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Drane K, Sheehan M, Whelan A, Ariel E, Kinobe R. The Role of Wastewater Treatment Plants in Dissemination of Antibiotic Resistance: Source, Measurement, Removal and Risk Assessment. Antibiotics (Basel) 2024; 13:668. [PMID: 39061350 PMCID: PMC11274174 DOI: 10.3390/antibiotics13070668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/05/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Antibiotic Resistance Genes (ARGs) are contaminants of emerging concern with marked potential to impact public and environmental health. This review focusses on factors that influence the presence, abundance, and dissemination of ARGs within Wastewater Treatment Plants (WWTPs) and associated effluents. Antibiotic-Resistant Bacteria (ARB) and ARGs have been detected in the influent and the effluent of WWTPs worldwide. Different levels of wastewater treatment (primary, secondary, and tertiary) show different degrees of removal efficiency of ARGs, with further differences being observed when ARGs are captured as intracellular or extracellular forms. Furthermore, routinely used molecular methodologies such as quantitative polymerase chain reaction or whole genome sequencing may also vary in resistome identification and in quantifying ARG removal efficiencies from WWTP effluents. Additionally, we provide an overview of the One Health risk assessment framework, as well as future strategies on how WWTPs can be assessed for environmental and public health impact.
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Affiliation(s)
- Kezia Drane
- College of Public Health Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
| | - Madoc Sheehan
- College of Science, Technology, and Engineering, James Cook University, Townsville, QLD 4811, Australia;
| | - Anna Whelan
- Townsville Water and Waste, Wastewater Operations, Townsville, QLD 4810, Australia;
| | - Ellen Ariel
- College of Public Health Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
| | - Robert Kinobe
- College of Public Health Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
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2
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Rodriguez-Ruiz JP, Lin Q, Van Heirstraeten L, Lammens C, Stewardson AJ, Godycki-Cwirko M, Coenen S, Goossens H, Harbarth S, Malhotra-Kumar S. Long-term effects of ciprofloxacin treatment on the gastrointestinal and oropharyngeal microbiome are more pronounced after longer antibiotic courses. Int J Antimicrob Agents 2024; 64:107259. [PMID: 38936492 DOI: 10.1016/j.ijantimicag.2024.107259] [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: 02/09/2024] [Revised: 06/04/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Urinary tract infections (UTIs) are one of the main reasons for antibiotic prescriptions in primary care. Recent studies demonstrate similar clinical outcomes with short vs. long antibiotics courses. The aim of this study was to investigate the differential collateral effect of ciprofloxacin treatment duration on the gastrointestinal and oropharyngeal microbiome in patients presenting with uncomplicated UTI to primary care practices in Switzerland, Belgium and Poland. METHODS Stool and oropharyngeal samples were obtained from 36 treated patients and 14 controls at the beginning of antibiotic therapy, end of therapy and one month after the end of therapy. Samples underwent shotgun metagenomics. RESULTS At the end of therapy, patients treated with both short (≤7 days) and long (>7 days) ciprofloxacin courses showed similar changes in the gastrointestinal microbiome compared to non-treated controls. After one month, most changes in patients receiving short courses were reversed; however, long courses led to increased abundance of the genera Roseburia, Faecalicatena and Escherichia. Changes in the oropharynx were minor and reversed to baseline levels within one month. Ciprofloxacin resistance encoding mutations in gyrA/B and parC/E reads were observed in both short and long treatment groups but decreased to baseline levels after one month. An increased abundance of resistance genes was observed in the gastrointestinal microbiome after longer treatment, and correlated to increased prevalence of aminoglycoside, β-lactam, sulphonamide, and tetracycline resistance genes. CONCLUSION Collateral effects on the gastrointestinal community, including an increased prevalence of antimicrobial resistance genes, persists for up to at least one month following longer ciprofloxacin therapy. These data support the use of shorter antimicrobial treatment duration.
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Affiliation(s)
- J P Rodriguez-Ruiz
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Q Lin
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - L Van Heirstraeten
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - C Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - A J Stewardson
- Department of Infectious Diseases, The Alfred and Central Clinical School, Monash University, Melbourne, Australia
| | - M Godycki-Cwirko
- Centre for Family and Community Medicine, Medical University of Lodz, Lodz, Poland
| | - S Coenen
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - H Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - S Harbarth
- Infection Control Program & Division of Infectious Diseases, University of Geneva and Faculty of Medicine, Geneva
| | - S Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium.
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3
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Yuu EY, Bührer C, Eckmanns T, Fulde M, Herz M, Kurzai O, Lindstedt C, Panagiotou G, Piro VC, Radonic A, Renard BY, Reuss A, Siliceo SL, Thielemann N, Thürmer A, Vorst KV, Wieler LH, Haller S. The gut microbiome, resistome, and mycobiome in preterm newborn infants and mouse pups: lack of lasting effects by antimicrobial therapy or probiotic prophylaxis. Gut Pathog 2024; 16:27. [PMID: 38735967 PMCID: PMC11089716 DOI: 10.1186/s13099-024-00616-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 04/13/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Enhancing our understanding of the underlying influences of medical interventions on the microbiome, resistome and mycobiome of preterm born infants holds significant potential for advancing infection prevention and treatment strategies. We conducted a prospective quasi-intervention study to better understand how antibiotics, and probiotics, and other medical factors influence the gut development of preterm infants. A controlled neonatal mice model was conducted in parallel, designed to closely reflect and predict exposures. Preterm infants and neonatal mice were stratified into four groups: antibiotics only, probiotics only, antibiotics followed by probiotics, and none of these interventions. Stool samples from both preterm infants and neonatal mice were collected at varying time points and analyzed by 16 S rRNA amplicon sequencing, ITS amplicon sequencing and whole genome shotgun sequencing. RESULTS The human infant microbiomes showed an unexpectedly high degree of heterogeneity. Little impact from medical exposure (antibiotics/probiotics) was observed on the strain patterns, however, Bifidobacterium bifidum was found more abundant after exposure to probiotics, regardless of prior antibiotic administration. Twenty-seven antibiotic resistant genes were identified in the resistome. High intra-variability was evident within the different treatment groups. Lastly, we found significant effects of antibiotics and probiotics on the mycobiome but not on the microbiome and resistome of preterm infants. CONCLUSIONS Although our analyses showed transient effects, these results provide positive motivation to continue the research on the effects of medical interventions on the microbiome, resistome and mycobiome of preterm infants.
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Affiliation(s)
- Elizabeth Y Yuu
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
| | | | | | - Marcus Fulde
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | - Michaela Herz
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
| | | | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07745, Jena, Germany
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Vitor C Piro
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | | | - Bernhard Y Renard
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
| | - Annicka Reuss
- Robert Koch Institute, Berlin, Germany
- Ministry of Justice and Health, Schleswig-Holstein, Kiel , Germany
| | - Sara Leal Siliceo
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
| | - Nadja Thielemann
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | | | - Kira van Vorst
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | - Lothar H Wieler
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
- Robert Koch Institute, Berlin, Germany
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4
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Zheng L, Shen J, Chen R, Hu Y, Zhao W, Leung ELH, Dai L. Genome engineering of the human gut microbiome. J Genet Genomics 2024; 51:479-491. [PMID: 38218395 DOI: 10.1016/j.jgg.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
The human gut microbiome, a complex ecosystem, significantly influences host health, impacting crucial aspects such as metabolism and immunity. To enhance our comprehension and control of the molecular mechanisms orchestrating the intricate interplay between gut commensal bacteria and human health, the exploration of genome engineering for gut microbes is a promising frontier. Nevertheless, the complexities and diversities inherent in the gut microbiome pose substantial challenges to the development of effective genome engineering tools for human gut microbes. In this comprehensive review, we provide an overview of the current progress and challenges in genome engineering of human gut commensal bacteria, whether executed in vitro or in situ. A specific focus is directed towards the advancements and prospects in cargo DNA delivery and high-throughput techniques. Additionally, we elucidate the immense potential of genome engineering methods to enhance our understanding of the human gut microbiome and engineer the microorganisms to enhance human health.
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Affiliation(s)
- Linggang Zheng
- Dr Neher's Biophysics Laboratory for Innovative Drug Discovery/State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Juntao Shen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ruiyue Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yucan Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Elaine Lai-Han Leung
- Cancer Center, Faculty of Health Science, University of Macau, Macau 999078, China; MOE Frontiers Science Center for Precision Oncology, University of Macau, Macau 999078, China.
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Tang H, Liu Z, Hu B, Zhu L. D-Ring Modifications of Tetracyclines Determine Their Ability to Induce Resistance Genes in the Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1338-1348. [PMID: 38157442 DOI: 10.1021/acs.est.3c07559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The widespread utilization of tetracyclines (TCs) in agriculture and medicine has led to the borderless spread of tetracycline resistance in humans, animals, and the environment, posing huge risks to both the ecosystem and human society. Changes in the functional group modifications resulted in a higher bacteriostatic efficacy of the new generation of TCs, but their effect on the emergence and evolution of antibiotic resistance genes (ARGs) is not yet known. To this end, four TCs from three generations were chosen to compare their structural effects on influencing the evolution of ARGs in soil microbial communities. The findings revealed that low-generation TCs, such as tetracycline and oxytetracycline, exhibited a greater propensity to stimulate the production and proliferation of ARGs than did high-generation tigecycline. Molecular docking analysis demonstrated that modifications of the D-ring functional group determined the binding capacity of TCs to the substrate-binding pocket of transcriptional regulators and efflux pumps mainly involved in drug resistance. This can be further evidenced by reverse transcription-quantitative polymerase chain reaction quantification and intracellular antibiotic accumulation assessment. This study sheds light on the mechanism of the structural effect of antibiotic-induced ARG production from the perspective of compound-protein binding, therefore providing theoretical support for controlling the dissemination of antibiotic resistance.
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Affiliation(s)
- Huiming Tang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China
| | - Zishu Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China
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6
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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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7
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Duarte DJ, Zillien C, Kox M, Oldenkamp R, van der Zaan B, Roex E, Ragas AMJ. Characterization of urban sources of antibiotics and antibiotic-resistance genes in a Dutch sewer catchment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167439. [PMID: 37774886 DOI: 10.1016/j.scitotenv.2023.167439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/08/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
A one year study was conducted in the city of Nijmegen, The Netherlands, to characterize various urban sources of antibiotics and antibiotic resistant genes (ARGs) in wastewater within a single sewer catchment. Prevalence of ermB, tet(W), sul1, sul2, intl1, and 16S rRNA gene was determined at 10 locations within the city. Sampling locations included a nursing home, a student residence, a hospital and an industrial area, among others. Wastewater concentrations of 23 antibiotics were measured using passive sampling. Additionally, excreted loads of 22 antibiotics were estimated based on ambulatory prescription and clinical usage data. Genes sul1 and intl1 were most abundant across most locations. Ciprofloxacin and amoxicillin together contributed over 92 % of the total estimated antibiotic selective pressure at all sampling points. The present study highlights the prominent role that hospitals can have in the prevalence and proliferation of ARGs in urban wastewater. Furthermore, results suggest that even short-term changes in the therapeutic regimen prescribed in hospitals may translate into shifting ARG abundance patterns in hospital wastewater. The methods applied present an opportunity to identify emission hotspots and prioritize intervention options to limit ARG spread from urban wastewater to the environment.
