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Samarra A, Cabrera-Rubio R, Martínez-Costa C, Collado MC. Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life. Ann Clin Microbiol Antimicrob 2024; 23:72. [PMID: 39138497 PMCID: PMC11323388 DOI: 10.1186/s12941-024-00725-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/12/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Alongside microbiota development, the evolution of the resistome is crucial in understanding the early-life acquisition and persistence of Antibiotic Resistance Genes (ARGs). Therefore, the aim of this study is to provide a comprehensive view of the evolution and dynamics of the neonatal resistome from 7 days to 4 months of age using a high-throughput qPCR platform. METHODS In the initial phase, a massive screening of 384 ARGs using a high-throughput qPCR in pooled healthy mother-infant pairs feces from the MAMI cohort was carried out to identify the most abundant and prevalent ARGs in infants and in mothers. This pre-analysis allowed for later targeted profiling in a large number of infants in a longitudinal manner during the first 4 months of life. 16S rRNA V3-V4 amplicon sequencing was performed to asses microbial composition longitudinally. Potential factors influencing the microbiota and ARGs in this period were also considered, such as mode of birth and breastfeeding type. RESULTS Following the massive screening, the top 45 abundant ARGs and mobile genetic elements were identified and studied in 72 infants during their first months of life (7 days, 1, 2, and 4 months). These genes were associated with resistance to aminoglycosides, beta-lactams and tetracyclines, among others, as well as integrons, and other mobile genetic elements. Changes in both ARG composition and quantity were observed during the first 4 months of life: most ARGs abundance increased over time, but mobile genetic elements decreased significantly. Further exploration of modulating factors highlighted the effect on ARG composition of specific microbial genus, and the impact of mode of birth at 7 days and 4 months. The influence of infant formula feeding was observed at 4-month-old infants, who exhibited a distinctive resistome composition. CONCLUSIONS This study illustrates the ARG evolution and dynamics in the infant gut by use of a targeted, high-throughput, quantitative PCR-based method. An increase in antibiotic resistance over the first months of life were observed with a fundamental role of delivery mode in shaping resistance profiles. Further, we highlighted the influence of feeding methods on the resistome development. These findings offer pivotal insights into dynamics of and factors influencing early-life resistome, with potential avenues for intervention strategies.
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Affiliation(s)
- Anna Samarra
- Departament of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Raúl Cabrera-Rubio
- Departament of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Cecilia Martínez-Costa
- Department of Pediatrics, School of Medicine, University of Valencia, Valencia, Spain
- Pediatric Gastroenterology and Nutrition Section, Hospital Clínico Universitario Valencia, INCLIVA, Valencia, Spain
| | - Maria Carmen Collado
- Departament of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Paterna, Valencia, Spain.
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2
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Trosvik P, Noordzij HT, de Muinck EJ. Antibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life. Sci Rep 2024; 14:18701. [PMID: 39134593 PMCID: PMC11319485 DOI: 10.1038/s41598-024-69275-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
Colonization of the infant gut is an important developmental process characterized by high carriage of antimicrobial resistance genes (ARGs) and high abundances of pathobionts. The horizontal transfer of ARGs to pathogenic bacteria represents a major public health concern. However, there is still a paucity of longitudinal studies surveilling ARGs in healthy infant guts at high temporal resolution. Furthermore, we do not yet have a clear view of how temporal variation in ARG carriage relates to the dynamics of specific bacterial populations, as well as community virulence potential. Here, we performed deep shotgun metagenomic sequencing of monthly fecal samples from a cohort of 12 infants, covering the first year of life to interrogate the infant gut microbiome for ARG content. We further relate ARG dynamics to the dynamics of taxa, virulence potential, as well as the potential for ARG mobilization. We identify a core resistome dominated by efflux systems typically associated with Enterobacteriaceae. Overall ARG carriage declined over the first year of life and showed strong contemporaneous correlation with the population dynamics of Proteobacteria. Furthermore, the majority of ARGs could be further mapped to metagenome-assembled genomes (MAGs) classified to this phylum. We were able to assign a large number of ARGs to E. coli by correlating the temporal dynamics of individual genes with species dynamics, and we show that the temporal dynamics of ARGs and virulence factors are highly correlated, suggesting close taxonomic associations between these two gene classes. Finally, we identify ARGs linked with various categories of mobile genetic elements, demonstrating preferential linkage among mobility categories and resistance to different drug classes. While individual variation in ARG carriage is substantial during infancy there is a clear reduction over the first year of life. With few exceptions, ARG abundances closely track the dynamics of pathobionts and community virulence potential. These findings emphasize the potential for development of resistant pathogens in the developing infant gut, and the importance of effective surveillance in order to detect such events.
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Affiliation(s)
- Pål Trosvik
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Hanna Theodora Noordzij
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Eric Jacques de Muinck
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Pharmacy, University of Oslo, Oslo, Norway
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Wang J, Li Y, Mu Y, Huang K, Li D, Lan C, Cui Y, Wang J. Missing microbes in infants and children in the COVID-19 pandemic: a study of 1,126 participants in Beijing, China. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1739-1750. [PMID: 38748355 DOI: 10.1007/s11427-023-2488-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/16/2023] [Indexed: 08/09/2024]
Abstract
The COVID-19 pandemic has caused many fatalities worldwide and continues to affect the health of the recovered patients in the form of long-COVID. In this study, we compared the gut microbiome of uninfected infants and children before the pandemic began (BEFORE cohort, n=906) to that of after the pandemic (AFTER cohort, n=220) to examine the potential impact of social distancing and life habit changes on infant/children gut microbiome. Based on 16S rRNA sequencing, we found a significant change in microbiome composition after the pandemic, with Bacteroides enterotype increasing to 35.45% from 30.46% before the pandemic. qPCR quantification indicated that the bacterial loads of seven keystone taxa decreased by 91.69%-19.58%. Quantitative microbiome profiling, used to enhance the resolution in detecting microbiome differences, revealed a greater explained variance of pandemic on microbiome compared to gender, as well as a significant decrease in bacterial loads in 15 of the 20 major genera. The random forest age-predictor indicated the gut microbiomes were less mature in the after-pandemic cohort than in the before-pandemic cohort in the children group (3-12 years old) and had features of a significantly younger age (average of 1.86 years). Lastly, body weight and height were significantly lower in the after-pandemic cohort than in the before-pandemic cohort in infants (<1 year of age), which was associated with a decrease in bacterial loads in the fecal microbiome.
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Affiliation(s)
- Jiejing Wang
- CAS Key Lab for Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuejuan Li
- CAS Key Lab for Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Mu
- Beijing Dr. CUIYUTAO Clinic, Beijing, 100028, China
| | - Kefei Huang
- Beijing Dr. CUIYUTAO Clinic, Beijing, 100028, China
| | - Danyi Li
- R-Institute Co. Ltd., Beijing, 100011, China
| | - Canhui Lan
- R-Institute Co. Ltd., Beijing, 100011, China
| | - Yutao Cui
- Beijing Dr. CUIYUTAO Clinic, Beijing, 100028, China.
| | - Jun Wang
- CAS Key Lab for Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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Dhariwal A, Rajar P, Salvadori G, Åmdal HA, Berild D, Saugstad OD, Fugelseth D, Greisen G, Dahle U, Haaland K, Petersen FC. Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants. Nat Commun 2024; 15:6024. [PMID: 39019886 PMCID: PMC11255206 DOI: 10.1038/s41467-024-50433-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 07/10/2024] [Indexed: 07/19/2024] Open
Abstract
Respiratory pathogens, commonly colonizing nasopharynx, are among the leading causes of death due to antimicrobial resistance. Yet, antibiotic resistance determinants within nasopharyngeal microbial communities remain poorly understood. In this prospective cohort study, we investigate the nasopharynx resistome development in preterm infants, assess early antibiotic impact on its trajectory, and explore its association with clinical covariates using shotgun metagenomics. Our findings reveal widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) with resistomes undergoing transient changes, including increased ARG diversity, abundance, and composition alterations due to early antibiotic exposure. ARGs associated with the critical nosocomial pathogen Serratia marcescens persist up to 8-10 months of age, representing a long-lasting hospitalization signature. The nasopharyngeal resistome strongly correlates with microbiome composition, with inter-individual differences and postnatal age explaining most of the variation. Our report on the collateral effects of antibiotics and prolonged hospitalization underscores the urgency of further studies focused on this relatively unexplored reservoir of pathogens and ARGs.
