mL/kg, and 4.32 kPa-5.64 kPa, respectively). Infants admitted to the neonatal unit with TTN had significantly lower RRs from 2 min of age compared with infants not admitted for TTN.

CONCLUSIONS

TV and EtCO₂ values are correlated and increase significantly over the first few minutes following ECS. RR increases gradually from birth, and rates were lower in infants that develop TTN.

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity

Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU’s (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome.

Parental And Clinician Views Of Consent In Neonatal Research

AIM

To determine parental and clinician views of the informed consent process in neonatal research.

METHODS

A questionnaire-based study on the informed consent process. Two questionnaires were developed and distributed to parents and clinicians over a four-month period.

RESULTS

Thirty-four parents (79%) surveyed had consented their baby to a research study. The majority of clinicians (72%) had a preference for antenatal provision of information. A desire to help future babies (97%, n=32) and a belief that their baby's healthcare would directly benefit (72%, n=28) were primary reasons for consenting. The majority (76% n=28) of parents were not in favour of a waiver of consent. However twenty clinicians (56%) agreed that a waiver of consent may be appropriate in neonatal research. Thirty-one (86%) clinicians rated GCP training as important.

DISCUSSION

Parents are generally supportive of neonatal research. Good clinical practice training is essential for clinicians involved in neonatal research.

Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains

Background

Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach.

Results

We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO).

Conclusions

The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4388-9) contains supplementary material, which is available to authorized users.

Perinatal outcomes following Helping Babies Breathe training and regular peer-peer skills practice among village midwives in Sudan

BACKGROUND

Over 80% of deliveries in Sudan occur in rural areas, attended by village midwives (VMWs).

OBJECTIVE

To determine the impact of Helping Babies Breathe training and regular peer-peer skills practice (HBBT^+RPPSP) on VMW resuscitation practices and outcomes.

METHODS

In a prospective community-based intervention study, 71/82 VMWs, reporting to six East Nile rural medical centres, with previous experience in community health research, consented to HBBT^+RPPSP. Outcomes included changes in the resuscitation practices, fresh stillbirths (FSB) and early neonatal deaths <1 week (ENND).

RESULTS

There were 1350 and 3040 deliveries before and after HBBT^+RPPSP, respectively, with no significant differences between the two cohorts regarding maternal age, education or area of birth. Drying of the newborn increased almost tenfold (8.4%, n=113 to 74.9%, n=1011) while suctioning of the mouth/nose decreased fivefold (80.3%, n=2442 to 14.4%, n=437) following HBBT^+RPPSP. Pre-HBBT^+RPPSP9/18 (50%) newborns who had mouth-to-mouth ventilation died, compared with 13/119 (11%) who received bag-mask ventilation post-HBBT^+RPPSP. Excluding 11 macerated fetuses, there were 55 perinatal deaths: 14 FSB/18 ENND (6 months pre-HBBT^+RPPSP) and 10 FSB/13 ENND (18 months post-HBBT^+RPPSP). FSB rates decreased from 10.5 to 3.3 per 1000 births ((χ²)=8.6209, p=0.003), while ENND rates decreased from 13.5 to 4.3 per 1000 live births ((χ²)=10.9369, p=0.001) pre-HBBT^+RPPSP and post-HBBT^+RPPSP, respectively.

CONCLUSION

In a selected group of VMWs, HBBT^+RPPSP was associated with improvements in newborn resuscitation and perinatal outcomes. HBBT^+RPPSP could have immense benefits if propagated nationally to all 17 000 VMWs in Sudan.

Intervention strategies for cesarean section-induced alterations in the microbiota-gut-brain axis

Microbial colonization of the gastrointestinal tract is an essential process that modulates host physiology and immunity. Recently, researchers have begun to understand how and when these microorganisms colonize the gut and the early-life factors that impact their natural ecological establishment. The vertical transmission of maternal microbes to the offspring is a critical factor for host immune and metabolic development. Increasing evidence also points to a role in the wiring of the gut-brain axis. This process may be altered by various factors such as mode of delivery, gestational age at birth, the use of antibiotics in early life, infant feeding, and hygiene practices. In fact, these early exposures that impact the intestinal microbiota have been associated with the development of diseases such as obesity, type 1 diabetes, asthma, allergies, and even neurodevelopmental disorders. The present review summarizes the impact of cesarean birth on the gut microbiome and the health status of the developing infant and discusses possible preventative and restorative strategies to compensate for early-life microbial perturbations.

