1
|
Hutchinson RA, Costeloe KL, Wade WG, Millar MR, Ansbro K, Stacey F, Fleming PF. Intravenous antibiotics in preterm infants have a negative effect upon microbiome development throughout preterm life. Gut Pathog 2023; 15:18. [PMID: 37085896 PMCID: PMC10120188 DOI: 10.1186/s13099-023-00544-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/09/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Intestinal dysbiosis is implicated in the origins of necrotising enterocolitis and late-onset sepsis in preterm babies. However, the effect of modulators of bacterial growth (e.g. antibiotics) upon the developing microbiome is not well-characterised. In this prospectively-recruited, retrospectively-classified, case-control study, high-throughput 16S rRNA gene sequencing was combined with contemporaneous clinical data collection, to assess the within-subject relationship between antibiotic administration and microbiome development, in comparison to preterm infants with minimal antibiotic exposure. RESULTS During courses of antibiotics, diversity progression fell in comparison to that seen outside periods of antibiotic use (-0.71units/week vs. + 0.63units/week, p < 0.01); Enterobacteriaceae relative abundance progression conversely rose (+ 10.6%/week vs. -8.9%/week, p < 0.01). After antibiotic cessation, diversity progression remained suppressed (+ 0.2units/week, p = 0.02). CONCLUSIONS Antibiotic use has an acute and longer-lasting impact on the developing preterm intestinal microbiome. This has clinical implications with regard to the contribution of antibiotic use to evolving dysbiosis, and affects the interpretation of existing microbiome studies where this effect modulator is rarely accounted for.
Collapse
Affiliation(s)
- R A Hutchinson
- Queen Mary University of London, London, UK.
- Homerton University Hospital NHS Foundation Trust, London, UK.
| | | | - W G Wade
- Queen Mary University of London, London, UK
- King's College London, London, UK
- The Forsyth Institute, Cambridge, MA, USA
| | - M R Millar
- Queen Mary University of London, London, UK
| | - K Ansbro
- Queen Mary University of London, London, UK
| | - F Stacey
- Homerton University Hospital NHS Foundation Trust, London, UK
| | - P F Fleming
- Queen Mary University of London, London, UK
- Homerton University Hospital NHS Foundation Trust, London, UK
| |
Collapse
|
2
|
Embleton ND, Sproat T, Uthaya S, Young GR, Garg S, Vasu V, Masi AC, Beck L, Modi N, Stewart CJ, Berrington JE. Effect of an Exclusive Human Milk Diet on the Gut Microbiome in Preterm Infants: A Randomized Clinical Trial. JAMA Netw Open 2023; 6:e231165. [PMID: 36857051 PMCID: PMC9978942 DOI: 10.1001/jamanetworkopen.2023.1165] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
IMPORTANCE The effect of using an exclusive human milk diet compared with one that uses bovine products in preterm infants is uncertain, but some studies demonstrate lower rates of key neonatal morbidities. A potential mediating pathway is the gut microbiome. OBJECTIVE To determine the effect of an exclusive human milk diet on gut bacterial richness, diversity, and proportions of specific taxa in preterm infants from enrollment to 34 weeks' postmenstrual age. DESIGN, SETTING, AND PARTICIPANTS In this randomized clinical trial conducted at 4 neonatal intensive care units in the United Kingdom from 2017 to 2020, microbiome analyses were blind to group. Infants less than 30 weeks' gestation who had only received own mother's milk were recruited before 72 hours of age. Statistical analysis was performed from July 2019 to September 2021. INTERVENTIONS Exclusive human milk diet using pasteurized human milk for any shortfall in mother's own milk supply and human milk-derived fortifiers (intervention) compared with bovine formula and bovine-derived fortifier (control) until 34 weeks' postmenstrual age. Fortifier commenced less than 48 hours of tolerating 150 mL/kg per day. MAIN OUTCOMES AND MEASURES Gut microbiome profile including alpha and beta diversity, and presence of specific bacterial taxa. RESULTS Of 126 preterm infants enrolled in the study, 63 were randomized to control (median [IQR] gestation: 27.0 weeks [26.0-28.1 weeks]; median [IQR] birthweight: 910 g [704-1054 g]; 32 [51%] male) and 63 were randomized to intervention (median [IQR] gestation: 27.1 weeks [25.7-28.1 weeks]; median [IQR] birthweight: 930 g [733-1095 g]; 38 [60%] male); 472 stool samples from 116 infants were analyzed. There were no differences in bacterial richness or Shannon diversity over time, or at 34 weeks between trial groups. The exclusive human milk diet group had reduced relative abundance of Lactobacillus after adjustment for confounders (coefficient estimate, 0.056; P = .03), but not after false discovery rate adjustment. There were no differences in time to full feeds, necrotizing enterocolitis, or other key neonatal morbidities. CONCLUSIONS AND RELEVANCE In this randomized clinical trial in preterm infants using human milk-derived formula and/or fortifier to enable an exclusive human milk diet, there were no effects on overall measures of gut bacterial diversity but there were effects on specific bacterial taxa previously associated with human milk receipt. These findings suggest that the clinical impact of human milk-derived products is not modulated via microbiomic mechanisms. TRIAL REGISTRATION ISRCTN trial registry identifier: ISRCTN16799022.