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Affiliation(s)
- Achal Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Polona Rajar
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
- Department of Neonatal Intensive Care, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Gabriela Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Heidi Aarø Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Dag Berild
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Drude Fugelseth
- Department of Neonatal Intensive Care, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gorm Greisen
- Department of Neonatology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Ulf Dahle
- Centre for Antimicrobial Resistance, Norwegian Institute of Public Health, Oslo, Norway
| | - Kirsti Haaland
- Department of Neonatal Intensive Care, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
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Xu X, Feng Q, Zhang T, Gao Y, Cheng Q, Zhang W, Wu Q, Xu K, Li Y, Nguyen N, Taft DH, Mills DA, Lemay DG, Zhu W, Mao S, Zhang A, Xu K, Liu J. Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life. IMETA 2024; 3:e169. [PMID: 38882494 PMCID: PMC11170968 DOI: 10.1002/imt2.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 06/18/2024]
Abstract
The infant gut microbiome is increasingly recognized as a reservoir of antibiotic resistance genes, yet the assembly of gut resistome in infants and its influencing factors remain largely unknown. We characterized resistome in 4132 metagenomes from 963 infants in six countries and 4285 resistance genes were observed. The inherent resistome pattern of healthy infants (N = 272) could be distinguished by two stages: a multicompound resistance phase (Months 0-7) and a tetracycline-mupirocin-β-lactam-dominant phase (Months 8-14). Microbial taxonomy explained 40.7% of the gut resistome of healthy infants, with Escherichia (25.5%) harboring the most resistance genes. In a further analysis with all available infants (N = 963), we found age was the strongest influencer on the resistome and was negatively correlated with the overall resistance during the first 3 years (p < 0.001). Using a random-forest approach, a set of 34 resistance genes could be used to predict age (R 2 = 68.0%). Leveraging microbial host inference analyses, we inferred the age-dependent assembly of infant resistome was a result of shifts in the gut microbiome, primarily driven by changes in taxa that disproportionately harbor resistance genes across taxa (e.g., Escherichia coli more frequently harbored resistance genes than other taxa). We performed metagenomic functional profiling and metagenomic assembled genome analyses whose results indicate that the development of gut resistome was driven by changes in microbial carbohydrate metabolism, with an increasing need for carbohydrate-active enzymes from Bacteroidota and a decreasing need for Pseudomonadota during infancy. Importantly, we observed increased acquired resistance genes over time, which was related to increased horizontal gene transfer in the developing infant gut microbiome. In summary, infant age was negatively correlated with antimicrobial resistance gene levels, reflecting a composition shift in the gut microbiome, likely driven by the changing need for microbial carbohydrate metabolism during early life.
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Affiliation(s)
- Xinming Xu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
- Department of Nutrition and Food Hygiene, School of Public Health, Institute of Nutrition Fudan University Shanghai China
| | - Qingying Feng
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
- Biological Engineering Division Massachusetts Institute of Technology (MIT) Cambridge Massachusetts USA
| | - Tao Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Yunlong Gao
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Qu Cheng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Wanqiu Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Qinglong Wu
- Department of Pathology and Immunology Baylor College of Medicine Houston Texas USA
| | - Ke Xu
- Department of Statistics University of Chicago Chicago Illinois
| | - Yucan Li
- State Key Laboratory of Genetic Engineering, Human Phenome Institute Fudan University Shanghai China
| | - Nhu Nguyen
- Department of Food Science and Technology University of California, Davis Davis California USA
| | - Diana H Taft
- Department of Food Science and Technology University of California, Davis Davis California USA
| | - David A Mills
- Department of Food Science and Technology University of California, Davis Davis California USA
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science University of California, Davis Davis California USA
| | - Danielle G Lemay
- USDA ARS Western Human Nutrition Research Center Davis California USA
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences Sichuan University Chengdu China
| | - Kelin Xu
- Department of Biostatistics, Key Laboratory of Public Health Safety, NHC Key Laboratory of Health Technology Assessment, School of Public Health Fudan University Shanghai China
| | - Jinxin Liu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
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Zhao L, Yang X, Liang Y, Zhang Z, Ding Y, Wang Y, Chen B, Wu J, Jin C, Zhao G, Li Z, Zhang L. Temporal development and potential interactions between the gut microbiome and resistome in early childhood. Microbiol Spectr 2024; 12:e0317723. [PMID: 38193687 PMCID: PMC10846076 DOI: 10.1128/spectrum.03177-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/03/2023] [Indexed: 01/10/2024] Open
Abstract
Antimicrobial resistance-associated infections have become a major threat to global health. The gut microbiome serves as a major reservoir of bacteria with antibiotic resistance genes; whereas, the temporal development of gut resistome during early childhood and the factors influencing it remain unclear. Moreover, the potential interactions between gut microbiome and resistome still need to be further explored. In this study, we found that antibiotic treatment led to destabilization of the gut microbiome and resistome structural communities, exhibiting a greater impact on the resistome than on the microbiome. The composition of the gut resistome at various developmental stages was influenced by the abundance and richness of different core microbes. First exposure to antibiotics led to a dramatic increase in the number of opportunistic pathogens carrying multidrug efflux pump encoding genes. Multiple factors could influence the gut microbiome and resistome formation. The data may provide new insights into early-life research.IMPORTANCEIn recent years, the irrational or inappropriate use of antibiotics, an important life-saving medical intervention, has led to the emergence and increase of drug-resistant and even multidrug-resistant bacteria. It remains unclear how antibiotic exposure affects various developmental stages of early childhood and how gut core microbes under antibiotic exposure affect the structural composition of the gut resistome. In this study, we focused on early antibiotic exposure and analyzed these questions in detail using samples from infants at various developmental stages. The significance of our research is to elucidate the impact of early antibiotic exposure on the dynamic patterns of the gut resistome in children and to provide new insights for early-life studies.
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Affiliation(s)
- Lanlan Zhao
- MicrobiomeX, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiao Yang
- MicrobiomeX, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yijia Liang
- MicrobiomeX, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ziyi Zhang
- MicrobiomeX, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yanwen Ding
- MicrobiomeX, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yihui Wang
- MicrobiomeX, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bin Chen
- MicrobiomeX, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiacheng Wu
- MicrobiomeX, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chuandi Jin
- MicrobiomeX, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Guoping Zhao
- MicrobiomeX, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ziyun Li
- MicrobiomeX, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lei Zhang
- MicrobiomeX, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Patangia DV, Grimaud G, O'Shea CA, Ryan CA, Dempsey E, Stanton C, Ross RP. Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome. MICROBIOME 2024; 12:19. [PMID: 38310316 PMCID: PMC10837951 DOI: 10.1186/s40168-023-01732-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/24/2023] [Indexed: 02/05/2024]
Abstract
BACKGROUND Infant gut microbiota is highly malleable, but the long-term longitudinal impact of antibiotic exposure in early life, together with the mode of delivery on infant gut microbiota and resistome, is not extensively studied. METHODS Two hundred and eight samples from 45 infants collected from birth until 2 years of age over five time points (week 1, 4, 8, 24, year 2) were analysed. Based on shotgun metagenomics, the gut microbial composition and resistome profile were compared in the early life of infants divided into three groups: vaginal delivery/no-antibiotic in the first 4 days of life, C-section/no-antibiotic in the first 4 days of life, and C-section/antibiotic exposed in first 4 days of life. Gentamycin and benzylpenicillin were the most commonly administered antibiotics during this cohort's first week of life. RESULTS Newborn gut microbial composition differed in all three groups, with higher diversity and stable composition seen at 2 years of age, compared to week 1. An increase in microbial diversity from week 1 to week 4 only in the C-section/antibiotic-exposed group reflects the effect of antibiotic use in the first 4 days of life, with a gradual increase thereafter. Overall, a relative abundance of Actinobacteria and Bacteroides was significantly higher in vaginal delivery/no-antibiotic while Proteobacteria was higher in C-section/antibiotic-exposed infants. Strains from species belonging to Bifidobacterium and Bacteroidetes were generally persistent colonisers, with Bifidobacterium breve and Bifidobacterium bifidum species being the major persistent colonisers in all three groups. Bacteroides persistence was dominant in the vaginal delivery/no-antibiotic group, with species Bacteroides ovatus and Phocaeicola vulgatus found to be persistent colonisers in the no-antibiotic groups. Most strains carrying antibiotic-resistance genes belonged to phyla Proteobacteria and Firmicutes, with the C-section/antibiotic-exposed group presenting a higher frequency of antibiotic-resistance genes (ARGs). CONCLUSION These data show that antibiotic exposure has an immediate and persistent effect on the gut microbiome in early life. As such, the two antibiotics used in the study selected for strains (mainly Proteobacteria) which were multiple drug-resistant (MDR), presumably a reflection of their evolutionary lineage of historical exposures-leading to what can be an extensive and diverse resistome. Video Abstract.
