One third of newborn babies in the US are exposed to antibiotics and, after discharge from the nursery, antibiotics are the most common prescription medication given to young children. Moreover, a large proportion of these perinatal and infant antibiotic exposures are unnecessary. While adverse effects of antibiotics such as the development of antibiotic resistance are well described, the patient-specific effects of antibiotic use on the long-term health of children remains unclear. The forming microbiome of the human infant is highly susceptible to disruptions, and alterations in gut bacterial species in early life during a critical period of normal colonization can have long-term effects. Early life antibiotic exposures have been associated with increased risks of obesity, allergy, and asthma. However, the potential links between varied early life antibiotic exposures, alterations in microbiome function or maturation, and health outcomes generally remain unknown. To address these knowledge gaps, we will assemble and follow longitudinally a large, diverse birth cohort to determine the relationship between (1) antibiotic exposure and gut microbiome development; (2) antibiotic exposure and weight gain/adiposity; (3) and microbiome development and weight gain/adiposity. We will examine routine intrapartum, neonatal, and infant antibiotic exposures; use bacterial taxonomic marker gene sequencing, metatranscriptomics, and metabolomics to measure antibiotic-related shifts in microbiome taxonomic carriage, biodiversity, and rate of maturation of the infant gut microbiome; and perform serial anthropometric measurements to assess weight gain and adiposity over the first 24 months of life. This project leverages complementary strengths in epidemiology, pediatrics, neonatology, infectious diseases, obesity research, clinical bioinformatics, and microbiome analysis from investigators at the University of Pennsylvania, the Children's Hospital of Philadelphia (CHOP), and the University of Minnesota. Our prior work demonstrates that (1) the investigators have extensive experience with defining the epidemiology and outcomes of antimicrobial use; the study of the mother-infant dyad in the perinatal period; the collection, processing, and analysis of human gut microbiome data; and assessing and characterizing infant and early childhood growth; 2) that antibiotic use across this population is both frequent and variable-an ideal environment to evaluate the proposed hypothesis; and 3) longitudinal early life anthropometric measurements of a cohort enrolled from birth is feasible. Through CHOP we have access to a large birthing center feeding one of the largest pediatric healthcare networks in the US using a common electronic health record. This large heterogeneous cohort is one of the key strengths of our proposal, and will enable us to recruit, follow, and monitor health records of all cohort members in real time. The establishment of a large birth cohort in which the microbiome is defined and patient health information is prospectively recorded will lead to unique future opportunities to directly link changes in the structure and function of the developing microbiome with additional health outcomes.
Perinatal and infant antibiotic exposures are common and have been linked to changes in the gut microbiome, which plays a central role in health and disease. Childhood obesity is an epidemic and animal models have linked antibiotic induced changes in the microbiome with increased adiposity. Using a large, diverse pediatric primary care network fed by a large birthing center, we will assemble and longitudinally follow a heterogeneous birth cohort from the womb through 24 months of age in order to determine the effects of early-life antibiotic exposure on microbiome taxonomy, gene expression, and metabolic activity and how this affects growth trajectory in the first 2 years of life.
|Mukhopadhyay, Sagori; Sengupta, Shaon; Puopolo, Karen M (2018) Challenges and opportunities for antibiotic stewardship among preterm infants. Arch Dis Child Fetal Neonatal Ed :|
|Ward, Tonya L; Dominguez-Bello, Maria Gloria; Heisel, Tim et al. (2018) Development of the Human Mycobiome over the First Month of Life and across Body Sites. mSystems 3:|
|Burns, Michael B; Montassier, Emmanuel; Abrahante, Juan et al. (2018) Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment. PLoS Genet 14:e1007376|
|Hillmann, Benjamin; Al-Ghalith, Gabriel A; Shields-Cutler, Robin R et al. (2018) Evaluating the Information Content of Shallow Shotgun Metagenomics. mSystems 3:|
|Al-Ghalith, Gabriel A; Montassier, Emmanuel; Ward, Henry N et al. (2016) NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes. PLoS Comput Biol 12:e1004658|