Collapse
Affiliation(s)
- Nicholas D. Embleton
- Newcastle Hospitals NHS Trust, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas Sproat
- Newcastle Hospitals NHS Trust, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sabita Uthaya
- Section of Neonatal Medicine, School of Public Health, Imperial College London, London, United Kingdom
- Chelsea and Westminster Hospital, NHS Foundation Trust, London, United Kingdom
| | | | - Shalabh Garg
- James Cook University Hospital, Middlesbrough, United Kingdom
| | - Vimal Vasu
- William Harvey Hospital, Ashford, Kent, United Kingdom
| | - Andrea C. Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lauren Beck
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Neena Modi
- Section of Neonatal Medicine, School of Public Health, Imperial College London, London, United Kingdom
- Chelsea and Westminster Hospital, NHS Foundation Trust, London, United Kingdom
| | - Christopher J. Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Janet E. Berrington
- Newcastle Hospitals NHS Trust, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
3
|
Shen R, Embleton N, Lyng Forman J, Gale C, Griesen G, Sangild PT, Uthaya S, Berrington J. Early antibiotic use and incidence of necrotising enterocolitis in very preterm infants: a protocol for a UK based observational study using routinely recorded data. BMJ Open 2022; 12:e065934. [PMID: 36379645 PMCID: PMC9667987 DOI: 10.1136/bmjopen-2022-065934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
INTRODUCTION Necrotising enterocolitis (NEC) remains a major contributor to preterm mortality and morbidity. Prolonged duration of antibiotic therapy after delivery is associated with later NEC development but recent evidence suggests that absence of antibiotic treatment after delivery may also increase NEC risk. We will explore this controversy using a large pre-existing dataset of preterm infants in the UK. METHODS AND ANALYSIS This is a retrospective cohort study using data from UK National Neonatal Research Database (NNRD) for infants born 1 January 2012 to 31 December 2020. Eligible infants will be <32 weeks gestation, alive on day 3. Primary outcome is development of severe NEC, compared in infants receiving early antibiotics (days 1-2 after birth) and those not. Subgroup analysis on duration of early antibiotic exposure will also occur. Secondary outcomes are: late onset sepsis, total antibiotic use, predischarge mortality, retinopathy of prematurity, intraventricular haemorrhage, bronchopulmonary dysplasia, focal intestinal perforation and any abdominal surgery. To address competing risks, incidence of death before day 7, 14 and 28 will be analysed. We will perform logistic regression and propensity score matched analyses. Statistical analyses will be guided by NEC risk factors, exposures and outcome presented in a causal diagram. These covariates include but are not limited to gestational age, birth weight, small for gestational age, sex, ethnicity, delivery mode, delivery without labour, Apgar score, early feeding and probiotic use. Sensitivity analyses of alternate NEC definitions, specific antibiotics and time of initiation will occur. ETHICS AND DISSEMINATION We will use deidentified data from NNRD, which holds permissions for the original data, from which parents can opt out and seek study-specific research ethics approval. The results will help to determine optimal use of early antibiotics for very preterm infants. IMPLICATIONS This data will help optimise early antibiotic use in preterm infants. TRIAL REGISTRATION NUMBER ISRCTN55101779.