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Affiliation(s)
- Dhrati V Patangia
- School of Microbiology, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Ghjuvan Grimaud
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | | | - C A Ryan
- APC Microbiome Ireland, Cork, Ireland
| | - Eugene Dempsey
- APC Microbiome Ireland, Cork, Ireland
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
- Infant Research Centre, University College Cork, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - R Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
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Allert M, Ferretti P, Johnson KE, Heisel T, Gonia S, Knights D, Fields DA, Albert FW, Demerath EW, Gale CA, Blekhman R. Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother's milk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.28.577594. [PMID: 38328166 PMCID: PMC10849666 DOI: 10.1101/2024.01.28.577594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as the sole source of nutrition for the human infant, little is known about how variation in milk composition, and especially the milk microbiome, shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiome using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. We found that the microbial taxonomic overlap between milk and the infant gut was driven by bifidobacteria, in particular by B. longum. Infant stool samples dominated by B. longum also showed higher temporal stability compared to samples dominated by other species. We identified two instances of strain sharing between maternal milk and the infant gut, one involving a commensal (B. longum) and one a pathobiont (K. pneumoniae). In addition, strain sharing between unrelated infants was higher among infants born at the same hospital compared to infants born in different hospitals, suggesting a potential role of the hospital environment in shaping the infant gut microbiome composition. The infant gut microbiome at one month compared to six months of age was enriched in metabolic pathways associated with de-novo molecule biosynthesis, suggesting that early colonisers might be more versatile and metabolically independent compared to later colonizers. Lastly, we found a significant overlap in antimicrobial resistance genes carriage between the mother's milk and their infant's gut microbiome. Taken together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.
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Affiliation(s)
- Mattea Allert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Pamela Ferretti
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kelsey E Johnson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Timothy Heisel
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Sara Gonia
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - David A Fields
- Department of Pediatrics, the University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ellen W Demerath
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Cheryl A Gale
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
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9
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Zhang T, Mu Y, Gao Y, Tang Y, Mao S, Liu J. Fecal microbial gene transfer contributes to the high-grain diet-induced augmentation of aminoglycoside resistance in dairy cattle. mSystems 2024; 9:e0081023. [PMID: 38085089 PMCID: PMC10805029 DOI: 10.1128/msystems.00810-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/31/2023] [Indexed: 01/24/2024] Open
Abstract
A high-grain (HG) diet can rapidly lower the rumen pH and thus modify the gastrointestinal microbiome in dairy cattle. Although the prevalence of antibiotic resistance is strongly linked with the gut microbiome, the influences of HG diet on animals' gut resistome remain largely unexplored. Here, we examined the impact and mechanism of an HG diet on the fecal resistome in dairy cattle by metagenomically characterizing the gut microbiome. Eight lactating Holstein cattle were randomly allocated into two groups and fed either a conventional (CON) or HG diet for 3 weeks. The fecal microbiome and resistome were significantly altered in dairy cattle from HG, demonstrating an adaptive response that peaks at day 14 after the dietary transition. Importantly, we determined that feeding an HG diet specifically elevated the prevalence of resistance to aminoglycosides (0.11 vs 0.24 RPKG, P < 0.05). This diet-induced resistance increase is interrelated with the disproportional propagation of microbes in Lachnospiraceae, indicating a potential reservoir of aminoglycosides resistance. We further showed that the prevalence of acquired resistance genes was also modified by introducing a different diet, likely due to the augmented frequency of lateral gene transfer (LGT) in microbes (CON vs HG: 254 vs 287 taxa) such as Lachnospiraceae. Consequently, we present that diet transition is associated with fecal resistome modification in dairy cattle and an HG diet specifically enriched aminoglycosides resistance that is likely by stimulating microbial LGT.IMPORTANCEThe increasing prevalence of antimicrobial resistance is one of the most severe threats to public health, and developing novel mitigation strategies deserves our top priority. High-grain (HG) diet is commonly applied in dairy cattle to enhance animals' performance to produce more high-quality milk. We present that despite such benefits, the application of an HG diet is correlated with an elevated prevalence of resistance to aminoglycosides, and this is a combined effect of the expansion of antibiotic-resistant bacteria and increased frequency of lateral gene transfer in the fecal microbiome of dairy cattle. Our results provided new knowledge in a typically ignored area by showing an unexpected enrichment of antibiotic resistance under an HG diet. Importantly, our findings laid the foundation for designing potential dietary intervention strategies to lower the prevalence of antibiotic resistance in dairy production.
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Affiliation(s)
- Tao Zhang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yingyu Mu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yunlong Gao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yijun Tang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jinxin Liu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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10
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Jokela R, Pärnänen KMM, Ponsero AJ, Lahti L, Kolho KL, de Vos WM, Salonen A. A cohort study in family triads: impact of gut microbiota composition and early life exposures on intestinal resistome during the first two years of life. Gut Microbes 2024; 16:2383746. [PMID: 39092808 PMCID: PMC11299627 DOI: 10.1080/19490976.2024.2383746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/20/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Antibiotic resistance genes (ARGs) are prevalent in the infant gut microbiota and make up the intestinal resistome, representing a community ARG reservoir. This study focuses on the dynamics and persistence of ARGs in the early gut microbiota, and the effect of early exposures therein. We leveraged 2,328 stool metagenomes from 475 children in the HELMi cohort and the available parental samples to study the diversity, dynamics, and intra-familial sharing of the resistome during the first two years of life. We found higher within-family similarity of the gut resistome composition and ARG load in infant-mother pairs, and between spouses, but not in father-infant pairs. Early gut microbiota composition and development correlated with the ARG load; Bacteroides correlated positively and Bifidobacterium negatively with the load, reflecting the typical resistance levels in these taxa. Caesarean delivered infants harbored lower ARG loads, partly reflecting the scarcity of Bacteroides compared to vaginally delivered. Exposure to intrapartum or post-natal antibiotics showed only modest associations with the ARG load and composition, mainly before 12 months. Our results indicate that the resistome is strongly driven by the normal development of the microbiota in early life, and suggest importance of longer evolution of ARGs over effects of recent antibiotic exposure.
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Affiliation(s)
- Roosa Jokela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Alise J Ponsero
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Kaija-Leena Kolho
- Children’s Hospital, University of Helsinki and Helsinki University Hospital (HUS), Helsinki, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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11
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Patangia DV, Grimaud G, Wang S, Ross RP, Stanton C. Influence of age, socioeconomic status, and location on the infant gut resistome across populations. Gut Microbes 2024; 16:2297837. [PMID: 38217470 PMCID: PMC10793692 DOI: 10.1080/19490976.2023.2297837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/18/2023] [Indexed: 01/15/2024] Open
Abstract
Antibiotic resistance is a growing global concern, with many ecological niches showing a high abundance of antibiotic resistance genes (ARGs), including the human gut. With increasing indications of ARGs in infants, this study aims to investigate the gut resistome profile during early life at a wider geographic level. To achieve this objective, we utilized stool samples data from 26 studies involving subjects aged up to 3 years from different geographical locations. The 32,277 Metagenome Assembled Genomes (MAGs) previously generated from shotgun sequencing reads from these studies were used for resistome analysis using RGI with the CARD database. This analysis showed that the distribution of ARGs across the countries in our study differed in alpha diversity and compositionally. In particular, the abundance of ARGs was found to vary by socioeconomic status and healthcare access and quality (HAQ) index. Surprisingly, countries having lower socioeconomic status and HAQ indices showed lower ARG abundance, which was contradictory to previous reports. Gram-negative genera, including Escherichia, Enterobacter, Citrobacter, and Klebsiella harbored a particularly rich set of ARGs, which included antibiotics that belong to the Reserve, Access or Watch category, such as glycopeptides, fluoroquinolones, sulfonamides, macrolides, and tetracyclines. We showed that ARG abundance exponentially decreased with time during the first 3 years of life. Many highly ARG-abundant species including Escherichia, Klebsiella, Citrobacter species that we observed are well-known pathobionts found in the infant gut in early life. High abundance of these species and a diverse range of ARGs in their genomes point toward the infant gut, acting as an ARG reservoir. This is a concern and further studies are needed to examine the causal effect and its consequences on long-term health.
