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Samarra A, Cabrera-Rubio R, Martínez-Costa C, Collado MC. The role of Bifidobacterium genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life. Gut Microbes 2024; 16:2357176. [PMID: 38798019 PMCID: PMC11135851 DOI: 10.1080/19490976.2024.2357176] [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: 12/17/2023] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
Resistance to antibiotics in newborns is a huge concern as their immune system is still developing, and infections and resistance acquisition in early life have short- and long-term consequences for their health. Bifidobacterium species are important commensals capable of dominating the infant gut microbiome and are known to be less prone to possess antimicrobial resistance genes than other taxa that may colonize infants. We aimed to study the association between Bifidobacterium-dominated infant gut microbiota and the antibiotic resistant gene load in neonates, and to ascertain the perinatal factors that may contribute to the antibiotic resistance acquisition. Two hundred infant fecal samples at 7 days and 1 month of age from the MAMI birth cohort were included in the study and for whom maternal-neonatal clinical records were available. Microbiota profiling was carried out by 16S rRNA amplicon sequencing, and targeted antibiotic resistance genes (ARGs) including tetM, tetW, tetO, blaTEM, blaSHV and ermB were quantified by qPCR. Infant microbiota clustered into two distinct groups according to their Bifidobacterium genus abundance: high and low. The main separation of groups or clusters at each time point was performed with an unsupervised non-linear algorithm of k-means partitioning to cluster data by time points based on Bifidobacterium genus relative abundance. Microbiota composition differed significantly between both groups, and specific bifidobacterial species were enriched in each cluster. Lower abundance of Bifidobacterium in the infant gut was associated with a higher load of antibiotic resistance genes. Our results highlight the relevance of Bifidobacterium genus in the early acquisition and establishment of antibiotic resistance in the gut. Further studies are needed to develop strategies to promote a healthy early colonization and fight against the spread of antibiotic resistances.
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Affiliation(s)
- Anna Samarra
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Raúl Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National 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, Valencia, Spain
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Paterna, Valencia, Spain
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Heston SM, Young RR, Jenkins K, Martin PL, Stokhuyzen A, Ward DV, Bhattarai SK, Bucci V, Arshad M, Chao NJ, Seed PC, Kelly MS. The effects of antibiotic exposures on the gut resistome during hematopoietic cell transplantation in children. Gut Microbes 2024; 16:2333748. [PMID: 38555499 PMCID: PMC10984140 DOI: 10.1080/19490976.2024.2333748] [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: 01/30/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
Antibiotic resistance is a global threat driven primarily by antibiotic use. We evaluated the effects of antibiotic exposures on the gut microbiomes and resistomes of children at high risk of colonization by antibiotic-resistant bacteria. We performed shotgun metagenomic sequencing of 691 serially collected fecal samples from 80 children (<18 years) undergoing hematopoietic cell transplantation. We evaluated the effects of aerobic (cefepime, vancomycin, fluoroquinolones, aminoglycosides, macrolides, and trimethoprim-sulfamethoxazole) and anaerobic (piperacillin-tazobactam, carbapenems, metronidazole, and clindamycin) antibiotic exposures on the diversity and composition of the gut microbiome and resistome. We identified 372 unique antibiotic resistance genes (ARGs); the most frequent ARGs identified encode resistance to tetracyclines (n = 88), beta-lactams (n = 84), and fluoroquinolones (n = 79). Both aerobic and anaerobic antibiotic exposures were associated with a decrease in the number of bacterial species (aerobic, β = 0.71, 95% CI: 0.64, 0.79; anaerobic, β = 0.66, 95% CI: 0.53, 0.82) and the number of unique ARGs (aerobic, β = 0.81, 95% CI: 0.74, 0.90; anaerobic, β = 0.73, 95% CI: 0.61, 0.88) within the gut metagenome. However, only antibiotic regimens that included anaerobic activity were associated with an increase in acquisition of new ARGs (anaerobic, β = 1.50; 95% CI: 1.12, 2.01) and an increase in the relative abundance of ARGs in the gut resistome (anaerobic, β = 1.62; 95% CI: 1.15, 2.27). Specific antibiotic exposures were associated with distinct changes in the number and abundance of ARGs for individual antibiotic classes. Our findings detail the impact of antibiotics on the gut microbiome and resistome and demonstrate that anaerobic antibiotics are particularly likely to promote acquisition and expansion of antibiotic-resistant bacteria.
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Affiliation(s)
- Sarah M. Heston
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Rebecca R. Young
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Insitute, Duke University School of Medicine, Durham, NC, USA
| | - Kirsten Jenkins
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Paul L. Martin
- Division of Pediatric Transplant and Cellular Therapy, Duke University School of Medicine, Durham, NC, USA
| | - Andre Stokhuyzen
- Division of Pediatric Transplant and Cellular Therapy, Duke University School of Medicine, Durham, NC, USA
| | - Doyle V. Ward
- Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shakti K. Bhattarai
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mehreen Arshad
- Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Nelson J. Chao
- Division of Hematologic Malignancies and Cellular Therapy, Duke University School of Medicine, Durham, NC, USA
| | - Patrick C. Seed
- Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
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Wang S, Wei L, Gao Y, Rong Y, Zha Z, Lv Y, Feng Z. Novel amikacin resistance genes identified from human gut microbiota by functional metagenomics. J Appl Microbiol 2022; 133:898-907. [PMID: 35543338 DOI: 10.1111/jam.15615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/10/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022]
Abstract
AIMS The aim of this study was to evaluate the diversity and potential for horizontal transfer of amikacin resistance genes from the human gut. METHODS AND RESULTS A library of human fecal microbiota was constructed and subjected to functional screening for amikacin resistance. In total, five amikacin resistance genes that conferred relatively high amikacin resistance, with minimum inhibitory concentrations (MICs) ranging from 64 to >512, were identified from the library, including a novel aminoglycoside acetyltransferase gene and a 16S rRNA methyltransferase (MTase) gene, labeled aac(6')-Iao and rmtI respectively. AAC(6')-Iao showed the highest identity of 48% to AAC(6')-Ian from a clinical isolate Serratia marcescens, whereas RmtI shared the closest amino acid identity of 32% with ArmA from Klebsiella pneumonia. The MICs of these five subclones to six commonly used aminoglycosides were determined. Susceptibility analysis indicated that RmtI was associated with high resistance phenotype to 4,6-disubstituted 2-DOS aminoglycosides, whereas AAC(6')-Iao conferred resistance to amikacin and kanamycin. In addition, kinetic parameters of AAC(6')-Iao were determined, suggesting a strong catalytic effect on amikacin and kanamycin. CONCLUSIONS Antibiotic resistance genes with low identity to known sequences can be uncovered by functional metagenomics. In addition, the diversity and prevalence of amikacin resistance genes merit further investigation in extended habitats, especially the 16S rRNA MTase gene that might have been underestimated in previous cognition. SIGNIFICANCE AND IMPACT OF STUDY Two novel amikacin resistance genes were identified in this study, including a 16S rRNA methyltransferase gene rmtI and an aminoglycoside acetyltransferase gene aac(6')-Iao. This work would contribute to the in-depth study of the diversity and horizontal transfer potential of amikacin resistance genes in the microbiome of the human gut.
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Affiliation(s)
- Shaochen Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Lin Wei
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuejiao Gao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yufeng Rong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhengqi Zha
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yunbin Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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Crits-Christoph A, Hallowell HA, Koutouvalis K, Suez J. Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome. Gut Microbes 2022; 14:2055944. [PMID: 35332832 PMCID: PMC8959533 DOI: 10.1080/19490976.2022.2055944] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.
