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Jiayi C, Jinying W, Yanhan Y, Tianyu L, Juanjuan C, Feng Z, Xiaohui F, Jinping Z. Probiotics' effects on gut microbiota in jaundiced neonates: a randomized controlled trial protocol. Front Pediatr 2024; 12:1296517. [PMID: 38523836 PMCID: PMC10957549 DOI: 10.3389/fped.2024.1296517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/16/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction Recent evidence suggests that blue-light phototherapy impacts gut microbiota composition in jaundiced newborns, leading to disturbances closely related to the therapy's side effects. As a result, gut microbiota may serve as a potential intervention target to mitigate these side effects. In this study, we aim to examine the effects of AB-GG (Lactobacillus rhamnosus LGG), Bb-12 (Bifidobacterium animalis Bb-12) and M-16V (Bifidobacterium breve M-16V) and their combination on the intestinal microbiota, metabolomics and phototherapy-related side effects in neonates with jaundice. Methods and analysis A total of 100 jaundiced newborns aged two weeks or younger will be included in this randomized, single-blind (the parents knew, but the neonatologists did not know), single-center controlled trial to receive either 109 colony-forming units of AB-GG, Bb-12, M-16V, a combination of the three probiotics with blue-light phototherapy, or blue-light phototherapy alone. The experimental group will be treated with oral probiotics once daily for 30 days, while the control group will receive only blue-light phototherapy. The follow-up duration will last 30 days. The primary outcomes include changes in gut microbiota, metabolomics, and the incidence of phototherapy side effects, assessed after each phototherapy session, as well as on days 10, 20, and 30. Ethics and dissemination The study protocol has been approved by the Ethics Committee of our institution. The findings of this trial will be submitted to a peer-reviewed pediatric journal. Its abstracts will be submitted to relevant national and international conferences. Clinical Trial Registration http://www.chictr.org.cn/index.aspx, identifer (ChiCTR2000036013).
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Affiliation(s)
- Chen Jiayi
- Pediatrics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Jinying
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yuan Yanhan
- Pediatrics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liu Tianyu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Chen Juanjuan
- Pediatrics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhang Feng
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Fang Xiaohui
- Pediatrics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhang Jinping
- Pediatrics, Shanghai Sixth People’s Hospital, Shanghai, China
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Liu Y, Zhang R, Wang B, Song S, Zhang F. Evaluation of penicillin-resistance and probiotic traits in Lactobacillus plantarum during laboratory evolution. Gene 2024; 891:147823. [PMID: 37741594 DOI: 10.1016/j.gene.2023.147823] [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: 02/16/2023] [Revised: 06/29/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
The aim of this study was to obtain the Lactobacillus plantarum ATCC14917 with high-level resistance to penicillin and evaluate their probiotic traits using laboratory evolution assay and whole-genome sequencing. In penicillin environment, the minimum inhibitory concentration (MIC) of L. plantarum to penicillin increased from 1 μg/mL to 16 μg/mL and remained stable after the removal of antibiotic pressure, suggesting that the resistance acquisition to penicillin was an irreversible process. Subsequently, change of probiotic characteristics was further evaluated, and the results showed that the acid tolerance, bile tolerance and adhesion ability were significantly declined in the highly resistant strains. Whole-genome sequencing indicated that genes encoding hypothetical protein, LPXTG-motif cell wall anchor domain protein and acetyltransferase were detected in highly resistant L. plantarum, and these genes were still present after the following subculture in the absence of penicillin, suggesting that these three mutants might be the main reason for the development of penicillin resistance. The homology-based analysis of surrounding DNA regions of mutant genes was further performed and indicated that no resistant genes were located on mobile elements in evolved L. plantarum strains, signifying that the spread of antibiotic resistance genes in the gut would not occur for these mutant genes. This study provided a basis for the combined use of highly resistant L. plantarum and penicillin in the treatment of pathogen induced gut diseases.
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Affiliation(s)
- Yufang Liu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an City, Shaanxi Province, China
| | - Rueyue Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an City, Shaanxi Province, China
| | - Bini Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an City, Shaanxi Province, China
| | - Shuanghong Song
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an City, Shaanxi Province, China
| | - Fuxin Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an City, Shaanxi Province, China.
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Nogacka AM, Saturio S, Alvarado-Jasso GM, Salazar N, de los Reyes Gavilán CG, Martínez-Faedo C, Suarez A, Wang R, Miyazawa K, Harata G, Endo A, Arboleya S, Gueimonde M. Probiotic-Induced Modulation of Microbiota Composition and Antibiotic Resistance Genes Load, an In Vitro Assessment. Int J Mol Sci 2024; 25:1003. [PMID: 38256076 PMCID: PMC10816173 DOI: 10.3390/ijms25021003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
The imbalance of the gut microbiota (GM) is known as dysbiosis and is associated with disorders such as obesity. The increasing prevalence of microorganisms harboring antibiotic resistance genes (ARG) in the GM has been reported as a potential risk for spreading multi-drug-resistant pathogens. The objective of this work was the evaluation, in a fecal culture model, of different probiotics for their ability to modulate GM composition and ARG levels on two population groups, extremely obese (OB) and normal-weight (NW) subjects. Clear differences in the basal microbiota composition were observed between NW and OB donors. The microbial profile assessed by metataxonomics revealed the broader impact of probiotics on the OB microbiota composition. Also, supplementation with probiotics promoted significant reductions in the absolute levels of tetM and tetO genes. Regarding the blaTEM gene, a minor but significant decrease in both donor groups was detected after probiotic addition. A negative association between the abundance of Bifidobacteriaceae and the tetM gene was observed. Our results show the ability of some of the tested strains to modulate GM. Moreover, the results suggest the potential application of probiotics for reducing the levels of ARG, which constitutes an interesting target for the future development of probiotics.
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Affiliation(s)
- Alicja Maria Nogacka
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain; (A.M.N.); (S.S.); (G.M.A.-J.); (N.S.); (C.G.d.l.R.G.); (S.A.)
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (DIMISA-ISPA), 33011 Oviedo, Spain;
| | - Silvia Saturio
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain; (A.M.N.); (S.S.); (G.M.A.-J.); (N.S.); (C.G.d.l.R.G.); (S.A.)
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (DIMISA-ISPA), 33011 Oviedo, Spain;
| | - Guadalupe Monserrat Alvarado-Jasso
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain; (A.M.N.); (S.S.); (G.M.A.-J.); (N.S.); (C.G.d.l.R.G.); (S.A.)
| | - Nuria Salazar
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain; (A.M.N.); (S.S.); (G.M.A.-J.); (N.S.); (C.G.d.l.R.G.); (S.A.)
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (DIMISA-ISPA), 33011 Oviedo, Spain;
| | - Clara G. de los Reyes Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain; (A.M.N.); (S.S.); (G.M.A.-J.); (N.S.); (C.G.d.l.R.G.); (S.A.)
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (DIMISA-ISPA), 33011 Oviedo, Spain;
| | - Ceferino Martínez-Faedo
- Endocrinology and Nutrition Service, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain;
- Endocrinology, Nutrition, Diabetes and Obesity Group, Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Spain
| | - Adolfo Suarez
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (DIMISA-ISPA), 33011 Oviedo, Spain;
- Digestive Service, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain
| | - Ruipeng Wang
- Technical Research Laboratory, Takanashi Milk Products Co., Ltd., Yokohama 241-0021, Japan; (R.W.); (K.M.); (G.H.)
| | - Kenji Miyazawa
- Technical Research Laboratory, Takanashi Milk Products Co., Ltd., Yokohama 241-0021, Japan; (R.W.); (K.M.); (G.H.)
| | - Gaku Harata
- Technical Research Laboratory, Takanashi Milk Products Co., Ltd., Yokohama 241-0021, Japan; (R.W.); (K.M.); (G.H.)
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan;
| | - Silvia Arboleya
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain; (A.M.N.); (S.S.); (G.M.A.-J.); (N.S.); (C.G.d.l.R.G.); (S.A.)
