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.

The Role of the Microbiome in Oral Squamous Cell Carcinoma with Insight into the Microbiome-Treatment Axis.

Oral squamous cell carcinoma (OSCC) is one of the leading presentations of head and neck cancer (HNC). The first part of this review will describe the highlights of the oral microbiome in health and normal development while demonstrating how both the oral and gut microbiome can map OSCC development, progression, treatment and the potential side effects associated with its management. We then scope the dynamics of the various microorganisms of the oral cavity, including bacteria, mycoplasma, fungi, archaea and viruses, and describe the characteristic roles they may play in OSCC development. We also highlight how the human immunodeficiency viruses (HIV) may impinge on the host microbiome and increase the burden of oral premalignant lesions and OSCC in patients with HIV. Finally, we summarise current insights into the microbiome-treatment axis pertaining to OSCC, and show how the microbiome is affected by radiotherapy, chemotherapy, immunotherapy and also how these therapies are affected by the state of the microbiome, potentially determining the success or failure of some of these treatments.

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.

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.

The microbiology and treatment of human mastitis.

Mastitis, which is generally described as an inflammation of breast tissue, is a common and debilitating disease which frequently results in the cessation of exclusive breastfeeding and affects up to 33% of lactating women. The condition is a primary cause of decreased milk production and results in organoleptic and nutritional alterations in milk quality. Recent studies employing culture-independent techniques, including metagenomic sequencing, have revealed a loss of bacterial diversity in the microbiome of mastitic milk samples compared to healthy milk samples. In those infected, the pathogens Staphylococcus aureus, Staphylococcus epidermidis and members of corynebacteria have been identified as the predominant etiological agents in acute, subacute and granulomatous mastitis, respectively. The increased incidence of antibiotic resistance in the causative species is also a key cause of concern for treatment of the disease, thus leading to the need to develop novel therapies. In this respect, probiotics and bacteriocins have revealed potential as alternative treatments.

End user bag-mask ability and perceptions of two infant resuscitation mannequins.

AIM: To examine user ability and preference in performing bag-mask ventilation (BMV) with four different configurations of infant mannequins. METHODS: Participants provided a 30-second period of BMV to a Resusci Baby mannequin (RB), NeoNatalie mannequin (NN), NN filled with air (NNA), NN filled with water (NNW) and NN filled with 50% air and 50% water mix (NNAW). Participants rated the fidelity of each configuration. RESULTS: Of the 20 participants, 65% rated NNW as having a high level of fidelity (HLF) 'to hold' (50% for NNAW, 10% for RB and 0% for NNA) (p < 0.001). Half rated NNAW as having a HLF in 'tone' (40% for NNW, 20% for RB and 5% for NNA) (p = 0.008). About 45% of participants rated NNAW as having a HLF in 'appearance' (45% for the RB, 20% for NNA and 15% for NNW) (p = 0.035). About 35% of participants rated NNAW as having a HLF in how it 'felt to touch' (30% for NNW, 15% for RB and 10% for NNA) (p = 0.008). Half of participants rated NNAW as having a HLF in terms of 'weight' (45% for NNW, 40% for RB and 0% for NNA) (p = 0.003). Participants delivered the greatest number of effective ventilations to the NNW mannequin. CONCLUSION: The NNW and NNAW configurations had the highest fidelity and had the highest percentage of effective ventilations delivered.

Perceptions of webcams in the neonatal intensive care unit: here's looking at you kid!

INTRODUCTION: Many tertiary neonatal units employ a restricted visiting policy. Webcams have previously been implemented in the neonatal unit setting in several countries. OBJECTIVES: This study aims to determine the views from parents, physicians, and nursing staff before implementation of a webcam system. METHODS: A questionnaire-based study. RESULTS: There were 101 responses. Parental computer usage was 83%. The majority of parents indicated that they would use the webcam system. Parents felt that a webcam system would reduce stress. Members of the nursing staff were most concerned about privacy risks (68%), compared with parents who were confident in the security of these systems (92%, p-value < 0.001). Seventy two percent of nurses felt that a webcam system would increase the stress levels of staff as compared with less than 20% of the physicians (p-value < 0.001). DISCUSSION: The majority of parents who completed the questionnaire have positive attitudes toward implementation of a webcam system in the NICU. Education of health care staff is required before implementation.

Addressing the taboo of medical error through IGBOs: I got burnt once!

BACKGROUND: An I Got Burnt Once (IGBO) is a near-miss or actual clinical event, related to patient safety, that leaves a lasting impact on the health professional (HP) involved. The purpose of this study was to collect and categorize IGBOs from a variety of pediatric HPs and to determine whether the individual's clinical practice was altered as a result. METHODS: Semistructured interviews involved recollection of an IGBO and subsequent changes in clinical practice. The IGBOs were classified into one of the seven Canadian Medical Education Directives for Specialists (CanMEDS) roles and outcome of the event. RESULTS: Of the 38 pediatric HPs approached (25 doctors and 13 female nurses), 35 recalled an IGBO. Most (74 %) were classified to the CanMEDS Medical Expert role (with subcategorization into diagnostics (37 %), treatment (34 %), and clinical management (31 %) followed by communicator (14 %) and collaborator (12 %) roles). Half (55 %) of the respondents considered the IGBO event to be potentially life threatening event to the patient, resulting in no harm (63 %), disability (14 %), and fatality in 17 % of the cases. Most respondents (92 %) stated that IGBOs affected their medical practice for months and sometimes years after the event. CONCLUSIONS: Most practitioners can recall an IGBO in their clinical practice. IGBOs may be a potential source of medical risk avoidance and reduction strategies, and worthy of further investigation by "deep dives" or root cause analysis.