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Affiliation(s)
- Alexander Crits-Christoph
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Haley Anne Hallowell
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Kalia Koutouvalis
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jotham Suez
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA,CONTACT Jotham Suez Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, Maryland, USA, 21205
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Zhang Y, Xu S, Yang Y, Chou SH, He J. A 'time bomb' in the human intestine-the multiple emergence and spread of antibiotic-resistant bacteria. Environ Microbiol 2021; 24:1231-1246. [PMID: 34632679 DOI: 10.1111/1462-2920.15795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022]
Abstract
Antibiotics have a strong killing effect on bacteria and are the first choice for the prevention and treatment of bacterial infectious diseases. Therefore, they have been widely used in the medical field, animal husbandry and planting industry. However, with the massive use of antibiotics, more and more antibiotic-resistant bacteria (ARB) have emerged. Because human intestines are rich in nutrients, have suitable temperature, and are high in bacterial abundance, they can easily become a hotbed for the spread of ARB and antibiotic-resistant genes (ARGs). When opportunistic pathogenic bacteria in the intestine acquire ARGs, the infectious diseases caused by such opportunistic pathogens will become more difficult to treat, or even impossible to cure. Therefore, ARB in the human intestine are like a 'time bomb'. In this review, we discuss the sources of intestinal ARB and the transmission routes of ARGs in the human intestine from the perspective of One Health. Further, we describe various methods to prevent the emergence of ARB and inhibit the spread of ARGs in the human intestine. Finally, we may be able to overcome ARB in the human intestine using an interdisciplinary 'One Health' approach.
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Affiliation(s)
- Yuling Zhang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Siyang Xu
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yijun Yang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Distribution of Antimicrobial Resistance and Virulence Genes within the Prophage-Associated Regions in Nosocomial Pathogens. mSphere 2021; 6:e0045221. [PMID: 34232073 PMCID: PMC8386436 DOI: 10.1128/msphere.00452-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Prophages are often involved in host survival strategies and contribute toward increasing the genetic diversity of the host genome. Prophages also drive horizontal propagation of various genes as vehicles. However, there are few retrospective studies contributing to the propagation of antimicrobial resistance (AMR) and virulence factor (VF) genes by prophage. We extracted the complete genome sequences of seven pathogens, including ESKAPE bacteria and Escherichia coli from a public database, and examined the distribution of both the AMR and VF genes in prophage-like regions. We found that the ratios of AMR and VF genes greatly varied among the seven species. More than 70% of Enterobacter cloacae strains had VF genes, but only 1.2% of Klebsiella pneumoniae strains had VF genes from prophages. AMR and VF genes are unlikely to exist together in the same prophage region except in E. coli and Staphylococcus aureus, and the distribution patterns of prophage types containing AMR genes are distinct from those of VF gene-carrying prophage types. AMR genes in the prophage were located near transposase and/or integrase. The prophage containing class 1 integrase possessed a significantly greater number of AMR genes than did prophages with no class 1 integrase. The results of this study present a comprehensive picture of AMR and VF genes present within, or close to, prophage-like elements and different prophage patterns between AMR- or VF-encoding prophage-like elements. IMPORTANCE Although we believe phages play an important role in horizontal gene transfer in exchanging genetic material, we do not know the distribution of the antimicrobial resistance (AMR) and/or virulence factor (VF) genes in prophages. We collected different prophage elements from the complete genome sequences of seven species—Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae, and Escherichia coli—and characterized the distribution of antimicrobial resistance and virulence genes located in the prophage region. While virulence genes in prophage were species specific, antimicrobial resistance genes in prophages were highly conserved in various species. An integron structure was detected within specific prophage regions such as P1-like prophage element. Maximum of 10 antimicrobial resistance genes were found in a single prophage region, suggesting that prophages act as a reservoir for antimicrobial resistance genes. The results of this study show the different characteristic structures between AMR- or VF-encoding prophages.
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Scaccia N, Vaz-Moreira I, Manaia CM. Persistence of wastewater antibiotic resistant bacteria and their genes in human fecal material. FEMS Microbiol Ecol 2020; 96:5815073. [PMID: 32239211 DOI: 10.1093/femsec/fiaa058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/27/2020] [Indexed: 01/11/2023] Open
Abstract
Domestic wastewater is a recognized source of antibiotic resistant bacteria and antibiotic resistance genes (ARB&ARGs), whose risk of transmission to humans cannot be ignored. The fitness of wastewater ARB in the complex fecal microbiota of a healthy human was investigated in feces-based microcosm assays (FMAs). FMAs were inoculated with two wastewater isolates, Escherichia coli strain A2FCC14 (MLST ST131) and Enterococcus faecium strain H1EV10 (MLST ST78), harboring the ARGs blaTEM, blaCTX, blaOXA-A and vanA, respectively. The FMAs, incubated in the presence or absence of oxygen or in the presence or absence of the antibiotics cefotaxime or vancomycin, were monitored based on cultivation, ARGs quantification and bacterial community analysis. The fecal bacterial community was dominated by members of the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The ARGs harbored by the wastewater isolates could be quantified after one week, in FMAs incubated under both aerobic and anaerobic conditions. These observations were not significantly different in FMAs incubated anaerobically, supplemented with sub-inhibitory concentrations of cefotaxime or vancomycin. The observation that ARGs of wastewater ARB persisted in presence of the human fecal microbiota for at least one week supports the hypothesis of a potential transmission to humans, a topic that deserves further investigation.
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Affiliation(s)
- Nazareno Scaccia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
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8
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Loo EXL, Zain A, Yap GC, Purbojati RW, Drautz-Moses DI, Koh YQ, Chong YS, Tan KH, Gluckman PD, Yap F, Eriksson JG, Tham E, Shek LPC, Kjelleberg S, Schuster SC, Banerjee R, Lee BW. Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema. BMC Infect Dis 2020; 20:312. [PMID: 32345218 PMCID: PMC7189448 DOI: 10.1186/s12879-020-05000-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/29/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND While there is increasing knowledge about the gut microbiome, the factors influencing and the significance of the gut resistome are still not well understood. Infant gut commensals risk transferring multidrug-resistant antibiotic resistance genes (ARGs) to pathogenic bacteria. The rapid spread of multidrug-resistant pathogenic bacteria is a worldwide public health concern. Better understanding of the naïve infant gut resistome may build the evidence base for antimicrobial stewardship in both humans and in the food industry. Given the high carriage rate of extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in Asia, we aimed to evaluate community prevalence, dynamics, and longitudinal changes in antibiotic resistance gene (ARG) profiles and prevalence of ESBL-producing E. coli and K. pneumoniae in the intestinal microbiome of infants participating in the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) study, a longitudinal cohort study of pregnant women and their infants. METHODS We analysed ARGs in the first year of life among 75 infants at risk of eczema who had stool samples collected at multiple timepoints using metagenomics. RESULTS The mean number of ARGs per infant increased with age. The most common ARGs identified confer resistance to aminoglycoside, beta-lactam, macrolide and tetracycline antibiotics; all infants harboured these antibiotic resistance genes at some point in the first year of life. Few ARGs persisted throughout the first year of life. Beta-lactam resistant Escherichia coli and Klebsiella pneumoniae were detected in 4 (5.3%) and 32 (42.7%) of subjects respectively. CONCLUSION In this longitudinal cohort study of infants living in a region with high endemic antibacterial resistance, we demonstrate that majority of the infants harboured several antibiotic resistance genes in their gut and showed that the infant gut resistome is diverse and dynamic over the first year of life.