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (DIMISA-ISPA), 33011 Oviedo, Spain;
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain; (A.M.N.); (S.S.); (G.M.A.-J.); (N.S.); (C.G.d.l.R.G.); (S.A.)
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (DIMISA-ISPA), 33011 Oviedo, Spain;
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Diebold PJ, Rhee MW, Shi Q, Trung NV, Umrani F, Ahmed S, Kulkarni V, Deshpande P, Alexander M, Thi Hoa N, Christakis NA, Iqbal NT, Ali SA, Mathad JS, Brito IL. Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. Nat Commun 2023; 14:7366. [PMID: 37963868 PMCID: PMC10645880 DOI: 10.1038/s41467-023-42998-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinase CTX-M and carbapenemases KPC, IMP, NDM, and VIM, remain taxonomically restricted to Proteobacteria. Even cfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted to Bacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity single-cell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted to Bacteroides species, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.
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Affiliation(s)
- Peter J Diebold
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Matthew W Rhee
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Qiaojuan Shi
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Nguyen Vinh Trung
- Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Ho Chi Minh city, Viet Nam
| | | | | | - Vandana Kulkarni
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Prasad Deshpande
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Mallika Alexander
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Ho Chi Minh city, Viet Nam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Microbiology Department and Center for Tropical Medicine Research, Ngoc Thach University of Medicine, Ho Chi Minh city, Vietnam
| | | | | | | | | | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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Samantray D, Tanwar AS, Murali TS, Brand A, Satyamoorthy K, Paul B. A Comprehensive Bioinformatics Resource Guide for Genome-Based Antimicrobial Resistance Studies. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:445-460. [PMID: 37861712 DOI: 10.1089/omi.2023.0140] [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: 10/21/2023]
Abstract
The use of high-throughput sequencing technologies and bioinformatic tools has greatly transformed microbial genome research. With the help of sophisticated computational tools, it has become easier to perform whole genome assembly, identify and compare different species based on their genomes, and predict the presence of genes responsible for proteins, antimicrobial resistance, and toxins. These bioinformatics resources are likely to continuously improve in quality, become more user-friendly to analyze the multiple genomic data, efficient in generating information and translating it into meaningful knowledge, and enhance our understanding of the genetic mechanism of AMR. In this manuscript, we provide an essential guide for selecting the popular resources for microbial research, such as genome assembly and annotation, antibiotic resistance gene profiling, identification of virulence factors, and drug interaction studies. In addition, we discuss the best practices in computer-oriented microbial genome research, emerging trends in microbial genomic data analysis, integration of multi-omics data, the appropriate use of machine-learning algorithms, and open-source bioinformatics resources for genome data analytics.
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Affiliation(s)
- Debyani Samantray
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Ankit Singh Tanwar
- United Nations University-Maastricht Economic and Social Research Institute on Innovation and Technology (UNU-MERIT), Maastricht, The Netherlands
- Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Thokur Sreepathy Murali
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Angela Brand
- United Nations University-Maastricht Economic and Social Research Institute on Innovation and Technology (UNU-MERIT), Maastricht, The Netherlands
- Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
- Department of Health Information, Prasanna School of Public Health (PSPH), Manipal Academy of Higher Education, Manipal, India
| | - Kapaettu Satyamoorthy
- SDM College of Medical Sciences and Hospital, Shri Dharmasthala Manjunatheshwara (SDM) University, Dharwad, India
| | - Bobby Paul
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
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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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Malin JJ, von Wintersdorff CJH, Penders J, Savelkoul PHM, Wolffs PFG. Longitudinal fluctuations of common antimicrobial resistance genes in the gut microbiomes of healthy Dutch individuals. Int J Antimicrob Agents 2023; 61:106716. [PMID: 36640847 DOI: 10.1016/j.ijantimicag.2023.106716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 11/22/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
The human gut microbiome is an important reservoir of antimicrobial resistance genes (ARGs), collectively termed the 'resistome'. To date, few studies have examined the dynamics of the human gut resistome in healthy individuals. Previously, the authors observed high rates of ARG acquisition and significant abundance shifts during international travel. In order to provide insight into commonly occurring dynamics, this study investigated longitudinal fluctuations in prevalent ARGs (cfxA, tetM and ermB) in the resistomes of non-travelling healthy volunteers. In addition, this study assessed the prevalence of acquirable ARGs (blaCTX-M, qnrB, qnrS, vanA and vanB) over time. Faecal samples from 23 participants were collected at baseline and after 2 and 4 weeks. DNA was isolated, and ARG quantification was performed by quantitative polymerase chain reaction adjusting for the total amount of bacterial 16S rDNA. vanA and qnrS were not detected in any of the samples, while the prevalence rates of vanB of non-enterococcal origin and qnrB were 73.9% and 5.7%, respectively. The ß-lactamase encoding blaCTX-M was detected in 17.4% of healthy participants. The results were compared with previous data from 122 travellers. ARG acquisitions observed in travellers were rare in non-travelling individuals during 4 weeks of follow-up, supporting the hypothesis of ARG acquisition during international travel. However, median -1.04- to 1.04-fold abundance changes were observed for 100% of cfxA, tetM and ermB, which did not differ from those found in travellers. Thus, common abundance shifts in prevalent ARGs of the gut resistome were found to occur independent of travel behaviour.
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Affiliation(s)
- Jakob J Malin
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Christian J H von Wintersdorff
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands.
| | - John Penders
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Petra F G Wolffs
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
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Leinyuy JF, Ali IM, Ousenu K, Tume CB. Molecular characterization of antimicrobial resistance related genes in E. coli, Salmonella and Klebsiella isolates from broilers in the West Region of Cameroon. PLoS One 2023; 18:e0280150. [PMID: 36630464 PMCID: PMC9833522 DOI: 10.1371/journal.pone.0280150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Antibiotic resistance has become an enduring threat to human health. This has prompted extensive research to identify the determinants responsible in a bid to fight the spread of resistance and also develop new antibiotics. However, routine procedures focus on identifying genetic determinants of resistance only on phenotypically resistant isolates. We aimed to characterise plasmid mediated resistance determinants in key Enterobacteriaceae isolates with differential phenotypic susceptibility profiles and evaluated the contribution of resistance genes on phenotypic expression of susceptibility. METHODS The study was carried out on 200 Enterobacteriaceae isolates belonging to the genera E. coli, Salmonella, and Klebsiella; 100 resistant and 100 susceptible to quinolones, aminoglycosides, and ESBL-producing as determined by disk diffusion. Reduced susceptibility in susceptible isolates was determined as an increased MIC by broth microdilution. Plasmid-borne resistance genes were sought in all isolates by endpoint PCR. We performed correlations tests to determine the relationship between the occurrence of resistance genes and increased MIC in susceptible isolates. We then used the notion of penetrance to show adequacy between resistance gene carriage and phenotypic resistance as well as diagnostic odds ratio to evaluate how predictable phenotypic susceptibility profile could determine the presence of resistant genes in the isolates. RESULTS Reduced susceptibility was detected in 30% (9/30) ESBL negative, 50% (20/40) quinolone-susceptible and 53.33% (16/30) aminoglycoside-susceptible isolates. Plasmid-borne resistance genes were detected in 50% (15/30) of ESBL negative, 65% (26/40) quinolone susceptible and 66.67% (20/30) aminoglycoside susceptible isolates. Reduced susceptibility increased the risk of susceptible isolates carrying resistance genes (ORs 4.125, 8.36, and 8.89 respectively for ESBL, quinolone, and aminoglycoside resistance genes). Resistance gene carriage correlated significantly to reduced susceptibility for quinolone and aminoglycoside resistance genes (0.002 and 0.015 at CI95). Gene carriage correlated with phenotypic resistance at an estimated 64.28% for ESBL, 56.90% for quinolone, and 58.33% for aminoglycoside resistance genes. CONCLUSIONS A high carriage of plasmid-mediated genes for ESBL, quinolone, and aminoglycoside resistance was found among the Enterobacteriaceae tested. However, gene carriage was not always correlated with phenotypic expression. This allows us to suggest that assessing genetic determinants of resistance should not be based on AST profile only. Further studies, including assessing the role of chromosomal determinants will shed light on other factors that undermine antimicrobial susceptibility locally.