Microbial Therapeutics Designed for Infant Health

Acknowledgment of the gut microbiome as a vital asset to health has led to multiple studies attempting to elucidate its mechanisms of action. During the first year of life, many factors can cause fluctuation in the developing gut microbiome. Host genetics, maternal health status, mode of delivery, gestational age, feeding regime, and perinatal antibiotic usage, are known factors which can influence the development of the infant gut microbiome. Thus, the microbiome of vaginally born, exclusively breastfed infants at term, with no previous exposure to antibiotics, either directly or indirectly from the mother, is to be considered the "gold standard." Moreover, the use of prebiotics as an aid for the development of a healthy gut microbiome is equally as important in maintaining gut homeostasis. Breastmilk, a natural prebiotic source, provides optimal active ingredients for the growth of beneficial microbial species. However, early life disorders such as necrotising enterocolitis, childhood obesity, and even autism have been associated with an altered/disturbed gut microbiome. Subsequently, microbial therapies have been introduced, in addition to suitable prebiotic ingredients, which when administered, may aid in the prevention of a microbial disturbance in the gastrointestinal tract. The aim of this mini-review is to highlight the beneficial effects of different probiotic and prebiotic treatments in early life, with particular emphasis on the different conditions which negatively impact microbial colonisation at birth.

The ability of early serial developmental assessment to predict outcome at 5years following neonatal hypoxic-ischaemic encephalopathy

BACKGROUND

Neurodevelopmental difficulties in children following hypoxic-ischaemic encephalopathy (HIE) may not emerge until school age.

AIMS

To evaluate the value and stability of early serial developmental assessments in predicting long-term outcome.

STUDY DESIGN

Prospective study of infants with neonatal HIE and early continuous EEG at birth.

SUBJECTS

Term infants with HIE were recruited at birth. Development was measured at 6, 12 and 24months using the Revised Griffiths' Scales (GMDS-R).

OUTCOME MEASURES

Intellectual abilities at age five were measured using the Wechsler Preschool & Primary Scale of Intelligence (WPPSI-III^UK) and the 'numbers' subtest from the Children's Memory Scale. Overall five-year outcome was also reported.

RESULTS

IQ outcome was available in forty-seven surviving children (28 male, 19 female: mean (SD) age 64.0(5.7) months. Mean processing speed (p=0.01) and short-term verbal memory (p=0.005) were below the norm. Global development (GDQ) at 6, 12 and 24months correlated (p<0.01) with five-year global, verbal and performance IQ with improved correlation over time. Normal GDQ throughout early childhood predicted normal IQ at 5years (24month AUROC value=0.941, p=0.001). An abnormal early GDQ score at any stage in the first 24months had excellent negative predictive values, superior to those for neonatal Sarnat and EEG grading.

CONCLUSIONS

Normal early development predicts normal 5year IQ with prediction increasing over time. Repeated measurement is warranted due to instability of findings across the first two years. Follow-up for children with abnormal early development is warranted given high sensitivity for school-age global abnormal outcome.

Consent for routine neonatal procedures: A study of practices in Irish neonatal units. How do we compare with the gold standard BAPM guidelines?

The Irish National Consent Policy (NCP) proposes that the legal requirement for consent extends to all forms of interventions, investigations and treatment, carried out on or behalf of the Health Service Executive (HSE). This study employs a quantitative descriptive approach to investigate the practices for obtaining consent for an identified group of routine neonatal procedures in neonatal facilities throughout Ireland. The BAPM (British Association of Perinatal Medicine) guidelines were identified as 'gold standard' for the purposes of this study. The results indicated a lack of consistency between participating units pertaining to the modes of consent utilised and notable variances from 'gold standard' guidelines. Unanimity was evident for 3 procedures only (administering BCG, 6-in-1, and donor breast milk to infant). Significant findings related to EEG with video recordings, MRI/CT and gastro intestinal imaging, screening of an infant with suspected substance abuse or retinopathy of prematurity screening (ROP), administration of Vitamin K, and the carrying out of a lumbar puncture.

Emergency uncross-matched blood transfusions in a tertiary neonatal unit

AIM

To determine the neonatal incidence, indications and outcomes following transfusions with emergency uncross-matched O-negative blood.

METHODS

A five-year retrospective review in a single tertiary neonatal unit was conducted. The blood transfusion laboratory's database was analysed for all infants who had received an emergency released blood transfusion (ERBT) between January 2010 and December 2014.