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Affiliation(s)
- Evelyn Xiu Ling Loo
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Amanda Zain
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
| | - Gaik Chin Yap
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rikky W Purbojati
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Yan Qing Koh
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Kok Hian Tan
- Department of Maternal Fetal Medicine, KK Women's and Children's Hospital (KKH), Singapore, Singapore
| | - Peter D Gluckman
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Fabian Yap
- Department of Endocrinology KK Women's and Children's Hospital (KKH), Singapore, Singapore
| | - Johan Gunnar Eriksson
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Elizabeth Tham
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
| | - Lynette Pei-Chi Shek
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Stephan C Schuster
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Ritu Banerjee
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bee Wah Lee
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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Van Daele E, Knol J, Belzer C. Microbial transmission from mother to child: improving infant intestinal microbiota development by identifying the obstacles. Crit Rev Microbiol 2019; 45:613-648. [DOI: 10.1080/1040841x.2019.1680601] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Emmy Van Daele
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Jan Knol
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Gut Biology and Microbiology, Danone Nutricia Research, Utrecht, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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10
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Abstract
Antimicrobial resistance (AMR) has emerged as an obstacle in the supple administration of antimicrobial agents to critical diarrheal patients. Most diarrheal pathogens have developed resistance against the major classes of antibiotics commonly used for assuaging diarrheal symptoms. Antimicrobial resistance develops when pathogens acquire antimicrobial resistance genes (ARGs) through genetic recombination from commensals and pathogens. These are the constituents of the complex microbiota in all ecological niches. The recombination events may occur in the environment or in the gut. Containment of AMR can be achieved through a complete understanding of the complex and diverse structure and function of the microbiota. Its taxonomic entities serve as focal points for the dissemination of antimicrobial resistance genetic determinants. Molecular methods complemented with culture-based diagnostics have been historically implemented to document these natural events. However, the advent of next-generation sequencing has revolutionized the field of molecular epidemiology. It has revolutionized the method of addressing relevant problems like diagnosis and surveillance of infectious diseases and the issue of antimicrobial resistance. Metagenomics is one such next-generation technique that has proved to be a monumental advancement in the area of molecular taxonomy. Current understanding of structure, function and dysbiosis of microbiota associated with antimicrobial resistance was realized due to its conception. This review describes the major milestones achieved due to the advent and implementation of this new technique in the context of antimicrobial resistance. These achievements span a wide panorama from the discovery of novel microorganisms to invention of translational value.
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Das L, Virmani R, Sharma V, Rawat D, Singh Y. Human Milk Microbiota: Transferring the Antibiotic Resistome to Infants. Indian J Microbiol 2019; 59:410-416. [PMID: 31762502 DOI: 10.1007/s12088-019-00824-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Commensal bacterial population is believed to be a reservoir for antibiotic resistance genes (ARGs). The infant gut microbiota has relatively higher abundance of ARGs than the adults. These genes can get transferred from commensals to pathogens by horizontal gene transfer, which magnifies the spectrum of antibiotic resistance in the environment. The presence of ARGs in neo-nates and infants, with no prior antibiotic exposure, questions their origin in the naïve commensal population. Breast milk microbiota that is responsible for the initial seeding of infant gut microbiota has also been found to harbour a vast array of ARGs. This review discusses the recent findings that indicate the potential of breast milk microbiota to act as a vehicle for transmission of ARGs to infants.
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Affiliation(s)
- Lahari Das
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Richa Virmani
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vishal Sharma
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Deepti Rawat
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India
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Zhao G, Luo Z, Wang Y, Liu J, Wu D, Zhang L, Yang X. Draft genome sequencing and annotation of a low-virulence Morganella morganii strain CQ-M7, a multidrug-resistant isolate from the giant salamander in China. J Glob Antimicrob Resist 2019; 20:248-252. [PMID: 31449965 DOI: 10.1016/j.jgar.2019.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/13/2019] [Accepted: 08/17/2019] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES A multidrug-resistant Morganella morganii strain (CQ-M7), isolated from the kidney of a diseased Chinese giant salamander in China, was examined with whole genome sequencing to better understand drug tolerance and its pathogenicity. METHODS The draft genome of the investigated strain was assembled using HGA assembler and annotated using Rapid Annotations Subsystems Technology (RAST) server. The contigs were annotated by the appropriate bioinformatics tools available on the National Center for Biotechnology Information (NCBI) website. Antibiotic resistance genes were detected by PCR. Pathogenicity of the isolate was performed on 30 healthy Chinese giant salamanders with different infection dosages. RESULTS The CQ-M7 strain showed resistance to multiple antimicrobials, especially to aminoglycoside and β-lactam antibiotics. Seventeen drug-resistance genes were detected, which were related to β-lactams, aminoglycosides, fluoroquinolones, tetracyclines, peptide antibiotic, and fosfomycin resistance. Sequence analysis showed the assembled genome size to be 4 966 326bp with 51.16% of GC content, containing 4587 protein-coding genes, 71 pseudogenes, five rRNAs, 80 tRNAs, and five noncoding RNAs. The genome sequence was deposited in GenBank under accession number RQIJ00000000. Artificial infection results indicated that the CQ-M7 strain was a low-virulence strain for the Chinese giant salamander. CONCLUSION It is believed that this is the first draft genome of Chinese giant salamander original Morganella morganii strain harbouring multiple antibiotic resistance genes in China. The reported genome sequence could provide insights into antibiotic resistance mechanisms and control strategies of Morganella morganii.
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Affiliation(s)
- Guangwei Zhao
- College of Animal Science, Southwest University, No. 160, Xueyuan Road, Chongqing, 402460, PR China; Chongqing Sanjiezhongxin Bioengineering Co, Ltd, No.3 Southern Section of Yingbin Avenue, Chongqing, 402460, PR China
| | - Zeli Luo
- College of Animal Science, Southwest University, No. 160, Xueyuan Road, Chongqing, 402460, PR China
| | - Yan Wang
- Shanghai Customs, No.1208, Minsuring Road, Shanghai Pudong District, Shanghai, 200135, PR China
| | - Jia Liu
- College of Animal Science, Southwest University, No. 160, Xueyuan Road, Chongqing, 402460, PR China
| | - Di Wu
- College of Animal Science, Southwest University, No. 160, Xueyuan Road, Chongqing, 402460, PR China
| | - Liwu Zhang
- Chongqing Sanjiezhongxin Bioengineering Co, Ltd, No.3 Southern Section of Yingbin Avenue, Chongqing, 402460, PR China
| | - Xiaowei Yang
- College of Animal Science, Southwest University, No. 160, Xueyuan Road, Chongqing, 402460, PR China; Chongqing Sanjiezhongxin Bioengineering Co, Ltd, No.3 Southern Section of Yingbin Avenue, Chongqing, 402460, PR China.