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Affiliation(s)
- Jude Fonbah Leinyuy
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
| | - Innocent Mbulli Ali
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
- The Biotechnology Centre, University of Yaoundé 1, Yaoundé, Cameroon
- * E-mail:
| | - Karimo Ousenu
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
| | - Christopher B. Tume
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
- Department of Biochemistry, Faculty of Science, University of Bamenda, Bamenda, Cameroon
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Doster E, Pinnell LJ, Noyes NR, Parker JK, Anderson CA, Booker CW, Hannon SJ, McAllister TA, Gow SP, Belk KE, Morley PS. Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle. Front Microbiol 2022; 13:970358. [PMID: 36583056 PMCID: PMC9792868 DOI: 10.3389/fmicb.2022.970358] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/10/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction Use of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Escherichia coli. However, genes conferring AMR are known to be distributed and shared throughout microbial communities. The objectives of this study were to employ target-enriched metagenomic sequencing and 16S rRNA gene amplicon sequencing to investigate the effects of AMD use, in the context of other management and environmental factors, on the resistome and microbiome in beef feedlot cattle. Methods This study leveraged samples collected during a previous longitudinal study of cattle at beef feedlots in Canada. This included fecal samples collected from randomly selected individual cattle, as well as composite-fecal samples from randomly selected pens of cattle. All AMD use was recorded and characterized across different drug classes using animal defined daily dose (ADD) metrics. Results Overall, fecal resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin (MLS) drug classes. The diversity of bacterial phyla was greater early in the feeding period and decreased over time in the feedlot. This decrease in diversity occurred concurrently as the microbiome represented in different individuals and different pens shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Some antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but the amount of variance explained by these important factors was very small (<0.6% variance each), and smaller than associations with other factors measured in this study such as time and feedlot ID. Time in the feedlot was associated with greater changes in the resistome for both individual animals and composite pen-floor samples, although the proportion of the variance associated with this factor was small (2.4% and 1.2%, respectively). Discussion Results of this study are consistent with other investigations showing that, compared to other factors, AMD exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle.
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Affiliation(s)
- Enrique Doster
- Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, CO, United States,Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, United States
| | - Lee J. Pinnell
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, United States
| | - Noelle R. Noyes
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Jennifer K. Parker
- Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, CO, United States
| | - Cameron A. Anderson
- Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, CO, United States
| | | | | | | | - Sheryl P. Gow
- Public Health Agency of Canada, Saskatoon, SK, Canada
| | - Keith E. Belk
- Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, CO, United States
| | - Paul S. Morley
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, United States,*Correspondence: Paul S. Morley,
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Nwaokorie FO, Edet UO, Joseph AP, Phylis K, Folasade O. Prediction of functional proteins associated with the gut microbiome of an adult population in Lagos State, Nigeria. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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11
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Liu Y, Zhang F. Changes of antibiotic resistance genes and gut microbiota after the ingestion of goat milk. J Dairy Sci 2022; 105:4804-4817. [PMID: 35346469 DOI: 10.3168/jds.2021-21325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/28/2022] [Indexed: 11/19/2022]
Abstract
Antibiotic resistance genes, as newly emerging contaminants, have become a serious challenge to public health through the food chain. The gut of humans and animals is an important reservoir for the development and dissemination of antibiotic resistance genes because of the great abundance and diversity of intestinal microbiota. In the present study, we evaluated the influence of goat milk on the diversity and abundance of antibiotic resistance genes and gut microbial communities, especially pathogenic bacteria. Male mice were used, 12 for each of the 2 groups: a control group that received sterile distilled water and a treated group that received goat milk, and gut microbiota and antibiotic resistance genes were compared in these groups using metagenomic analysis. The results revealed that ingestion of goat milk decreased the diversity and abundance of antibiotic resistance genes in the mice gut. The relative abundance of fluoroquinolone, peptide, macrolide, and β-lactam resistance genes in the total microbial genes significantly decreased after the intervention. Goat milk intake also significantly reduced the abundance of pathogenic bacteria, such as Clostridium bolteae, Clostridium symbiosum, Helicobacter cinaedi, and Helicobacter bilis. Therefore, goat milk intake might decrease the transfer potential of antibiotic resistance gene to pathogenic bacteria in the gut. In addition, bacteria with multiple resistance mechanisms accounted for approximately 4.5% of total microbial communities in the control group, whereas it was not detectable in the goat milk group, indicating the total inhibition by goat milk intake. This study highlights the influence of goat milk on antibiotic resistome and microbial communities in the gut, and provides a new insight into the function of goat milk for further study.
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Affiliation(s)
- Yufang Liu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Fuxin Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China.
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12
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Omoniyi AA, Adebisi SS, Musa SA, Nzalak JO, Bauchi ZM, Bako KW, Olatomide OD, Zachariah R, Nyengaard JR. In silico design and analyses of a multi-epitope vaccine against Crimean-Congo hemorrhagic fever virus through reverse vaccinology and immunoinformatics approaches. Sci Rep 2022; 12:8736. [PMID: 35610299 PMCID: PMC9127496 DOI: 10.1038/s41598-022-12651-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/12/2022] [Indexed: 12/16/2022] Open
Abstract
Crimean Congo Hemorrhagic Fever virus (CCHFV) is a deadly human pathogen that causes an emerging zoonotic disease with a broad geographic spread, especially in Africa, Asia, and Europe, and the second most common viral hemorrhagic fever and widely transmitted tick-borne viral disease. Following infection, the patients are presented with a variety of clinical manifestations and a fatality rate of 40%. Despite the high fatality rate, there are unmet clinical interventions, as no antiviral drugs or vaccines for CCHF have been approved. Immunoinformatics pipeline and reverse vaccinology were used in this study to design a multi-epitope vaccine that may elicit a protective humoral and cellular immune response against Crimean-Congo hemorrhagic fever virus infection. Three essential virulent and antigenic proteins (S, M, and L) were used to predict seven CTL and 18 HTL epitopes that were non-allergenic, antigenic, IFN-γ inducing, and non-toxic. The epitopes were connected using linkers and 50S ribosomal protein L7/L12 was used as an adjuvant and raised a multi-epitope vaccine (MEV) that is 567 amino acids long. Molecular docking and simulation of the predicted 3D structure of the MEV with the toll-like (TLR2, TLR3, and TLR4) receptors and major histocompatibility complex (MCH-I and MCH-II) indicate high interactions and stability of the complexes, MM-GBSA free binding energy calculation revealed a favourable protein-protein complex. Maximum MEV expression was achieved with a CAI value of 0.98 through in silico cloning in the Drosophila melanogaster host. According to the immune simulation, IgG1, T-helper cells, T-cytotoxic cells, INF-γ, and IL-2 were predicted to be significantly elevated. These robust computational analyses demonstrated that the proposed MEV is effective in preventing CCHFV infections. However, it is still necessary to conduct both in vitro and in vivo experiments to validate the potential of the vaccine.
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Affiliation(s)
- Akinyemi Ademola Omoniyi
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria.
- Department of Clinical Medicine, Core Centre for Molecular Morphology, Section for Stereology and Microscopy, Aarhus University, Aarhus, Denmark.