RESULTS

We calculated a total ERBT rate of 0.91 per 1000 live births (39/42 657) and a rate of 0.43 per 1000 in infants >34 weeks' gestation (18/41 637). A rate of 0.14 per 1000 births (6/42 657) received an ERBT as part of newborn stabilisation despite almost half of our infant cohort having intrapartum haemorrhages (n = 18, 46%). One-third (13/39) of all infants who were transfused died. Outcome varied depending on underlying aetiology, gestation and birthweight. The highest mortality was in preterm infants weighing <1000 g, of whom 70% died.

CONCLUSION

This study establishes an ERBT rate of <1 per 1000 births, and 0.14 per 1000 infants received an ERBT as part of newborn delivery room stabilisation. ERBTs are associated with a high mortality rate. This study highlights the need for further research and guidelines that clarify the role of ERBTs in newborn stabilisations.

Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort

BACKGROUND

The gut is the most extensively studied niche of the human microbiome. The aim of this study was to characterise the initial gut microbiota development of a cohort of breastfed infants (n = 192) from 1 to 24 weeks of age.

METHODS

V4-V5 region 16S rRNA amplicon Illumina sequencing and, in parallel, bacteriological culture. The metabolomic profile of infant urine at 4 weeks of age was also examined by LC-MS.

RESULTS

Full-term (FT), spontaneous vaginally delivered (SVD) infants' microbiota remained stable at both phylum and genus levels during the 24-week period examined. FT Caesarean section (CS) infants displayed an increased faecal abundance of Firmicutes (p < 0.01) and lower abundance of Actinobacteria (p < 0.001) after the first week of life compared to FT-SVD infants. FT-CS infants gradually progressed to harbouring a microbiota closely resembling FT-SVD (which remained stable) by week 8 of life, which was maintained at week 24. The gut microbiota of preterm (PT) infants displayed a significantly greater abundance of Proteobacteria compared to FT infants (p < 0.001) at week 1. Metabolomic analysis of urine at week 4 indicated PT-CS infants have a functionally different metabolite profile than FT (both CS and SVD) infants. Co-inertia analysis showed co-variation between the urine metabolome and the faecal microbiota of the infants. Tryptophan and tyrosine metabolic pathways, as well as fatty acid and bile acid metabolism, were found to be affected by delivery mode and gestational age.

CONCLUSIONS

These findings confirm that mode of delivery and gestational age both have significant effects on early neonatal microbiota composition. There is also a significant difference between the metabolite profile of FT and PT infants. Prolonged breastfeeding was shown to have a significant effect on the microbiota composition of FT-CS infants at 24 weeks of age, but interestingly not on that of FT-SVD infants. Twins had more similar microbiota to one another than between two random infants, reflecting the influence of similarities in both host genetics and the environment on the microbiota..

The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study

Human milk contains a diverse array of bioactives and is also a source of bacteria for the developing infant gut. The aim of this study was to characterize the bacterial communities in human milk and infant faeces over the first 3 months of life, in 10 mother-infant pairs. The presence of viable Bifidobacterium and Lactobacillus in human milk was also evaluated. MiSeq sequencing revealed a large diversity of the human milk microbiota, identifying over 207 bacterial genera in milk samples. The phyla Proteobacteria and Firmicutes and the genera Pseudomonas, Staphylococcus and Streptococcus were the predominant bacterial groups. A core of 12 genera represented 81% of the microbiota relative abundance in milk samples at week 1, 3 and 6, decreasing to 73% at week 12. Genera shared between infant faeces and human milk samples accounted for 70–88% of the total relative abundance in infant faecal samples, supporting the hypothesis of vertical transfer of bacteria from milk to the infant gut. In addition, identical strains of Bifidobacterium breve and Lactobacillus plantarum were isolated from the milk and faeces of one mother-infant pair. Vertical transfer of bacteria via breastfeeding may contribute to the initial establishment of the microbiota in the developing infant intestine.

Optimising Intravenous Volume Resuscitation of the Newborn in the Delivery Room: Practical Considerations and Gaps in Knowledge

Volume resuscitation (VR) for the treatment of newborn shock is a rare but potentially lifesaving intervention. Conducting clinical studies to assess the effectiveness of VR in the delivery room during newborn stabilization is challenging. We review the available literature and current management guidelines to determine which infants will benefit from VR, the frequency of VR, and the choice of agents used. In addition, the potential role for placental transfusion in the prevention of newborn shock is explored.