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13
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Casaburi G, Duar RM, Vance DP, Mitchell R, Contreras L, Frese SA, Smilowitz JT, Underwood MA. Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria. Antimicrob Resist Infect Control 2019; 8:131. [PMID: 31423298 PMCID: PMC6693174 DOI: 10.1186/s13756-019-0583-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 07/22/2019] [Indexed: 01/21/2023] Open
Abstract
Background Antibiotic-resistant (AR) bacteria are a global threat. AR bacteria can be acquired in early life and have long-term sequelae. Limiting the spread of antibiotic resistance without triggering the development of additional resistance mechanisms is of immense clinical value. Here, we show how the infant gut microbiome can be modified, resulting in a significant reduction of AR genes (ARGs) and the potentially pathogenic bacteria that harbor them. Methods The gut microbiome was characterized using shotgun metagenomics of fecal samples from two groups of healthy, term breastfed infants. One group was fed B. infantis EVC001 in addition to receiving lactation support (n = 29, EVC001-fed), while the other received lactation support alone (n = 31, controls). Coliforms were isolated from fecal samples and genome sequenced, as well as tested for minimal inhibitory concentrations against clinically relevant antibiotics. Results Infants fed B. infantis EVC001 exhibited a change to the gut microbiome, resulting in a 90% lower level of ARGs compared to controls. ARGs that differed significantly between groups were predicted to confer resistance to beta lactams, fluoroquinolones, or multiple drug classes, the majority of which belonged to Escherichia, Clostridium, and Staphylococcus. Minimal inhibitory concentration assays confirmed the resistance phenotypes among isolates with these genes. Notably, we found extended-spectrum beta lactamases among healthy, vaginally delivered breastfed infants who had never been exposed to antibiotics. Conclusions Colonization of the gut of breastfed infants by a single strain of B. longum subsp. infantis had a profound impact on the fecal metagenome, including a reduction in ARGs. This highlights the importance of developing novel approaches to limit the spread of these genes among clinically relevant bacteria. Future studies are needed to determine whether colonization with B. infantis EVC001 decreases the incidence of AR infections in breastfed infants. Trial registration This clinical trial was registered at ClinicalTrials.gov, NCT02457338.
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Affiliation(s)
| | | | | | | | | | - Steven A. Frese
- Evolve Biosystems, Inc, Davis, CA 95618 USA
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588 USA
| | - Jennifer T. Smilowitz
- Department of Food Science and Technology, University of California, Davis, CA 95616 USA
- Foods for Health Institute, University of California, Davis, CA 95616 USA
| | - Mark A. Underwood
- Foods for Health Institute, University of California, Davis, CA 95616 USA
- Department of Pediatrics, UC Davis Children’s Hospital, Sacramento, CA 95817 USA
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14
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Jacob JJ, Veeraraghavan B, Vasudevan K. Metagenomic next-generation sequencing in clinical microbiology. Indian J Med Microbiol 2019; 37:133-140. [PMID: 31745012 DOI: 10.4103/ijmm.ijmm_19_401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, Tamil Nadu, India
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, Tamil Nadu, India
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15
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McConnell MJ. Where are we with monoclonal antibodies for multidrug-resistant infections? Drug Discov Today 2019; 24:1132-1138. [PMID: 30853568 DOI: 10.1016/j.drudis.2019.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/21/2019] [Accepted: 03/01/2019] [Indexed: 01/17/2023]
Abstract
Widespread antibiotic resistance threatens the continued efficacy of antimicrobial therapy based on small-molecule antibiotics. Infections caused by multidrug-resistant Gram-negative bacteria are particularly worrisome owing to the lack of antimicrobials retaining sufficient activity against these microorganisms. Despite the explosion in monoclonal antibody therapies that have been developed for oncologic and rheumatic indications, only three antibacterial monoclonal antibodies have been approved for clinical use. In the present review, the therapeutic potential of this drug class for treating multidrug-resistant infections is discussed, and considerations for the development of antibacterial monoclonal antibodies are presented. Finally, the state of development of monoclonal antibody therapies for some of the most problematic multidrug-resistant Gram-negative infections is summarized.
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Affiliation(s)
- Michael J McConnell
- Antimicrobial Resistance and Hospital Acquired Infections Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain.
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16
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17
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Casals-Pascual C, Vergara A, Vila J. Intestinal microbiota and antibiotic resistance: Perspectives and solutions. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.humic.2018.05.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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18
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Nogacka AM, Salazar N, Arboleya S, Suárez M, Fernández N, Solís G, de Los Reyes-Gavilán CG, Gueimonde M. Early microbiota, antibiotics and health. Cell Mol Life Sci 2018; 75:83-91. [PMID: 28988290 PMCID: PMC11105232 DOI: 10.1007/s00018-017-2670-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/19/2022]
Abstract
The colonization of the neonatal digestive tract provides a microbial stimulus required for an adequate maturation towards the physiological homeostasis of the host. This colonization, which is affected by several factors, begins with facultative anaerobes and continues with anaerobic genera. Accumulating evidence underlines the key role of the early neonatal period for this microbiota-induced maturation, being a key determinant factor for later health. Therefore, understanding the factors that determine the establishment of the microbiota in the infant is of critical importance. Exposure to antibiotics, either prenatally or postnatally, is common in early life mainly due to the use of intrapartum prophylaxis or to the administration of antibiotics in C-section deliveries. However, we are still far from understanding the impact of early antibiotics and their long-term effects. Increased risk of non-communicable diseases, such as allergies or obesity, has been observed in individuals exposed to antibiotics during early infancy. Moreover, the impact of antibiotics on the establishment of the infant gut resistome, and on the role of the microbiota as a reservoir of resistance genes, should be evaluated in the context of the problems associated with the increasing number of antibiotic resistant pathogenic strains. In this article, we review and discuss the above-mentioned issues with the aim of encouraging debate on the actions needed for understanding the impact of early life antibiotics upon human microbiota and health and for developing strategies aimed at minimizing this impact.
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Affiliation(s)
- Alicja M Nogacka
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Nuria Salazar
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Silvia Arboleya
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Marta Suárez
- Pediatrics Service, Hospital Universitario Central de Asturias, SESPA, Oviedo, Asturias, Spain
| | - Nuria Fernández
- Pediatrics Service, Hospital Universitario Central de Asturias, SESPA, Oviedo, Asturias, Spain
| | - Gonzalo Solís
- Pediatrics Service, Hospital Universitario Central de Asturias, SESPA, Oviedo, Asturias, Spain
| | - Clara G de Los Reyes-Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300, Villaviciosa, Asturias, Spain.
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Esaiassen E, Hjerde E, Cavanagh JP, Pedersen T, Andresen JH, Rettedal SI, Støen R, Nakstad B, Willassen NP, Klingenberg C. Effects of Probiotic Supplementation on the Gut Microbiota and Antibiotic Resistome Development in Preterm Infants. Front Pediatr 2018; 6:347. [PMID: 30505830 PMCID: PMC6250747 DOI: 10.3389/fped.2018.00347] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/26/2018] [Indexed: 12/15/2022] Open
Abstract
Objectives: In 2014 probiotic supplementation (Lactobacillus acidophilus and Bifidobacterium longum subspecies infantis; InfloranⓇ) was introduced as standard of care to prevent necrotizing enterocolitis (NEC) in extremely preterm infants in Norway. We aimed to evaluate the influence of probiotics and antibiotic therapy on the developing gut microbiota and antibiotic resistome in extremely preterm infants, and to compare with very preterm infants and term infants not given probiotics. Study design: A prospective, observational multicenter study in six tertiary-care neonatal units. We enrolled 76 infants; 31 probiotic-supplemented extremely preterm infants <28 weeks gestation, 35 very preterm infants 28-31 weeks gestation not given probiotics and 10 healthy full-term control infants. Taxonomic composition and collection of antibiotic resistance genes (resistome) in fecal samples, collected at 7 and 28 days and 4 months age, were analyzed using shotgun-metagenome sequencing. Results: Median (IQR) birth weight was 835 (680-945) g and 1,290 (1,150-1,445) g in preterm infants exposed and not exposed to probiotics, respectively. Two extremely preterm infants receiving probiotic developed NEC requiring surgery. At 7 days of age we found higher median relative abundance of Bifidobacterium in probiotic supplemented infants (64.7%) compared to non-supplemented preterm infants (0.0%) and term control infants (43.9%). Lactobacillus was only detected in small amounts in all groups, but the relative abundance increased up to 4 months. Extremely preterm infants receiving probiotics had also much higher antibiotic exposure, still overall microbial diversity and resistome was not different than in more mature infants at 4 weeks and 4 months. Conclusion: Probiotic supplementation may induce colonization resistance and alleviate harmful effects of antibiotics on the gut microbiota and antibiotic resistome. Clinical Trial Registration: Clinicaltrials.gov: NCT02197468. https://clinicaltrials.gov/ct2/show/NCT02197468.