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark.
| | - Samuel Sunday Adebisi
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Sunday Abraham Musa
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - James Oliver Nzalak
- Department of Veterinary Anatomy, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Zainab Mahmood Bauchi
- Department of Human Anatomy, Faculty of Basic Medical Sciences, Abubakar Tafawa Balewa University, Bauchi, Nigeria
| | - Kerkebe William Bako
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Oluwasegun Davis Olatomide
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Richard Zachariah
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Jens Randel Nyengaard
- Department of Clinical Medicine, Core Centre for Molecular Morphology, Section for Stereology and Microscopy, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
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Xiang L, Ying Z, Xue M, Xiaoxian P, Xiaorong L, Chunyang L, Yu W, Mingcheng L, Binxian L. A novel Lactobacillus bulgaricus isolate can maintain the intestinal health, improve the growth performance and reduce the colonization of E. coli O157:H7 in broilers. Br Poult Sci 2022; 63:621-632. [PMID: 35383527 DOI: 10.1080/00071668.2022.2062220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. This study aimed at the effects of a novel Lactobacillus bulgaricus (L. bulgaricus) strain and Enterohemorrhagic Escherichia coli (E. coli) O157: H7 on intestinal flora and growth performance of broilers, and the protective effect of L. bulgaricus on broilers in challenged experiment by E. coli O157: H7.2. In vitro bacteriostatic test showed that the cell-free supernatant (CFS) of L. bulgaricus isolate had obvious inhibitory effect on E. coli O157: H7.3. Eighty 1-day-old male broilers were randomly assigned into 4 treatment groups with 4 replicate per treatment. All group received basic diet in addition to the specific treatments: NC group, gavage with normal saline; In LBP group, gavage with L. bulgaricus isolate (1×109 CFU/mL) during the whole process, and challenged with E. coli O157: H7 (3×109 CFU/mL); EC group, gavage with E. coli O157: H7 (3×109 CFU/mL); LB Group, gavage with L. bulgaricus isolate. At the age of 21 days, broilers were weighed and feed conversion ratio (FCR) was calculated. Cecum and cecal contents, ileum and feces samples were taken after slaughter.4. The challenge of E. coli O157: H7 resulted in an increase in TLR-4, NF-κB and IL-8 mRNA in cecal tissue, a decrease in Villus: crypt ratio in ileum, a decrease in overall diversity of intestinal microflora and a poor FCR.5. The L. bulgaricus isolate decreased the mRNA expression of TLR-4, NF-κB and IL-8 induced by E. coli O157: H7, reduced the content of E. coli O157: H7 in the cecum of broilers, increased the Villus: crypt ratio, increased the abundance of beneficial bacteria and overall diversity of intestinal microflora, made good FCR.6. The L. bulgaricus isolate can maintain the intestinal health, improve the growth performance of broilers and reduce the colonization of E. coli O157:H7 in the cecum.
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Affiliation(s)
- Li Xiang
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Zhang Ying
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Meng Xue
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Pei Xiaoxian
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Liu Xiaorong
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Lan Chunyang
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Wang Yu
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Li Mingcheng
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Li Binxian
- Dept. of Clinical Microbiology, Associated Hospital, Beihua University, Jilin, Jilin 132013, China
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Differences in Gut Microbiome Composition and Antibiotic Resistance Gene Distribution between Chinese and Pakistani University Students from a Common Peer Group. Microorganisms 2021; 9:microorganisms9061152. [PMID: 34072124 PMCID: PMC8229524 DOI: 10.3390/microorganisms9061152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/13/2022] Open
Abstract
Gut microbiomes play important functional roles in human health and are also affected by many factors. However, few studies concentrate on gut microbiomes under exercise intervention. Additionally, antibiotic resistance genes (ARGs) carried by gut microbiomes may constantly pose a threat to human health. Here, ARGs and microbiomes of Chinese and Pakistanis participants were investigated using 16S rRNA gene sequencing and high-throughput quantitative PCR techniques. The exercise had no impact on gut microbiomes in the 12 individuals investigated during the observation period, while the different distribution of gut microbiomes was found in distinct nationalities. Overall, the dominant microbial phyla in the participants’ gut were Bacteroidota, Firmicutes and Proteobacteria. Some genera such as Prevotella and Dialister were more abundant in Pakistani participants and some other genera such as Bacteroides and Faecalibacterium were more abundant in Chinese participants. The microbial diversity in Chinese was higher than that in Pakistanis. Furthermore, microbial community structures were also different between Chinese and Pakistanis. For ARGs, the distribution of all detected ARGs is not distinct at each time point. Among these ARGs, floR was distributed differently in Chinese and Pakistani participants, and some ARGs such as tetQ and sul2 are positively correlated with several dominant microbiomes, particularly Bacteroidota and Firmicutes bacteria that did not fluctuate over time.
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15
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Sheikh SW, Ali A, Ahsan A, Shakoor S, Shang F, Xue T. Insights into Emergence of Antibiotic Resistance in Acid-Adapted Enterohaemorrhagic Escherichia coli. Antibiotics (Basel) 2021; 10:522. [PMID: 34063307 PMCID: PMC8147483 DOI: 10.3390/antibiotics10050522] [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: 03/08/2021] [Revised: 04/15/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of multidrug-resistant pathogens presents a global challenge for treating and preventing disease spread through zoonotic transmission. The water and foodborne Enterohaemorrhagic Escherichia coli (EHEC) are capable of causing intestinal and systemic diseases. The root cause of the emergence of these strains is their metabolic adaptation to environmental stressors, especially acidic pH. Acid treatment is desired to kill pathogens, but the protective mechanisms employed by EHECs cross-protect against antimicrobial peptides and thus facilitate opportunities for survival and pathogenesis. In this review, we have discussed the correlation between acid tolerance and antibiotic resistance, highlighting the identification of novel targets for potential production of antimicrobial therapeutics. We have also summarized the molecular mechanisms used by acid-adapted EHECs, such as the two-component response systems mediating structural modifications, competitive inhibition, and efflux activation that facilitate cross-protection against antimicrobial compounds. Moving beyond the descriptive studies, this review highlights low pH stress as an emerging player in the development of cross-protection against antimicrobial agents. We have also described potential gene targets for innovative therapeutic approaches to overcome the risk of multidrug-resistant diseases in healthcare and industry.
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Affiliation(s)
- Salma Waheed Sheikh
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
| | - Ahmad Ali
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China;
| | - Asma Ahsan
- Faculty of Life Sciences, University of Central Punjab, Lahore 54000, Punjab, Pakistan;
| | - Sidra Shakoor
- Station de Neucfchateau, CIRAD, 97130 Sainte-Marie, Capesterre Belle Eau, Guadeloupe, France;
| | - Fei Shang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
| | - Ting Xue
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
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Zhong C, Zhou Y, Zhao J, Fu J, Jiang T, Liu B, Chen F, Cao G. High throughput sequencing reveals the abundance and diversity of antibiotic-resistant bacteria in aquaculture wastewaters, Shandong, China. 3 Biotech 2021; 11:104. [PMID: 33552832 PMCID: PMC7847479 DOI: 10.1007/s13205-021-02656-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
An innovative investigation was undertaken into the abundance and diversity of high antibiotic-resistant bacteria in aquaculture waters in Shandong Province, China, through cumulation incubation, PCR amplification of 16S rDNA, and high-throughput sequencing. The results showed that Vibrio, Bacillus, Vagococcus, Acinetobacter, Shewanella, Psychrobacter, Lactococcus, Enterococcus, Marinimonus and Myroids were abundant in the aquaculture waters, whereas other phylum including Actinobacteria, Deinococcus-Thermus, Omnitrophica and Nitrospirae had relatively lower abundance. Our studies revealed the presence of different bacteria in different locations in the aquaculture waters, most of which were resistant to multiple antibiotics. That is, the same microbial species from the same aquaculture wastewater can resist different antibiotics. Altogether, a considerable portion of the microbial community were found to be multi-drug resistant. It is essential that the spread of the antibiotic-resistant bacteria is controlled so that the distribution of antibiotic resistance genes to other environments is avoided. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02656-4.
