The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms.
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ABSTRACT:
SUBMITTER: Brooks B
PROVIDER: S-EPMC6011520 | biostudies-literature | 2018 Jun
REPOSITORIES: biostudies-literature
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The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms.
Brooks Brandon B Olm Matthew R MR Firek Brian A BA Baker Robyn R Geller-McGrath David D Reimer Sophia R SR Soenjoyo Karina R KR Yip Jennifer S JS Dahan Dylan D Thomas Brian C BC Morowitz Michael J MJ Banfield Jillian F JF
Microbiome 20180620 1
<h4>Background</h4>The neonatal intensive care unit (NICU) contains a unique cohort of patients with underdeveloped immune systems and nascent microbiome communities. Patients often spend several months in the same room, and it has been previously shown that the gut microbiomes of these infants often resemble the microbes found in the NICU. Little is known, however, about the identity, persistence, and absolute abundance of NICU room-associated bacteria over long stretches of time. Here, we coup ...[more]
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Project description:IntroductionThe infant gut microbiome is thought to play a key role in developing metabolic and immunologic pathways. Antibiotics have been shown to disrupt the human microbiome, but the impact they have on infants during this key window of development remains poorly understood. Through this study, we further characterize the effect antibiotics have on the gut microbiome of infants by looking at metagenomic sequencing data over time.Materials and methodsStool samples were collected on infants from a large tertiary care neonatal intensive care unit. After DNA extraction, metagenomics libraries were generated and sequenced. Taxonomic and functional analyses were then performed. Further directed specimen sequencing for fungal species was also performed.ResultsA total of 51 stool samples from 25 infants were analyzed: seven infants were on antibiotics during at least one of their collection time points. Antibiotics given at birth altered the microbiome (PERMANOVA R2 = 0.044, p = .002) but later courses did not (R2 = 0.023, p = .114). Longitudinal samples collected while off antibiotics were more similar than those collected during a transition on or off antibiotics (mean Bray-Curtis distance 0.29 vs. 0.63, Wilcoxon p = .06). Functional analysis revealed four microbial pathways that were disrupted by antibiotics given at-birth (p < .1, folate synthesis, glycerolipid metabolism, fatty acid biosynthesis, and glycolysis). No functional changes associated with current antibiotic use were identified. In a limited sample set, we saw little evidence of fungal involvement in the overall infant microbiome.ConclusionThrough this study, we have further characterized the role antibiotics have in the development of the infant microbiome. Antibiotics given at birth were associated with alterations in the microbiome and had significant impact on the functional pathways involved in folate synthesis and multiple metabolic pathways. Later courses of antibiotics led to stochastic dysbiosis and a significant decrease in Escherichia coli. Further characterization of the infant mycobiome is still needed.
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Project description:Every year in the United States, more than 300,000 infants are admitted to neonatal intensive care units (NICU) where they are exposed to a chemical-intensive hospital environment during a developmentally vulnerable period. The neurodevelopmental impact of environmental exposure to phthalates during the NICU stay is unknown. As phthalate exposure during the third trimester developmental window has been implicated in neurobehavioral deficits in term-born children that are strikingly similar to a phenotype of neurobehavioral morbidity common among children born premature, the role of early-life phthalate exposure on the neurodevelopmental trajectory of premature infants may be clinically important. In this study, premature newborns with birth weight <1500g were recruited to participate in a prospective environmental health cohort study, NICU-HEALTH (Hospital Exposures and Long-Term Health), part of the DINE (Developmental Impact of NICU Exposures) cohort of the ECHO (Environmental influences on Child Health Outcomes) program. Seventy-six percent of eligible infants enrolled in the study. Sixty-four of 81 infants survived and are included in this analysis. 164 urine specimens were analyzed for phthalate metabolites using high-performance liquid chromatography/tandem mass spectrometry. The NICU Network Neurobehavioral Scale (NNNS) was performed prior to NICU discharge. Linear and weighted quantile sum regression quantified associations between phthalate biomarkers and NNNS performance, and between phthalate biomarkers and intensity of medical intervention. The sum of di(2-ethylhexyl) phthalate metabolites (?DEHP) was associated with improved performance on the Attention and Regulation scales. Specific mixtures of phthalate biomarkers were also associated with improved NNNS performance. More intense medical intervention was associated with higher ?DEHP exposure. NICU-based exposure to phthalates mixtures was associated with improved attention and social response. This suggests that the impact of phthalate exposure on neurodevelopment may follow a non-linear trajectory, perhaps accelerating the development of certain neural networks. The long-term neurodevelopmental impact of NICU-based phthalate exposure needs to be evaluated.