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Affiliation(s)
- Daniel J Duarte
- Radboud University Nijmegen, Radboud Institute for Biological and Environmental Sciences, Department of Environmental Science, 6500 GL Nijmegen, Netherlands
| | - Caterina Zillien
- Radboud University Nijmegen, Radboud Institute for Biological and Environmental Sciences, Department of Environmental Science, 6500 GL Nijmegen, Netherlands.
| | - Martine Kox
- Deltares, Subsurface and Groundwater Systems, Daltonlaan 600, 3584 KB Utrecht, the Netherlands
| | - Rik Oldenkamp
- Department of Global Health-Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Paasheuvelweg 25, 1105 BP Amsterdam, the Netherlands
| | - Bas van der Zaan
- Deltares, Subsurface and Groundwater Systems, Daltonlaan 600, 3584 KB Utrecht, the Netherlands
| | - Erwin Roex
- National Institute for Public Health and the Environment (RIVM), Centre for Zoonoses and Environmental Microbiology, 3721 MA Bilthoven, the Netherlands
| | - Ad M J Ragas
- Radboud University Nijmegen, Radboud Institute for Biological and Environmental Sciences, Department of Environmental Science, 6500 GL Nijmegen, Netherlands
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Hill MS, Gilbert JA. Microbiology of the built environment: harnessing human-associated built environment research to inform the study and design of animal nests and enclosures. Microbiol Mol Biol Rev 2023; 87:e0012121. [PMID: 38047636 PMCID: PMC10732082 DOI: 10.1128/mmbr.00121-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
SUMMARYOver the past decade, hundreds of studies have characterized the microbial communities found in human-associated built environments (BEs). These have focused primarily on how the design and use of our built spaces have shaped human-microbe interactions and how the differential selection of certain taxa or genetic traits has influenced health outcomes. It is now known that the more removed humans are from the natural environment, the greater the risk for the development of autoimmune and allergic diseases, and that indoor spaces can be harsh, selective environments that can increase the emergence of antimicrobial-resistant and virulent phenotypes in surface-bound communities. However, despite the abundance of research that now points to the importance of BEs in determining human-microbe interactions, only a fraction of non-human animal structures have been comparatively explored. It is here, in the context of human-associated BE research, that we consider the microbial ecology of animal-built natural nests and burrows, as well as artificial enclosures, and point to areas of primary interest for future research.
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Affiliation(s)
- Megan S. Hill
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, California, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, California, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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Igo M, Xu L, Krishna A, Stewart S, Xu L, Li Z, Weaver JL, Stone H, Sacks L, Bensman T, Florian J, Rouse R, Han X. A metagenomic analysis for combination therapy of multiple classes of antibiotics on the prevention of the spread of antibiotic-resistant genes. Gut Microbes 2023; 15:2271150. [PMID: 37908118 PMCID: PMC10621307 DOI: 10.1080/19490976.2023.2271150] [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: 06/06/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023] Open
Abstract
Antibiotics used systemically to treat infections may have off-target effects on the gut microbiome, potentially resulting in the emergence of drug-resistant bacteria or selection of pathogenic species. These organisms may present a risk to the host and spread to the environment with a risk of transmission in the community. To investigate the risk of emergent antibiotic resistance in the gut microbiome following systemic treatment with antibiotics, this metagenomic analysis project used next-generation sequencing, a custom-built metagenomics pipeline, and differential abundance analysis to study the effect of antibiotics (ampicillin, ciprofloxacin, and fosfomycin) in monotherapy and different combinations at high and low doses, to determine the effect on resistome and taxonomic composition in the gut of Balb/c mice. The results showed that low-dose monotherapy treatments showed little change in microbiome composition but did show an increase in expression of many antibiotic-resistant genes (ARGs) posttreatment. Dual combination treatments allowed the emergence of some conditionally pathogenic bacteria and some increase in the abundance of ARGs despite a general decrease in microbiota diversity. Triple combination treatment was the most successful in inhibiting emergence of relevant opportunistic pathogens and completely suppressed all ARGs after 72 h of treatment. The relative abundances of mobile genetic elements that can enhance transmission of antibiotic resistance either decreased or remained the same for combination therapy while increasing for low-dose monotherapy. Combination therapy prevented the emergence of ARGs and decreased bacterial diversity, while low-dose monotherapy treatment increased ARGs and did not greatly change bacterial diversity.
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Affiliation(s)
- Matthew Igo
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Lei Xu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Ashok Krishna
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Sharron Stewart
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Lin Xu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - James L. Weaver
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Heather Stone
- Office of Medical Policy, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Leonard Sacks
- Office of Medical Policy, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Timothy Bensman
- Division of Infectious Disease Pharmacology, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Jeffry Florian
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Rodney Rouse
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Xiaomei Han
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
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Lai C, Chen L, Zhong X, Tang Z, Zhang B, Luo Y, Li C, Jin M, Chen X, Li J, Shi Y, Sun Y, Guo L. Long-term effects on liver metabolism induced by ceftriaxone sodium pretreatment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 335:122238. [PMID: 37506808 DOI: 10.1016/j.envpol.2023.122238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Abstract
Ceftriaxone is an emerging contaminant due to its potential harm, while its effects on liver are still need to be clarified. In this study, we first pretreated the 8-week-old C57BL/6J mice with high dose ceftriaxone sodium (Cef, 400 mg/mL, 0.2 mL per dose) for 8 days to prepare a gut dysbiosis model, then treated with normal feed for a two-month recovery period, and applied non-targeted metabolomics (including lipidomics) to investigate the variations of fecal and liver metabolome, and coupled with targeted determination of fecal short-chain fatty acids (SCFAs) and bile acids (BAs). Lastly, the correlations and mediation analysis between the liver metabolism and gut metabolism/microbes were carried, and the potential mechanisms of the mal-effects on gut-liver axis induced by Cef pretreatment were accordingly discussed. Compared to the control group, Cef pretreatment reduced the rate of weight gain and hepatosomatic index, induced bile duct epithelial cells proliferated around the central vein and appearance of binucleated hepatocytes, decreased the ratio of total branching chains amino acids (BCAAs) to total aromatic amino acids (AAAs) in liver metabolome. In fecal metabolome, the total fecal SCFAs and BAs did not change significantly while butyric acid decreased and the primary BAs increased after Cef pretreatment. Correlation and mediation analysis revealed one potential mechanism that Cef may first change the intestinal microbiota (such as destroying its normal structure, reducing its abundance and the stability of the microbial network or certain microbe abundance like Alistipes), and then change the intestinal metabolism (such as acetate, caproate, propionate), leading to liver metabolic disorder (such as spermidine, inosine, cinnamaldehyde). This study proved the possibility of Cef-induced liver damage, displayed the overall metabolic profile of the liver following Cef pretreatment and provided a theoretical framework for further research into the mechanism of Cef-induced liver damage.
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Affiliation(s)
- Chengze Lai
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China; Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Linkang Chen
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Xiaoting Zhong
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Zeli Tang
- Department of Pathology, School of Basic Medical Sciences, Guangdong Medical University, Dongguan, China
| | - Bin Zhang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Yu Luo
- Guangzhou Liwan District Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Chengji Li
- Yunfu Disease Control and Prevention Center, Guang Dong Province, China
| | - Mengcheng Jin
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Xu Chen
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Jinglin Li
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Yinying Shi
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Yanqin Sun
- Department of Pathology, School of Basic Medical Sciences, Guangdong Medical University, Dongguan, China
| | - Lianxian Guo
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China; Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.
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11
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Lim EY, Song EJ, Shin HS. Gut Microbiome as a Possible Cause of Occurrence and Therapeutic Target in Chronic Obstructive Pulmonary Disease. J Microbiol Biotechnol 2023; 33:1111-1118. [PMID: 37164760 PMCID: PMC10580882 DOI: 10.4014/jmb.2301.01033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 05/12/2023]
Abstract
As a long-term condition that affects the airways and lungs, chronic obstructive pulmonary disease (COPD) is characterized by inflammation, emphysema, breathlessness, chronic cough, and sputum production. Currently, the bronchodilators and anti-inflammatory drugs prescribed for COPD are mostly off-target, warranting new disease management strategies. Accumulating research has revealed the gut-lung axis to be a bidirectional communication system. Cigarette smoke, a major exacerbating factor in COPD and lung inflammation, affects gut microbiota composition and diversity, causing gut microbiota dysbiosis, a condition that has recently been described in COPD patients and animal models. For this review, we focused on the gut-lung axis, which is influenced by gut microbial metabolites, bacterial translocation, and immune cell modulation. Further, we have summarized the findings of preclinical and clinical studies on the association between gut microbiota and COPD to provide a basis for using gut microbiota in therapeutic strategies against COPD. Our review also proposes that further research on probiotics, prebiotics, short-chain fatty acids, and fecal microbiota transplantation could assist therapeutic approaches targeting the gut microbiota to alleviate COPD.
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Affiliation(s)
- Eun Yeong Lim
- Food Functionality Research Division, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Eun-Ji Song
- Food Functionality Research Division, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hee Soon Shin
- Food Functionality Research Division, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
- Department of Food Biotechnology, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
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12
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Lee SY, Lee DY, Kang HJ, Yun SH, Mariano EJ, Lee J, Kim JH, Hur SJ. Analysis of changes in antibiotic resistance in the human body using an in vitro digestion model incorporating human gut microbiota. Heliyon 2023; 9:e16128. [PMID: 37251864 PMCID: PMC10209409 DOI: 10.1016/j.heliyon.2023.e16128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/12/2023] [Accepted: 05/06/2023] [Indexed: 05/31/2023] Open
Abstract
Residual antibiotics may affect human health by increasing challenges related to infection treatment due to antibiotic resistance development. Hence, determining whether residual antibiotics in the body can lead to antibiotic resistance is important. We developed a model to predict possible antibiotic resistance caused by residual antibiotics by simulating human digestion in vitro. Increased antibiotic resistance was found to be dependent on the digestion process. Ethical prediction of antibiotic resistance using fewer animals and no humans was possible by simulating the internal environment. Thus, preliminary studies to monitor antibiotic resistance that can affect human health may be safely conducted using this model.