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Affiliation(s)
- Dhrati V. Patangia
- School of Microbiology, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Ghjuvan Grimaud
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Shaopu Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - R. Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
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12
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Clark JA, Curran MD, Gouliouris T, Conway Morris A, Bousfield R, Navapurkar V, Kean IRL, Daubney E, White D, Baker S, Pathan N. Rapid Detection of Antimicrobial Resistance Genes in Critically Ill Children Using a Custom TaqMan Array Card. Antibiotics (Basel) 2023; 12:1701. [PMID: 38136735 PMCID: PMC10740637 DOI: 10.3390/antibiotics12121701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Bacteria are identified in only 22% of critically ill children with respiratory infections treated with antimicrobial therapy. Once an organism is isolated, antimicrobial susceptibility results (phenotypic testing) can take another day. A rapid diagnostic test identifying antimicrobial resistance (AMR) genes could help clinicians make earlier, informed antimicrobial decisions. Here we aimed to validate a custom AMR gene TaqMan Array Card (AMR-TAC) for the first time and assess its feasibility as a screening tool in critically ill children. An AMR-TAC was developed using a combination of commercial and bespoke targets capable of detecting 23 AMR genes. This was validated using isolates with known phenotypic resistance. The card was then tested on lower respiratory tract and faecal samples obtained from mechanically ventilated children in a single-centre observational study of respiratory infection. There were 82 children with samples available, with a median age of 1.2 years. Major comorbidity was present in 29 (35%) children. A bacterial respiratory pathogen was identified in 13/82 (16%) of children, of which 4/13 (31%) had phenotypic AMR. One AMR gene was detected in 49/82 (60%), and multiple AMR genes were detected in 14/82 (17%) children. Most AMR gene detections were not associated with the identification of phenotypic AMR. AMR genes are commonly detected in samples collected from mechanically ventilated children with suspected respiratory infections. AMR-TAC may have a role as an adjunct test in selected children in whom there is a high suspicion of antimicrobial treatment failure.
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Affiliation(s)
- John A. Clark
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
| | - Martin D. Curran
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Theodore Gouliouris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Andrew Conway Morris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge CB2 2QQ, UK
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Rachel Bousfield
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Vilas Navapurkar
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
| | - Iain R. L. Kean
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Esther Daubney
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Deborah White
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK;
| | - Nazima Pathan
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
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13
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Goh SG, Haller L, Ng C, Charles FR, Jitxin L, Chen H, He Y, Gin KYH. Assessing the additional health burden of antibiotic resistant Enterobacteriaceae in surface waters through an integrated QMRA and DALY approach. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:132058. [PMID: 37459761 DOI: 10.1016/j.jhazmat.2023.132058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/15/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
Antibiotic resistant Enterobacteriaceae pose a significant threat to public health. However, limited studies have evaluated the health risks associated with exposure to antibiotic-resistant bacteria (ARB), especially in natural environments. While quantitative microbial risk assessment (QMRA) assesses microbial risks in terms of the probability of infection, it does not account for the severity of health outcomes. In this study, a QMRA-DALY model was developed to integrate QMRA with health burden (disability-adjusted life years (DALY)) from infections caused by ARB. The model considers uncertainties in probability of infection and health burden assessment using Monte Carlo simulations. The study collected antimicrobial resistance (AMR) surveillance data from surface waters with different land uses. Results revealed water bodies with agricultural land use to be the main AMR hotspots, with the highest additional health burden observed in infections caused by meropenem-resistant E. coli (∆DALY = 0.0105 DALY/event) compared to antibiotic-susceptible E. coli. The estimated ∆DALY for antibiotic-resistant K. pneumoniae was lower than for antibiotic-resistant E. coli (highest ∆DALY = 0.00048 DALY/event). The study highlights the need for better evaluation of AMR associated health burden, and effective measures to mitigate the risks associated with antibiotic-resistant bacteria in natural environments.
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Affiliation(s)
- Shin Giek Goh
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Laurence Haller
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Charmaine Ng
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Francis Rathinam Charles
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Lim Jitxin
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Hongjie Chen
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore; Department of Civil & Environmental Engineering, National University of Singapore, Singapore 117576, Singapore.
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14
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Mills M, Lee S, Piperata BA, Garabed R, Choi B, Lee J. Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua. MICROBIOME 2023; 11:207. [PMID: 37715296 PMCID: PMC10503196 DOI: 10.1186/s40168-023-01636-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/31/2023] [Indexed: 09/17/2023]
Abstract
BACKGROUND Early life plays a vital role in the development of the gut microbiome and subsequent health. While many factors that shape the gut microbiome have been described, including delivery mode, breastfeeding, and antibiotic use, the role of household environments is still unclear. Furthermore, the development of the gut antimicrobial resistome and its role in health and disease is not well characterized, particularly in settings with water insecurity and less sanitation infrastructure. RESULTS This study investigated the gut microbiome and resistome of infants and young children (ages 4 days-6 years) in rural Nicaragua using Oxford Nanopore Technology's MinION long-read sequencing. Differences in gut microbiome diversity and antibiotic resistance gene (ARG) abundance were examined for associations with host factors (age, sex, height for age z-score, weight for height z-score, delivery mode, breastfeeding habits) and household environmental factors (animals inside the home, coliforms in drinking water, enteric pathogens in household floors, fecal microbial source tracking markers in household floors). We identified anticipated associations of higher gut microbiome diversity with participant age and vaginal delivery. However, novel to this study were the significant, positive associations between ruminant and dog fecal contamination of household floors and gut microbiome diversity. We also identified greater abundance of potential pathogens in the gut microbiomes of participants with higher fecal contamination on their household floors. Path analysis revealed that water quality and household floor contamination independently and significantly influenced gut microbiome diversity when controlling for age. These gut microbiome contained diverse resistome, dominated by multidrug, tetracycline, macrolide/lincosamide/streptogramin, and beta-lactam resistance. We found that the abundance of ARGs in the gut decreased with age. The bacterial hosts of ARGs were mainly from the family Enterobacteriaceae, particularly Escherichia coli. CONCLUSIONS This study identified the role of household environmental contamination in the developing gut microbiome and resistome of young children and infants with a One Health perspective. We found significant relationships between host age, gut microbiome diversity, and the resistome. Understanding the impact of the household environment on the development of the resistome and microbiome in early life is essential to optimize the relationship between environmental exposure and human health. Video Abstract.
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Affiliation(s)
- Molly Mills
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Seungjun Lee
- Department of Food Science and Nutrition, College of Fisheries Science, Pukyong National University, Busan, Republic of Korea
| | - Barbara A Piperata
- Department of Anthropology, The Ohio State University, Columbus, OH, USA
| | - Rebecca Garabed
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Boseung Choi
- Division of Big Data Science, Korea University, Sejong, Republic of Korea
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA.
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA.
- Department of Food Science & Technology, The Ohio State University, Columbus, OH, USA.
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15
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Mallott EK, Sitarik AR, Leve LD, Cioffi C, Camargo CA, Hasegawa K, Bordenstein SR. Human microbiome variation associated with race and ethnicity emerges as early as 3 months of age. PLoS Biol 2023; 21:e3002230. [PMID: 37590208 PMCID: PMC10434942 DOI: 10.1371/journal.pbio.3002230] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 07/03/2023] [Indexed: 08/19/2023] Open
Abstract
Human microbiome variation is linked to the incidence, prevalence, and mortality of many diseases and associates with race and ethnicity in the United States. However, the age at which microbiome variability emerges between these groups remains a central gap in knowledge. Here, we identify that gut microbiome variation associated with race and ethnicity arises after 3 months of age and persists through childhood. One-third of the bacterial taxa that vary across caregiver-identified racial categories in children are taxa reported to also vary between adults. Machine learning modeling of childhood microbiomes from 8 cohort studies (2,756 samples from 729 children) distinguishes racial and ethnic categories with 87% accuracy. Importantly, predictive genera are also among the top 30 most important taxa when childhood microbiomes are used to predict adult self-identified race and ethnicity. Our results highlight a critical developmental window at or shortly after 3 months of age when social and environmental factors drive race and ethnicity-associated microbiome variation and may contribute to adult health and health disparities.
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Affiliation(s)
- Elizabeth K. Mallott
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Alexandra R. Sitarik
- Department of Public Health Sciences, Henry Ford Health, Detroit, Michigan, United States of America
| | - Leslie D. Leve
- Prevention Science Institute, University of Oregon, Eugene, Oregon, United States of America
| | - Camille Cioffi
- Prevention Science Institute, University of Oregon, Eugene, Oregon, United States of America
| | - Carlos A. Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Seth R. Bordenstein
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, School of Medicine, Nashville, Tennessee, United States of America
- Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
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16
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Bargheet A, Klingenberg C, Esaiassen E, Hjerde E, Cavanagh JP, Bengtsson-Palme J, Pettersen VK. Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments. EBioMedicine 2023; 92:104613. [PMID: 37187112 DOI: 10.1016/j.ebiom.2023.104613] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Gestational age (GA) and associated level of gastrointestinal tract maturation are major factors driving the initial gut microbiota composition in preterm infants. Besides, compared to term infants, premature infants often receive antibiotics to treat infections and probiotics to restore optimal gut microbiota. How GA, antibiotics, and probiotics modulate the microbiota's core characteristics, gut resistome and mobilome, remains nascent. METHODS We analysed metagenomic data from a longitudinal observational study in six Norwegian neonatal intensive care units to describe the bacterial microbiota of infants of varying GA and receiving different treatments. The cohort consisted of probiotic-supplemented and antibiotic-exposed extremely preterm infants (n = 29), antibiotic-exposed very preterm (n = 25), antibiotic-unexposed very preterm (n = 8), and antibiotic-unexposed full-term (n = 10) infants. The stool samples were collected on days of life 7, 28, 120, and 365, and DNA extraction was followed by shotgun metagenome sequencing and bioinformatical analysis. FINDINGS The top predictors of microbiota maturation were hospitalisation length and GA. Probiotic administration rendered the gut microbiota and resistome of extremely preterm infants more alike to term infants on day 7 and ameliorated GA-driven loss of microbiota interconnectivity and stability. GA, hospitalisation, and both microbiota-modifying treatments (antibiotics and probiotics) contributed to an elevated carriage of mobile genetic elements in preterm infants compared to term controls. Finally, Escherichia coli was associated with the highest number of antibiotic-resistance genes, followed by Klebsiella pneumoniae and Klebsiella aerogenes. INTERPRETATION Prolonged hospitalisation, antibiotics, and probiotic intervention contribute to dynamic alterations in resistome and mobilome, gut microbiota characteristics relevant to infection risk. FUNDING Odd-Berg Group, Northern Norway Regional Health Authority.