T-piece gas flow palpation as a clinical indicator of endotracheal intubation in neonates.

We aimed to determine if providers could detect simulated spontaneous respirations of an intubated neonate by palpating gas flow changes at the positive end expiratory pressure valve of a T-piece resuscitation device in an in vitro setting. We also aimed to demonstrate whether the sensitivity of this methodology was related to the exhaled tidal volumes and/or the gas flow settings on the resuscitation device. A T-piece resuscitator (Neopuff®) circuit was connected to a neonatal silicon test lung. Expiratory tidal volumes of 5, 10 and 15 ml were provided via the test lung, with the Neopuff® set at gas flow rates of 5, 10 and 15 L/min. Physician volunteers were asked to identify whether they could detect expiratory gas from the test lung at the circuit T-piece with the volar surface of their wrist, at different tidal volumes and gas flows. Ten doctors detected 315 of 450 expirations; 95, 73 and 42 % of tidal volumes of 15, 10 and 5 ml, respectively, were detected with an overall positive predictive value of 98.7 %. Detection of exhalations was similar at different gas flow rates for each tidal volume. No exhalations were detected at zero gas flow. We concluded that T-piece gas flow palpation may be a useful and previously unreported clinical sign, which may help to reassure clinicians that they have successfully intubated the trachea. As with any clinical sign, it should not be considered in isolation but within the context of the clinical picture.

Perfusion index in the very preterm infant.

AIM: Perfusion Index (PI) is a quantifiable measurement of peripheral perfusion and may be a useful adjunct to the assessment of circulatory status in the newborn. (i) To assess reproducibility of PI and (ii) To determine whether there is a difference between simultaneously obtained limb measurements of PI in newborns <32 weeks GA in the transitional period. METHODS: Perfusion Index was measured in newborns <32 weeks during the first 48 h of life. To examine reproducibility, the pulse oximetry probe was replaced on the same limb consecutively by the same operator. Upper and lower limbs were then simultaneously evaluated over a 5-min period. Heart rate, blood pressure, birth weight, ventilation requirement, inotrope use, lactate, PCO2 and CRIB-II score were also recorded. RESULTS: Thirty infants were assessed. Intraclass correlation coefficient for reproducibility in the same limb was high (r value = 0.982 p < 0.001). Measurements obtained in the right upper limb were consistently higher than either lower limb. The median (IQR) PI for the entire cohort was 0.70 (0.29-1.35). No correlation existed between gestational age, birth weight, CRIB scores, systolic and diastolic blood pressure, mean blood pressure and median PI values. CONCLUSION: Perfusion Index measurement is reproducible, and values are highest in the right upper limb. Wide differences between right upper and lower limb readings are most likely related to transitional circulatory changes.

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.

High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin.

The infant gut microbiota undergoes dramatic changes during the first 2 years of life. The acquisition and development of this population can be influenced by numerous factors, and antibiotic treatment has been suggested as one of the most significant. Despite this, however, there have been relatively few studies which have investigated the short-term recovery of the infant gut microbiota following antibiotic treatment. The aim of this study was to use high-throughput sequencing (employing both 16S rRNA and rpoB-specific primers) and quantitative PCR to compare the gut microbiota of nine infants who underwent parenteral antibiotic treatment with ampicillin and gentamicin (within 48 h of birth), 4 and 8 weeks after the conclusion of treatment, relative to that of nine matched healthy controls. The investigation revealed that the gut microbiota of the antibiotic-treated infants had significantly higher proportions of Proteobacteria (P = 0.0049) and significantly lower proportions of Actinobacteria (P = 0.00001) (and the associated genus Bifidobacterium [P = 0.0132]) as well as the genus Lactobacillus (P = 0.0182) than the untreated controls 4 weeks after the cessation of treatment. By week 8, the Proteobacteria levels remained significantly higher in the treated infants (P = 0.0049), but the Actinobacteria, Bifidobacterium, and Lactobacillus levels had recovered and were similar to those in the control samples. Despite this recovery of total Bifidobacterium numbers, rpoB-targeted pyrosequencing revealed that the number of different Bifidobacterium species present in the antibiotic-treated infants was reduced. It is thus apparent that the combined use of ampicillin and gentamicin in early life can have significant effects on the evolution of the infant gut microbiota, the long-term health implications of which remain unknown.

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.

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.

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.

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.

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.

The Neopuff's PEEP valve is flow sensitive.

AIM: The current recommendation in setting up the Neopuff is to use a gas flow of 5-15 L/min. We investigated if the sensitivity of the positive end expiratory pressure (PEEP) valve varies at different flow rates within this range. METHODS: Five Neopuffs were set up to provide a PEEP of 5 cm H(2) O. The number of clockwise revolutions to complete occlusion of the PEEP valve and the mean and range of pressures at each quarter clockwise revolution were recorded at gas flow rates between 5 and 15 L/min. RESULTS: At 5, 10 and 15 L/min, 0.5, 1.7 and 3.4 full clockwise rotations were required to completely occlude the PEEP valve, and pressures rose from 5 to 11.4, 18.4 and 21.5 cm H(2) O, respectively. At a flow rate of 5 L/min, half a rotation of the PEEP dial resulted in a rise in PEEP from 5 to 11.4cm H(2) O. At 10 L/min, half a rotation resulted in a rise from 5 to 7.7cm H(2) O, and at 15 L/min PEEP rose from 5 to 6.8cm H(2) O. CONCLUSION: Users of the Neopuff should be aware that the PEEP valve is more sensitive at lower flow rates and that half a rotation of the dial at 5 L/min gas flow can more than double the PEEP.