1
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Gasparrini AJ, Markley JL, Kumar H, Wang B, Fang L, Irum S, Symister CT, Wallace M, Burnham CAD, Andleeb S, Tolia NH, Wencewicz TA, Dantas G. Tetracycline-inactivating enzymes from environmental, human commensal, and pathogenic bacteria cause broad-spectrum tetracycline resistance. Commun Biol 2020; 3:241. [PMID: 32415166 PMCID: PMC7229144 DOI: 10.1038/s42003-020-0966-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/17/2020] [Indexed: 12/19/2022] Open
Abstract
Tetracycline resistance by antibiotic inactivation was first identified in commensal organisms but has since been reported in environmental and pathogenic microbes. Here, we identify and characterize an expanded pool of tet(X)-like genes in environmental and human commensal metagenomes via inactivation by antibiotic selection of metagenomic libraries. These genes formed two distinct clades according to habitat of origin, and resistance phenotypes were similarly correlated. Each gene isolated from the human gut encodes resistance to all tetracyclines tested, including eravacycline and omadacycline. We report a biochemical and structural characterization of one enzyme, Tet(X7). Further, we identify Tet(X7) in a clinical Pseudomonas aeruginosa isolate and demonstrate its contribution to tetracycline resistance. Lastly, we show anhydrotetracycline and semi-synthetic analogues inhibit Tet(X7) to prevent enzymatic tetracycline degradation and increase tetracycline efficacy against strains expressing tet(X7). This work improves our understanding of resistance by tetracycline-inactivation and provides the foundation for an inhibition-based strategy for countering resistance.
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Affiliation(s)
- Andrew J Gasparrini
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jana L Markley
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Hirdesh Kumar
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Luting Fang
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Sidra Irum
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Chanez T Symister
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Meghan Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Carey-Ann D Burnham
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Saadia Andleeb
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Niraj H Tolia
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | | | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Department of Biomedical Engineering, Washington University, St. Louis, MO, 63130, USA.
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2
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Knoop KA, Coughlin PE, Floyd AN, Ndao IM, Hall-Moore C, Shaikh N, Gasparrini AJ, Rusconi B, Escobedo M, Good M, Warner BB, Tarr PI, Newberry RD. Maternal activation of the EGFR prevents translocation of gut-residing pathogenic Escherichia coli in a model of late-onset neonatal sepsis. Proc Natl Acad Sci U S A 2020; 117:7941-7949. [PMID: 32179676 PMCID: PMC7148560 DOI: 10.1073/pnas.1912022117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Late-onset sepsis (LOS) is a highly consequential complication of preterm birth and is defined by a positive blood culture obtained after 72 h of age. The causative bacteria can be found in patients' intestinal tracts days before dissemination, and cohort studies suggest reduced LOS risk in breastfed preterm infants through unknown mechanisms. Reduced concentrations of epidermal growth factor (EGF) of maternal origin within the intestinal tract of mice correlated to the translocation of a gut-resident human pathogen Escherichia coli, which spreads systemically and caused a rapid, fatal disease in pups. Translocation of Escherichia coli was associated with the formation of colonic goblet cell-associated antigen passages (GAPs), which translocate enteric bacteria across the intestinal epithelium. Thus, maternally derived EGF, and potentially other EGFR ligands, prevents dissemination of a gut-resident pathogen by inhibiting goblet cell-mediated bacterial translocation. Through manipulation of maternally derived EGF and alteration of the earliest gut defenses, we have developed an animal model of pathogen dissemination which recapitulates gut-origin neonatal LOS.
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Affiliation(s)
- Kathryn A Knoop
- Department of Immunology, Mayo Clinic, Rochester, MN 55905;
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Paige E Coughlin
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Alexandria N Floyd
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - I Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Carla Hall-Moore
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Nurmohammad Shaikh
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Andrew J Gasparrini
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110
| | - Brigida Rusconi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Marilyn Escobedo
- Department of Pediatrics, University of Oklahoma School of Medicine, Oklahoma City, OK 73019
| | - Misty Good
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Barbara B Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Rodney D Newberry
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110
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3
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Gasparrini AJ, Wang B, Sun X, Kennedy EA, Hernandez-Leyva A, Ndao IM, Tarr PI, Warner BB, Dantas G. Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome. Nat Microbiol 2019; 4:2285-2297. [PMID: 31501537 PMCID: PMC6879825 DOI: 10.1038/s41564-019-0550-2] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 07/26/2019] [Indexed: 12/29/2022]
Abstract
Hospitalized preterm infants receive frequent and often prolonged exposures to antibiotics because they are vulnerable to infection. It is not known whether the short-term effects of antibiotics on the preterm infant gut microbiota and resistome persist after discharge from neonatal intensive care units. Here, we use complementary metagenomic, culture-based and machine learning techniques to study the gut microbiota and resistome of antibiotic-exposed preterm infants during and after hospitalization, and we compare these readouts to antibiotic-naive healthy infants sampled synchronously. We find a persistently enriched gastrointestinal antibiotic resistome, prolonged carriage of multidrug-resistant Enterobacteriaceae and distinct antibiotic-driven patterns of microbiota and resistome assembly in extremely preterm infants that received early-life antibiotics. The collateral damage of early-life antibiotic treatment and hospitalization in preterm infants is long lasting. We urge the development of strategies to reduce these consequences in highly vulnerable neonatal populations.