Collapse
Affiliation(s)
- Rene Shen
- Comparative Pediatrics and Nutrition, University of Copenhagen, Copenhgaen, Denmark
| | - Nicholas Embleton
- Neonatology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Population Health Sciences, Newcastle University Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | | | - Chris Gale
- Neonatal Medicine, School of Public Health, Imperial College London, London, UK
| | - Gorm Griesen
- Neonatology, Odense University Hospital, Odense, Denmark
| | - Per Torp Sangild
- Comparative Pediatrics and Nutrition, University of Copenhagen, Copenhgaen, Denmark
- Department of Neonatology, Rigshospitalet, Copenhagen, Denmark
| | - Sabita Uthaya
- Faculty of Medicine, Imperial College London, London, UK
| | - Janet Berrington
- Neonatology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Clinical and Translational Research Institute, Newcastle University Faculty of Medical Sciences, Newcastle upon Tyne, UK
| |
Collapse
|
4
|
Moschino L, Verlato G, Duci M, Cavicchiolo ME, Guiducci S, Stocchero M, Giordano G, Fascetti Leon F, Baraldi E. The Metabolome and the Gut Microbiota for the Prediction of Necrotizing Enterocolitis and Spontaneous Intestinal Perforation: A Systematic Review. Nutrients 2022; 14:nu14183859. [PMID: 36145235 PMCID: PMC9506026 DOI: 10.3390/nu14183859] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 11/26/2022] Open
Abstract
Necrotizing enterocolitis (NEC) is the most devastating gastrointestinal emergency in preterm neonates. Research on early predictive biomarkers is fundamental. This is a systematic review of studies applying untargeted metabolomics and gut microbiota analysis to evaluate the differences between neonates affected by NEC (Bell’s stage II or III), and/or by spontaneous intestinal perforation (SIP) versus healthy controls. Five studies applying metabolomics (43 cases, 95 preterm controls) and 20 applying gut microbiota analysis (254 cases, 651 preterm controls, 22 term controls) were selected. Metabolomic studies utilized NMR spectroscopy or mass spectrometry. An early urinary alanine/histidine ratio >4 showed good sensitivity and predictive value for NEC in one study. Samples collected in proximity to NEC diagnosis demonstrated variable pathways potentially related to NEC. In studies applying untargeted gut microbiota analysis, the sequencing of the V3−V4 or V3 to V5 regions of the 16S rRNA was the most used technique. At phylum level, NEC specimens were characterized by increased relative abundance of Proteobacteria compared to controls. At genus level, pre-NEC samples were characterized by a lack or decreased abundance of Bifidobacterium. Finally, at the species level Bacteroides dorei, Clostridium perfringens and perfringens-like strains dominated early NEC specimens, whereas Clostridium butyricum, neonatale and Propionibacterium acnei those at disease diagnosis. Six studies found a lower Shannon diversity index in cases than controls. A clear separation of cases from controls emerged based on UniFrac metrics in five out of seven studies. Importantly, no studies compared NEC versus SIP. Untargeted metabolomics and gut microbiota analysis are interrelated strategies to investigate NEC pathophysiology and identify potential biomarkers. Expression of quantitative measurements, data sharing via biorepositories and validation studies are fundamental to guarantee consistent comparison of results.