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Affiliation(s)
- Seung Yun Lee
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, 52725, South Korea
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52725, South Korea
| | - Da Young Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, South Korea
| | - Hea Jin Kang
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, South Korea
| | - Seung Hyeon Yun
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, South Korea
| | - Ermie Jr. Mariano
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, South Korea
| | - Juhyun Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, South Korea
| | - Jong Hyuk Kim
- Department of Animal Science, Chungbuk National University, Cheongju, 28644, South Korea
| | - Sun Jin Hur
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, South Korea
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13
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Takimoto Y, Chu PS, Nakamoto N, Hagihara Y, Mikami Y, Miyamoto K, Morikawa R, Teratani T, Taniki N, Fujimori S, Suzuki T, Koda Y, Ishihara R, Ichikawa M, Honda A, Kanai T. Myeloid TLR4 signaling promotes post-injury withdrawal resolution of murine liver fibrosis. iScience 2023; 26:106220. [PMID: 36876136 PMCID: PMC9982274 DOI: 10.1016/j.isci.2023.106220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/25/2022] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
The fate of resolution of liver fibrosis after withdrawal of liver injury is still incompletely elucidated. Toll-like receptor 4 (TLR4) in tissue fibroblasts is pro-fibrogenic. After withdrawal of liver injury, we unexpectedly observed a significant delay of fibrosis resolution as TLR4 signaling was pharmacologically inhibited in vivo in two murine models. Single-cell transcriptome analysis of hepatic CD11b+ cells, main producers of matrix metalloproteinases (MMPs), revealed a prominent cluster of restorative Tlr4-expressing Ly6c2-low myeloid cells. Delayed resolution after gut sterilization suggested its microbiome-dependent nature. Enrichment of a metabolic pathway linking to a significant increase of bile salt hydrolase-possessing family Erysipelotrichaceae during resolution. Farnesoid X receptor-stimulating secondary bile acids including 7-oxo-lithocholic acids upregulated MMP12 and TLR4 in myeloid cells in vitro. Fecal material transplant in germ-free mice confirmed phenotypical correlations in vivo. These findings highlight a pro-fibrolytic role of myeloid TLR4 signaling after injury withdrawal and may provide targets for anti-fibrotic therapy.
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Affiliation(s)
- Yoichi Takimoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Po-Sung Chu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Nobuhiro Nakamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yuya Hagihara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kentaro Miyamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.,Miyarisan Pharmaceutical Co., Ltd, Kita-ku, Tokyo 114-0016, Japan
| | - Rei Morikawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Toshiaki Teratani
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Nobuhito Taniki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Sota Fujimori
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.,Research Unit/Immunology and Inflammation, Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama, Kanagawa 227-0033, Japan
| | - Takahiro Suzuki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.,Miyarisan Pharmaceutical Co., Ltd, Kita-ku, Tokyo 114-0016, Japan
| | - Yuzo Koda
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.,Research Unit/Immunology and Inflammation, Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama, Kanagawa 227-0033, Japan
| | - Rino Ishihara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masataka Ichikawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Akira Honda
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Tokyo Medical University Ibaraki Medical Center, Inashiki-gun, Ibaraki 300-0395, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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14
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Matzaras R, Nikopoulou A, Protonotariou E, Christaki E. Gut Microbiota Modulation and Prevention of Dysbiosis as an Alternative Approach to Antimicrobial Resistance: A Narrative Review. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2022; 95:479-494. [PMID: 36568836 PMCID: PMC9765331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background: The importance of gut microbiota in human health is being increasingly studied. Imbalances in gut microbiota have been associated with infection, inflammation, and obesity. Antibiotic use is the most common and significant cause of major alterations in the composition and function of the gut microbiota and can result in colonization with multidrug-resistant bacteria. Methods: The purpose of this review is to present existing evidence on how microbiota modulation and prevention of gut dysbiosis can serve as tools to combat antimicrobial resistance. Results: While the spread of antibiotic-resistant pathogens requires antibiotics with novel mechanisms of action, the number of newly discovered antimicrobial classes remains very low. For this reason, the application of alternative modalities to combat antimicrobial resistance is necessary. Diet, probiotics/prebiotics, selective oropharyngeal or digestive decontamination, and especially fecal microbiota transplantation (FMT) are under investigation with FMT being the most studied. But, as prevention is better than cure, the implementation of antimicrobial stewardship programs and strict infection control measures along with newly developed chelating agents could also play a crucial role in decreasing colonization with multidrug resistant organisms. Conclusion: New alternative tools to fight antimicrobial resistance via gut microbiota modulation, seem to be effective and should remain the focus of further research and development.
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Affiliation(s)
- Rafail Matzaras
- Infectious Diseases Unit, Department of Medicine,
University General Hospital of Ioannina, University of Ioannina, Ioannina,
Greece
| | - Anna Nikopoulou
- Department of Internal Medicine, G. Papanikolaou
General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Efthimia Protonotariou
- Department of Microbiology, AHEPA University Hospital,
Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eirini Christaki
- Infectious Diseases Unit, Department of Medicine,
University General Hospital of Ioannina, University of Ioannina, Ioannina,
Greece,To whom all correspondence should be addressed:
Eirini Christaki, University General Hospital of Ioannina, St. Niarchou,
Ioannina, Greece; ; ORCID:
https://www.orcid.org/0000-0002-8152-6367
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15
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Yoon S, Lee G, Yu J, Lee K, Lee K, Si J, You HJ, Ko G. Distinct Changes in Microbiota-Mediated Intestinal Metabolites and Immune Responses Induced by Different Antibiotics. Antibiotics (Basel) 2022; 11:antibiotics11121762. [PMID: 36551419 PMCID: PMC9774394 DOI: 10.3390/antibiotics11121762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The cocktails of antibiotics are utilized to study the functions of microbiota. There have been studies on the alteration of not only the microbiota composition but also the host's metabolism or immunity. However, the bacterial species associated with these altered physiologic markers are still unclear. Therefore, we supplied mice with drinking water containing ampicillin (AMP), vancomycin (VAN), neomycin (NEO), or metronidazole (MET) to observe the effect of each antibiotic on helper T cells and inflammation-related gene expression and metabolism, including amino acid metabolism and changes in gut microbiota. We observed major changes in gut microbiota in mice treated with AMP and VAN, respectively, immediately after administration. The abundance of the genera Parabacteroides and Akkermansia increased in the AMP and VAN groups, while Prevotella almost disappeared from both groups. The compositional changes in intestinal metabolites in the AMP and VAN groups were more distinct than those in the NEO and MET groups, which was similar to the microbiome results. In particular, the most distinct changes were observed in amino acid related metabolism in AMP and VAN groups; the amounts of phenylalanine and tyrosine were increased in the AMP group while those were decreased in the VAN group. The changed amounts of intestinal amino acids in each of the AMP and VAN groups were correlated with increases in the abundance of the genera Parabacteroides and Akkermansia in the AMP and VAN groups, respectively. The most distinctive changes in intestinal gene expression were observed in the ileum, especially the expression Th17-related genes such as rorgt, il17a, and il17f, which decreased dramatically in the guts of most of the antibiotic-treated groups. These changes were also associated with a significant decrease in Prevotella in both the AMP and VAN groups. Taken together, these findings indicate that changes in gut microbiota as well as host physiology, including host metabolism and immunity, differ depending on the types of antibiotics, and the antibiotic-induced gut microbiota alteration has a correlation with host physiology such as host metabolic or immunological status. Thus, the immune and metabolic status of the host should be taken into account when administering antibiotics.
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Affiliation(s)
- Sunghyun Yoon
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
| | - Giljae Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
- Bio-MAX/N-Bio, Seoul National University, Seoul 08826, Republic of Korea
| | - Junsun Yu
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
| | - Kiuk Lee
- KoBioLabs, Inc., Seoul 13488, Republic of Korea
| | - Kyeongju Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
| | - Jiyeon Si
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Health and Environment, Seoul National University, Seoul 08826, Republic of Korea
- Natural Products Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea
- Center for Human and Environmental Microbiome, Institute of Health and Environment, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyun Ju You
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
- KoBioLabs, Inc., Seoul 13488, Republic of Korea
- Institute of Health and Environment, Seoul National University, Seoul 08826, Republic of Korea
- Center for Human and Environmental Microbiome, Institute of Health and Environment, Seoul National University, Seoul 08826, Republic of Korea
- Correspondence: (H.J.Y.); (G.K.)
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
- Bio-MAX/N-Bio, Seoul National University, Seoul 08826, Republic of Korea
- KoBioLabs, Inc., Seoul 13488, Republic of Korea
- Center for Human and Environmental Microbiome, Institute of Health and Environment, Seoul National University, Seoul 08826, Republic of Korea
- Correspondence: (H.J.Y.); (G.K.)
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16
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Zhou Y, Zhang Z, Awasthi MK. Exploring the impact of biochar supplement on the dynamics of antibiotic resistant fungi during pig manure composting. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120235. [PMID: 36165829 DOI: 10.1016/j.envpol.2022.120235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/16/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
The purpose of this study was to investigate antibiotic resistant fungal (ARF) communities in pig manure (PM) composting employing two different biochar (coconut shell-CSB and bamboo biochar-BB) as amendment. Three treatments (Control, 10% CSB and 10% BB) were designed and indicated with T1 to T3. Experimental results declared that the fungal abundance significantly reduced among the both biochar applied treatments but three dominant phyla Ascomycota, Basidiomycota and Mucoromycota were still relatively greater abundance present. There were significant differences (p < 0.05) in the relative abundance and diversity of fungi among all three treatments. Interestingly, biochar addition regulated the overall fungal community in final compost. Compared with the control group, the abundance of fungi was positively mobilized, and especially CSB showed a better effect. Conclusively, biochar has potential to inhibit and reduce the ARGs population and mobility in compost. Thus, these findings offer new insight to understand the succession of ARFs during PM composting.