Reporting on data monitoring committees in neonatal randomised controlled trials is inconsistent

AIM

To evaluate the reported use of data monitoring committees (DMCs), the frequency of interim analysis, prespecified stopping rules and early trial termination in neonatal randomised controlled trials (RCTs).

METHODS

We reviewed neonatal RCTs published in four high-impact general medical journals, specifically looking at safety issues including documented involvement of a DMC, stated interim analysis, stopping rules and early trial termination. We searched all journal issues over an 11-year period (2003-2013) and recorded predefined parameters on each item for RCTs meeting inclusion criteria.

RESULTS

Seventy neonatal trials were identified in four general medical journals: Lancet, New England Journal of Medicine (NEJM), British Medical Journal and Journal of American Medical Association. A total of 43 (61.4%) studies reported the presence of a DMC, 36 (51.4%) explicitly mentioned interim analysis, stopping rules were reported in 15 (21.4%) RCTs and seven (10%) trials were terminated early. The NEJM most frequently reported these parameters compared to the other three journals reviewed.

CONCLUSION

While the majority of neonatal RCTs report on DMC involvement and interim analysis, there is still scope for improvement. Clear documentation of safety-related issues should be a central component of reporting in neonatal trials involving newborn infants.

Early EEG Grade and Outcome at 5 Years After Mild Neonatal Hypoxic Ischemic Encephalopathy

OBJECTIVE

More than half of all infants with neonatal hypoxic ischemic encephalopathy (HIE) are graded as mild and do not meet current criteria for therapeutic hypothermia. These infants are often not enrolled in follow-up, and hence our knowledge of their long-term outcome is sparse. We wished to compare 5-year outcomes in a group of infants with mild, moderate, and severe HIE, graded with both early EEG and clinical assessment, none of whom were treated with therapeutic hypothermia.

METHODS

Term infants with HIE and a healthy comparison group were recruited at birth. Both groups had early continuous EEG recordings. Cognitive and motor outcome was assessed at 5 years.

RESULTS

Outcome was available in 53 infants with HIE and 30 infants in the comparison group at 5 years. Infants with mild HIE at birth (n = 22) had significantly lower full-scale IQ, verbal IQ, and performance IQ than comparison infants (n = 30) at 5 years (P = .001, .001, and 0.004, respectively). No difference in cognitive measures was seen between infants with mild and moderate grades HIE. Intact survival at 5 years varied across EEG grade HIE at 6 hours after birth; 75% in mild, 46% in moderate, 43% in major abnormalities, and 0% with inactive EEGs, compared with 97% in the comparison group.

CONCLUSIONS

Survivors of mild HIE, graded clinically or by early EEG, have higher rates of disability than their peers and have cognitive outcomes similar to that of children with moderate encephalopathy in an uncooled HIE cohort.

Systems 1 and 2 thinking processes and cognitive reflection testing in medical students

BACKGROUND

Diagnostic decision-making is made through a combination of Systems 1 (intuition or pattern-recognition) and Systems 2 (analytic) thinking. The purpose of this study was to use the Cognitive Reflection Test (CRT) to evaluate and compare the level of Systems 1 and 2 thinking among medical students in pre-clinical and clinical programs.

METHODS

The CRT is a three-question test designed to measure the ability of respondents to activate metacognitive processes and switch to System 2 (analytic) thinking where System 1 (intuitive) thinking would lead them astray. Each CRT question has a correct analytical (System 2) answer and an incorrect intuitive (System 1) answer. A group of medical students in Years 2 & 3 (pre-clinical) and Years 4 (in clinical practice) of a 5-year medical degree were studied.

RESULTS

Ten percent (13/128) of students had the intuitive answers to the three questions (suggesting they generally relied on System 1 thinking) while almost half (44%) answered all three correctly (indicating full analytical, System 2 thinking). Only 3-13% had incorrect answers (i.e. that were neither the analytical nor the intuitive responses). Non-native English speaking students (n = 11) had a lower mean number of correct answers compared to native English speakers (n = 117: 1.0 s 2.12 respectfully: p < 0.01). As students progressed through questions 1 to 3, the percentage of correct System 2 answers increased and the percentage of intuitive answers decreased in both the pre-clinical and clinical students.