Collapse
Affiliation(s)
- Laura Moschino
- Neonatal Intensive Care Unit, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
- Institute of Paediatric Research, Città della Speranza, Laboratory of Mass Spectrometry and Metabolomics, 35127 Padova, Italy
- Correspondence: ; Tel.: +39-049-821-3548
| | - Giovanna Verlato
- Neonatal Intensive Care Unit, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Miriam Duci
- Paediatric Surgery, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Maria Elena Cavicchiolo
- Neonatal Intensive Care Unit, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Silvia Guiducci
- Neonatal Intensive Care Unit, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Matteo Stocchero
- Institute of Paediatric Research, Città della Speranza, Laboratory of Mass Spectrometry and Metabolomics, 35127 Padova, Italy
- Laboratory of Mass Spectrometry and Metabolomics, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Giuseppe Giordano
- Institute of Paediatric Research, Città della Speranza, Laboratory of Mass Spectrometry and Metabolomics, 35127 Padova, Italy
- Laboratory of Mass Spectrometry and Metabolomics, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Francesco Fascetti Leon
- Paediatric Surgery, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Eugenio Baraldi
- Neonatal Intensive Care Unit, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
- Institute of Paediatric Research, Città della Speranza, Laboratory of Mass Spectrometry and Metabolomics, 35127 Padova, Italy
| |
Collapse
|
5
|
Westaway JAF, Huerlimann R, Miller CM, Kandasamy Y, Norton R, Rudd D. Methods for exploring the faecal microbiome of premature infants: a review. Matern Health Neonatol Perinatol 2021; 7:11. [PMID: 33685524 PMCID: PMC7941982 DOI: 10.1186/s40748-021-00131-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
The premature infant gut microbiome plays an important part in infant health and development, and recognition of the implications of microbial dysbiosis in premature infants has prompted significant research into these issues. The approaches to designing investigations into microbial populations are many and varied, each with its own benefits and limitations. The technique used can influence results, contributing to heterogeneity across studies. This review aimed to describe the most common techniques used in researching the preterm infant microbiome, detailing their various limitations. The objective was to provide those entering the field with a broad understanding of available methodologies, so that the likely effects of their use can be factored into literature interpretation and future study design. We found that although many techniques are used for characterising the premature infant microbiome, 16S rRNA short amplicon sequencing is the most common. 16S rRNA short amplicon sequencing has several benefits, including high accuracy, discoverability and high throughput capacity. However, this technique has limitations. Each stage of the protocol offers opportunities for the injection of bias. Bias can contribute to variability between studies using 16S rRNA high throughout sequencing. Thus, we recommend that the interpretation of previous results and future study design be given careful consideration.
Collapse
Affiliation(s)
- Jacob A F Westaway
- James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia.
| | - Roger Huerlimann
- James Cook University, 1 James Cook Dr, Douglas, QLD, 4811, Australia
| | - Catherine M Miller
- James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia
| | - Yoga Kandasamy
- Townsville University Hospital, 100 Angus Smith Dr, Douglas, QLD, 4814, Australia
| | - Robert Norton
- Pathology Queensland, 100 Angus Smith Dr, Douglas, QLD, 4814, Australia
| | - Donna Rudd
- James Cook University, 1 James Cook Dr, Douglas, QLD, 4811, Australia
| |
Collapse
|
6
|
Abstract
Late-onset sepsis (LOS) and necrotising enterocolitis (NEC) account for the highest number of deaths in premature infants and often cause severe morbidity in survivors. NEC is an inflammatory mediated condition, but its pathophysiology remains poorly understood. There is increasing evidence that in LOS the causative organism most often translocates from the gut. No causative microorganism has been consistently associated with either LOS or NEC, but an aberrant gut microbiome development could play a pivotal role. A low bacterial diversity and a delay in anaerobic bacteria colonization may predispose preterm infants to disease development. Conversely, a predominance of Bifidobacterium species and breast milk feeding might help to prevent disease onset. With numerous studies reporting conflicting results, further research is needed to better understand the role of microorganisms and type of feeding in the health status of preterm infants.
Collapse
Affiliation(s)
- Andrea C Masi
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | |
Collapse
|
7
|
Abstract
Probiotic administration to preterm infants is not universal despite randomised trial data from >10,000 infants, significant observational data and multiple meta-analyses. Advocates point to reductions in necrotising enterocolitis and sepsis, 'sceptics' hold concerns over data quality/interpretation or risks. Issues revolve around different products, primary outcomes, uncertain dosing strategies and individual large 'negative' trials alongside probiotic associated sepsis and quality control concerns. We review concerns and how to move probiotic use forward. Surprisingly little is known about parental perspectives, vital to inform next steps. How to share information and decisions around probiotic use now, and how this impacts on future available strategies is discussed. We address placebo controlled trials and propose alternate designs, including head to head studies, using 'routine' data collection systems, opt out consents and 'learning technologies' embedded in health care systems. We also raise the importance of underpinning mechanistic work to inform future trials.