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Affiliation(s)
- Yuwen Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
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17
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Kowallik V, Das A, Mikheyev AS. Experimental inheritance of antibiotic acquired dysbiosis affects host phenotypes across generations. Front Microbiol 2022; 13:1030771. [PMID: 36532456 PMCID: PMC9751584 DOI: 10.3389/fmicb.2022.1030771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/24/2022] [Indexed: 04/12/2024] Open
Abstract
Microbiomes can enhance the health, fitness and even evolutionary potential of their hosts. Many organisms propagate favorable microbiomes fully or partially via vertical transmission. In the long term, such co-propagation can lead to the evolution of specialized microbiomes and functional interdependencies with the host. However, microbiomes are vulnerable to environmental stressors, particularly anthropogenic disturbance such as antibiotics, resulting in dysbiosis. In cases where microbiome transmission occurs, a disrupted microbiome may then become a contagious pathology causing harm to the host across generations. We tested this hypothesis using the specialized socially transmitted gut microbiome of honey bees as a model system. By experimentally passaging tetracycline-treated microbiomes across worker 'generations' we found that an environmentally acquired dysbiotic phenotype is heritable. As expected, the antibiotic treatment disrupted the microbiome, eliminating several common and functionally important taxa and strains. When transmitted, the dysbiotic microbiome harmed the host in subsequent generations. Particularly, naïve bees receiving antibiotic-altered microbiomes died at higher rates when challenged with further antibiotic stress. Bees with inherited dysbiotic microbiomes showed alterations in gene expression linked to metabolism and immunity, among other pathways, suggesting effects on host physiology. These results indicate that there is a possibility that sublethal exposure to chemical stressors, such as antibiotics, may cause long-lasting changes to functional host-microbiome relationships, possibly weakening the host's progeny in the face of future ecological challenges. Future studies under natural conditions would be important to examine the extent to which negative microbiome-mediated phenotypes could indeed be heritable and what role this may play in the ongoing loss of biodiversity.
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Affiliation(s)
- Vienna Kowallik
- Okinawa Institute of Science and Technology, Tancha Onna-son, Okinawa, Japan
| | - Ashutosh Das
- Australian National University, Canberra, ACT, Australia
- Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram, Bangladesh
| | - Alexander S. Mikheyev
- Okinawa Institute of Science and Technology, Tancha Onna-son, Okinawa, Japan
- Australian National University, Canberra, ACT, Australia
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18
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Anand U, Vaishnav A, Sharma SK, Sahu J, Ahmad S, Sunita K, Suresh S, Dey A, Bontempi E, Singh AK, Proćków J, Shukla AK. Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156641. [PMID: 35700781 DOI: 10.1016/j.scitotenv.2022.156641] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Anukool Vaishnav
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh 281406, India; Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland; Plant-Soil Interaction Group, Agroscope (Reckenholz), Reckenholzstrasse 191, 8046 Zürich, Switzerland
| | - Sushil K Sharma
- National Agriculturally Important Microbial Culture Collection (NAIMCC), ICAR-National Bureau of Agriculturally Important Microorganisms (ICAR-NBAIM), Mau 275 103, Uttar Pradesh, India.
| | - Jagajjit Sahu
- GyanArras Academy, Gothapatna, Malipada, Bhubaneswar, Odisha 751029, India
| | - Sarfaraz Ahmad
- Department of Botany, Jai Prakash University, Saran, Chhapra 841301, Bihar, India
| | - Kumari Sunita
- Department of Botany, Faculty of Science, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh 273009, India
| | - S Suresh
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal 462 003, Madhya Pradesh, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, West Bengal, India
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy
| | - Amit Kishore Singh
- Department of Botany, Bhagalpur National College, (A Constituent unit of Tilka Manjhi Bhagalpur University), Bhagalpur 812007, Bihar, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631 Wrocław, Poland.
| | - Awadhesh Kumar Shukla
- Department of Botany, K.S. Saket P.G. College, Ayodhya (affiliated to Dr. Rammanohar Lohia Avadh University, Ayodhya) 224123, Uttar Pradesh, India.
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19
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Nausch B, Bittner CB, Höller M, Abramov-Sommariva D, Hiergeist A, Gessner A. Contribution of Symptomatic, Herbal Treatment Options to Antibiotic Stewardship and Microbiotic Health. Antibiotics (Basel) 2022; 11:1331. [PMID: 36289988 PMCID: PMC9598931 DOI: 10.3390/antibiotics11101331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/16/2022] [Accepted: 09/24/2022] [Indexed: 12/03/2022] Open
Abstract
Epithelial surfaces in humans are home to symbiotic microbes (i.e., microbiota) that influence the defensive function against pathogens, depending on the health of the microbiota. Healthy microbiota contribute to the well-being of their host, in general (e.g., via the gut-brain axis), and their respective anatomical site, in particular (e.g., oral, urogenital, skin, or respiratory microbiota). Despite efforts towards a more responsible use of antibiotics, they are often prescribed for uncomplicated, self-limiting infections and can have a substantial negative impact on the gut microbiota. Treatment alternatives, such as non-steroidal anti-inflammatory drugs, may also influence the microbiota; thus, they can have lasting adverse effects. Herbal drugs offer a generally safe treatment option for uncomplicated infections of the urinary or respiratory tract. Additionally, their microbiota preserving properties allow for a more appropriate therapy of uncomplicated infections, without contributing to an increase in antibiotic resistance or disturbing the gut microbiota. Here, herbal treatments may be a more appropriate therapy, with a generally favorable safety profile.
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Affiliation(s)
- Bernhard Nausch
- Bionorica SE, Research and Development, Kerschensteinerstraße 11-15, 92318 Neumarkt in der Oberpfalz, Germany
| | - Claudia B. Bittner
- Bionorica SE, Research and Development, Kerschensteinerstraße 11-15, 92318 Neumarkt in der Oberpfalz, Germany
| | - Martina Höller
- Bionorica SE, Research and Development, Kerschensteinerstraße 11-15, 92318 Neumarkt in der Oberpfalz, Germany
| | - Dimitri Abramov-Sommariva
- Bionorica SE, Research and Development, Kerschensteinerstraße 11-15, 92318 Neumarkt in der Oberpfalz, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
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20
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Shi F, Huang Y, Yang M, Lu Z, Li Y, Zhan F, Lin L, Qin Z. Antibiotic-induced alternations in gut microflora are associated with the suppression of immune-related pathways in grass carp (Ctenopharyngodon idellus). Front Immunol 2022; 13:970125. [PMID: 36032163 PMCID: PMC9403240 DOI: 10.3389/fimmu.2022.970125] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/20/2022] [Indexed: 11/19/2022] Open
Abstract
Gut microbiota play a vital role in fish health homeostasis. Antibiotics are known to alter microbial community composition and diversity; however, the substantial effects of antibiotics upon the gut microbiome with respect to immune-related pathways in healthy fish remain unclear. Accordingly, here we explored the impact of two antibiotics on the intestinal health, immune response, microbiome dynamics, and transcriptome profiles of grass carp. A two-week feeding trial was carried out in which the basal diet was complemented with enrofloxacin (10 mg/kg) or florfenicol (10 mg/kg). The results showed that: (1) Enrofloxacin and florfenicol both induced intestinal oxidative stress and reduced the digestive enzyme activity of grass carp. (2) High-throughput sequencing of 16S rDNA revealed that enrofloxacin but not the florfenicol treatment influenced gut microbiota diversity in grass carp by shifting α/β-diversity with more abundant pathogens detected. (3) Transcriptome profiling demonstrated that florfenicol down-regulated the immune-related pathways of grass carp, and the network analysis revealed that IgA was negatively correlated with certain pathogens, such as Shewanella and Aeromonas. (4) Antibiotic-induced alternations of gut core microbes were revealed via immune-related transcripts, as were lower mRNA expression levels of mucosal-related genes. (5) Apoptosis and histopathological changes were detected in the enrofloxacin- and florfenicol-treated groups compared with the control group. Overall, administering antibiotics will promote oxidative stress, cause intestinal flora dysbiosis, inhibit the mucosal immune system, and induce apoptosis in grass carp.
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Affiliation(s)
| | | | | | | | | | | | - Li Lin
- *Correspondence: Li Lin, ; Zhendong Qin,
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21
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Ibrahim NA, Elmorshedy KE, Radwan DA, Buabeid MA. The impact of oral ciprofloxacin on the structure and functions of rat gastric mucosa. Saudi J Biol Sci 2022; 29:2187-2198. [PMID: 35531231 PMCID: PMC9073028 DOI: 10.1016/j.sjbs.2021.11.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/07/2021] [Accepted: 11/17/2021] [Indexed: 11/27/2022] Open
Abstract
Ciprofloxacin (CPX), is a fluoroquinolone antibiotic used to treat a number of gram-negative and gram-positive bacterial infections. Ciprofloxacin can cause severe side effects, ranging from tendon problems, nerve damage, to serious mood or behavior changes. The purpose of this study was to investigate how ciprofloxacin affects gastric cell lines in rats with a distinctive emphasis on physiological, histopathological, and bacteriological changes. Male albino rats (n = 21) were distributed into three groups; control, CPX, and CPX-withdrawal groups. The treated rats were given CPX tablets (12.5 mg/kg) dissolved in carboxymethyl cellulose (CMC) 0.5% orally once daily via gavage for sixty consecutive days. Control rats received only the vehicle. The withdrawal group was treated for 60 days and the drug was withdrawn for another sixty days. After completion of the experiment, all rats were sacrificed and gastric tissues were treated for light, immunohistochemical, and scanning electron microscopic examination. Image J software was used to measure immune-labeled gastric epithelial cells. Blood samples were also collected for H. Pylori immunoglobulins IgM, IgA, and IgG. Results showed that treated rats acquired significantly strongly positive tumor necrosis factor (TNFα) and significant reduction of serum level of H. pylori IgM, IgA, and IgG in all the study groups. It could be concluded that prolonged oral CPX administration to albino rats changes the gastric mucosal architecture and bacteriology.
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Affiliation(s)
- Nihal A Ibrahim
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, United Arab Emirates.,Centre of Medical and Bio-allied Health Sciences Research (CMBAHSR), Ajman University, Ajman, United Arab Emirates
| | - Kadreya E Elmorshedy
- Anatomy Department, Tanta College of Medicine, Egypt.,Almaakal University, Basra, Iraq
| | - Doaa A Radwan
- Anatomy Department, Tanta College of Medicine, Egypt
| | - Manal A Buabeid
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, United Arab Emirates.,Centre of Medical and Bio-allied Health Sciences Research (CMBAHSR), Ajman University, Ajman, United Arab Emirates
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22
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Evolution of the murine gut resistome following broad-spectrum antibiotic treatment. Nat Commun 2022; 13:2296. [PMID: 35484157 PMCID: PMC9051133 DOI: 10.1038/s41467-022-29919-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/06/2022] [Indexed: 12/29/2022] Open
Abstract
The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and timescales shaping this resistome remain elusive. Using an antibiotic cocktail administered to a murine model along with a longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire antimicrobial resistance genes (ARGs) after a single antibiotic course. While most of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Enterobacteriaceae, Enterococcaceae, and Lactobacillaceae families acquire resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotics in the corresponding metagenome-assembled genomes (MAGs) and trace their origins within each genome. Here we show that, while mobile genetic elements (MGEs), including bacteriophages and plasmids, contribute to the spread of ARGs, integrons represent key factors mediating AMR in the antibiotic-treated mice. Our findings suggest that a single course of antibiotics alone may act as the selective sweep driving ARG acquisition and incidence in gut commensals over a single mammalian lifespan. Antimicrobial resistance represents an ongoing silent pandemic. Here, de Nies et al. show that a single antibiotic treatment leads to resistance in bacteria such as Akkermansia muciniphila and that integrons play a key role in mediating this resistance.