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Affiliation(s)
- Andrew J Gasparrini
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Xiaoqing Sun
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Elizabeth A Kennedy
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Ariel Hernandez-Leyva
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - I Malick Ndao
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Phillip I Tarr
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Barbara B Warner
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA.
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4
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Markley JL, Fang L, Gasparrini AJ, Symister CT, Kumar H, Tolia NH, Dantas G, Wencewicz TA. Semisynthetic Analogues of Anhydrotetracycline as Inhibitors of Tetracycline Destructase Enzymes. ACS Infect Dis 2019; 5:618-633. [PMID: 30835428 DOI: 10.1021/acsinfecdis.8b00349] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The synthesis and biological evaluation of semisynthetic anhydrotetracycline analogues as small molecule inhibitors of tetracycline-inactivating enzymes are reported. Inhibitor potency was found to vary as a function of enzyme (major) and substrate-inhibitor pair (minor), and anhydrotetracycline analogue stability to enzymatic and nonenzymatic degradation in solution contributes to their ability to rescue tetracycline activity in whole cell Escherichia coli expressing tetracycline destructase enzymes. Taken collectively, these results provide the framework for the rational design of next-generation inhibitor libraries en route to a viable and proactive adjuvant approach to combat the enzymatic degradation of tetracycline antibiotics.
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Affiliation(s)
| | | | - Andrew J. Gasparrini
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, 4513 Clayton Ave., Campus Box 8510, St. Louis, Missouri 63108, United States
| | | | - Hirdesh Kumar
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, BG 29B Rm 4NN08, Bethesda, Maryland 20814, United States
| | - Niraj H. Tolia
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, BG 29B Rm 4NN08, Bethesda, Maryland 20814, United States
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, 4513 Clayton Ave., Campus Box 8510, St. Louis, Missouri 63108, United States
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Department of Molecular Microbiology, Washington University School of Medicine, 4515 McKinley Avenue, fifth Floor, Room 5314, St. Louis, Missouri 63110, United States
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5
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Crook N, Ferreiro A, Gasparrini AJ, Pesesky MW, Gibson MK, Wang B, Sun X, Condiotte Z, Dobrowolski S, Peterson D, Dantas G. Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut. Cell Host Microbe 2019; 25:499-512.e8. [PMID: 30926240 PMCID: PMC6487504 DOI: 10.1016/j.chom.2019.02.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/06/2019] [Accepted: 02/19/2019] [Indexed: 12/14/2022]
Abstract
Probiotics are living microorganisms that are increasingly used as gastrointestinal therapeutics by virtue of their innate or engineered genetic function. Unlike abiotic therapeutics, probiotics can replicate in their intended site, subjecting their genomes and therapeutic properties to natural selection. We exposed the candidate probiotic E. coli Nissle (EcN) to the mouse gastrointestinal tract over several weeks, systematically altering the diet and background microbiota complexity. In-transit EcN accumulates genetic mutations that modulate carbohydrate utilization, stress response, and adhesion to gain competitive fitness, while previous exposure to antibiotics reveals an acquisition of resistance. We then leveraged these insights to generate an EcN strain that shows therapeutic efficacy in a mouse model of phenylketonuria and found that it was genetically stable over 1 week, thereby validating EcN's utility as a chassis for engineering. Collectively, we demonstrate a generalizable pipeline that can be applied to other probiotics to better understand their safety and engineering potential.