Collapse
|
8
|
Stewart CJ, Fatemizadeh R, Parsons P, Lamb CA, Shady DA, Petrosino JF, Hair AB. Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue. BMC Microbiol 2019; 19:52. [PMID: 30832576 PMCID: PMC6398254 DOI: 10.1186/s12866-019-1426-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 02/22/2019] [Indexed: 12/16/2022] Open
Abstract
Background Necrotising enterocolitis (NEC) is a common cause of death in preterm infants and is closely linked to the gut microbiota. Spontaneous intestinal perforation (SIP) also occurs in preterm neonates, but results in lower mortality and less adverse neonatal outcomes than NEC. Existing studies are largely limited to non-invasive stool samples, which may not be reflective of the anatomical site of disease. Therefore, we analysed historical formalin-fixed paraffin-embedded (FFPE) tissue from NEC and SIP preterm infants. A total of 13 NEC and 16 SIP infants were included. Extracted DNA from FFPE tissue blocks underwent 16S rRNA gene sequencing. For a subset of infants, diseased tissue and marginal healthy tissue from the same infant were compared. Results Xylene provided a cost and time effective means of deparaffinization. Tissue from the site of disease was highly comparable to adjacent healthier tissue. Comparing only diseased tissue from all infants showed significantly lower Shannon diversity in NEC (P = 0.026). The overall bacterial communities were also significantly different in NEC samples compared to SIP (P = 0.038), and large variability within NEC infants was observed. While no single OTU or genus was significantly associated with NEC or SIP, at the phylum level Proteobacteria (P = 0.045) and Bacteroidetes (P = 0.024) were significantly higher in NEC and SIP infants, respectively. Conclusions Existing banks of intestinal FFPE blocks provide a robust and specific sample for profiling the microbiota at the site of disease. We showed preterm infants with NEC have lower diversity and different bacterial communities when compared to SIP controls. Electronic supplementary material The online version of this article (10.1186/s12866-019-1426-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA. .,Institute of Cellular Medicine, Newcastle University, Medical School, Leech Building, M3.121, Newcastle upon Tyne, NE2 4HH, UK.
| | - Roxana Fatemizadeh
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Pamela Parsons
- Texas Medical Center Digestive Diseases Center, Core B Cellular and Molecular Morphology, Houston, TX, USA
| | - Christopher A Lamb
- Institute of Cellular Medicine, Newcastle University, Medical School, Leech Building, M3.121, Newcastle upon Tyne, NE2 4HH, UK.,Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Deborah A Shady
- Texas Medical Center Digestive Diseases Center, Core B Cellular and Molecular Morphology, Houston, TX, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Amy B Hair
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| |
Collapse
|
9
|
Ma B, McComb E, Gajer P, Yang H, Humphrys M, Okogbule-Wonodi AC, Fasano A, Ravel J, Viscardi RM. Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants. Front Microbiol 2018; 9:2755. [PMID: 30487786 PMCID: PMC6246636 DOI: 10.3389/fmicb.2018.02755] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/29/2018] [Indexed: 12/24/2022] Open
Abstract
Intestinal barrier immaturity, or "leaky gut," is the proximate cause of susceptibility to necrotizing enterocolitis in preterm neonates. However, the impact of intestinal microbiota development on intestinal mucosal barrier maturation has not been evaluated in this population. In this study, we investigated a longitudinally sampled cohort of 38 preterm infants < 33 weeks gestation monitored for intestinal permeability (IP) and fecal microbiota during the first 2 weeks of life. Rapid decrease in IP indicating intestinal barrier function maturation correlated with significant increase in community diversity. In particular, members of the Clostridiales and Bifidobacterium were highly transcriptionally active, and progressively increasing abundance in Clostridiales was significantly associated with decreased intestinal permeability. Further, neonatal factors previously identified to promote intestinal barrier maturation, including early exclusive breastmilk feeding and shorter duration antibiotic exposure, associate with the early colonization of the intestinal microbiota by members of the Clostridiales, which altogether are associated with improved intestinal barrier function in preterm infants.