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Affiliation(s)
- Ahmed Bargheet
- Host-Microbe Interaction Research Group, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway; Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Center for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway
| | - Claus Klingenberg
- Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Center for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway; Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway
| | - Eirin Esaiassen
- Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway
| | - Erik Hjerde
- Center for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway; Department of Chemistry, Norstruct, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jorunn Pauline Cavanagh
- Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Center for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway
| | - Johan Bengtsson-Palme
- Division of Systems Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10A, Gothenburg, SE-413 46, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Veronika Kuchařová Pettersen
- Host-Microbe Interaction Research Group, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway; Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Center for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway.
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17
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Gaire TN, Scott HM, Noyes NR, Ericsson AC, Tokach MD, Menegat MB, Vinasco J, Roenne B, Ray T, Nagaraja TG, Volkova VV. Age influences the temporal dynamics of microbiome and antimicrobial resistance genes among fecal bacteria in a cohort of production pigs. Anim Microbiome 2023; 5:2. [PMID: 36624546 PMCID: PMC9830919 DOI: 10.1186/s42523-022-00222-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The pig gastrointestinal tract hosts a diverse microbiome, which can serve to select and maintain a reservoir of antimicrobial resistance genes (ARG). Studies suggest that the types and quantities of antimicrobial resistance (AMR) in fecal bacteria change as the animal host ages, yet the temporal dynamics of AMR within communities of bacteria in pigs during a full production cycle remains largely unstudied. RESULTS A longitudinal study was performed to evaluate the dynamics of fecal microbiome and AMR in a cohort of pigs during a production cycle; from birth to market age. Our data showed that piglet fecal microbial communities assemble rapidly after birth and become more diverse with age. Individual piglet fecal microbiomes progressed along similar trajectories with age-specific community types/enterotypes and showed a clear shift from E. coli/Shigella-, Fusobacteria-, Bacteroides-dominant enterotypes to Prevotella-, Megaspheara-, and Lactobacillus-dominated enterotypes with aging. Even when the fecal microbiome was the least diverse, the richness of ARGs, quantities of AMR gene copies, and counts of AMR fecal bacteria were highest in piglets at 2 days of age; subsequently, these declined over time, likely due to age-related competitive changes in the underlying microbiome. ARGs conferring resistance to metals and multi-compound/biocides were detected predominately at the earliest sampled ages. CONCLUSIONS The fecal microbiome and resistome-along with evaluated descriptors of phenotypic antimicrobial susceptibility of fecal bacteria-among a cohort of pigs, demonstrated opposing trajectories in diversity primarily driven by the aging of pigs.
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Affiliation(s)
- Tara N. Gaire
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
| | - H. Morgan Scott
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Noelle R. Noyes
- grid.17635.360000000419368657Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108 USA
| | - Aaron C. Ericsson
- grid.134936.a0000 0001 2162 3504Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211 USA
| | - Michael D. Tokach
- grid.36567.310000 0001 0737 1259Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS 66506 USA
| | - Mariana B. Menegat
- grid.36567.310000 0001 0737 1259Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS 66506 USA
| | - Javier Vinasco
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Boyd Roenne
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
| | - Tui Ray
- grid.17635.360000000419368657Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108 USA
| | - T. G. Nagaraja
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
| | - Victoriya V. Volkova
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
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18
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YI R, LIU T, XUE R, YANG Z. Effect of Lactobacillus isolated from Chinese fermented food on antibiotic induced intestinal microflora disorder in early life of mice. FOOD SCIENCE AND TECHNOLOGY 2023. [DOI: 10.1590/fst.121422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Ruokun YI
- Beijing Technology and Business University, China
| | - Tongji LIU
- Beijing Technology and Business University, China
| | - Rui XUE
- Beijing Technology and Business University, China
| | - Zhennai YANG
- Beijing Technology and Business University, China
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19
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Lebeaux RM, Madan JC, Nguyen QP, Coker MO, Dade EF, Moroishi Y, Palys TJ, Ross BD, Pettigrew MM, Morrison HG, Karagas MR, Hoen AG. Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies. Pediatr Res 2022; 92:1757-1766. [PMID: 35568730 PMCID: PMC9659678 DOI: 10.1038/s41390-022-02104-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/04/2022] [Accepted: 03/29/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Young children are frequently exposed to antibiotics, with the potential for collateral consequences to the gut microbiome. The impact of antibiotic exposures to off-target microbes (i.e., bacteria not targeted by treatment) and antibiotic resistance genes (ARGs) is poorly understood. METHODS We used metagenomic sequencing data from paired stool samples collected prior to antibiotic exposure and at 1 year from over 200 infants and a difference-in-differences approach to assess the relationship between subsequent exposures and the abundance or compositional diversity of microbes and ARGs while adjusting for covariates. RESULTS By 1 year, the abundance of multiple species and ARGs differed by antibiotic exposure. Compared to infants never exposed to antibiotics, Bacteroides vulgatus relative abundance increased by 1.72% (95% CI: 0.19, 3.24) while Bacteroides fragilis decreased by 1.56% (95% CI: -4.32, 1.21). Bifidobacterium species also exhibited opposing trends. ARGs associated with exposure included class A beta-lactamase gene CfxA6. Among infants attending day care, Escherichia coli and ARG abundance were both positively associated with antibiotic use. CONCLUSION Novel findings, including the importance of day care attendance, were identified through considering microbiome data at baseline and post-intervention. Thus, our study design and approach have important implications for future studies evaluating the unintended impacts of antibiotics. IMPACT The impact of antibiotic exposure to off-target microbes and antibiotic resistance genes in the gut is poorly defined. We quantified these impacts in two cohort studies using a difference-in-differences approach. Novel to microbiome studies, we used pre/post-antibiotic data to emulate a randomized controlled trial. Compared to infants unexposed to antibiotics between baseline and 1 year, the relative abundance of multiple off-target species and antibiotic resistance genes was altered. Infants who attended day care and were exposed to antibiotics within the first year had a higher abundance of Escherichia coli and antibiotic resistance genes; a novel finding warranting further investigation.
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Affiliation(s)
- Rebecca M Lebeaux
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Juliette C Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Pediatrics, Children's Hospital at Dartmouth, Lebanon, NH, USA
- Children's Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Quang P Nguyen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Modupe O Coker
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - Erika F Dade
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Yuka Moroishi
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Thomas J Palys
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Benjamin D Ross
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Orthopaedics, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Melinda M Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Children's Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
- Center for Molecular Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Anne G Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
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20
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Kim J, Kim E, Kim B, Kim J, Lee HJ, Park JS, Hwang S, Rho M, Pai H. Different maturation of gut microbiome in Korean children. Front Microbiol 2022; 13:1036533. [PMID: 36504822 PMCID: PMC9726757 DOI: 10.3389/fmicb.2022.1036533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction Gut microbiome plays a crucial role in maintaining human health and is influenced by food intake, age, and other factors. Methods In this study based in Korea, we examined the bacterial taxonomic composition of the gut microbiota in infants (≤ 1 year), toddlers (1-<4 years), and school-aged children (4-13 years) and compared them with those of healthy adults to investigate the microbiota changes in early life and their association with the resistome. We used whole metagenome sequences obtained by Illumina HiSeq sequencing and clinical information of 53 healthy children, and sequence data of 61 adults from our previous study. Results Our results indicate that the bacterial proportion of the gut in the population ranging from infants to adults forms three clusters: the Ruminococcus-Eubacterium (G1), Bifidobacterium-Escherichia (G2), and Bacteroides-Faecalibacterium (G3) groups. The gut microbiota of infants and toddlers (100% of infants and 85% of toddlers) constituted mostly of G2 and G3 groups, whereas 90% of adults showed G1-type gut microbiota. School-aged children showed a transitional gut microbiota composition of both infants and adults (31%, 38%, and 31% in G1, G2, and G3, respectively). Notably, the three clusters of microbiota showed significantly different patterns of bacterial diversity (p < 0.001): G2 showed the lowest Shannon index, followed by G3 and G1 (1.41, 2.08, and 2.48, respectively; median Shannon index). When combined with the adult group, alpha diversity showed a positive correlation with age (R2 = 0.3). Furthermore, clustering the composition of antibiotic resistance genes (ARG) identified two clusters (A1 and A2), and most of G1 (95%) and G3 (80%) belonged to A1. However, G2 showed the least diversity and the highest abundance of ARGs. Nine ARG families showed a significant difference among age groups; three tetracycline resistance genes, tet32, tetO, and tetW, showed a positive correlation, and six other genes, ampC, TEM, ileS, bacA, pmr transferase, and cepA, showed a negative correlation with age. Discussion In conclusion, our results highlighted that a delayed persistence of the Bifidobacterium-dominant enterotype with a lower bacterial diversity was observed in Korean children up to 13 years of age, which suggests a different maturation process with a delayed maturation time.