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Project description:The neonatal/infant intensive care unit (N/IICU) at the Children's Hospital of Philadelphia is a 98-bed, level IV unit through which second-year pediatric residents rotate monthly. We developed a quality improvement project to improve the resident educational experience using goal setting. Primary objectives were to increase resident educational goal identification to 65% and goal achievement to 85% by June 2017. Secondary objectives were to (1) increase in-person feedback from fellows and/or attendings to 90% by June 2017 and (2) sustain improvements through June 2018.MethodsThe quality improvement team developed a driver diagram and administered a baseline survey to 48 residents who had rotated through the N/IICU in the 18 months before the project. Plan-Do-Study-Act cycles targeted project awareness and trialing of 3 different methods to elicit goals and track feedback, from July 2016 through June 2018.ResultsThe baseline survey response rate was 52% (n = 25). Among 60 rotating residents, the median resident-reported rate of goal achievement increased from 37.5% to 50%, and residents receiving in-person feedback increased from 25% to 50%. Of the 63% (n = 38) of residents who participated in data collection, goal identification and achievement increased from 38% to 100% between academic year 2016 and academic year 2017, and in-person feedback increased from 24% to 82%.ConclusionsInstituting a goal-setting framework for residents during their N/IICU rotation increased goal achievement and in-person feedback. Consistent resident participation in postrotation data collection made measuring project outcomes challenging. These data support goal-oriented learning as an approach to enhance learner engagement and improve goal achievement.
| S-EPMC7591117 | biostudies-literature
Project description:BACKGROUND: The source inoculum of gastrointestinal tract (GIT) microbes is largely influenced by delivery mode in full-term infants, but these influences may be decoupled in very low birth weight (VLBW, <1,500 g) neonates via conventional broad-spectrum antibiotic treatment. We hypothesize the built environment (BE), specifically room surfaces frequently touched by humans, is a predominant source of colonizing microbes in the gut of premature VLBW infants. Here, we present the first matched fecal-BE time series analysis of two preterm VLBW neonates housed in a neonatal intensive care unit (NICU) over the first month of life. RESULTS: Fresh fecal samples were collected every 3 days and metagenomes sequenced on an Illumina HiSeq2000 device. For each fecal sample, approximately 33 swabs were collected from each NICU room from 6 specified areas: sink, feeding and intubation tubing, hands of healthcare providers and parents, general surfaces, and nurse station electronics (keyboard, mouse, and cell phone). Swabs were processed using a recently developed 'expectation maximization iterative reconstruction of genes from the environment' (EMIRGE) amplicon pipeline in which full-length 16S rRNA amplicons were sheared and sequenced using an Illumina platform, and short reads reassembled into full-length genes. Over 24,000 full-length 16S rRNA sequences were produced, generating an average of approximately 12,000 operational taxonomic units (OTUs) (clustered at 97% nucleotide identity) per room-infant pair. Dominant gut taxa, including Staphylococcus epidermidis, Klebsiella pneumoniae, Bacteroides fragilis, and Escherichia coli, were widely distributed throughout the room environment with many gut colonizers detected in more than half of samples. Reconstructed genomes from infant gut colonizers revealed a suite of genes that confer resistance to antibiotics (for example, tetracycline, fluoroquinolone, and aminoglycoside) and sterilizing agents, which likely offer a competitive advantage in the NICU environment. CONCLUSIONS: We have developed a high-throughput culture-independent approach that integrates room surveys based on full-length 16S rRNA gene sequences with metagenomic analysis of fecal samples collected from infants in the room. The approach enabled identification of discrete ICU reservoirs of microbes that also colonized the infant gut and provided evidence for the presence of certain organisms in the room prior to their detection in the gut.