Collapse
Affiliation(s)
- Bing Ma
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Elias McComb
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Pawel Gajer
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Hongqiu Yang
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Mike Humphrys
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Adora C. Okogbule-Wonodi
- Department of Pediatrics and Child Health, Howard University College of Medicine, Washington, DC, United States
| | - Alessio Fasano
- Department of Pediatrics, Basic, Clinical and Translational Research, MassGeneral Hospital for Children, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Jacques Ravel
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Rose M Viscardi
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| |
Collapse
|
10
|
Effect of fecal microbiota transplantation route of administration on gut colonization and host response in preterm pigs. ISME JOURNAL 2018; 13:720-733. [PMID: 30367124 DOI: 10.1038/s41396-018-0301-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/26/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023]
Abstract
This study examined gut colonization patterns and host responses to fecal microbiota transplantation (FMT) by different administration routes after preterm birth. In two separate experiments, cesarean-delivered, preterm pigs were administered combined oral + rectal, or exclusively rectal donor feces, and compared with saline controls. After 5 days, stomach and colon bacterial compositions were determined by 16S rRNA gene amplicon sequencing, and organic acid metabolites measured. Further, gut pathology, mucosa bacterial adherence, and goblet cell density were assessed. FMT increased the relative abundance of obligate anaerobes in the colon without affecting total bacterial load. Bacteroides colonized recipients despite low abundance in the donor feces, whereas highly abundant Prevotella and Ruminococcaceae did not. Further, FMT changed carbohydrate metabolism from lactate to propionate production thereby increasing colonic pH. Besides, FMT preserved goblet cell mucin stores and reduced necrotizing enterocolitis incidence. Only rectal FMT increased the stomach-to-colon pH gradient and resistance to mucosa bacterial adhesion. Conversely, oral + rectal FMT increased bacterial adhesion, internal organ colonization, and overall mortality. Our results uncovered distinctions in bacterial colonization patterns along the gastrointestinal tract, as well as host tolerability between oral and rectal FMT administration in preterm newborns. Besides, FMT showed the potential to prevent necrotizing enterocolitis.
Collapse
|
11
|
Embleton ND, Berrington JE, Dorling J, Ewer AK, Juszczak E, Kirby JA, Lamb CA, Lanyon CV, McGuire W, Probert CS, Rushton SP, Shirley MD, Stewart CJ, Cummings SP. Mechanisms Affecting the Gut of Preterm Infants in Enteral Feeding Trials. Front Nutr 2017; 4:14. [PMID: 28534028 PMCID: PMC5420562 DOI: 10.3389/fnut.2017.00014] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022] Open
Abstract
Large randomized controlled trials (RCTs) in preterm infants offer unique opportunities for mechanistic evaluation of the risk factors leading to serious diseases, as well as the actions of interventions designed to prevent them. Necrotizing enterocolitis (NEC) a serious inflammatory gut condition and late-onset sepsis (LOS) are common feeding and nutrition-related problems that may cause death or serious long-term morbidity and are key outcomes in two current UK National Institutes for Health Research (NIHR) trials. Speed of increasing milk feeds trial (SIFT) randomized preterm infants to different rates of increases in milk feeds with a primary outcome of survival without disability at 2 years corrected age. Enteral lactoferrin in neonates (ELFIN) randomizes infants to supplemental enteral lactoferrin or placebo with a primary outcome of LOS. This is a protocol for the mechanisms affecting the gut of preterm infants in enteral feeding trials (MAGPIE) study and is funded by the UK NIHR Efficacy and Mechanistic Evaluation programme. MAGPIE will recruit ~480 preterm infants who were enrolled in SIFT or ELFIN. Participation in MAGPIE does not change the main trial protocols and uses non-invasive sampling of stool and urine, along with any residual resected gut tissue if infants required surgery. Trial interventions may involve effects on gut microbes, metabolites (e.g., short-chain fatty acids), and aspects of host immune function. Current hypotheses suggest that NEC and/or LOS are due to a dysregulated immune system in the context of gut dysbiosis, but mechanisms have not been systematically studied within large RCTs. Microbiomic analysis will use next-generation sequencing, and metabolites will be assessed by mass spectrometry to detect volatile organic and other compounds produced by microbes or the host. We will explore differences between disease cases and controls, as well as exploring the actions of trial interventions. Impacts of this research are multiple: translation of knowledge of mechanisms promoting gut health may explain outcomes or suggest alternate strategies to improve health. Results may identify new non-invasive diagnostic or monitoring techniques, preventative or treatment strategies for NEC or LOS, or provide data useful for risk stratification in future studies. Mechanistic evaluation might be especially informative where there are not clear effects on the primary outcome (ISRCTN 12554594).