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Affiliation(s)
- Jieun Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea
| | - Erin Kim
- Department of Computer Science and Engineering, Hanyang University, Seoul, South Korea
| | - Bongyoung Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea
| | - Jinsup Kim
- Department of Clinical Development, Novel Pharma Inc., Seoul, South Korea
| | - Hyun Ju Lee
- Department of Pediatrics, College of Medicine, Hanyang University, Seoul, South Korea
| | - Jun-Sun Park
- Translational Research Center, Research Institute of Public Health, National Medical Center, Seoul, Republic of Korea
| | - Sehee Hwang
- Cancer Information Center, Yonsei University Health System, Yonsei Cancer Center, Seoul, South Korea,Sehee Hwang,
| | - Mina Rho
- Department of Computer Science and Engineering, Hanyang University, Seoul, South Korea,Department of Biomedical Informatics, Hanyang University, Seoul, South Korea,Mina Rho,
| | - Hyunjoo Pai
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea,*Correspondence: Hyunjoo Pai,
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Guitor AK, Yousuf EI, Raphenya AR, Hutton EK, Morrison KM, McArthur AG, Wright GD, Stearns JC. Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation. MICROBIOME 2022; 10:136. [PMID: 36008821 PMCID: PMC9414150 DOI: 10.1186/s40168-022-01327-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/14/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND Probiotic use in preterm infants can mitigate the impact of antibiotic exposure and reduce rates of certain illnesses; however, the benefit on the gut resistome, the collection of antibiotic resistance genes, requires further investigation. We hypothesized that probiotic supplementation of early preterm infants (born < 32-week gestation) while in hospital reduces the prevalence of antibiotic resistance genes associated with pathogenic bacteria in the gut. We used a targeted capture approach to compare the resistome from stool samples collected at the term corrected age of 40 weeks for two groups of preterm infants (those that routinely received a multi-strain probiotic during hospitalization and those that did not) with samples from full-term infants at 10 days of age to identify if preterm birth or probiotic supplementation impacted the resistome. We also compared the two groups of preterm infants up to 5 months of age to identify persistent antibiotic resistance genes. RESULTS At the term corrected age, or 10 days of age for the full-term infants, we found over 80 antibiotic resistance genes in the preterm infants that did not receive probiotics that were not identified in either the full-term or probiotic-supplemented preterm infants. More genes associated with antibiotic inactivation mechanisms were identified in preterm infants unexposed to probiotics at this collection time-point compared to the other infants. We further linked these genes to mobile genetic elements and Enterobacteriaceae, which were also abundant in their gut microbiomes. Various genes associated with aminoglycoside and beta-lactam resistance, commonly found in pathogenic bacteria, were retained for up to 5 months in the preterm infants that did not receive probiotics. CONCLUSIONS This pilot survey of preterm infants shows that probiotics administered after preterm birth during hospitalization reduced the diversity and prevented persistence of antibiotic resistance genes in the gut microbiome. The benefits of probiotic use on the microbiome and the resistome should be further explored in larger groups of infants. Due to its high sensitivity and lower sequencing cost, our targeted capture approach can facilitate these surveys to further address the implications of resistance genes persisting into infancy without the need for large-scale metagenomic sequencing. Video Abstract.
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Affiliation(s)
- Allison K Guitor
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Efrah I Yousuf
- Department of Pediatrics, McMaster University, Hamilton, Canada
| | - Amogelang R Raphenya
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Eileen K Hutton
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, Canada
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada
| | - Katherine M Morrison
- Department of Pediatrics, McMaster University, Hamilton, Canada
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Jennifer C Stearns
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada.
- Department of Medicine, McMaster University, Hamilton, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada.
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22
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Sindi AS, Stinson LF, Lean SS, Chooi YH, Leghi GE, Netting MJ, Wlodek ME, Muhlhausler BS, Geddes DT, Payne MS. Effect of a reduced fat and sugar maternal dietary intervention during lactation on the infant gut microbiome. Front Microbiol 2022; 13:900702. [PMID: 36060782 PMCID: PMC9428759 DOI: 10.3389/fmicb.2022.900702] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveA growing body of literature has shown that maternal diet during pregnancy is associated with infant gut bacterial composition. However, whether maternal diet during lactation affects the exclusively breastfed infant gut microbiome remains understudied. This study sets out to determine whether a two-week of a reduced fat and sugar maternal dietary intervention during lactation is associated with changes in the infant gut microbiome composition and function.DesignStool samples were collected from four female and six male (n = 10) infants immediately before and after the intervention. Maternal baseline diet from healthy mothers aged 22–37 was assessed using 24-h dietary recall. During the 2-week dietary intervention, mothers were provided with meals and their dietary intake was calculated using FoodWorks 10 Software. Shotgun metagenomic sequencing was used to characterize the infant gut microbiome composition and function.ResultsIn all but one participant, maternal fat and sugar intake during the intervention were significantly lower than at baseline. The functional capacity of the infant gut microbiome was significantly altered by the intervention, with increased levels of genes associated with 28 bacterial metabolic pathways involved in biosynthesis of vitamins (p = 0.003), amino acids (p = 0.005), carbohydrates (p = 0.01), and fatty acids and lipids (p = 0.01). Although the dietary intervention did not affect the bacterial composition of the infant gut microbiome, relative difference in maternal fiber intake was positively associated with increased abundance of genes involved in biosynthesis of storage compounds (p = 0.016), such as cyanophycin. Relative difference in maternal protein intake was negatively associated with Veillonella parvula (p = 0.006), while positively associated with Klebsiella michiganensis (p = 0.047). Relative difference in maternal sugar intake was positively associated with Lactobacillus paracasei (p = 0.022). Relative difference in maternal fat intake was positively associated with genes involved in the biosynthesis of storage compounds (p = 0.015), fatty acid and lipid (p = 0.039), and metabolic regulator (p = 0.038) metabolic pathways.ConclusionThis pilot study demonstrates that a short-term maternal dietary intervention during lactation can significantly alter the functional potential, but not bacterial taxonomy, of the breastfed infant gut microbiome. While the overall diet itself was not able to change the composition of the infant gut microbiome, changes in intakes of maternal protein and sugar during lactation were correlated with changes in the relative abundances of certain bacterial species.Clinical trial registration: Australian New Zealand Clinical Trials Registry (ACTRN12619000606189).