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Affiliation(s)
- Chuanqing Zhong
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
- Resources and Environment Innovation Research Institute, Shandong Jianzhu University, Jinan, China
| | - Yingping Zhou
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Jia Zhao
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Jiafang Fu
- College of Biomedical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117 China
| | - Tianyi Jiang
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Bing Liu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
- Resources and Environment Innovation Research Institute, Shandong Jianzhu University, Jinan, China
| | - Feiyong Chen
- Resources and Environment Innovation Research Institute, Shandong Jianzhu University, Jinan, China
| | - Guangxiang Cao
- College of Biomedical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117 China
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de Abreu VAC, Perdigão J, Almeida S. Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview. Front Genet 2021; 11:575592. [PMID: 33537056 PMCID: PMC7848172 DOI: 10.3389/fgene.2020.575592] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/04/2020] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance is a major global public health problem, which develops when pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic recombination between commensal and pathogenic microbes. The resistome is a collection of all ARGs. In microorganisms, the primary method of ARG acquisition is horizontal gene transfer (HGT). Thus, understanding and identifying HGTs, can provide insight into the mechanisms of antimicrobial resistance transmission and dissemination. The use of high-throughput sequencing technologies has made the analysis of ARG sequences feasible and accessible. In particular, the metagenomic approach has facilitated the identification of community-based antimicrobial resistance. This approach is useful, as it allows access to the genomic data in an environmental sample without the need to isolate and culture microorganisms prior to analysis. Here, we aimed to reflect on the challenges of analyzing metagenomic data in the three main approaches for studying antimicrobial resistance: (i) analysis of microbial diversity, (ii) functional gene analysis, and (iii) searching the most complete and pertinent resistome databases.
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Affiliation(s)
- Vinicius A C de Abreu
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, Belém, Brazil
| | - José Perdigão
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, Belém, Brazil
| | - Sintia Almeida
- Central de Genômica e Bioinformática (CeGenBio), Núcleo de Pesquisa e Desenvolvimento de Medicamentos (NPDM), Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, Brazil
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Li J, Si H, Du H, Guo H, Dai H, Xu S, Wan J. Comparison of gut microbiota structure and Actinobacteria abundances in healthy young adults and elderly subjects: a pilot study. BMC Microbiol 2021; 21:13. [PMID: 33407122 PMCID: PMC7788997 DOI: 10.1186/s12866-020-02068-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/10/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The aim was to determine the potential association of the gut microbiota composition, especially the abundance of Actinobacteria, as well as the differentiation of functional and resistance genes with age (young adults vs elderly subjects) in China. RESULTS The patterns of relative abundance of all bacteria isolated from fecal samples differed between young adults and elderly subjects, but the alpha diversity (Chao1 P = 0.370, Shannon P = 0.560 and Simpson P = 0.270) and beta diversity (ANOSIM R = 0.031, P = 0.226) were not significantly different. There were 3 Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways (carbon metabolism, inositol phosphate metabolism, and sesquiterpenoid and triterpenoid biosynthesis) and 7 antibiotic resistant genes (ARGs) (macrolide lincosamide-streptogramin B (MLSB), tetracycline, aminoglycoside, sulfonamide, fosmidomycin, lincomycin, and vancomycin) that showed significant differences between the 2 groups (all P < 0.05). The abundance of Actinomycetes was enriched (about 2.4-fold) in young adults. Bifidobacteria dominated in both young adults and elderly subjects, with overall higher abundances in young adults (P > 0.05). Only the Bifidobacterium_dentium species showed significant differences between the 2 groups (P = 0.013), with a higher abundance in elderly subjects but absent in young adults. CONCLUSIONS The present study revealed that there were 3 KEGG metabolic pathways and 7 ARGs as well as enhanced Bifidobacterium_dentium species abundance in elderly compared to young subjects.
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Affiliation(s)
- Jun Li
- Department of Gastroenterology, 2nd Medical Center, Chinese People's Liberation Army General Hospital, No. 28 Fuxing Road, Beijing, 100853, China
| | - Haiyan Si
- Department of Oncology, First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Haitao Du
- Department of Gastroenterology, 2nd Medical Center, Chinese People's Liberation Army General Hospital, No. 28 Fuxing Road, Beijing, 100853, China
| | - Hongxia Guo
- Department of Oncology, First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Huanqin Dai
- Chinese Academy Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shiping Xu
- Department of Gastroenterology, 2nd Medical Center, Chinese People's Liberation Army General Hospital, No. 28 Fuxing Road, Beijing, 100853, China.
| | - Jun Wan
- Department of Gastroenterology, 2nd Medical Center, Chinese People's Liberation Army General Hospital, No. 28 Fuxing Road, Beijing, 100853, China.
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Hemmadi V, Biswas M. An overview of moonlighting proteins in Staphylococcus aureus infection. Arch Microbiol 2020; 203:481-498. [PMID: 33048189 PMCID: PMC7551524 DOI: 10.1007/s00203-020-02071-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 01/01/2023]
Abstract
Staphylococcus aureus is responsible for numerous instances of superficial, toxin-mediated, and invasive infections. The emergence of methicillin-resistant (MRSA), as well as vancomycin-resistant (VRSA) strains of S. aureus, poses a massive threat to human health. The tenacity of S. aureus to acquire resistance against numerous antibiotics in a very short duration makes the effort towards developing new antibiotics almost futile. S. aureus owes its destructive pathogenicity to the plethora of virulent factors it produces among which a majority of them are moonlighting proteins. Moonlighting proteins are the multifunctional proteins in which a single protein, with different oligomeric conformations, perform multiple independent functions in different cell compartments. Peculiarly, proteins involved in key ancestral functions and metabolic pathways typically exhibit moonlighting functions. Pathogens mainly employ those proteins as virulent factors which exhibit high structural conservation towards their host counterparts. Consequentially, the host immune system counteracts these invading bacterial virulent factors with minimal protective action. Additionally, many moonlighting proteins also play multiple roles in various stages of pathogenicity while augmenting the virulence of the bacterium. This has necessitated elaborative studies to be conducted on moonlighting proteins of S. aureus that can serve as drug targets. This review is a small effort towards understanding the role of various moonlighting proteins in the pathogenicity of S. aureus.
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Affiliation(s)
- Vijay Hemmadi
- Department of Biological Sciences, Birla Institute of Technology and Science, BITS-Pilani, K. K. Birla Goa Campus, NH17B, Zuarinagar, Goa, 403726, India
| | - Malabika Biswas
- Department of Biological Sciences, Birla Institute of Technology and Science, BITS-Pilani, K. K. Birla Goa Campus, NH17B, Zuarinagar, Goa, 403726, India.
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The Toothbrush Microbiome: Impact of User Age, Period of Use and Bristle Material on the Microbial Communities of Toothbrushes. Microorganisms 2020; 8:microorganisms8091379. [PMID: 32916797 PMCID: PMC7563892 DOI: 10.3390/microorganisms8091379] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 11/24/2022] Open
Abstract
Toothbrushes play a central role in oral hygiene and must be considered one of the most common articles of daily use. We analysed the bacterial colonization of used toothbrushes by next generation sequencing (NGS) and by cultivation on different media. Furthermore, we determined the occurrence of antibiotic resistance genes (ARGs) and the impact of different bristle materials on microbial growth and survival. NGS data revealed that Enterobacteriaceae, Micrococcaceae, Actinomycetaceae, and Streptococcaceae comprise major parts of the toothbrush microbiome. The composition of the microbiome differed depending on the period of use or user age. While higher fractions of Actinomycetales, Lactobacillales, and Enterobacterales were found after shorter periods, Micrococcales dominated on both toothbrushes used for more than four weeks and on toothbrushes of older users, while in-vitro tests revealed increasing counts of Micrococcus on all bristle materials as well. Compared to other environments, we found a rather low frequency of ARGs. We determined bacterial counts between 1.42 × 106 and 1.19 × 107 cfu/toothbrush on used toothbrushes and no significant effect of different bristles materials on bacterial survival or growth. Our study illustrates that toothbrushes harbor various microorganisms and that both period of use and user age might affect the microbial composition.
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Van Daele E, Knol J, Belzer C. Microbial transmission from mother to child: improving infant intestinal microbiota development by identifying the obstacles. Crit Rev Microbiol 2019; 45:613-648. [DOI: 10.1080/1040841x.2019.1680601] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Emmy Van Daele
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Jan Knol
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Gut Biology and Microbiology, Danone Nutricia Research, Utrecht, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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Kumar H, Park W, Lim D, Srikanth K, Kim JM, Jia XZ, Han JL, Hanotte O, Park JE, Oyola SO. Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes. Genomics 2019; 112:1988-1999. [PMID: 31759120 DOI: 10.1016/j.ygeno.2019.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/11/2019] [Accepted: 11/18/2019] [Indexed: 12/24/2022]
Abstract
We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.