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Affiliation(s)
- Nathan Crook
- Equal Contribution
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Present address: Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA
| | - Aura Ferreiro
- Equal Contribution
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Andrew J. Gasparrini
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Present address: VL55, 55 Cambridge Pwky, Cambridge, MA 02142, USA
| | - Mitchell W. Pesesky
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Present address: Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Molly K. Gibson
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Present address: Flagship Pioneering, 55 Cambridge Pkwy, Cambridge, MA 02142, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoqing Sun
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zevin Condiotte
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Present address: Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen Dobrowolski
- Department of Pathology, Children’s Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Daniel Peterson
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Present address: Eli Lilly & Company, 307 East McCarty Street, Indianapolis, IN 46225, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Lead Contact: Gautam Dantas, Ph.D. ()
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6
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Park J, Gasparrini AJ, Reck MR, Symister CT, Elliott JL, Vogel JP, Wencewicz TA, Dantas G, Tolia NH. Plasticity, dynamics, and inhibition of emerging tetracycline resistance enzymes. Nat Chem Biol 2017; 13:730-736. [PMID: 28481346 PMCID: PMC5478473 DOI: 10.1038/nchembio.2376] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/08/2017] [Indexed: 12/18/2022]
Abstract
While tetracyclines are an important class of antibiotics in agriculture and the clinic, their efficacy is threatened by increasing resistance. Resistance to tetracyclines can occur through efflux, ribosomal protection, or enzymatic inactivation. Surprisingly, tetracycline enzymatic inactivation has remained largely unexplored despite providing the distinct advantage of antibiotic clearance. The tetracycline destructases are a recently-discovered family of tetracycline-inactivating flavoenzymes from pathogens and soil metagenomes with a high potential for broad dissemination. Here, we show tetracycline destructases accommodate tetracycline-class antibiotics in diverse and novel orientations for catalysis, and antibiotic binding drives unprecedented structural dynamics facilitating tetracycline inactivation. We identify a key inhibitor binding mode that locks the flavin adenine dinucleotide cofactor in an inactive state, functionally rescuing tetracycline activity. Our results reveal the potential of a novel tetracycline/tetracycline destructase inhibitor combination therapy strategy to overcome resistance by enzymatic inactivation and restore the use of an important class of antibiotics.
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Affiliation(s)
- Jooyoung Park
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrew J Gasparrini
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Margaret R Reck
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Chanez T Symister
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jennifer L Elliott
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Joseph P Vogel
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Timothy A Wencewicz
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Gautam Dantas
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Niraj H Tolia
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
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7
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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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8
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Adu-Oppong B, Gasparrini AJ, Dantas G. Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes. Ann N Y Acad Sci 2016; 1388:42-58. [PMID: 27768825 DOI: 10.1111/nyas.13257] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/16/2016] [Accepted: 08/22/2016] [Indexed: 02/07/2023]
Abstract
Microbial communities contain diverse bacteria that play important roles in every environment. Advances in sequencing and computational methodologies over the past decades have illuminated the phylogenetic and functional diversity of microbial communities from diverse habitats. Among the activities encoded in microbiomes are the abilities to synthesize and resist small molecules, yielding antimicrobial activity. These functions are of particular interest when viewed in light of the public health emergency posed by the increase in clinical antimicrobial resistance and the dwindling antimicrobial discovery and approval pipeline, and given the intimate ecological and evolutionary relationship between antimicrobial biosynthesis and resistance. Here, we review genomic and functional methods that have been developed for accessing the antimicrobial biosynthesis and resistance capacity of microbiomes and highlight outstanding examples of their applications.
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Affiliation(s)
- Boahemaa Adu-Oppong
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Andrew J Gasparrini
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Gautam Dantas
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri.,Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri
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9
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Abstract
The gut microbiota plays important roles in nutrient absorption, immune system development, and pathogen colonization resistance. Perturbations early in life may be detrimental to host health in the short and the long-term. Antibiotics are among the many factors that influence the development of the microbiota. Because antibiotics are heavily administered during the first critical years of gut microbiota development, it is important to understand the effects of these interventions. Infants, particularly those born prematurely, represent an interesting population because they receive early and often extensive antibiotic therapy in the first months after birth. Gibson et al. recently demonstrated that antibiotic therapy in preterm infants can dramatically affect the gut microbiome. While meropenem, ticarcillin-clavulanate, and cefotaxime treatments were associated with decreased species richness, gentamicin and vancomycin had variable effects on species richness. Interestingly, the direction of species richness response could be predicted based on the abundance of 2 species and 2 genes in the microbiome prior to gentamicin or vancomycin treatment. Nonetheless, all antibiotic treatments enriched the presence of resistance genes and multidrug resistant organisms. Treatment with different antibiotics further resulted in unique population shifts of abundant organisms and selection for different sets of resistance genes. In this addendum, we provide an extended discussion of these recent findings, and outline important future directions for elucidating the interplay between antibiotics and preterm infant gut microbiota development.
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Affiliation(s)
- Andrew J. Gasparrini
- Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St Louis, MO,
USA
| | - Terence S. Crofts
- Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St Louis, MO,
USA,Department of Pathology and Immunology,
Washington University School of Medicine, St Louis, MO,
USA
| | - Molly K. Gibson
- Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St Louis, MO,
USA
| | - Phillip I. Tarr
- Department of Pediatrics, Washington
University School of Medicine, St Louis, MO, USA,Department of Molecular Microbiology,
Washington University School of Medicine, St Louis, MO,
USA
| | - Barbara B. Warner
- Department of Pediatrics, Washington
University School of Medicine, St Louis, MO, USA
| | - Gautam Dantas
- Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St Louis, MO,
USA,Department of Pathology and Immunology,
Washington University School of Medicine, St Louis, MO,
USA,Department of Molecular Microbiology,
Washington University School of Medicine, St Louis, MO,
USA,Department of Biomedical Engineering,
Washington University, St Louis, MO, USA
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