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Affiliation(s)
- 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
- 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.,Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway
| | - Tanja Pedersen
- Department of Paediatrics, Haukeland University Hospital, Bergen, Norway
| | - Jannicke H Andresen
- Department of Neonatal Intensive Care, Oslo University Hospital, Oslo, Norway
| | - Siren I Rettedal
- Department of Paediatrics, Stavanger University Hospital, Stavanger, Norway
| | - Ragnhild Støen
- Department of Paediatrics, St. Olavs University Hospital, Trondheim, Norway.,Department of Laboratory Medicine, Children's and Women's Health, University of Science and Technology, Trondheim, Norway
| | - Britt Nakstad
- Department of Paediatric and Adolescents Medicine, Akershus University Hospital, Nordbyhagen, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Nils P Willassen
- Department of Chemistry, Norstruct, 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.,Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway
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Boddu RS, Divakar K. Metagenomic Insights into Environmental Microbiome and Their Application in Food/Pharmaceutical Industry. Microb Biotechnol 2018. [DOI: 10.1007/978-981-10-7140-9_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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21
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Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M, Xavier RJ. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med 2017; 8:343ra81. [PMID: 27306663 DOI: 10.1126/scitranslmed.aad0917] [Citation(s) in RCA: 613] [Impact Index Per Article: 87.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 05/27/2016] [Indexed: 12/12/2022]
Abstract
The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. We report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, about half of whom received multiple courses of antibiotics during the first 3 years of life. Whereas the gut microbiome of most children born by vaginal delivery was dominated by Bacteroides species, the four children born by cesarean section and about 20% of vaginally born children lacked Bacteroides in the first 6 to 18 months of life. Longitudinal sampling, coupled with whole-genome shotgun sequencing, allowed detection of strain-level variation as well as the abundance of antibiotic resistance genes. The microbiota of antibiotic-treated children was less diverse in terms of both bacterial species and strains, with some species often dominated by single strains. In addition, we observed short-term composition changes between consecutive samples from children treated with antibiotics. Antibiotic resistance genes carried on microbial chromosomes showed a peak in abundance after antibiotic treatment followed by a sharp decline, whereas some genes carried on mobile elements persisted longer after antibiotic therapy ended. Our results highlight the value of high-density longitudinal sampling studies with high-resolution strain profiling for studying the establishment and response to perturbation of the infant gut microbiome.
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Affiliation(s)
- Moran Yassour
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA. Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Tommi Vatanen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA. Department of Computer Science, Aalto University School of Science, 02150 Espoo, Finland
| | - Heli Siljander
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland. Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland. Department of Pediatrics, Tampere University Hospital, 33521 Tampere, Finland
| | - Anu-Maaria Hämäläinen
- Department of Pediatrics, Jorvi Hospital, Helsinki University Hospital, 02740 Espoo, Finland
| | - Taina Härkönen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland. Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland
| | - Samppa J Ryhänen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland. Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland
| | - Eric A Franzosa
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Hera Vlamakis
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA
| | - Curtis Huttenhower
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA. Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Dirk Gevers
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA
| | - Eric S Lander
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA. Department of Biology, MIT, Cambridge, MA 02139, USA. Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA
| | - Mikael Knip
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland. Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland. Department of Pediatrics, Tampere University Hospital, 33521 Tampere, Finland. Folkhälsan Research Center, 00290 Helsinki, Finland
| | | | - Ramnik J Xavier
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA. Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA.
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22
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Brinkac L, Voorhies A, Gomez A, Nelson KE. The Threat of Antimicrobial Resistance on the Human Microbiome. MICROBIAL ECOLOGY 2017; 74:1001-1008. [PMID: 28492988 PMCID: PMC5654679 DOI: 10.1007/s00248-017-0985-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 04/18/2017] [Indexed: 05/22/2023]
Abstract
Ubiquitous in nature, antimicrobial resistance (AMR) has existed long before the golden age of antimicrobials. While antimicrobial agents are beneficial to combat infection, their widespread use contributes to the increase in and emergence of novel resistant microbes in virtually all environmental niches. The human microbiome is an important reservoir of AMR with initial exposure occurring in early life. Once seeded with AMR, commensal organisms may be key contributors to the dissemination of resistance due to the interconnectedness of microbial communities. When acquired by pathogens however, AMR becomes a serious public health threat worldwide. Our ability to combat the threat of emerging resistance relies on accurate AMR detection methods and the development of therapeutics that function despite the presence of antimicrobial resistance.
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Affiliation(s)
- Lauren Brinkac
- J. Craig Venter Institute|, Rockville, MD, 20850, USA.
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4000, South Africa.
| | | | - Andres Gomez
- J. Craig Venter Institute|, Rockville, MD, 20850, USA
| | - Karen E Nelson
- J. Craig Venter Institute|, Rockville, MD, 20850, USA
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4000, South Africa
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A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis. Sci Rep 2017; 7:6685. [PMID: 28751714 PMCID: PMC5532234 DOI: 10.1038/s41598-017-06880-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/19/2017] [Indexed: 12/15/2022] Open
Abstract
Cystic Fibrosis (CF) and its treatment result in an altered gut microbiota composition compared to non-CF controls. However, the impact of this on gut microbiota functionality has not been extensively characterised. Our aim was to conduct a proof-of-principle study to investigate if measurable changes in gut microbiota functionality occur in adult CF patients compared to controls. Metagenomic DNA was extracted from faecal samples from six CF patients and six non-CF controls and shotgun metagenomic sequencing was performed on the MiSeq platform. Metabolomic analysis using gas chromatography-mass spectrometry was conducted on faecal water. The gut microbiota of the CF group was significantly different compared to the non-CF controls, with significantly increased Firmicutes and decreased Bacteroidetes. Functionality was altered, with higher pathway abundances and gene families involved in lipid (e.g. PWY 6284 unsaturated fatty acid biosynthesis (p = 0.016)) and xenobiotic metabolism (e.g. PWY-5430 meta-cleavage pathway of aromatic compounds (p = 0.004)) in CF patients compared to the controls. Significant differences in metabolites occurred between the two groups. This proof-of-principle study demonstrates that measurable changes in gut microbiota functionality occur in CF patients compared to controls. Larger studies are thus needed to interrogate this further.