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Affiliation(s)
- Himansu Kumar
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Republic of Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Republic of Korea
| | - Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Xin-Zheng Jia
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, PR China; International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, PR China; International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Nairobi, Kenya; Faculty of Medicine & Health Sciences, University of Nottingham, UK; International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Republic of Korea.
| | - Samuel O Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya.
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Abstract
Antimicrobial resistance (AMR) has emerged as an obstacle in the supple administration of antimicrobial agents to critical diarrheal patients. Most diarrheal pathogens have developed resistance against the major classes of antibiotics commonly used for assuaging diarrheal symptoms. Antimicrobial resistance develops when pathogens acquire antimicrobial resistance genes (ARGs) through genetic recombination from commensals and pathogens. These are the constituents of the complex microbiota in all ecological niches. The recombination events may occur in the environment or in the gut. Containment of AMR can be achieved through a complete understanding of the complex and diverse structure and function of the microbiota. Its taxonomic entities serve as focal points for the dissemination of antimicrobial resistance genetic determinants. Molecular methods complemented with culture-based diagnostics have been historically implemented to document these natural events. However, the advent of next-generation sequencing has revolutionized the field of molecular epidemiology. It has revolutionized the method of addressing relevant problems like diagnosis and surveillance of infectious diseases and the issue of antimicrobial resistance. Metagenomics is one such next-generation technique that has proved to be a monumental advancement in the area of molecular taxonomy. Current understanding of structure, function and dysbiosis of microbiota associated with antimicrobial resistance was realized due to its conception. This review describes the major milestones achieved due to the advent and implementation of this new technique in the context of antimicrobial resistance. These achievements span a wide panorama from the discovery of novel microorganisms to invention of translational value.
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Hong Y, Cheng Y, Li Y, Li X, Zhou Z, Shi D, Li Z, Xiao Y. Preliminary Study on the Effect of Bacillus amyloliquefaciens TL on Cecal Bacterial Community Structure of Broiler Chickens. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5431354. [PMID: 31687392 PMCID: PMC6794981 DOI: 10.1155/2019/5431354] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/11/2019] [Indexed: 02/01/2023]
Abstract
Probiotics can promote the health and growth performance of animals through modulation of intestinal microbiota. When used as a feed additive, they have the potential to minimize or abolish the use of antibiotics. In this study, we investigated the effect of the probiotic strain Bacillus amyloliquefaciens TL on the growth performance and cecum microflora composition in Cobb 500 broiler chickens. In total, 180 broilers were randomly divided into three groups-each group comprised 4 pens, and each pen contained 15 chickens. The three groups were fed either a control diet, or a diet supplemented with either the antibiotic chlortetracycline or B. amyloliquefaciens TL. Broilers were weighed, and cecum contents were collected on days 7, 14, 21, and 35, respectively. The broilers in both the antibiotic and probiotic groups exhibited significant weight gain compared with controls, exhibiting increases of 16.02% and 13.40%, respectively, after 35 days (P < 0.01). Similarly, the feed conversion ratio (FCR, 1-35 days) of broilers in the chlortetracycline and B. amyloliquefaciens TL groups was lower than that of the controls. HiSeq high-throughput sequencing of 16S rRNA of the cecal microbiota was performed on days 7, 14, 21, and 35, respectively. The Firmicutes/Bacteroidetes ratio was higher in the chlortetracycline and B. amyloliquefaciens TL groups than in the control group on days 14, 21, and 35, and especially on day 21. The prevalence of genera Oscillospira, Ruminococcus, Butyricicoccus, and Faecalibacterium (Firmicutes) was higher in the antibiotic and probiotic groups, while that of Bacteroides, Parabacteroides (Bacteroidetes), and Lactobacillus was higher in the control group. In this study, the changes in the microbiota of the probiotic group were similar to those in the antibiotic group. These results suggest that the probiotic strain B. amyloliquefaciens TL can modulate the cecal microbiota of broilers similar to chlortetracycline.
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Affiliation(s)
- Yuxuan Hong
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yingxian Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yanjuan Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Xiaowen Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zutao Zhou
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Deshi Shi
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zili Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yuncai Xiao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
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Senapati T, Kothidar A, Banerjee SK, DAS B. Insights into the gastrointestinal tract microbiomes of Indian population. J Biosci 2019; 44:113. [PMID: 31719222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trillions of microbes living in the gastrointestinal tract (GIT) of the human body finely tune homeostatic equilibrium in the GIT ecosystem and encode key functionalities that play crucial role in host metabolic functions, synthesis of macro- and micronutrients, xenobiotics metabolisms, development of innate and adaptive immune systems, tissue and organ developments and resistance against invasion of enteric pathogens. The microbial diversity and richness of GIT ecosystem varies greatly between individuals and over time. Extent of taxonomic and functional variations in GIT ecosystem is linked with dietary habit, pharmaceuticals usages, age, sex, body mass index, ethnicity, geography, altitude and civilization. Understanding a holistic picture of GIT microbiome of healthy people living across geography and identifying population specific 'keystone' taxa is of immense importance for identifying microbial species that may provide protection against chronic and metabolic diseases. Knowledge on geographic or ethnicity specific microbial signatures may also help us to understand the varied efficacy of different drugs and vaccines in different population. India is the home of more than 1.36 billion people belonging to 2000 human communities residing in well distinct geography. In the present review, we discuss the microbial signatures in health and diseases of the rural and urban Indians living in sea level and high altitude areas.
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Affiliation(s)
- Tarosi Senapati
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121 001, India
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Senapati T, Kothidar A, Banerjee SK, Das B. Insights into the gastrointestinal tract microbiomes of Indian population. J Biosci 2019. [DOI: 10.1007/s12038-019-9927-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Escudeiro P, Pothier J, Dionisio F, Nogueira T. Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes. mSphere 2019; 4:e00135-19. [PMID: 31043514 PMCID: PMC6495336 DOI: 10.1128/msphere.00135-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/11/2019] [Indexed: 01/12/2023] Open
Abstract
Human beings have used large amounts of antibiotics, not only in medical contexts but also, for example, as growth factors in agriculture and livestock, resulting in the contamination of the environment. Even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are affected as well. Therefore, both pathogenic and nonpathogenic bacteria have gradually become resistant to antibiotics. We tested whether there is still cooccurrence of resistance and virulence determinants. We performed a comparative study of environmental and human gut metagenomes from different individuals and from distinct human populations across the world. We found a great diversity of antibiotic resistance determinants (AR diversity [ARd]) and virulence factors (VF diversity [VFd]) in metagenomes. Importantly there is a correlation between ARd and VFd, even after correcting for protein family richness. In the human gut, there are less ARd and VFd than in more diversified environments, and yet correlations between the ARd and VFd are stronger. They can vary from very high in Malawi, where antibiotic consumption is unattended, to nonexistent in the uncontacted Amerindian population. We conclude that there is cooccurrence of resistance and virulence determinants in human gut microbiomes, suggesting a possible coselective mechanism.IMPORTANCE Every year, thousands of tons of antibiotics are used, not only in human and animal health but also as growth promoters in livestock. Consequently, during the last 75 years, antibiotic-resistant bacterial strains have been selected in human and environmental microbial communities. This implies that, even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are also affected. Here, we performed a comparative study of environmental and human gut microbial communities issuing from different individuals and from distinct human populations across the world. We found that antibiotic resistance and pathogenicity are correlated and speculate that, by selecting for resistant bacteria, we may be selecting for more virulent strains as a side effect of antimicrobial therapy.