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Project description:IntroductionLate preterm births represent the largest category of preterm deliveries. Although these infants are frequently managed in normal newborn nurseries, they have an increased risk of readmissions and mortality. Thus, we designed this PowerPoint-based learning module to provide learners with a computer-based educational resource on late preterm infants in the level II neonatal intensive care unit.MethodsThis module can be completed using the included pretest and posttest to assess for change in knowledge. The module should take approximately 20 to 30 minutes to complete.ResultsBetween May and June of 2016, members of the pediatric hospitalist division at Children's National Health System in Washington, DC participated in a study of the module as a self-directed learning tool and completed the pretest, posttest, and postmodule evaluation forms. There was an overall increase in knowledge, with an increase in posttest score from 64% to 94%. Furthermore, this module was well-received by learners, as 55% of learners agreed or strongly agreed that the material presented in the module would change their clinical practice, and 100% agreed or strongly agreed that the module increased their comfort with teaching on this topic.DiscussionInitial implementation of the module indicates it could be a valuable tool to address a perceived educational need in the area of late preterm infant care in the level II neonatal intensive care unit.
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Project description:AIM:To investigate the frequency, etiology, and current management strategies for diarrhea in newborn. METHODS:Retrospective, nationwide study involving 5801 subjects observed in neonatal intensive care units during 3 years. The main anamnesis and demographic characteristics, etiology and characteristics of diarrhea, nutritional and therapeutic management, clinical outcomes were evaluated. RESULTS:Thirty-nine cases of diarrhea (36 acute, 3 chronic) were identified. The occurrence rate of diarrhea was 6.72 per 1000 hospitalized newborn. Etiology was defined in 29 of 39 newborn (74.3%): food allergy (20.5%), gastrointestinal infections (17.9%), antibiotic-associated diarrhea (12.8%), congenital defects of ion transport (5.1%), withdrawal syndrome (5.1%), Hirschsprung's disease (2.5%), parenteral diarrhea (2.5%), cystic fibrosis (2.5%), and metabolic disorders (2.5%). Three patients died due to complications related to diarrhea (7.7%). In 19 of 39 patients (48.7%), rehydration was performed exclusively by the enteral route. CONCLUSION:Diarrhea in neonates is a challenging clinical condition due to the possible heterogeneous etiologies and severe outcomes. Specific guidelines are advocated in order to optimize management of diarrhea in this particular setting.
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Project description:The purpose of this study is to develop nursing standard guidelines for nurses in a neonatal intensive care unit. The Delphi method was used in this study to elicit expert consensus. Thirteen experts who were nurses and pediatric adolescent specialists working in the neonatal intensive care unit participated in the study. In this study, 178 items were developed based on 5 nursing practice standards and 7 standards of professional practice. An additional 10 items were included based on observation in the neonatal intensive care unit. After expert validation, a final total of 184 items was developed. The standard guidelines for high-risk neonatal care developed in this study for practical clinical education in nursing are significant because they reflect the nursing practice standards in Korea and characteristics of nursing practice in the neonatal intensive unit.