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Crofts TS, Gasparrini AJ, Dantas G. Next-generation approaches to understand and combat the antibiotic resistome. Nat Rev Microbiol 2017; 15:422-434. [PMID: 28392565 DOI: 10.1038/nrmicro.2017.28] [Citation(s) in RCA: 312] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antibiotic resistance is a natural feature of diverse microbial ecosystems. Although recent studies of the antibiotic resistome have highlighted barriers to the horizontal transfer of antibiotic resistance genes between habitats, the rapid global spread of genes that confer resistance to carbapenem, colistin and quinolone antibiotics illustrates the dire clinical and societal consequences of such events. Over time, the study of antibiotic resistance has grown from focusing on single pathogenic organisms in axenic culture to studying antibiotic resistance in pathogenic, commensal and environmental bacteria at the level of microbial communities. As the study of antibiotic resistance advances, it is important to incorporate this comprehensive approach to better inform global antibiotic resistance surveillance and antibiotic development. It is increasingly becoming apparent that although not all resistance genes are likely to geographically and phylogenetically disseminate, the threat presented by those that are is serious and warrants an interdisciplinary research focus. In this Review, we highlight seminal work in the resistome field, discuss recent advances in the studies of resistomes, and propose a resistome paradigm that can pave the way for the improved proactive identification and mitigation of emerging antibiotic resistance threats.
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Affiliation(s)
- Terence S Crofts
- Center for Genome Sciences &Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, Missouri 63110, USA
| | - Andrew J Gasparrini
- Center for Genome Sciences &Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, Missouri 63110, USA
| | - Gautam Dantas
- Center for Genome Sciences &Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, Missouri 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine.,Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, Missouri 63110, USA.,Department of Biomedical Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, Missouri 63130, USA
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25
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A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements. Antimicrob Agents Chemother 2017; 61:AAC.02054-16. [PMID: 28137804 DOI: 10.1128/aac.02054-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/17/2017] [Indexed: 12/28/2022] Open
Abstract
The antimicrobial resistance (AMR) rates and levels recorded for Clostridium difficile are on the rise. This study reports the nature, levels, diversity, and genomic context of the antimicrobial resistance of human C. difficile isolates of the NAPCR1/RT012/ST54 genotype, which caused an outbreak in 2009 and is endemic in Costa Rican hospitals. To this end, we determined the susceptibilities of 38 NAPCR1 isolates to 10 antibiotics from seven classes using Etests or macrodilution tests and examined 31 NAPCR1 whole-genome sequences to identify single nucleotide polymorphisms (SNPs) and genes that could explain the resistance phenotypes observed. The NAPCR1 isolates were multidrug resistant (MDR) and commonly exhibited very high resistance levels. By sequencing their genomes, we showed that they possessed resistance-associated SNPs in gyrA and rpoB and carried eight to nine acquired antimicrobial resistance (AMR) genes. Most of these genes were located on known or novel mobile genetic elements shared by isolates recovered at different hospitals and at different time points. Metronidazole and vancomycin remain the first-line treatment options for these isolates. Overall, the NAPCR1 lineage showed an enhanced ability to acquire AMR genes through lateral gene transfer. On the basis of this finding, we recommend further vigilance and the adoption of improved control measures to limit the dissemination of this lineage and the emergence of more C. difficile MDR strains.
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Rose G, Shaw AG, Sim K, Wooldridge DJ, Li MS, Gharbia S, Misra R, Kroll JS. Antibiotic resistance potential of the healthy preterm infant gut microbiome. PeerJ 2017; 5:e2928. [PMID: 28149696 PMCID: PMC5270596 DOI: 10.7717/peerj.2928] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/20/2016] [Indexed: 01/06/2023] Open
Abstract
Background Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. Results Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples. Conclusions We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities.
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Affiliation(s)
- Graham Rose
- Genomics Research Unit, Public Health England , London , United Kingdom
| | - Alexander G Shaw
- Department of Medicine, Imperial College London , London , United Kingdom
| | - Kathleen Sim
- Department of Medicine, Imperial College London , London , United Kingdom
| | | | - Ming-Shi Li
- Department of Medicine, Imperial College London , London , United Kingdom
| | - Saheer Gharbia
- Genomics Research Unit, Public Health England , London , United Kingdom
| | - Raju Misra
- Genomics Research Unit, Public Health England , London , United Kingdom
| | - John Simon Kroll
- Section of Paediatrics, Department of Medicine, Imperial College London , London , United Kingdom
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Willmann M, Peter S. Translational metagenomics and the human resistome: confronting the menace of the new millennium. J Mol Med (Berl) 2016; 95:41-51. [PMID: 27766372 PMCID: PMC5225160 DOI: 10.1007/s00109-016-1478-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/19/2016] [Accepted: 09/26/2016] [Indexed: 12/21/2022]
Abstract
The increasing threat of antimicrobial resistance poses one of the greatest challenges to modern medicine. The collection of all antimicrobial resistance genes carried by various microorganisms in the human body is called the human resistome and represents the source of resistance in pathogens that can eventually cause life-threatening and untreatable infections. A deep understanding of the human resistome and its multilateral interaction with various environments is necessary for developing proper measures that can efficiently reduce the spread of resistance. However, the human resistome and its evolution still remain, for the most part, a mystery to researchers. Metagenomics, particularly in combination with next-generation-sequencing technology, provides a powerful methodological approach for studying the human microbiome as well as the pathogenome, the virolume and especially the resistome. We summarize below current knowledge on how the human resistome is shaped and discuss how metagenomics can be employed to improve our understanding of these complex processes, particularly as regards a rapid translation of new findings into clinical diagnostics, infection control and public health.
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Affiliation(s)
- Matthias Willmann
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Elfriede-Aulhorn-Str. 6, 72076, Tuebingen, Germany. .,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany.
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Elfriede-Aulhorn-Str. 6, 72076, Tuebingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
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Noyes NR, Yang X, Linke LM, Magnuson RJ, Cook SR, Zaheer R, Yang H, Woerner DR, Geornaras I, McArt JA, Gow SP, Ruiz J, Jones KL, Boucher CA, McAllister TA, Belk KE, Morley PS. Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems. Sci Rep 2016; 6:24645. [PMID: 27095377 PMCID: PMC4837390 DOI: 10.1038/srep24645] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/04/2016] [Indexed: 11/08/2022] Open
Abstract
It has been proposed that livestock production effluents such as wastewater, airborne dust and manure increase the density of antimicrobial resistant bacteria and genes in the environment. The public health risk posed by this proposed outcome has been difficult to quantify using traditional microbiological approaches. We utilized shotgun metagenomics to provide a first description of the resistome of North American dairy and beef production effluents, and identify factors that significantly impact this resistome. We identified 34 mechanisms of antimicrobial drug resistance within 34 soil, manure and wastewater samples from feedlot, ranch and dairy operations. The majority of resistance-associated sequences found in all samples belonged to tetracycline resistance mechanisms. We found that the ranch samples contained significantly fewer resistance mechanisms than dairy and feedlot samples, and that the resistome of dairy operations differed significantly from that of feedlots. The resistome in soil, manure and wastewater differed, suggesting that management of these effluents should be tailored appropriately. By providing a baseline of the cattle production waste resistome, this study represents a solid foundation for future efforts to characterize and quantify the public health risk posed by livestock effluents.