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23
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Awasthi MK, Liu H, Liu T, Awasthi SK, Zhang Z. Effect of biochar addition on the dynamics of antibiotic resistant bacteria during the pig manure composting. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152688. [PMID: 34974024 DOI: 10.1016/j.scitotenv.2021.152688] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
In present study, the taxonomic variation of antibiotic resistant bacteria (ARB) in pig manure (PM) composting with coconut shell biochar (CSB) and bamboo biochar (BB) addition was investigated. The experiment was divided into three treatments: T1 (as control or without biochar amendment), T2 was added 10% coconut shell biochar and T3 supplemented with 10% bamboo biochar. The initial feed stock were properly homogenized using a mechanical crusher. PM and wheat straw (WS) were mixed in a 5: 1 dry weight ratio to adjust the initial carbon/nitrogen ratio 25:1, bulk density to ~0.5 (kg/L) and ~60% moisture content, respectively. This experiment was lasted for 42 days. The results indicated the bacterial communities in the three treatments were more different in terms of relative abundance and diversity of dominant bacteria. The control group had the highest abundance of Kingdome bacteria. The changes in ARB was noticed by variation in the relative abundances of Actinobacteria, Proteobacteria, Firmicutes and Bacteroidota. At the end of composting (on day 42), the total RAs of ARB at the class, order, and family levels were considerably reduced in T2 and T3 by ~35.78-38.75%, 36.42-40.63% and 45.82-47.70%, respectively. But in T1 was decreased by 6.16-8.62%, 7.93-8.72% and 8.70-10.15%, as compared with the day 0 sample. However, the CSB was much more effective to reduce 55 to 60% of ARB than T3 or BB applied treatment has 40 to 42% ARB reduction, while control has certainly very less RAa of ARB reduction. Finally, the biochar amendment was significant approach to mitigate the total ARB abundance in compost and it's further used for organic farming purposes.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China.
| | - Hong Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Sanjeev Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
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24
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Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing. Microbiol Spectr 2022; 10:e0190121. [PMID: 35196800 PMCID: PMC8865484 DOI: 10.1128/spectrum.01901-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The microbiota plays an important role in human health and disease development. The lung microbiota profile in pulmonary tuberculosis (TB) patients and the effects of anti-TB treatment on the profile need to be determined thoroughly and comprehensively. This study primarily aimed to determine the lung microbiota profile associated with pulmonary TB and characterize the longitudinal changes during anti-TB treatment. A total of 53 participants, comprising 8 healthy individuals, 12 untreated pulmonary TB patients, 15 treated pulmonary TB patients, 11 cured pulmonary TB patients, and 7 lung cancer patients, were recruited in the present study. Bronchioalveolar lavage fluid (BALF) samples were collected from the above participants, and throat swabs were taken from healthy individuals. Microbiomes in the samples were examined using metagenomic next-generation sequencing (mNGS). Differences in microbiota profiles were determined through a comparison of the indicated groups. Our findings indicated that the BALF samples displayed decreased richness and diversity of the microbiota compared to those of the throat swab samples, and these two kinds of samples exhibited obvious separation on principal-coordinate analysis (PCoA) plots. Untreated pulmonary TB patients displayed a unique lung microbiota signature distinct from that of healthy individuals and lung cancer patients. Our data first demonstrated that anti-TB treatment with first-line drugs increases alpha diversity and significantly affects the beta diversity of the lung microbiota, while it also induces antibiotic resistance genes (ARGs). IMPORTANCE Characterization of the lung microbiota could lead to a better understanding of the pathogenesis of pulmonary TB. Here, we applied the metagenomic shotgun sequencing instead of 16S rRNA sequencing method to characterize the lung microbiota using the BALF samples instead of sputum. We found that alterations in the lung microbiota are associated with TB infection and that anti-TB treatment significantly affects the alpha and beta diversity of the lung microbiota in pulmonary TB patients. These findings could help us better understand TB pathogenesis.
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25
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Isles NS, Mu A, Kwong JC, Howden BP, Stinear TP. Gut microbiome signatures and host colonization with multidrug-resistant bacteria. Trends Microbiol 2022; 30:853-865. [DOI: 10.1016/j.tim.2022.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/17/2022]
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26
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The significance of maternal asymptomatic bacteriuria during pregnancy on long-term offspring infectious hospitalizations. J Dev Orig Health Dis 2021; 13:508-513. [PMID: 34709145 DOI: 10.1017/s2040174421000593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Asymptomatic bacteriuria (ASB) is a well-acknowledged infectious entity during pregnancy; yet its long-term implications are not well investigated. The present study aimed to test the association between maternal ASB during pregnancy and long-term offspring infectious hospitalizations. A population-based cohort analysis was conducted, comparing the incidence of long-term infectious-related hospitalizations of offspring born to mothers who were diagnosed with ASB during pregnancy, and those who did not have ASB. The study was conducted at a tertiary medical center and included all singleton deliveries between the years 1991 and 2014. Infectious morbidities were based on a predefined set of International Classification of Disease-9 codes. A Kaplan-Meier survival curve compared cumulative infectious hospitalization incidence between the groups, and a Cox regression model was used to adjust for confounding variables. During the study period, 212,984 deliveries met inclusion criteria. Of them, 5378 (2.5%) were diagnosed with ASB. As compared to offspring of non-ASB mothers, total long-term infectious hospitalizations were significantly higher among children to mothers who were diagnosed with ASB (13.1% vs. 11.1%, OR = 1.2, 95% CI 1.11-1.30, P ≤ 0.001). Likewise, a Kaplan-Meier curve demonstrated higher cumulative incidence of infectious hospitalizations among children born to mothers with ASB (log rank, P = 0.006). In the Cox regression model, while controlling for maternal age, diabetes mellitus, ethnicity, hypertensive disorders, and gestational age, maternal ASB was noted as an independent risk factor for long-term infectious morbidity in the offspring (adjusted HR = 1.1, 95% CI 1.01-1.17, P = 0.042). ASB during pregnancy increases offspring susceptibility to long-term infectious hospitalizations.
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27
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Maity C, Gupta AK. Therapeutic efficacy of probiotic Alkalihalobacillus clausii 088AE in antibiotic-associated diarrhea: A randomized controlled trial. Heliyon 2021; 7:e07993. [PMID: 34585011 PMCID: PMC8453216 DOI: 10.1016/j.heliyon.2021.e07993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 09/10/2021] [Indexed: 01/22/2023] Open
Abstract
The use of probiotics in gastrointestinal ailments has shown therapeutic effects. The imbalance of the microbiota caused by antibiotic treatment or others has been shown to be restored to normal with probiotic treatment. In this study, a genomically and phenotypically safe probiotic Alkalihalobacillus clausii 088AE has been evaluated for ameliorating antibiotic-associated diarrhea (AAD) in pediatrics (PE, n = 60, 2-10 years), adolescent and adults (AA, n = 60, 11-65 years) through a randomized controlled clinical trial. A. clausii 088AE was administered for seven days (PE, 4 and AA, 6 billion/day) and primary and secondary endpoints were evaluated on different visits. Compared to the respective placebo arms, A. clausii 088AE improved the diarrheal (time to last unformed stool and diarrheal frequency) conditions in children, adolescents and adults. A. clausii 088AE treatment decreased AAD-severity score on visit 5 in both pediatric (0.12 ± 0.33, 12.39 folds), adult and adolescent (0.54 ± 0.36, 2.34 folds) groups compared to those respective placebo arm (p < 0.05). A. clausii 088AE was well tolerated, did not cause significant changes in vital and clinical safety parameters and subjects reported no adverse effects or serious adverse reactions. A. clausii 088AE is safe and therapeutically effective against AAD, reducing onset of diarrhea and related severity symptoms including abdominal discomfort and pain, bloating and flatulence. A. clausii 088AE may be recommended as a live bio-therapeutic agent for improving clinical pathophysiology of gastrointestinal ailments, in particular antibiotic-associated diarrhea and related symptoms.
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Affiliation(s)
- Chiranjit Maity
- Probiotics Laboratory, Advanced Enzyme Technologies Ltd., 5Th Floor, A-Wing, Sun Magnetica, LIC Service Road, Louiswadi, Thane (W), 400 604, Maharashtra, India
| | - Anil Kumar Gupta
- Probiotics Laboratory, Advanced Enzyme Technologies Ltd., 5Th Floor, A-Wing, Sun Magnetica, LIC Service Road, Louiswadi, Thane (W), 400 604, Maharashtra, India
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28
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Unveiling the Gut Microbiota and Resistome of Wild Cotton Mice, Peromyscus gossypinus, from Heavy Metal- and Radionuclide-Contaminated Sites in the Southeastern United States. Microbiol Spectr 2021; 9:e0009721. [PMID: 34431703 PMCID: PMC8552609 DOI: 10.1128/spectrum.00097-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The prevalence of antibiotic resistance genes (ARGs) can be driven by direct selection from antibiotic use and indirect selection from substances such as heavy metals (HMs). While significant progress has been made to characterize the influence of HMs on the enrichment and dissemination of ARGs in the environment, there is still much we do not know. To fill this knowledge gap, we present a comprehensive analysis of gut bacteria associated with wild cotton mice (Peromyscus gossypinus) trapped from several areas affected by legacies of HM and radionuclide contamination. We explore how these contaminants affect gut microbial community (GMC) composition and diversity and the enrichment of antibiotic, biocide, and metal resistance genes. Although we were able to identify that a myriad of co-occurring antimicrobial and HM resistance genes appear in mice from all areas, including those without a history of contamination, the proportions of co-occurring ARGs and metal resistance genes (MRGs) are higher in sites with radionuclide contamination. These results support those from several previous studies and enhance our understanding of the coselection process, while providing new insights into the ubiquity of antimicrobial resistance in the resistome of wild animals. IMPORTANCE Antimicrobial resistance is a serious global public health concern because of its prevalence and ubiquitous distribution. The rapid dissemination of antibiotic resistance genes is thought to be the result of the massive overuse of antibiotics in agriculture and therapeutics. However, previous studies have demonstrated that the spread of antibiotic resistance genes can also be influenced by heavy metal contamination. This coselection phenomenon, whereby different resistance determinants are genetically linked on the same genetic element (coresistance) or a single genetic element provides resistance to multiple antimicrobial agents (cross-resistance), has profound clinical and environmental implications. In contrast to antibiotics, heavy metals can persist in the environment as a selection pressure for long periods of time. Thus, it is important to understand how antibiotic resistance genes are distributed in the environment and to what extent heavy metal contaminants may be driving their selection, which we have done in one environmental setting.