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Affiliation(s)
- Azhar S. Sindi
- Division of Obstetrics and Gynecology, The University of Western Australia, Perth, WA, Australia
- College of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Lisa F. Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Soo Sum Lean
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Gabriela E. Leghi
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Merryn J. Netting
- Women and Kids Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- Discipline of Pediatrics, The University of Adelaide, Adelaide, SA, Australia
- Women’s and Children’s Hospital, Adelaide, SA, Australia
| | - Mary E. Wlodek
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Melbourne, VIC, Australia
| | - Beverly S. Muhlhausler
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
- CSIRO, Adelaide, SA, Australia
| | - Donna T. Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Matthew S. Payne
- Division of Obstetrics and Gynecology, The University of Western Australia, Perth, WA, Australia
- Women and Infants Research Foundation, Perth, WA, Australia
- *Correspondence: Matthew S. Payne,
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McDougall F, Boardman W, Power M. High Prevalence of Beta-Lactam-Resistant Escherichia coli in South Australian Grey-Headed Flying Fox Pups ( Pteropus poliocephalus). Microorganisms 2022; 10:1589. [PMID: 36014007 PMCID: PMC9416314 DOI: 10.3390/microorganisms10081589] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
The emergence of antimicrobial-resistant Escherichia coli in wildlife is concerning-especially resistance to clinically important beta-lactam antibiotics. Wildlife in closer proximity to humans, including in captivity and in rescue/rehabilitation centres, typically have a higher prevalence of antimicrobial-resistant E. coli compared to their free-living counterparts. Each year, several thousand Australian fruit bat pups, including the grey-headed flying fox (GHFF; Pteropus poliocephalus), require rescuing and are taken into care by wildlife rescue and rehabilitation groups. To determine the prevalence of beta-lactam-resistant E. coli in rescued GHFF pups from South Australia, faecal samples were collected from 53 pups in care. A combination of selective culture, PCR, antimicrobial susceptibility testing, whole-genome sequencing, and phylogenetic analysis was used to identify and genetically characterise beta-lactam-resistant E. coli isolates. The prevalence of amoxicillin-, amoxicillin-plus-clavulanic-acid-, and cephalosporin-resistant E. coli in the 53 pups was 77.4% (n = 41), 24.5% (n = 13), and 11.3% (n = 6), respectively. GHFF beta-lactam-resistant E. coli also carried resistance genes to aminoglycosides, trimethoprim plus sulphonamide, and tetracyclines in 37.7% (n = 20), 35.8% (n = 19), and 26.4% (n = 14) of the 53 GHFF pups, respectively, and 50.9% (n = 27) of pups carried multidrug-resistant E. coli. Twelve E. coli strain types were identified from the 53 pups, with six strains having extraintestinal pathogenic traits, indicating that they have the potential to cause blood, lung, or wound infections in GHFFs. Two lineages-E. coli ST963 and ST58 O8:H25-were associated with human extraintestinal infections. Phylogenetic analyses determined that all 12 strains were lineages associated with humans and/or domestic animals. This study demonstrates high transmission of anthropogenic-associated beta-lactam-resistant E. coli to GHFF pups entering care. Importantly, we identified potential health risks to GHFF pups and zoonotic risks for their carers, highlighting the need for improved antibiotic stewardship and biosafety measures for GHFF pups entering care.
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Affiliation(s)
- Fiona McDougall
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Wayne Boardman
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5371, Australia
| | - Michelle Power
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Gaire TN, Odland C, Zhang B, Ray T, Doster E, Nerem J, Dee S, Davies P, Noyes N. The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs. MICROBIOME 2022; 10:118. [PMID: 35922873 PMCID: PMC9351240 DOI: 10.1186/s40168-022-01312-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Antimicrobials are used in food-producing animals for purposes of preventing, controlling, and/or treating infections. In swine, a major driver of antimicrobial use is porcine reproductive and respiratory syndrome (PRRS), which is caused by a virus that predisposes infected animals to secondary bacterial infections. Numerous antimicrobial protocols are used to treat PRRS, but we have little insight into how these treatment schemes impact antimicrobial resistance (AMR) dynamics within the fecal microbiome of commercial swine. The aim of this study was to determine whether different PRRS-relevant antimicrobial treatment protocols were associated with differences in the fecal microbiome and resistome of growing pigs. To accomplish this, we used a metagenomics approach to characterize and compare the longitudinal wean-to-market resistome and microbiome of pigs challenged with PRRS virus and then exposed to different antimicrobial treatments, and a group of control pigs not challenged with PRRS virus and having minimal antimicrobial exposure. Genomic DNA was extracted from pen-level composite fecal samples from each treatment group and subjected to metagenomic sequencing and microbiome-resistome bioinformatic and statistical analysis. Microbiome-resistome profiles were compared over time and between treatment groups. RESULTS Fecal microbiome and resistome compositions both changed significantly over time, with a dramatic and stereotypic shift between weaning and 9 days post-weaning (dpw). Antimicrobial resistance gene (ARG) richness and diversity were significantly higher at earlier time points, while microbiome richness and diversity were significantly lower. The post-weaning shift was characterized by transition from a Bacteroides-dominated enterotype to Lactobacillus- and Streptococcus-dominated enterotypes. Both the microbiome and resistome stabilized by 44 dpw, at which point the trajectory of microbiome-resistome maturation began to diverge slightly between the treatment groups, potentially due to physical clustering of the pigs. Challenge with PRRS virus seemed to correspond to the re-appearance of many very rare and low-abundance ARGs within the feces of challenged pigs. Despite very different antimicrobial exposures after challenge with PRRS virus, resistome composition remained largely similar between the treatment groups. Differences in ARG abundance between the groups were mostly driven by temporal changes in abundance that occurred prior to antimicrobial exposures, with the exception of ermG, which increased in the feces of treated pigs, and was significantly more abundant in the feces of these pigs compared to the pigs that did not receive post-PRRS antimicrobials. CONCLUSIONS The fecal microbiome-resistome of growing pigs exhibited a stereotypic trajectory driven largely by weaning and physiologic aging of the pigs. Events such as viral illness, antimicrobial exposures, and physical grouping of the pigs exerted significant yet relatively minor influence over this trajectory. Therefore, the AMR profile of market-age pigs is the culmination of the life history of the individual pigs and the populations to which they belong. Disease status alone may be a significant driver of AMR in market-age pigs, and understanding the interaction between disease processes and antimicrobial exposures on the swine microbiome-resistome is crucial to developing effective, robust, and reproducible interventions to control AMR. Video Abstract.
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Affiliation(s)
- Tara N Gaire
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Carissa Odland
- Pipestone Veterinary Services, Pipestone, Minnesota, USA
| | - Bingzhou Zhang
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tui Ray
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Enrique Doster
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Joel Nerem
- Pipestone Applied Research, Pipestone, Minnesota, USA
| | - Scott Dee
- Pipestone Applied Research, Pipestone, Minnesota, USA
| | - Peter Davies
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Noelle Noyes
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA.
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Coker MO, Lebeaux RM, Hoen AG, Moroishi Y, Gilbert-Diamond D, Dade EF, Palys TJ, Madan JC, Karagas MR. Metagenomic analysis reveals associations between salivary microbiota and body composition in early childhood. Sci Rep 2022; 12:13075. [PMID: 35906254 PMCID: PMC9338228 DOI: 10.1038/s41598-022-14668-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 06/10/2022] [Indexed: 12/15/2022] Open
Abstract
Several studies have shown that body mass index is strongly associated with differences in gut microbiota, but the relationship between body weight and oral microbiota is less clear especially in young children. We aimed to evaluate if there is an association between child growth and the saliva microbiome. We hypothesized that associations between growth and the saliva microbiome would be moderate, similarly to the association between growth and the gut microbiome. For 236 toddlers participating in the New Hampshire Birth Cohort Study, we characterized the association between multiple longitudinal anthropometric measures of body height, body weight and body mass. Body Mass Index (BMI) z-scores were calculated, and dual-energy x-ray absorptiometry (DXA) was used to estimate body composition. Shotgun metagenomic sequencing of saliva samples was performed to taxonomically and functionally profile the oral microbiome. We found that within-sample diversity was inversely related to body mass measurements while community composition was not associated. Although the magnitude of associations were small, some taxa were consistently associated with growth and modified by sex. Certain taxa were associated with decreased weight or growth (including Actinomyces odontolyticus and Prevotella melaninogenica) or increased growth (such as Streptococcus mitis and Corynebacterium matruchotii) across anthropometric measures. Further exploration of the functional significance of this relationship will enhance our understanding of the intersection between weight gain, microbiota, and energy metabolism and the potential role of these relationships on the onset of obesity-associated diseases in later life.
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Affiliation(s)
- Modupe O Coker
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA.
- Department of Oral Biology, School of Dental Medicine, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA.
| | - Rebecca M Lebeaux
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Anne G Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Yuka Moroishi
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Diane Gilbert-Diamond
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Erika F Dade
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Thomas J Palys
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Juliette C Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
- Departments of Pediatrics and Psychiatry, Children's Hospital at Dartmouth, Lebanon, NH, 03766, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
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Cason C, D’Accolti M, Soffritti I, Mazzacane S, Comar M, Caselli E. Next-generation sequencing and PCR technologies in monitoring the hospital microbiome and its drug resistance. Front Microbiol 2022; 13:969863. [PMID: 35966671 PMCID: PMC9370071 DOI: 10.3389/fmicb.2022.969863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
The hospital environment significantly contributes to the onset of healthcare-associated infections (HAIs), which represent one of the most frequent complications occurring in healthcare facilities worldwide. Moreover, the increased antimicrobial resistance (AMR) characterizing HAI-associated microbes is one of the human health’s main concerns, requiring the characterization of the contaminating microbial population in the hospital environment. The monitoring of surface microbiota in hospitals is generally addressed by microbial cultural isolation. However, this has some important limitations mainly relating to the inability to define the whole drug-resistance profile of the contaminating microbiota and to the long time period required to obtain the results. Hence, there is an urgent need to implement environmental surveillance systems using more effective methods. Molecular approaches, including next-generation sequencing and PCR assays, may be useful and effective tools to monitor microbial contamination, especially the growing AMR of HAI-associated pathogens. Herein, we summarize the results of our recent studies using culture-based and molecular analyses in 12 hospitals for adults and children over a 5-year period, highlighting the advantages and disadvantages of the techniques used.