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Affiliation(s)
- Pedro Escudeiro
- cE3c-Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Joël Pothier
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Francisco Dionisio
- cE3c-Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa Nogueira
- cE3c-Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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Liss MA, Leach RJ, Rourke E, Sherrill A, Johnson-Pais T, Lai Z, Basler J, White JR, Patterson JE. Microbiome diversity in carriers of fluoroquinolone resistant Escherichia coli. Investig Clin Urol 2019; 60:75-83. [PMID: 30838339 PMCID: PMC6397931 DOI: 10.4111/icu.2019.60.2.75] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 02/03/2019] [Indexed: 12/18/2022] Open
Abstract
Purpose Fluoroquinolone-resistant (FQR) Escherichia coli causes transrectal prostate biopsy infections. In order to reduce colonization of these bacteria in carriers, we would like to understand the surrounding microbiome to determine targets for decolonization. Materials and Methods We perform an observational study to investigate the microbiome differences in men with and without FQR organisms found on rectal culture. A rectal swab with two culturettes was performed on men before an upcoming prostate biopsy procedure as standard of care to perform “targeted prophylaxis.” Detection of FQR was performed by the standard microbiology lab inoculates the swab onto MacConkey agar containing ciprofloxacin. The extra swab was sent for 16S rRNA amplicon sequencing (MiSeq paired-end) using the V1V2 primer. Alpha and beta-diversity analysis were performed using QIIME. We used PERMANOVA to evaluate the statistical significance of beta-diversity distances within and between groups of interest. Results We collected 116 rectal swab samples before biopsy for 16S rRNA amplicon sequencing. We identified 18 isolates (15.5%, 18/116) that were positive and had relative reduced diversity profiles (p<0.05). Enterobacteriaceae were significantly over-represented in the FQR subjects (adjusted p=0.03). Conclusions Microbiome analysis determined that men colonized with FQR bacteria have less diverse bacterial communities (dysbiosis), higher levels of Enterobacteriaceae and reduced levels of Prevotella disiens. These results may have implications in pre/probiotic intervention studies.
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Affiliation(s)
- Michael A Liss
- Department of Urology, UT Health San Antonio Long School of Medicine, San Antonio, TX, USA.,South Texas Veterans Healthcare System, San Antonio, TX, USA
| | - Robin J Leach
- Department of Urology, UT Health San Antonio Long School of Medicine, San Antonio, TX, USA.,Department of Cell Systems and Anatomy, UT Health San Antonio Long School of Medicine, San Antonio, TX, USA
| | - Elizabeth Rourke
- Department of Urology, UT Health San Antonio Long School of Medicine, San Antonio, TX, USA
| | - Allison Sherrill
- Department of Urology, UT Health San Antonio Long School of Medicine, San Antonio, TX, USA
| | - Teresa Johnson-Pais
- Department of Urology, UT Health San Antonio Long School of Medicine, San Antonio, TX, USA.,Department of Cell Systems and Anatomy, UT Health San Antonio Long School of Medicine, San Antonio, TX, USA
| | - Zhao Lai
- Genome Sequencing Facility (GSF) in the Greehey Children's Cancer Research Institute (Greehey CCRI), San Antonio, TX, USA
| | - Joseph Basler
- Department of Urology, UT Health San Antonio Long School of Medicine, San Antonio, TX, USA
| | | | - Jan E Patterson
- Department of Medicine, UT Health San Antonio Long School of Medicine, San Antonio, TX, USA
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Bag S, Ghosh TS, Banerjee S, Mehta O, Verma J, Dayal M, Desigamani A, Kumar P, Saha B, Kedia S, Ahuja V, Ramamurthy T, Das B. Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota. MICROBIAL ECOLOGY 2019; 77:546-557. [PMID: 30009332 DOI: 10.1007/s00248-018-1228-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Antimicrobial resistance (AMR) among bacterial species that resides in complex ecosystems is a natural phenomenon. Indiscriminate use of antimicrobials in healthcare, livestock, and agriculture provides an evolutionary advantage to the resistant variants to dominate the ecosystem. Ascendency of resistant variants threatens the efficacy of most, if not all, of the antimicrobial drugs commonly used to prevent and/or cure microbial infections. Resistant phenotype is very common in enteric bacteria. The most common mechanisms of AMR are enzymatic modifications to the antimicrobials or their target molecules. In enteric bacteria, most of the resistance traits are acquired by horizontal gene transfer from closely or distantly related bacterial population. AMR traits are generally linked with mobile genetic elements (MGEs) and could rapidly disseminate to the bacterial species through horizontal gene transfer (HGT) from a pool of resistance genes. Although prevalence of AMR genes among pathogenic bacteria is widely studied in the interest of infectious disease management, the resistance profile and the genetic traits that encode resistance to the commensal microbiota residing in the gut of healthy humans are not well-studied. In the present study, we have characterized AMR phenotypes and genotypes of five dominant commensal enteric bacteria isolated from the gut of healthy Indians. Our study revealed that like pathogenic bacteria, enteric commensals are also multidrug-resistant. The genes encoding antibiotic resistance are physically linked with MGEs and could disseminate vertically to the progeny and laterally to the distantly related microbial species. Consequently, the AMR genes present in the chromosome of commensal gut bacteria could be a potential source of resistance functions for other enteric pathogens.
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Affiliation(s)
- Satyabrata Bag
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Tarini Shankar Ghosh
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Sayantan Banerjee
- Division of Infectious Diseases, Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Ojasvi Mehta
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Jyoti Verma
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Mayanka Dayal
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Anbumani Desigamani
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Pawan Kumar
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Bipasa Saha
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Saurabh Kedia
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Thandavarayan Ramamurthy
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Bhabatosh Das
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India.
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Ruppé E, Ghozlane A, Tap J, Pons N, Alvarez AS, Maziers N, Cuesta T, Hernando-Amado S, Clares I, Martínez JL, Coque TM, Baquero F, Lanza VF, Máiz L, Goulenok T, de Lastours V, Amor N, Fantin B, Wieder I, Andremont A, van Schaik W, Rogers M, Zhang X, Willems RJL, de Brevern AG, Batto JM, Blottière HM, Léonard P, Léjard V, Letur A, Levenez F, Weiszer K, Haimet F, Doré J, Kennedy SP, Ehrlich SD. Prediction of the intestinal resistome by a three-dimensional structure-based method. Nat Microbiol 2018; 4:112-123. [PMID: 30478291 DOI: 10.1038/s41564-018-0292-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/11/2018] [Indexed: 12/21/2022]
Abstract
The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens via mobile genetic elements. Yet, this assumption is poorly supported by empirical evidence due to the distant homologies between known ARDs (mostly from culturable bacteria) and ARDs from the intestinal microbiota. Consequently, an accurate census of intestinal ARDs (that is, the intestinal resistome) has not yet been fully determined. For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. We found that the majority of predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino acid identity 29.8%) and found little evidence supporting their transfer between species. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n = 663) into six resistotypes that were connected to the previously described enterotypes. Finally, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. Altogether, our results indicate that the majority of intestinal microbiota ARDs can be considered intrinsic to the dominant commensal microbiota and that these genes are rarely shared with bacterial pathogens.
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Affiliation(s)
- Etienne Ruppé
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France. .,IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.