Collapse
Affiliation(s)
- Nicholas D Embleton
- Newcastle Neonatal Service, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
| | - Janet E Berrington
- Newcastle Neonatal Service, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Jon Dorling
- School of Medicine, University of Nottingham, Nottingham, UK
| | - Andrew K Ewer
- College of Medical and Dental Sciences, Institute of Metabolism and Systems Research, Birmingham University, Birmingham, UK
| | | | - John A Kirby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher A Lamb
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Clare V Lanyon
- Department for Biomedical Sciences, School of Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - William McGuire
- Centre for Reviews and Dissemination, University of York, York, UK
| | - Christopher S Probert
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | | | - Mark D Shirley
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher J Stewart
- Department for Biomedical Sciences, School of Life Sciences, Northumbria University, Newcastle upon Tyne, UK.,Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Stephen P Cummings
- School of Science and Engineering, Teesside University, Middlesbrough, UK
| |
Collapse
|
12
|
Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Nelson A, Abdulkadir B, Skeath T, Petrosino JF, Perry JD, Berrington JE, Cummings SP. Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease. MICROBIOME 2016; 4:67. [PMID: 28034304 PMCID: PMC5200962 DOI: 10.1186/s40168-016-0216-8] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 12/01/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND The preterm microbiome is crucial to gut health and may contribute to necrotising enterocolitis (NEC), which represents the most significant pathology affecting preterm infants. From a cohort of 318 infants, <32 weeks gestation, we selected 7 infants who developed NEC (defined rigorously) and 28 matched controls. We performed detailed temporal bacterial (n = 641) and metabolomic (n = 75) profiling of the gut microbiome throughout the disease. RESULTS A core community of Klebsiella, Escherichia, Staphyloccocus, and Enterococcus was present in all samples. Gut microbiota profiles grouped into six distinct clusters, termed preterm gut community types (PGCTs). Each PGCT reflected dominance by the core operational taxonomic units (OTUs), except of PGCT 6, which had high diversity and was dominant in bifidobacteria. While PGCTs 1-5 were present in infants prior to NEC diagnosis, PGCT 6 was comprised exclusively of healthy samples. NEC infants had significantly more PGCT transitions prior to diagnosis. Metabolomic profiling identified significant pathways associated with NEC onset, with metabolites involved in linoleate metabolism significantly associated with NEC diagnosis. Notably, metabolites associated with NEC were the lowest in PGCT 6. CONCLUSIONS This is the first study to integrate sequence and metabolomic stool analysis in preterm neonates, demonstrating that NEC does not have a uniform microbial signature. However, a diverse gut microbiome with a high abundance of bifidobacteria may protect preterm infants from disease. These results may inform biomarker development and improve understanding of gut-mediated mechanisms of NEC.
Collapse
MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- DNA, Bacterial/analysis
- DNA, Ribosomal/analysis
- Enterocolitis, Necrotizing/metabolism
- Enterocolitis, Necrotizing/microbiology
- Feces/microbiology
- Female
- Gastrointestinal Microbiome
- Humans
- Infant, Newborn
- Infant, Premature
- Infant, Premature, Diseases/metabolism
- Infant, Premature, Diseases/microbiology
- Linoleic Acid/metabolism
- Longitudinal Studies
- Male
- Metabolic Networks and Pathways
- Phylogeny
- Proteomics/methods
- RNA, Ribosomal, 16S/analysis
- Sequence Analysis, DNA/methods
Collapse
Affiliation(s)
- Christopher J Stewart
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Alkek Center for Metagenomics and Microbiome Research, Houston, Texas, 77030, USA.
| | - Nicholas D Embleton
- Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, United Kingdom
| | - Emma C L Marrs
- Department of Microbiology, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, United Kingdom
| | - Daniel P Smith
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Alkek Center for Metagenomics and Microbiome Research, Houston, Texas, 77030, USA
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
| | - Bashir Abdulkadir
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
| | - Tom Skeath
- Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, United Kingdom
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Alkek Center for Metagenomics and Microbiome Research, Houston, Texas, 77030, USA
| | - John D Perry
- Department of Microbiology, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, United Kingdom
| | - Janet E Berrington
- Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, United Kingdom
| | - Stephen P Cummings
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
- School of Science and Engineering, Teesside University, Middlesbrough, TS1 3BX, United Kingdom
| |
Collapse
|