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29
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Yamaguchi A, Teratani T, Chu PS, Suzuki T, Taniki N, Mikami Y, Shiba S, Morikawa R, Amiya T, Aoki R, Kanai T, Nakamoto N. Hepatic Adenosine Triphosphate Reduction Through the Short-Chain Fatty Acids-Peroxisome Proliferator-Activated Receptor γ-Uncoupling Protein 2 Axis Alleviates Immune-Mediated Acute Hepatitis in Inulin-Supplemented Mice. Hepatol Commun 2021; 5:1555-1570. [PMID: 34510840 PMCID: PMC8435281 DOI: 10.1002/hep4.1742] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/08/2021] [Accepted: 04/24/2021] [Indexed: 02/04/2023] Open
Abstract
How liver tolerance is disrupted in immune-mediated liver injury is currently unclear. There is also insufficient information available regarding susceptibility, precipitation, escalation, and perpetuation of autoimmune hepatitis. To explore how dietary fiber influences hepatic damage, we applied the concanavalin A (ConA)-induced acute immune-mediated liver injury model in mice fed a diet supplemented with 6.8% inulin, a water-soluble fermentable fiber. Twelve hours after ConA administration, inulin-supplemented diet-fed mice demonstrated significantly alleviated hepatic damage histologically and serologically, with down-regulation of hepatic interferon-γ and tumor necrosis factor and reduced myeloperoxidase (MPO)-producing neutrophil infiltration. Preconditioning with an inulin-supplemented diet for 2 weeks significantly reduced hepatic adenosine triphosphate (ATP) content; suramin, a purinergic P2 receptor antagonist, abolished the protective effect. Of note, the portal plasma derived from mice fed the inulin-supplemented diet significantly alleviated ConA-induced immune-mediated liver injury. Mechanistically, increased portal short-chain fatty acid (SCFA) levels, such as those of acetate and butyrate, by inulin supplementation leads to up-regulation of hepatic γ-type peroxisome proliferator-activated receptor (Pparg) and uncoupling protein 2 (Ucp2), which uncouples mitochondrial ATP synthesis downstream of PPARγ. Pparg down-regulating small interfering RNA cancelled the protective effect of inulin supplementation against MPO-producing neutrophil infiltration and the subsequent immune-mediated liver injury, suggesting that the SCFA-PPARγ-UCP2 axis plays a key role in the protective effect by inulin supplementation. Moreover, significant changes in the gut microbiota, including increased operational taxonomic units in genera Akkermansia and Allobaculum, also characterized the protective effect of the inulin-supplemented diet. Conclusion: There is a possible unraveled etiopathophysiological link between the maintenance of liver tolerance and dietary fiber. The SCFA-PPARγ-UCP2 axis may provide therapeutic targets for immune-mediated liver injury in the future.
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Affiliation(s)
- Akihiro Yamaguchi
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineKeio University School of MedicineTokyoJapan.,Department of Gastroenterology and HepatologyNational Hospital Organization Saitama HospitalSaitamaJapan
| | - Toshiaki Teratani
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineKeio University School of MedicineTokyoJapan
| | - Po-Sung Chu
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineKeio University School of MedicineTokyoJapan
| | - Takahiro Suzuki
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineKeio University School of MedicineTokyoJapan.,Miyarisan Pharmaceutical Co., Ltd.TokyoJapan
| | - Nobuhito Taniki
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineKeio University School of MedicineTokyoJapan
| | - Yohei Mikami
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineKeio University School of MedicineTokyoJapan
| | - Shunsuke Shiba
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineKeio University School of MedicineTokyoJapan
| | - Rei Morikawa
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineKeio University School of MedicineTokyoJapan
| | - Takeru Amiya
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineKeio University School of MedicineTokyoJapan.,Research Unit/Immunology and InflammationSohyaku Innovative Research DivisionMitsubishi Tanabe Pharma CoKanagawaJapan
| | - Ryo Aoki
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineKeio University School of MedicineTokyoJapan.,Institute of Health ScienceEzaki Glico Co., Ltd.OsakaJapan
| | - Takanori Kanai
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineKeio University School of MedicineTokyoJapan
| | - Nobuhiro Nakamoto
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineKeio University School of MedicineTokyoJapan
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30
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Abstract
ABSTRACT Burn injuries are a common form of traumatic injury that leads to significant morbidity and mortality worldwide. Burn injuries are characterized by inflammatory processes and alterations in numerous organ systems and functions. Recently, it has become apparent that the gastrointestinal bacterial microbiome is a key component of regulating the immune response and recovery from burn and can also contribute to significant detrimental sequelae after injury, such as sepsis and multiple organ failure. Microbial dysbiosis has been linked to multiple disease states; however, its role in exacerbating acute traumatic injuries, such as burn, is poorly understood. In this article, we review studies that document changes in the intestinal microbiome after burn injury, assess the implications in post-burn pathogenesis, and the potential for further discovery and research.
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Affiliation(s)
- Marisa E. Luck
- Burn & Shock Trauma Research Institute, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
- Alcohol Research Program, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
- Integrative Cell Biology Program, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
| | - Caroline J. Herrnreiter
- Burn & Shock Trauma Research Institute, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
- Alcohol Research Program, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
- Biochemistry and Molecular Biology Program, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
| | - Mashkoor A. Choudhry
- Burn & Shock Trauma Research Institute, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
- Alcohol Research Program, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
- Department of Surgery, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
- Integrative Cell Biology Program, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
- Biochemistry and Molecular Biology Program, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
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31
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Vallianou N, Dalamaga M, Stratigou T, Karampela I, Tsigalou C. Do Antibiotics Cause Obesity Through Long-term Alterations in the Gut Microbiome? A Review of Current Evidence. Curr Obes Rep 2021; 10:244-262. [PMID: 33945146 PMCID: PMC8093917 DOI: 10.1007/s13679-021-00438-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/21/2021] [Indexed: 02/08/2023]
Abstract
PURPOSE OF REVIEW In this review, we summarize current evidence on the association between antibiotics and the subsequent development of obesity through modulation of the gut microbiome. Particular emphasis is given on (i) animal and human studies and their limitations; (ii) the reservoir of antibiotics in animal feed, emerging antibiotic resistance, gut dysbiosis, and obesity; (iii) the role of infections, specifically viral infections, as a cause of obesity; and (iv) the potential therapeutic approaches other than antibiotics to modulate gut microbiome. RECENT FINDINGS Overall, the majority of animal studies and meta-analyses of human studies on the association between antibiotics and subsequent development of obesity are suggestive of a link between exposure to antibiotics, particularly early exposure in life, and the development of subsequent obesity as a result of alterations in the diversity of gut microbiota. The evidence is strong in animal models whereas evidence in humans is inconclusive requiring well-designed, long-term longitudinal studies to examine this association. Based on recent meta-analyses and epidemiologic studies in healthy children, factors, such as the administration of antibiotics during the first 6 months of life, repeated exposure to antibiotics for ≥ 3 courses, treatment with broad-spectrum antibiotics, and male gender have been associated with increased odds of overweight/obesity. Early antibiotic exposure in animal models has shown that reductions in the population size of specific microbiota, such as Lactobacillus, Allobaculum, Rikenellaceae, and Candidatus Arthromitus, are related to subsequent adiposity. These data suggest that the loss of diversity of the gut microbiome, especially early in life, may have potential long-term detrimental effects on the adult host gut microbiome and metabolic health. Genetic, environmental, and age-related factors influence the gut microbiome throughout the lifetime. More large-scale, longer-term, longitudinal studies are needed to determine whether changes that occur in the microbiome after exposure to antibiotics, particularly early exposure, are causal of subsequent weight gain or consequent of weight gain in humans. Further well-designed, large-scale RCTs in humans are required to evaluate the effects of administration of antibiotics, particularly early administration, and the subsequent development of overweight/obesity. Therapeutic interventions, such as bacteriophage treatment or the use of probiotics, especially genetically engineered ones, need to be evaluated in terms of prevention and management of obesity.
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Affiliation(s)
- Natalia Vallianou
- grid.414655.70000 0004 4670 4329Department of Internal Medicine and Endocrinology, ‘Evangelismos’ General Hospital of Athens, 45-47 Ypsilantou Street, 10676 Athens, Greece
| | - Maria Dalamaga
- grid.5216.00000 0001 2155 0800Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Mikras Asias 75, Goudi, 11527 Athens, Greece
| | - Theodora Stratigou
- grid.414655.70000 0004 4670 4329Department of Internal Medicine and Endocrinology, ‘Evangelismos’ General Hospital of Athens, 45-47 Ypsilantou Street, 10676 Athens, Greece
| | - Irene Karampela
- grid.5216.00000 0001 2155 0800Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Mikras Asias 75, Goudi, 11527 Athens, Greece
- grid.5216.00000 0001 2155 0800Second Department of Critical Care, Attikon General University Hospital, Medical School, National and Kapodistrian University of Athens, 1 Rimini St, Haidari, 12462 Athens, Greece
| | - Christina Tsigalou
- grid.12284.3d0000 0001 2170 8022Laboratory of Microbiology, Medical School, Democritus University of Thrace, 6th Km Alexandroupolis-Makri, Alexandroupolis, Greece
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Miethke M, Pieroni M, Weber T, Brönstrup M, Hammann P, Halby L, Arimondo PB, Glaser P, Aigle B, Bode HB, Moreira R, Li Y, Luzhetskyy A, Medema MH, Pernodet JL, Stadler M, Tormo JR, Genilloud O, Truman AW, Weissman KJ, Takano E, Sabatini S, Stegmann E, Brötz-Oesterhelt H, Wohlleben W, Seemann M, Empting M, Hirsch AKH, Loretz B, Lehr CM, Titz A, Herrmann J, Jaeger T, Alt S, Hesterkamp T, Winterhalter M, Schiefer A, Pfarr K, Hoerauf A, Graz H, Graz M, Lindvall M, Ramurthy S, Karlén A, van Dongen M, Petkovic H, Keller A, Peyrane F, Donadio S, Fraisse L, Piddock LJV, Gilbert IH, Moser HE, Müller R. Towards the sustainable discovery and development of new antibiotics. Nat Rev Chem 2021; 5:726-749. [PMID: 37118182 PMCID: PMC8374425 DOI: 10.1038/s41570-021-00313-1] [Citation(s) in RCA: 384] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 02/08/2023]
Abstract
An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations. ![]()
Antimicrobial resistance is an increasing threat to public health and encouraging the development of new antimicrobials is one of the most important ways to address the problem. This Roadmap article aims to bring together industrial, academic and political partners, and proposes both short-term and long-term solutions to this challenge.