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Project description:IntroductionThirdhand smoke (THS) is ultrafine particulate matter and residue resulting from tobacco combustion, with implications for health-related harm (eg, impaired wound healing), particularly among hospitalized infants. Project aims were to characterize nicotine (THS proxy) transported on neonatal intensive care unit (NICU) visitors and deposited on bedside furniture, as well as infant exposure.MethodsCross-sectional data were collected from participants in a metropolitan NICU. Participants completed a survey and carbon monoxide breath sample, and 41.9% (n = 88) of participants (n = 210) were randomly selected for finger-nicotine wipes during a study phase when all bedside visitors were screened for nicotine use and finger-nicotine levels. During an overlapping study phase, 80 mother-infant dyads consented to bedside furniture-nicotine wipes and an infant urine sample (for cotinine analyses).ResultsMost nonstaff visitors' fingers had nicotine above the limit of quantification (>LOQ; 61.9%). Almost all bedside furniture surfaces (93.8%) and infant cotinine measures (93.6%) had values >LOQ, regardless of household nicotine use. Participants who reported using (or lived with others who used) nicotine had greater furniture-nicotine contamination (Mdn = 0.6 [interquartile range, IQR = 0.2-1.6] µg/m2) and higher infant cotinine (Mdn = 0.09 [IQR = 0.04-0.25] ng/mL) compared to participants who reported no household-member nicotine use (Mdn = 0.5 [IQR = 0.2-0.7] µg/m2; Mdn = 0.04 [IQR = 0.03-0.07] ng/mL, respectively). Bayesian univariate regressions supported hypotheses that increased nicotine use/exposure correlated with greater nicotine contamination (on fingers/furniture) and infant THS exposure.ConclusionsPotential furniture-contamination pathways and infant-exposure routes (eg, dermal) during NICU hospitalization were identified, despite hospital prohibitions on tobacco/nicotine use. This work highlights the surreptitious spread of nicotine and potential THS-related health risks to vulnerable infants during critical stages of development.ImplicationsTHS contamination is underexplored in medical settings. Infants who were cared for in the NICU are vulnerable to health risks from THS exposure. This study demonstrated that 62% of nonstaff NICU visitors transport nicotine on their fingers to the NICU. Over 90% of NICU (bedside) furniture was contaminated with nicotine, regardless of visitors' reported household-member nicotine use or nonuse. Over 90% of infants had detectable levels of urinary cotinine during NICU hospitalizations. Results justify further research to better protect infants from unintended THS exposure while hospitalized.
| S-EPMC7822104 | biostudies-literature
Project description:Background: There is a growing move to provide care for premature infants in a single family, private room neonatal intensive care unit (NICU) in place of the traditional shared space, open bay NICU. The resultant effect on the developing neonatal microbiota is unknown. Study Design: Stool and groin skin swabs were collected from infants in a shared-space NICU (old NICU) and a single-family room NICU (new NICU) on the same hospital campus. Metagenomic sequencing was performed and data analyzed by CosmosID bioinformatics software package. Results: There were no significant differences between the cohorts in gestational age, length of stay, and delivery mode; infants in the old NICU received significantly more antibiotics (p = 0.03). Differentially abundant antimicrobial resistance genes and virulence associated genes were found between the cohorts in stool and skin, with more differentially abundant antimicrobial resistance genes in the new NICU. The entire bacterial microbiota analyzed to the genus level significantly differed between cohorts in skin (p = 0.0001) but not in stool samples. There was no difference in alpha diversity between the two cohorts. DNA viruses and fungi were detected but did not differ between cohorts. Conclusion: Differences were seen in the resistome and virulome between the two cohorts with more differentially abundant antimicrobial resistance genes in the new NICU. This highlights the influence that different NICU environments can have on the neonatal microbiota. Whether the differences were due to the new NICU being a single-family NICU or located in a newly constructed building warrants exploration. Long term health outcomes from the differences observed must be followed longitudinally.
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Project description:BACKGROUND:Risk factors for perinatal posttraumatic stress disorder (PTSD) among parents of an infant in the NICU have varied in previous literature. The relationships between perception of illness severity and objective measures of illness severity with PTSD are not well understood. AIMS:To determine if PTSD among parents after an infant NICU discharge can be predicted by 1) objective measures of infant illness severity or 2) perceptions of infant illness severity. STUDY DESIGN:A prospective, observational study. SUBJECTS:Parent/infant dyads who were in the NICU for ≥14 days. OUTCOME MEASURES:Objective measures of illness severity were obtained from the electronic health record. Perceptions of illness were measured by the response to the question, "How sick is your child/patient?" on a 5-point Likert scale. The Perinatal Post-Traumatic Stress Disorder Questionnaire (PPQ) was completed by parents three months after discharge. RESULTS:One hundred ninety-four dyads participated in the study, 86% of parents completed follow up screening. 25% of parents screened positive for PTSD. Parents perceived infants to be sick more often than hospital caregivers. In bivariate analysis many objective measures of illness severity were associated with PTSD. Parent perceptions of illness were also associated with PTSD after adjusting for objective measures of illness (OR 3.2, 95% CI 1.1-6.1, p = 0.008). CONCLUSIONS:PTSD in parents after NICU discharge is multifactorial. Objective illness risk factors can be used to screen parents at risk. Hospital caregivers should strive to understand parents' perception of illness and improve communication to potentially decrease PTSD after discharge.
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