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Affiliation(s)
- Carolina Cason
- Department of Advanced Translational Microbiology, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Maria D’Accolti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, Section of Microbiology and LTTA, University of Ferrara, Ferrara, Italy
- CIAS Research Centre, University of Ferrara, Ferrara, Italy
| | - Irene Soffritti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, Section of Microbiology and LTTA, University of Ferrara, Ferrara, Italy
- CIAS Research Centre, University of Ferrara, Ferrara, Italy
| | | | - Manola Comar
- Department of Advanced Translational Microbiology, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, Trieste, Italy
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Elisabetta Caselli
- Department of Chemical, Pharmaceutical and Agricultural Sciences, Section of Microbiology and LTTA, University of Ferrara, Ferrara, Italy
- CIAS Research Centre, University of Ferrara, Ferrara, Italy
- *Correspondence: Elisabetta Caselli,
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Arboleya S, Saturio S, Gueimonde M. Impact of intrapartum antibiotics on the developing microbiota: a review. MICROBIOME RESEARCH REPORTS 2022; 1:22. [PMID: 38046905 PMCID: PMC10688785 DOI: 10.20517/mrr.2022.04] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/26/2022] [Accepted: 07/07/2022] [Indexed: 12/02/2023]
Abstract
The perinatal period sets the basis for the later physiological and immune homeostasis of the individual, with the intestinal microbiota being an important contributor to driving this homeostasis development. Therefore, the initial establishment and later development of the microbiota during early life may play a key role in later health. This early establishment of the intestinal microbiota is known to be affected by several factors, with gestational age, delivery mode, and feeding habits being extensively studied ones. Other factors are not so well understood, although knowledge has been accumulating in the last years. Among them, a factor of great relevance is the effect of perinatal exposure to antibiotics. Administration of intrapartum antimicrobial prophylaxis (IAP) to women during the delivery process represents the most common form of exposure to antibiotics during the perinatal period, present in around 30% of deliveries. During the last decade, evidence has accumulated demonstrating that IAP alters intestinal microbiota development in neonates. Moreover, recent evidence indicates that this practice may also be altering the infant intestinal resistome by increasing the levels of some antibiotic resistance genes. This evidence, as reviewed in this manuscript, suggests the interest in promoting the rational use of IAP. This practice has significantly reduced the risk of neonatal infections, but now the accumulating knowledge suggests the need for strategies to minimize its impact on the neonatal microbiota establishment.
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Affiliation(s)
- Silvia Arboleya
- Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, Villaviciosa 33300, Spain
- Diet, Human Microbiota and Health Group, Institute of Health Research of the Principality of Asturias (ISPA), Oviedo 33011, Spain
| | - Silvia Saturio
- Diet, Human Microbiota and Health Group, Institute of Health Research of the Principality of Asturias (ISPA), Oviedo 33011, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, Villaviciosa 33300, Spain
- Diet, Human Microbiota and Health Group, Institute of Health Research of the Principality of Asturias (ISPA), Oviedo 33011, Spain
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Thänert R, Sawhney SS, Schwartz DJ, Dantas G. The resistance within: Antibiotic disruption of the gut microbiome and resistome dynamics in infancy. Cell Host Microbe 2022; 30:675-683. [PMID: 35550670 PMCID: PMC9173668 DOI: 10.1016/j.chom.2022.03.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/28/2022] [Accepted: 03/08/2022] [Indexed: 11/28/2022]
Abstract
Intestinal host-microbiota interactions during the first year of life are critical for infant development. Early-life antibiotic exposures disrupt stereotypical gut microbiota maturation and adversely affect childhood health. Furthermore, antibiotics increase the abundance of resistant bacteria and enrich the resistome-the compendium of antibiotic resistance genes-within the gut microbiota. Here, we discuss acute and persistent impacts of antibiotic exposure during infancy on pediatric health, the gut microbiome, and, particularly, the resistome. Reviewing our current understanding of antibiotic resistance acquisition and dissemination within and between microbiomes, we highlight open questions, which are imperative to resolve in the face of rising bacterial resistance.
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Affiliation(s)
- Robert Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sanjam S Sawhney
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Drew J Schwartz
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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29
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Abstract
Antimicrobial resistance (AMR) represents a significant source of morbidity and mortality worldwide, with expectations that AMR-associated consequences will continue to worsen throughout the coming decades. Since resistance to antibiotics is encoded in the microbiome, interventions aimed at altering the taxonomic composition of the gut might allow us to prophylactically engineer microbiomes that harbor fewer antibiotic resistant genes (ARGs). Diet is one method of intervention, and yet little is known about the association between diet and antimicrobial resistance. To address this knowledge gap, we examined diet using the food frequency questionnaire (FFQ; habitual diet) and 24-h dietary recalls (Automated Self-Administered 24-h [ASA24®] tool) coupled with an analysis of the microbiome using shotgun metagenome sequencing in 290 healthy adult participants of the United States Department of Agriculture (USDA) Nutritional Phenotyping Study. We found that aminoglycosides were the most abundant and prevalent mechanism of AMR in these healthy adults and that aminoglycoside-O-phosphotransferases (aph3-dprime) correlated negatively with total calories and soluble fiber intake. Individuals in the lowest quartile of ARGs (low-ARG) consumed significantly more fiber in their diets than medium- and high-ARG individuals, which was concomitant with increased abundances of obligate anaerobes, especially from the family Clostridiaceae, in their gut microbiota. Finally, we applied machine learning to examine 387 dietary, physiological, and lifestyle features for associations with antimicrobial resistance, finding that increased phylogenetic diversity of diet was associated with low-ARG individuals. These data suggest diet may be a potential method for reducing the burden of AMR. IMPORTANCE Antimicrobial resistance (AMR) represents a considerable burden to health care systems, with the public health community largely in consensus that AMR will be a major cause of death worldwide in the coming decades. Humans carry antibiotic resistance in the microbes that live in and on us, collectively known as the human microbiome. Diet is a powerful method for shaping the human gut microbiome and may be a tractable method for lessening antibiotic resistance, and yet little is known about the relationship between diet and AMR. We examined this relationship in healthy individuals who contained various abundances of antibiotic resistance genes and found that individuals who consumed diverse diets that were high in fiber and low in animal protein had fewer antibiotic resistance genes. Dietary interventions may be useful for lessening the burden of antimicrobial resistance and might ultimately motivate dietary guidelines which will consider how nutrition can reduce the impact of infectious disease.
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30
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Lebeaux RM, Karalis DB, Lee J, Whitehouse HC, Madan JC, Karagas MR, Hoen AG. The association between early life antibiotic exposure and the gut resistome of young children: a systematic review. Gut Microbes 2022; 14:2120743. [PMID: 36289062 PMCID: PMC9621065 DOI: 10.1080/19490976.2022.2120743] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/01/2022] [Accepted: 08/31/2022] [Indexed: 02/04/2023] Open
Abstract
Antimicrobial resistance is a growing public health burden, but little is known about the effects of antibiotic exposure on the gut resistome. As childhood (0-5 years) represents a sensitive window of microbiome development and a time of relatively high antibiotic use, the aims of this systematic review were to evaluate the effects of antibiotic exposure on the gut resistome of young children and identify knowledge gaps. We searched PubMed, Scopus, Web of Science, and the Cochrane Central Register of Controlled Trials. A PICO framework was developed to determine eligibility criteria. Our main outcomes were the mean or median difference in overall resistance gene load and resistome alpha diversity by antibiotic exposure groups. Bias assessment was completed using RoB 2 and ROBINS-I with quality of evidence assessed via the GRADE criteria. From 4885 records identified, 14 studies (3 randomized controlled trials and 11 observational studies) were included in the qualitative review. Eight studies that included information on antibiotic exposure and overall resistance gene load reported no or positive associations. Inconsistent associations were identified for the nine studies that assessed resistome alpha diversity. We identified three main groups of studies based on study design, location, participants, antibiotic exposures, and indication for antibiotics. Overall, the quality of evidence for our main outcomes was rated low or very low, mainly due to potential bias from the selective of reporting results and confounding. We found evidence that antibiotic exposure is associated with changes to the overall gut resistance gene load of children and may influence the diversity of antimicrobial resistance genes. Given the overall quality of the studies, more research is needed to assess how antibiotics impact the resistome of other populations. Nonetheless, this evidence indicates that the gut resistome is worthwhile to consider for antibiotic prescribing practices.
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Affiliation(s)
- Rebecca M. Lebeaux
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Despina B. Karalis
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Jihyun Lee
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Hanna C. Whitehouse
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Juliette C. Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Pediatrics, Children’s Hospital at Dartmouth, Lebanon, NH, USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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