CONCLUSIONS

Up to half of the medical students demonstrated full or partial reliance on System 1 (intuitive) thinking in response to these analytical questions. While their CRT performance has no claims to make as to their future expertise as clinicians, the test may be used in helping students to understand the importance of awareness and regulation of their thinking processes in clinical practice.

The local lymph node assay in practice: a current regulatory perspective

Following the formal acceptance of the local lymph node assay (LLNA) as an Organization for Economic Cooperation and Development (OECD) guideline in April 2002, the UK Health and Safety Executive (HSE) informed notifiers that this was now the method of choice for the assessment of skin sensitization potential under the EU notification scheme for new industrial chemicals (NONS). This paper summarizes the experience of the HSE for the 2-year period immediately following the issuing of this statement, during which 48 LLNA study reports were assessed for notification purposes. The issues discussed here include adherence to the OECD guideline, interpretation of results, and classification outcomes. Generally, notifying laboratories followed the OECD guideline successfully, with regard to the sex/ strain/numbers of mice used, the precise process used for measurement of cell proliferation, and the use of recommended vehicles and positive controls. Initially, use of the individual animal approach (measuring the cell proliferation in each animal rather than for a pooled dose group) highlighted problems caused by technical inexperience, but these were overcome by practice. Toxicity or irritation were found to be minor factors in dose selection; more important was the choice of vehicle to correctly maximize the test substance concentration, while maintaining appropriate application properties. Contrary to concerns that the LLNA would prove to be less sensitive or more sensitive than the traditionally used Guinea Pig Maximization Test (GPMT), the proportion of new substances classified as skin sensitizers was within the range observed in previous years. Although the sample size is relatively small, the experience of the HSE indicates that the LLNA is satisfactory for routine regulatory use.

High rates of sexually transmitted diseases among male transvestites in Jakarta, Indonesia

Many male transvestites ( waria) in Jakarta, Indonesia engage in unprotected receptive anal and oral intercourse with homosexual and bisexual men for pay. Although this behaviour clearly puts them at risk of sexually transmitted diseases (STDs), including HIV infection, little is known about the prevalence of STD among them. To learn the STD prevalence and its risk factors, we conducted an STD prevalence survey among waria in North Jakarta, Indonesia. From August to December 1999 we offered screening for rectal and pharyngeal infections with Neisseria gonorrhoeae (Ng), Chlamydia trachomatis (Ct) by DNA probe (GenProbe PACE 2) and for Treponema pallidum (Tp) by non-treponemal and treponemal serological tests. Of 296 participants (median age 28 years), 93% reported having been paid for sex. A total of 96% reported having had oral sex (median five times/week) and/or anal sex (median three times/week) in the last week. Ng was found in the rectum of 12.8% and the pharynx of 4.2%; Ct was found in 3.8% and 2.4%, respectively. A total of 43.6% had reactive non-treponemal and treponemal tests. Of the 129 with positive treponemal tests, 42.6% had non-treponemal test titres greater than 1:8. In the logistic regression model, waria who were younger (≥25 years old) had a significantly 3.5 times risk of Ng and/or Ct infections than older waria (>25 years old). Because only 12% of waria stated that they consistently used condoms during any sex act, it is important to warn them that STD/HIV transmission can occur with either anal or oral sex and that the risk of either anal or oral transmission can be reduced by condom use. In addition, high rates of asymptomatic syphilis and rectal gonorrhoea warrant a periodic screening and treatment for these infections in this population. Because waria have the highest rates of HIV and their clients consist of homosexual and bisexual men, successful prevention efforts in waria could help curb the spread of the epidemic.

Bosom Buddies: The Symbiotic Relationship Between Infants and Bifidobacterium longum ssp. longum and ssp. infantis. Genetic and Probiotic Features

The intestinal microbiota is a complex community that plays an important role in human health from the initial steps of its establishment. Its microbial composition has been suggested to result from selective pressures imposed by the host and is modulated by competition among its members. Bifidobacterium longum is one of the most abundant species of the Bifidobacterium genus in the gut microbiota of healthy breast-fed infants and adults. The recent advancements of 'omics techniques have facilitated the genetic and functional studies of different gut microbiota members. They have revealed the complex genetic pathways used to metabolize different compounds that likely contribute to the competitiveness and persistence of B. longum in the colon. The discovery of a genomic island in B. longum ssp. infantis that encodes specific enzymes for the metabolism of human milk oligosaccharides suggests a specific ecological adaptation. Moreover, B. longum is widely used as probiotic, and beneficial effects in infant health have been reported in several studies.