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Affiliation(s)
- Noelle R. Noyes
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Xiang Yang
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA
| | - Lyndsey M. Linke
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Roberta J. Magnuson
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Shaun R. Cook
- Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB, Canada
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB, Canada
| | - Hua Yang
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA
| | - Dale R. Woerner
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ifigenia Geornaras
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jessica A. McArt
- Department of Population Medicine & Diagnostic Sciences, Cornell University, Ithaca, NY, USA
| | - Sheryl P. Gow
- Centre for Food-borne, Environmental Zoonotic Infectious Diseases, Public Health Agency of Canada, University of Saskatoon, Saskatchewan, Canada
| | - Jaime Ruiz
- Department of Computer Sciences, College of Natural Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kenneth L. Jones
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Denver, CO, USA
| | - Christina A. Boucher
- Department of Computer Sciences, College of Natural Sciences, Colorado State University, Fort Collins, CO, USA
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB, Canada
| | - Keith E. Belk
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA
| | - Paul S. Morley
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
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29
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von Wintersdorff CJH, Wolffs PFG, Savelkoul PHM, Nijsen RRR, Lau S, Gerhold K, Hamelmann E, Penders J. The gut resistome is highly dynamic during the first months of life. Future Microbiol 2016; 11:501-10. [PMID: 27064174 DOI: 10.2217/fmb.15.154] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
AIM We investigated the longitudinal development of several antibiotic resistance genes (ARGs) of the infant gut resistome during the first months after birth. MATERIALS & METHODS Fecal samples from 120 infants collected at the ages of 5, 13 and 31 weeks were analyzed and subjected to qPCR for the detection of several ARGs. RESULTS The prevalence of ARGs significantly increased for ermB, tetM and tetQ, while it decreased for aac(6')-aph(2'). Birth mode and breastfeeding significantly affected tetQ prevalence. Correlations to bacterial taxa suggest that fluctuations in some ARGs are (partly) attributed to shifts in bacteroides colonization rates. CONCLUSION Acquisition of ARGs in the gut microbiota occurs shortly after birth and resistome composition fluctuates over the course of several months, reflecting changes in microbial community structure.
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Affiliation(s)
- Christian J H von Wintersdorff
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Petra F G Wolffs
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology, Caphri School for Public Health & Primary Care, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology, Caphri School for Public Health & Primary Care, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology & Infection Control, VU University Medical Center, Amsterdam
| | - Rianne R R Nijsen
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Susanne Lau
- Department of Pediatrics, Pneumology & Immunology, Charité Medical University Berlin, Berlin, Germany
| | - Kerstin Gerhold
- Department of Pediatrics & Child Health, Section of Pediatric Rheumatology, Winnipeg, Manitoba, Canada
| | - Eckard Hamelmann
- Children's Hospital, Ev. Hospital Bielefeld (EvKB), Bielefeld, Germany
| | - John Penders
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology, Caphri School for Public Health & Primary Care, Maastricht University Medical Center+, Maastricht, The Netherlands
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Abstract
PURPOSE OF REVIEW Antibiotics have not only saved lives and improved outcomes, but they also influence the evolving microbiome. This review summarizes reports on neonatal infections and variation in antibiotic utilization, discusses the emergence of resistant organisms, and presents data from human neonates and animal models demonstrating the impact of antibiotics on the microbiome, and how microbiome alterations impact health. The importance of antibiotic stewardship is also discussed. RECENT FINDINGS Infections increase neonatal morbidity and mortality. Furthermore, the clinical presentation of infections can be subtle, prompting clinicians to empirically start antibiotics when infection is a possibility. Antibiotic-resistant infections are a growing problem. Cohort studies have identified extensive center variations in antibiotic usage and associations between antibiotic exposures and outcomes. Studies of antibiotic-induced microbiome alterations and downstream effects on the developing immune system have increased our understanding of the mechanisms underlying the associations between antibiotics and adverse outcomes. The emergence of resistant microorganisms and recent evidence linking antibiotic practice variations with health outcomes has led to the initiation of antibiotic stewardship programs. SUMMARY The review encourages practitioners to assess local antibiotic use with regard to local microbiology, and to adopt steps to reduce infections and use antibiotics wisely.
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31
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von Wintersdorff CJH, Penders J, van Niekerk JM, Mills ND, Majumder S, van Alphen LB, Savelkoul PHM, Wolffs PFG. Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer. Front Microbiol 2016; 7:173. [PMID: 26925045 PMCID: PMC4759269 DOI: 10.3389/fmicb.2016.00173] [Citation(s) in RCA: 721] [Impact Index Per Article: 90.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of antibiotic resistance among pathogenic bacteria has been a rising problem for public health in recent decades. It is becoming increasingly recognized that not only antibiotic resistance genes (ARGs) encountered in clinical pathogens are of relevance, but rather, all pathogenic, commensal as well as environmental bacteria—and also mobile genetic elements and bacteriophages—form a reservoir of ARGs (the resistome) from which pathogenic bacteria can acquire resistance via horizontal gene transfer (HGT). HGT has caused antibiotic resistance to spread from commensal and environmental species to pathogenic ones, as has been shown for some clinically important ARGs. Of the three canonical mechanisms of HGT, conjugation is thought to have the greatest influence on the dissemination of ARGs. While transformation and transduction are deemed less important, recent discoveries suggest their role may be larger than previously thought. Understanding the extent of the resistome and how its mobilization to pathogenic bacteria takes place is essential for efforts to control the dissemination of these genes. Here, we will discuss the concept of the resistome, provide examples of HGT of clinically relevant ARGs and present an overview of the current knowledge of the contributions the various HGT mechanisms make to the spread of antibiotic resistance.
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Affiliation(s)
- Christian J H von Wintersdorff
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+ Maastricht, Netherlands
| | - John Penders
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+Maastricht, Netherlands
| | - Julius M van Niekerk
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Nathan D Mills
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Snehali Majumder
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Lieke B van Alphen
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology and Infection Control, VU University Medical CenterAmsterdam, Netherlands
| | - Petra F G Wolffs
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+Maastricht, Netherlands
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32
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Vaccines for Antibiotic-Resistant Bacteria: Possibility or Pipe Dream? Trends Pharmacol Sci 2016; 37:143-152. [DOI: 10.1016/j.tips.2015.10.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/13/2015] [Accepted: 10/16/2015] [Indexed: 11/19/2022]
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33
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Francino MP. Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances. Front Microbiol 2016; 6:1543. [PMID: 26793178 PMCID: PMC4709861 DOI: 10.3389/fmicb.2015.01543] [Citation(s) in RCA: 447] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/21/2015] [Indexed: 12/12/2022] Open
Abstract
The human microbiome is overly exposed to antibiotics, due, not only to their medical use, but also to their utilization in farm animals and crops. Microbiome composition can be rapidly altered by exposure to antibiotics, with potential immediate effects on health, for instance through the selection of resistant opportunistic pathogens that can cause acute disease. Microbiome alterations induced by antibiotics can also indirectly affect health in the long-term. The mutualistic microbes in the human body interact with many physiological processes, and participate in the regulation of immune and metabolic homeostasis. Therefore, antibiotic exposure can alter many basic physiological equilibria, promoting long-term disease. In addition, excessive antibiotic use fosters bacterial resistance, and the overly exposed human microbiome has become a significant reservoir of resistance genes, contributing to the increasing difficulty in controlling bacterial infections. Here, the complex relationships between antibiotics and the human microbiome are reviewed, with focus on the intestinal microbiota, addressing (1) the effects of antibiotic use on the composition and function of the gut microbiota, (2) the impact of antibiotic-induced microbiota alterations on immunity, metabolism, and health, and (3) the role of the gut microbiota as a reservoir of antibiotic resistances.