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Affiliation(s)
- Marcus Miethke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Marco Pieroni
- Food and Drug Department, University of Parma, Parma, Italy
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mark Brönstrup
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Chemical Biology (CBIO), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Peter Hammann
- Infectious Diseases & Natural Product Research at EVOTEC, and Justus Liebig University Giessen, Giessen, Germany
| | - Ludovic Halby
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance Unit, Microbiology Department, Institut Pasteur, CNRS UMR3525, Paris, France
| | | | - Helge B Bode
- Department of Biosciences, Goethe University Frankfurt, Frankfurt, Germany.,Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Rui Moreira
- Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Yanyan Li
- Unit MCAM, CNRS, National Museum of Natural History (MNHN), Paris, France
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC) & Microbiology Department, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Marc Stadler
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | | | | | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Kira J Weissman
- Molecular and Structural Enzymology Group, Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Evi Stegmann
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Myriam Seemann
- Institute for Chemistry UMR 7177, University of Strasbourg/CNRS, ITI InnoVec, Strasbourg, France
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Brigitta Loretz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Alexander Titz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Timo Jaeger
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Silke Alt
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | | | | | - Andrea Schiefer
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Kenneth Pfarr
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Achim Hoerauf
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Heather Graz
- Biophys Ltd., Usk, Monmouthshire, United Kingdom
| | - Michael Graz
- School of Law, University of Bristol, Bristol, United Kingdom
| | | | | | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | | | - Hrvoje Petkovic
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | | | | | - Laurent Fraisse
- Drugs for Neglected Diseases initiative (DNDi), Geneva, Switzerland
| | - Laura J V Piddock
- The Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Ian H Gilbert
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Heinz E Moser
- Novartis Institutes for BioMedical Research (NIBR), Emeryville, CA USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
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Tan LY, Yeo XY, Bae HG, Lee DPS, Ho RC, Kim JE, Jo DG, Jung S. Association of Gut Microbiome Dysbiosis with Neurodegeneration: Can Gut Microbe-Modifying Diet Prevent or Alleviate the Symptoms of Neurodegenerative Diseases? Life (Basel) 2021; 11:698. [PMID: 34357070 PMCID: PMC8305650 DOI: 10.3390/life11070698] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022] Open
Abstract
The central nervous system was classically perceived as anatomically and functionally independent from the other visceral organs. But in recent decades, compelling evidence has led the scientific community to place a greater emphasis on the role of gut microbes on the brain. Pathological observations and early gastrointestinal symptoms highlighted that gut dysbiosis likely precedes the onset of cognitive deficits in Alzheimer's disease (AD) and Parkinson's disease (PD) patients. The delicate balance in the number and functions of pathogenic microbes and alternative probiotic populations is critical in the modulation of systemic inflammation and neuronal health. However, there is limited success in restoring healthy microbial biodiversity in AD and PD patients with general probiotics interventions and fecal microbial therapies. Fortunately, the gut microflora is susceptible to long-term extrinsic influences such as lifestyle and dietary choices, providing opportunities for treatment through comparatively individual-specific control of human behavior. In this review, we examine the impact of restrictive diets on the gut microbiome populations associated with AD and PD. The overall evidence presented supports that gut dysbiosis is a plausible prelude to disease onset, and early dietary interventions are likely beneficial for the prevention and treatment of progressive neurodegenerative diseases.
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Affiliation(s)
- Li Yang Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore; (L.Y.T.); (X.Y.Y.)
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Xin Yi Yeo
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore; (L.Y.T.); (X.Y.Y.)
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Han-Gyu Bae
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea;
| | - Delia Pei Shan Lee
- Department of Food Science and Technology, Faculty of Science, National University of Singapore, Singapore 117542, Singapore;
| | - Roger C. Ho
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore
| | - Jung Eun Kim
- Department of Food Science and Technology, Faculty of Science, National University of Singapore, Singapore 117542, Singapore;
| | - Dong-Gyu Jo
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea;
| | - Sangyong Jung
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore; (L.Y.T.); (X.Y.Y.)
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
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34
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Meier MJ, Nguyen KC, Crosthwait J, Kawata A, Rigden M, Leingartner K, Wong A, Holloway A, Shwed PS, Beaudette L, Navarro M, Wade M, Tayabali AF. Low dose antibiotic ingestion potentiates systemic and microbiome changes induced by silver nanoparticles. NANOIMPACT 2021; 23:100343. [PMID: 35559844 DOI: 10.1016/j.impact.2021.100343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/29/2021] [Accepted: 07/12/2021] [Indexed: 06/15/2023]
Abstract
Changes in the mammalian gut microbiome are linked to the impairment of immunological function and numerous other pathologies. Antimicrobial silver nanoparticles (AgNPs) are incorporated into numerous consumer products (e.g., clothing, cosmetics, food packaging), which may directly impact the gut microbiome through ingestion. The human health impact of chronic AgNP ingestion is still uncertain, but evidence from exposure to other antimicrobials provides a strong rationale to assess AgNP effects on organ function, immunity, metabolism, and gut-associated microbiota. To investigate this, mice were gavaged daily for 5 weeks with saline, AgNPs, antibiotics (ciprofloxacin and metronidazole), or AgNPs combined with antibiotics. Animals were weighed daily, assessed for glucose tolerance, organ function, tissue and blood cytokine and leukocyte levels. At the end of the study, we used 16S rDNA amplicon and whole-metagenome shotgun sequencing to assess changes in the gut microbiome. In mice exposed to both AgNPs and antibiotics, silver was found in the stomach, and small and large intestines, but negligible amounts were present in other organs examined. Mice exposed to AgNPs alone showed minimal tissue silver levels. Antibiotics, but not AgNPs, altered glucose metabolism. Mice given AgNPs and antibiotics together demonstrated slower weight gain, reduced peripheral lymphocytes, and elevated splenic, but not circulatory markers of inflammation. 16S rDNA profiling of cecum and feces and metagenomic sequencing of fecal DNA demonstrated that combined AgNP-antibiotic treatment also significantly altered the structure and function of the gut microbiota, including depletion of the indicator species Akkermansia muciniphila. This study provides evidence for possible biological effects from repeated ingestion of AgNP-containing consumer products when antibiotics are also being used and raises concern that an impaired gut microbiome (e.g., through antibiotic use) can potentiate the harm from chemical exposures such as AgNPs.
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Affiliation(s)
- Matthew J Meier
- Environmental Health, Science and Research Bureau, Health Canada, Ottawa, Canada
| | - K C Nguyen
- Environmental Health, Science and Research Bureau, Health Canada, Ottawa, Canada; New Substances Assessment and Control Bureau, Health Canada, Ottawa, Canada
| | - J Crosthwait
- Environmental Health, Science and Research Bureau, Health Canada, Ottawa, Canada
| | - A Kawata
- Environmental Health, Science and Research Bureau, Health Canada, Ottawa, Canada
| | - M Rigden
- Environmental Health, Science and Research Bureau, Health Canada, Ottawa, Canada
| | - K Leingartner
- Environmental Health, Science and Research Bureau, Health Canada, Ottawa, Canada
| | - A Wong
- Department of Biology, Carleton University, Ottawa, Canada
| | - A Holloway
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, Canada
| | - P S Shwed
- Environmental Health, Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Lee Beaudette
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Ottawa, Canada
| | - M Navarro
- Bureau of Chemical Safety, Health Canada, Ottawa, Canada
| | - M Wade
- Environmental Health, Science and Research Bureau, Health Canada, Ottawa, Canada
| | - A F Tayabali
- Environmental Health, Science and Research Bureau, Health Canada, Ottawa, Canada.
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Biondi A, Basile F, Vacante M. Familial adenomatous polyposis and changes in the gut microbiota: New insights into colorectal cancer carcinogenesis. World J Gastrointest Oncol 2021; 13:495-508. [PMID: 34163569 PMCID: PMC8204352 DOI: 10.4251/wjgo.v13.i6.495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/15/2021] [Accepted: 05/08/2021] [Indexed: 02/06/2023] Open
Abstract
Patients with familial adenomatous polyposis (FAP), an autosomal dominant hereditary colorectal cancer syndrome, have a lifetime risk of developing cancer of nearly 100%. Recent studies have pointed out that the gut microbiota could play a crucial role in the development of colorectal adenomas and the consequent progression to colorectal cancer. Some gut bacteria, such as Fusobacterium nucleatum, Escherichia coli, Clostridium difficile, Peptostreptococcus, and enterotoxigenic Bacteroides fragilis, could be implicated in colorectal carcinogenesis through different mechanisms, including the maintenance of a chronic inflammatory state, production of bioactive tumorigenic metabolites, and DNA damage. Studies using the adenomatous polyposis coliMin/+ mouse model, which resembles FAP in most respects, have shown that specific changes in the intestinal microbial community could influence a multistep progression, the intestinal "adenoma-carcinoma sequence", which involves mucosal barrier injury, low-grade inflammation, activation of the Wnt pathway. Therefore, modulation of gut microbiota might represent a novel therapeutic target for patients with FAP. Administration of probiotics, prebiotics, antibiotics, and nonsteroidal anti-inflammatory drugs could potentially prevent the progression of the adenoma-carcinoma sequence in FAP. The aim of this review was to summarize the best available knowledge on the role of gut microbiota in colorectal carcinogenesis in patients with FAP.