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Affiliation(s)
- M P Francino
- Unitat Mixta d'Investigació en Genòmica i Salut, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública/Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
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34
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High frequencies of antibiotic resistance genes in infants' meconium and early fecal samples. J Dev Orig Health Dis 2015; 7:35-44. [PMID: 26353938 DOI: 10.1017/s2040174415001506] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The gastrointestinal tract (GIT) microbiota has been identified as an important reservoir of antibiotic resistance genes (ARGs) that can be horizontally transferred to pathogenic species. Maternal GIT microbes can be transmitted to the offspring, and recent work indicates that such transfer starts before birth. We have used culture-independent genetic screenings to explore whether ARGs are already present in the meconium accumulated in the GIT during fetal life and in feces of 1-week-old infants. We have analyzed resistance to β-lactam antibiotics (BLr) and tetracycline (Tcr), screening for a variety of genes conferring each. To evaluate whether ARGs could have been inherited by maternal transmission, we have screened perinatal fecal samples of the 1-week-old babies' mothers, as well as a mother-infant series including meconium, fecal samples collected through the infant's 1st year, maternal fecal samples and colostrum. Our results reveal a high prevalence of BLr and Tcr in both meconium and early fecal samples, implying that the GIT resistance reservoir starts to accumulate even before birth. We show that ARGs present in the mother may reach the meconium and colostrum and establish in the infant GIT, but also that some ARGs were likely acquired from other sources. Alarmingly, we identified in both meconium and 1-week-olds' samples a particularly elevated prevalence of mecA (>45%), six-fold higher than that detected in the mothers. The mecA gene confers BLr to methicillin-resistant Staphylococcus aureus, and although its detection does not imply the presence of this pathogen, it does implicate the young infant's GIT as a noteworthy reservoir of this gene.
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Coughlan LM, Cotter PD, Hill C, Alvarez-Ordóñez A. Biotechnological applications of functional metagenomics in the food and pharmaceutical industries. Front Microbiol 2015; 6:672. [PMID: 26175729 PMCID: PMC4485178 DOI: 10.3389/fmicb.2015.00672] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 06/19/2015] [Indexed: 12/31/2022] Open
Abstract
Microorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods. Metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat. Function-based screenings, following the cloning and expression of metagenomic DNA in a heterologous host, can be applied to the discovery of novel proteins of industrial interest encoded by the genes of previously inaccessible microorganisms. Functional metagenomics has considerable potential in the food and pharmaceutical industries, where it can, for instance, aid (i) the identification of enzymes with desirable technological properties, capable of catalyzing novel reactions or replacing existing chemically synthesized catalysts which may be difficult or expensive to produce, and able to work under a wide range of environmental conditions encountered in food and pharmaceutical processing cycles including extreme conditions of temperature, pH, osmolarity, etc; (ii) the discovery of novel bioactives including antimicrobials active against microorganisms of concern both in food and medical settings; (iii) the investigation of industrial and societal issues such as antibiotic resistance development. This review article summarizes the state-of-the-art functional metagenomic methods available and discusses the potential of functional metagenomic approaches to mine as yet unexplored environments to discover novel genes with biotechnological application in the food and pharmaceutical industries.
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Affiliation(s)
| | - Paul D Cotter
- Teagasc Food Research Centre Cork, Ireland ; Alimentary Pharmabiotic Centre Cork, Ireland
| | - Colin Hill
- Alimentary Pharmabiotic Centre Cork, Ireland ; School of Microbiology, University College Cork Cork, Ireland
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36
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Moore AM, Ahmadi S, Patel S, Gibson MK, Wang B, Ndao MI, Deych E, Shannon W, Tarr PI, Warner BB, Dantas G. Gut resistome development in healthy twin pairs in the first year of life. MICROBIOME 2015; 3:27. [PMID: 26113976 PMCID: PMC4480905 DOI: 10.1186/s40168-015-0090-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/05/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND The early life of the human host marks a critically important time for establishment of the gut microbial community, yet the developmental trajectory of gut community-encoded resistance genes (resistome) is unknown. We present a longitudinal study of the fecal antibiotic resistome of healthy amoxicillin-exposed and antibiotic-naive twins and their mothers during the first year of life. RESULTS We extracted metagenomic DNA (mgDNA) from fecal samples collected from three healthy twin pairs at three timepoints (1 or 2 months, 6 or 7 months, and 11 months) and from their mothers (collected at delivery). The mgDNA was used to construct metagenomic expression libraries in an Escherichia coli host. These libraries were screened for antibiotic resistance, and functionally selected resistance genes were sequenced and annotated. A diverse fecal resistome distinct from the maternal resistome was apparent by 2 months of age, and infants' fecal resistomes included resistance to clinically important broad-spectrum beta-lactam antibiotics (e.g., piperacillin-tazobactam, aztreonam, cefepime) not found in their mothers. Dissemination of resistance genes among members of a given family was positively correlated with sharing of those same resistance genes between unrelated families, potentially identifying within-family sharing as a marker of resistance genes emerging in the human community at large. Finally, we found a distinct developmental trajectory for a community-encoded function: chloramphenicol resistance. All study subjects at all timepoints harbored chloramphenicol resistance determinants, but multidrug efflux pumps (rarely found in mothers) were the primary effectors of chloramphenicol resistance in young infants. Chloramphenicol acetyltransferases were more common in mothers than in infants and were found in nearly all the infants at later timepoints. CONCLUSIONS Our results suggest that healthy 1-2-month-old infants' gut microbes harbor clinically relevant resistance genes distinct from those of their mothers, and that family-specific shared environmental factors early in life shape resistome development.
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Affiliation(s)
- Aimee M. Moore
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Sara Ahmadi
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Sanket Patel
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Molly K. Gibson
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Bin Wang
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Malick I. Ndao
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Elena Deych
- />Department of Biostatistics, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - William Shannon
- />Department of Biostatistics, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Phillip I. Tarr
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Department of Molecular Microbiology, Washington University in St. School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Barbara B. Warner
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Gautam Dantas
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
- />Department of Biomedical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130 USA
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Fouhy F, Stanton C, Cotter PD, Hill C, Walsh F. Proteomics as the final step in the functional metagenomics study of antimicrobial resistance. Front Microbiol 2015; 6:172. [PMID: 25784907 PMCID: PMC4347484 DOI: 10.3389/fmicb.2015.00172] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/15/2015] [Indexed: 01/23/2023] Open
Abstract
The majority of clinically applied antimicrobial agents are derived from natural products generated by soil microorganisms and therefore resistance is likely to be ubiquitous in such environments. This is supported by the fact that numerous clinically important resistance mechanisms are encoded within the genomes of such bacteria. Advances in genomic sequencing have enabled the in silico identification of putative resistance genes present in these microorganisms. However, it is not sufficient to rely on the identification of putative resistance genes, we must also determine if the resultant proteins confer a resistant phenotype. This will require an analysis pipeline that extends from the extraction of environmental DNA, to the identification and analysis of potential resistance genes and their resultant proteins and phenotypes. This review focuses on the application of functional metagenomics and proteomics to study antimicrobial resistance in diverse environments.
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Affiliation(s)
- Fiona Fouhy
- Teagasc - Moorepark Food Research Centre , Fermoy, Ireland
| | - Catherine Stanton
- Teagasc - Moorepark Food Research Centre , Fermoy, Ireland ; Alimentary Pharmabiotic Centre , Cork, Ireland
| | - Paul D Cotter
- Teagasc - Moorepark Food Research Centre , Fermoy, Ireland ; Alimentary Pharmabiotic Centre , Cork, Ireland
| | - Colin Hill
- Alimentary Pharmabiotic Centre , Cork, Ireland ; School of Microbiology, University College Cork , Cork, Ireland
| | - Fiona Walsh
- Department of Biology, National University of Ireland Maynooth , Maynooth, Ireland
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