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Affiliation(s)
- Antonio Biondi
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania 95123, Italy
- Multidisciplinary Research Center for Rare Diseases, University of Catania, Catania 95123, Italy
| | - Francesco Basile
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania 95123, Italy
- Multidisciplinary Research Center for Rare Diseases, University of Catania, Catania 95123, Italy
| | - Marco Vacante
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania 95123, Italy
- Multidisciplinary Research Center for Rare Diseases, University of Catania, Catania 95123, Italy
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Impact of Environmental and Pharmacologic Changes on the Upper Gastrointestinal Microbiome. Biomedicines 2021; 9:biomedicines9060617. [PMID: 34072493 PMCID: PMC8229529 DOI: 10.3390/biomedicines9060617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/23/2021] [Accepted: 05/26/2021] [Indexed: 02/08/2023] Open
Abstract
Diseases of the upper gastrointestinal tract have become more prevalent over time. Mechanisms of disease formation are still only partially understood. Recent literature has shown that the surrounding microbiome affects the propensity for disease formation in various parts of the upper gastrointestinal tract. A review was performed of any literature to our best knowledge concerning the effects of pharmacologic agents, environmental changes, and surgical intervention on the microbiome of the upper gastrointestinal tract. Searches of the literature were performed using specific keywords related to drugs, surgical procedures, and environmental factors. Many prescription and nonprescription drugs that are commonly used have varying effects on the upper gastrointestinal tract. Proton pump inhibitors may affect the relative prevalence of some organisms in the lower esophagus and have less effect in the proximal esophagus. Changes in the esophageal microbiome correlate with some esophageal diseases. Drugs that induce weight loss have also been shown to affect the microbiomes of the esophagus and stomach. Common surgical procedures are associated with shifts in the microbial community in the gastrointestinal tract. Environmental factors have been shown to affect the microbiome in the upper gastrointestinal tract, as geographic differences correlate with alterations in the microbiome of the gastrointestinal tract. Understanding the association of environmental and pharmacologic changes on the microbiome of the upper gastrointestinal tract will facilitate treatment plans to reduce morbidity from disease.
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Lorente-Picón M, Laguna A. New Avenues for Parkinson's Disease Therapeutics: Disease-Modifying Strategies Based on the Gut Microbiota. Biomolecules 2021; 11:433. [PMID: 33804226 PMCID: PMC7998286 DOI: 10.3390/biom11030433] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/13/2022] Open
Abstract
Parkinson's disease (PD) is a multifactorial neurodegenerative disorder that currently affects 1% of the population over the age of 60 years, and for which no disease-modifying treatments exist. Neurodegeneration and neuropathology in different brain areas are manifested as both motor and non-motor symptoms in patients. Recent interest in the gut-brain axis has led to increasing research into the gut microbiota changes in PD patients and their impact on disease pathophysiology. As evidence is piling up on the effects of gut microbiota in disease development and progression, another front of action has opened up in relation to the potential usage of microbiota-based therapeutic strategies in treating gastrointestinal alterations and possibly also motor symptoms in PD. This review provides status on the different strategies that are in the front line (i.e., antibiotics; probiotics; prebiotics; synbiotics; dietary interventions; fecal microbiota transplantation, live biotherapeutic products), and discusses the opportunities and challenges the field of microbiome research in PD is facing.
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Affiliation(s)
- Marina Lorente-Picón
- Neurodegenerative Diseases Research Group, Vall d'Hebron Research Institute (VHIR)-Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Ariadna Laguna
- Neurodegenerative Diseases Research Group, Vall d'Hebron Research Institute (VHIR)-Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
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Ishii A, Shigemura K, Kitagawa K, Harada M, Kan Y, Hayashi F, Osawa K, Kuntaman K, Shirakawa T, Fujisawa M. Cross-Resistance and the Mechanisms of Cephalosporin-Resistant Bacteria in Urinary Tract Infections Isolated in Indonesia. Curr Microbiol 2021; 78:1771-1777. [PMID: 33713209 DOI: 10.1007/s00284-021-02415-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/10/2021] [Indexed: 10/21/2022]
Abstract
Urinary tract infection (UTI) by antibiotic-resistant strains has become increasingly problematic, with trends that differ from country to country. This study examined cross-resistance and the mechanisms of cephalosporin resistance in UTI-causative bacteria isolated in Indonesia. Antibiotic susceptibility tests based on Clinical Laboratory Standards Institute (CLSI) standards were done for UTI-causative strains (n = 50) isolated from patients in Indonesia in 2015-2016 and showed resistance against the third-generation cephalosporin. Mechanistic studies were carried out to confirm the presence of extended-spectrum β-lactamase (ESBL) genes, carbapenemase-related genes, the fosA3 gene related to fosfomycin resistance, and mutations of quinolone-resistance-related genes. Isolated UTI-causative bacteria included Escherichia coli (64.0%), Pseudomonas aeruginosa (16.0%), Klebsiella pneumoniae (10.0%), and others (10.0%). These strains showed 96.0% susceptibility to amikacin, 76.0% to fosfomycin, 90.0% to imipenem, 28.0% to levofloxacin, 92.0% to meropenem, and 74.0% to tazobactam/piperacillin. ESBL was produced by 68.0% of these strains. Mechanistic studies found no strains with carbapenemase genes but 6.0% of strains had the fosA3 gene. Seventy-two % of the strains had mutations in the gyrA gene and 74.0% in the parC gene. Most E. coli strains (87.5%) had Ser-83 → Leu and Asp-87 → Asn in gyrA and 93.8% of E. coli had Ser-80 → Ile in parC. There were significant correlations among mutations in gyrA and parC, and fosA3 gene detection (P < 0.05), respectively. To our knowledge, this is the first mechanistic study of antibiotic-cross-resistant UTI-causative bacteria in Indonesia. Further studies with a longer period of observation are necessary, especially for changes in carbapenem resistance without carbapenemase-related genes.
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Affiliation(s)
- Aya Ishii
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Katsumi Shigemura
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan. .,Department of Urology, Kobe University Graduate School of Medicine, Kobe, Japan. .,Department of Infection Control, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Koichi Kitagawa
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan.,Department of Advanced Medical Science, Kobe University Graduate School of Science, Technology and Innovation, Kobe, Japan
| | - Mizuki Harada
- Central Laboratory Department, Local Independent Administrative Agency, Rinkuu General Medical Center, Osaka, Japan
| | - Yuki Kan
- Department of Medical Technology, School of Medicine Faculty of Health Sciences, Kobe University, Kobe, Japan
| | - Fuka Hayashi
- Department of Medical Technology, School of Medicine Faculty of Health Sciences, Kobe University, Kobe, Japan
| | - Kayo Osawa
- Department of Medical Technology, Kobe Tokiwa University, Kobe, Japan
| | - K Kuntaman
- Department of Microbiology, Faculty of Medicine, Airlangga University, Surabaya, Indonesia
| | - Toshiro Shirakawa
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan.,Department of Advanced Medical Science, Kobe University Graduate School of Science, Technology and Innovation, Kobe, Japan
| | - Masato Fujisawa
- Department of Urology, Kobe University Graduate School of Medicine, Kobe, Japan
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Raplee I, Walker L, Xu L, Surathu A, Chockalingam A, Stewart S, Han X, Rouse R, Li Z. Emergence of nosocomial associated opportunistic pathogens in the gut microbiome after antibiotic treatment. Antimicrob Resist Infect Control 2021; 10:36. [PMID: 33588951 PMCID: PMC7885457 DOI: 10.1186/s13756-021-00903-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Introduction According to the Centers for Disease Control’s 2015 Hospital Acquired Infection Hospital Prevalence Survey, 1 in 31 hospital patients was infected with at least one nosocomial pathogen while being treated for unrelated issues. Many studies associate antibiotic administration with nosocomial infection occurrence. However, to our knowledge, there is little to no direct evidence of antibiotic administration selecting for nosocomial opportunistic pathogens. Aim This study aims to confirm gut microbiota shifts in an animal model of antibiotic treatment to determine whether antibiotic use favors pathogenic bacteria. Methodology We utilized next-generation sequencing and in-house metagenomic assembly and taxonomic assignment pipelines on the fecal microbiota of a urinary tract infection mouse model with and without antibiotic treatment. Results Antibiotic therapy decreased the number of detectable species of bacteria by at least 20-fold. Furthermore, the gut microbiota of antibiotic treated mice had a significant increase of opportunistic pathogens that have been implicated in nosocomial infections, like Acinetobacter calcoaceticus/baumannii complex, Chlamydia abortus, Bacteroides fragilis, and Bacteroides thetaiotaomicron. Moreover, antibiotic treatment selected for antibiotic resistant gene enriched subpopulations for many of these opportunistic pathogens. Conclusions Oral antibiotic therapy may select for common opportunistic pathogens responsible for nosocomial infections. In this study opportunistic pathogens present after antibiotic therapy harbored more antibiotic resistant genes than populations of opportunistic pathogens before treatment. Our results demonstrate the effects of antibiotic therapy on induced dysbiosis and expansion of opportunistic pathogen populations and antibiotic resistant subpopulations of those pathogens. Follow-up studies with larger samples sizes and potentially controlled clinical investigations should be performed to confirm our findings.
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Affiliation(s)
- Isaac Raplee
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Lacey Walker
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Lei Xu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Anil Surathu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Ashok Chockalingam
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Sharron Stewart
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Xiaomei Han
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Rodney Rouse
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
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Subirats J, Murray R, Scott A, Lau CHF, Topp E. Composting of chicken litter from commercial broiler farms reduces the abundance of viable enteric bacteria, Firmicutes, and selected antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:141113. [PMID: 32768779 DOI: 10.1016/j.scitotenv.2020.141113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 06/11/2023]
Abstract
We examined the ability of composting to remove ARGs and enteric bacteria in litter obtained from broiler chickens fed with a diet supplemented with Bacitracin methylene disalicylate (BDM) (conventional chicken litter), or an antibiotic-free diet (raised without antibiotic (RWA) chicken litter). This was done by evaluating the litter before and after composting for the abundance of ten gene targets associated with antibiotic resistance or horizontal gene transfer, the composition of the bacterial communities, and the abundance of viable enteric bacteria. The abundance of gene targets was determined by qPCR and the microbial community composition of chicken litter determined by 16S rRNA gene amplicon sequencing. Enteric bacteria were enumerated by viable plate count. A majority of the gene targets were more abundant in conventional than in RWA litter. In both litter types, the absolute abundance of all of the target genes decreased after composting except sul1, intI1, incW and erm(F) that remained stable. Composting significantly reduced the abundance of enteric bacteria, including those carrying antibiotic resistance. The major difference in bacterial community composition between conventional and RWA litter was due to members affiliated to the genus Pseudomonas, which were 28% more abundant in conventional than in RWA litter. Composting favoured the presence of thermophilic bacteria, such as those affiliated with the genus Truepera, but decreased the abundance of those bacterial genera associated with cold-adapted species, such as Carnobacterium, Psychrobacter and Oceanisphaera. The present study shows that chicken litter from broilers fed with a diet supplemented with antibiotic has an increased abundance of some ARGs, even after composting. However, we can conclude that fertilization with composted litter represents a reduced risk of transmission of antibiotic resistance genes and enteric bacteria of poultry origin to soil and crops than will fertilization with raw litter.
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Affiliation(s)
- Jessica Subirats
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada; Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Roger Murray
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Andrew Scott
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Calvin Ho-Fung Lau
- Canadian Food Inspection Agency, 960 Carling Avenue, Ottawa, Ontario, Canada
| | - Edward Topp
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada; Department of Biology, University of Western Ontario, London, Ontario, Canada.
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