| | - Amine Ghozlane
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France.,Institut Pasteur - Biomics - CITECH, Paris, France
| | - Julien Tap
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Danone Nutricia Research, Palaiseau, France
| | - Nicolas Pons
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | | | - Nicolas Maziers
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | | | | | - Irene Clares
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | | | - Teresa M Coque
- Servicio de Microbiología Instituto, Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología Instituto, Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain
| | - Val F Lanza
- Servicio de Microbiología Instituto, Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - Luis Máiz
- Unit for Cystic Fibrosis, Ramon y Cajal University Hospital, Madrid, Spain
| | - Tiphaine Goulenok
- Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Victoire de Lastours
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Nawal Amor
- Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Bruno Fantin
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Ingrid Wieder
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Antoine Andremont
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands.,Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, UK
| | - Malbert Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Xinglin Zhang
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexandre G de Brevern
- INSERM UMR_S 1134, Paris Diderot University, Sorbonne Paris Cité, Université de la Réunion, Université des Antilles, INTS, GR-Ex, Paris, France
| | - Jean-Michel Batto
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Hervé M Blottière
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Pierre Léonard
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Véronique Léjard
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Aline Letur
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Florence Levenez
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Kevin Weiszer
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Florence Haimet
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Joël Doré
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Sean P Kennedy
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Institut Pasteur - Biomics - CITECH, Paris, France
| | - S Dusko Ehrlich
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Centre of Host Microbiome Interactions, King's College, London, UK
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32
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Nogueira T, David PHC, Pothier J. Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach. Drug Dev Res 2018; 80:86-97. [PMID: 30370682 DOI: 10.1002/ddr.21466] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/14/2018] [Accepted: 08/15/2018] [Indexed: 12/28/2022]
Abstract
The exposure of the human gut to antibiotics can have a great impact on human health. Antibiotics pertain to the preservation of human health and are useful tools for fighting bacterial infections. They can be used for curing infections and can play a critical role in immunocompromised or chronic patients, or in fighting childhood severe malnutrition. Yet, the genomic and phylogenetic diversity of the human gut changes under antibiotic exposure. Antibiotics can also have severe side effects on human gut health, due to the spreading of potential antibiotic resistance genetic traits and to their correlation with virulence of some bacterial pathogens. They can shape, and even disrupt, the composition and functioning diversity of the human gut microbiome. Traditionally bacterial antibiotic resistances have been evaluated at clone or population level. However, the understanding of these two apparently disparate perspectives as both friends and foes may come from the study of microbiomes as a whole and from the evaluation of both positive and negative effects of antibiotics on microbial community dynamics and diversity. In this review we present some metagenomic tools and databases that enable the studying of antibiotic resistance in human gut metagenomes, promoting the development of personalized medicine strategies, new antimicrobial therapy protocols and patient follow-up.
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Affiliation(s)
- Teresa Nogueira
- cE3c - Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro H C David
- cE3c - Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Joël Pothier
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, Muséum National d'Histoire naturelle, CNRS, EPHE, CP, Paris, France
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33
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Lim MY, Cho Y, Rho M. Diverse Distribution of Resistomes in the Human and Environmental Microbiomes. Curr Genomics 2018; 19:701-711. [PMID: 30532649 PMCID: PMC6225452 DOI: 10.2174/1389202919666180911130845] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 04/14/2018] [Accepted: 09/03/2018] [Indexed: 11/22/2022] Open
Abstract
The routine therapeutic use of antibiotics has caused resistance genes to be disseminated across microbial populations. In particular, bacterial strains having antibiotic resistance genes are frequently observed in the human microbiome. Moreover, multidrug-resistant pathogens are now widely spread, threatening public health. Such genes are transferred and spread among bacteria even in different environments. Advances in high throughput sequencing technology and computational algorithms have accelerated investigation into antibiotic resistance genes of bacteria. Such studies have revealed that the antibiotic resistance genes are located close to the mobility-associated genes, which promotes their dissemination. An increasing level of information on genomic sequences of resistome should expedite research on drug-resistance in our body and environment, thereby contributing to the development of public health policy. In this review, the high prevalence of antibiotic resistance genes and their exchange in the human and environmental microbiome is discussed with respect to the genomic contents. The relationships among diverse resistomes, related bacterial species, and the antibiotics are reviewed. In addition, recent advances in bioinformatics approaches to investigate such relationships are discussed.
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Affiliation(s)
- Mi Young Lim
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
| | - Youna Cho
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
| | - Mina Rho
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
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34
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Obiakor CV, Tun HM, Bridgman SL, Arrieta MC, Kozyrskyj AL. The association between early life antibiotic use and allergic disease in young children: recent insights and their implications. Expert Rev Clin Immunol 2018; 14:841-855. [PMID: 30198345 DOI: 10.1080/1744666x.2018.1521271] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Greater prescribing of antibiotics to infants has coincided with an epidemic of allergic disease. Through meta-analytic synthesis, accumulating evidence from prospective or database cohorts suggests a link between infant antibiotic treatment and the development of atopy. Stronger associations seen with multiple course and broad-spectrum antibiotic treatment add to biological plausibility. A major bias, confounding by indication, has been addressed in studies on antibiotic treatment of conditions which do not precede allergic disease. Areas covered: Our review provides an up-to-date synthesis of the current literature on associations between infant antibiotic exposure and future allergic disease. We discuss methods that assist in reducing study bias and look at new insights from studies of the infant gut microbiome. Expert commentary: Large-scale profiling of the gut microbiome provides a new tool for disentangling biases found in observational studies of infant antibiotic use. To date, microbial dysbiosis of the infant gut has been reported to predict allergic disease independent of antibiotic exposure up to 3 months after birth. However, these studies have not accounted for antibiotic treatment in later infancy. Continued study of the infant gut microbiome, mycobiome, or resistome will provide a closer link to antibiotic treatment or refute it as a cause of allergic disease.
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Affiliation(s)
- Chinwe V Obiakor
- a School of Public Health , University of Alberta , Edmonton , Canada
| | - Hein M Tun
- b Department of Pediatrics , University of Alberta , Edmonton , Canada.,c HKU-Pasteur Research Pole, School of Public Health , The University of Hong Kong, Hong Kong , Hong Kong
| | - Sarah L Bridgman
- b Department of Pediatrics , University of Alberta , Edmonton , Canada
| | - Marie-Claire Arrieta
- d Departments of Physiology and Pharmacology & Pediatrics , Cumming School of Medicine, University of Calgary , Calgary , Canada
| | - Anita L Kozyrskyj
- a School of Public Health , University of Alberta , Edmonton , Canada.,b Department of Pediatrics , University of Alberta , Edmonton , Canada.,e Department of Obstetrics and Gynecology , University of Alberta , Edmonton , Canada
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35
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Alves LDF, Westmann CA, Lovate GL, de Siqueira GMV, Borelli TC, Guazzaroni ME. Metagenomic Approaches for Understanding New Concepts in Microbial Science. Int J Genomics 2018; 2018:2312987. [PMID: 30211213 PMCID: PMC6126073 DOI: 10.1155/2018/2312987] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/21/2018] [Accepted: 07/29/2018] [Indexed: 12/15/2022] Open
Abstract
Over the past thirty years, since the dawn of metagenomic studies, a completely new (micro) universe was revealed, with the potential to have profound impacts on many aspects of the society. Remarkably, the study of human microbiome provided a new perspective on a myriad of human traits previously regarded as solely (epi-) genetically encoded, such as disease susceptibility, immunological response, and social and nutritional behaviors. In this context, metagenomics has established a powerful framework for understanding the intricate connections between human societies and microbial communities, ultimately allowing for the optimization of both human health and productivity. Thus, we have shifted from the old concept of microbes as harmful organisms to a broader panorama, in which the signal of the relationship between humans and microbes is flexible and directly dependent on our own decisions and practices. In parallel, metagenomics has also been playing a major role in the prospection of "hidden" genetic features and the development of biotechnological applications, through the discovery of novel genes, enzymes, pathways, and bioactive molecules with completely new or improved biochemical functions. Therefore, this review highlights the major milestones over the last three decades of metagenomics, providing insights into both its potentialities and current challenges.
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Affiliation(s)
- Luana de Fátima Alves
- Department of Biochemistry, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Cauã Antunes Westmann
- Department of Cell Biology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Gabriel Lencioni Lovate
- Department of Biochemistry, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Tiago Cabral Borelli
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - María-Eugenia Guazzaroni
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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Abstract
AbstractAntibiotic resistance (AR) is ancient. Use of antibiotics is a selective driving force that enriches AR genes and promotes the emergence of resistant pathogens. It also has been widely accepted that horizontal gene transfer (HGT) occurs everywhere and plays a critical role in the transmission of AR genes among bacteria. However, our understanding of HGT processes primarily build on extensivein vitrostudies; to date, there is still a significant knowledge gap regardingin situHGT events as well as the factors that influence HGT in different ecological niches. This review is focused on the HGT process in the intestinal tract, a ‘melting pot’ for gene exchange. Several factors that potentially influencein vivoHGT efficiency in the intestine are identified and summarized, which include SOS-inducing agents, stress hormones, microbiota and microbiota-derived factors. We highlight recent discoveries demonstrating that certain antibiotics, which are widely used in animal industry, can enhance HGT in the intestine by serving as DNA-damaging, SOS-inducing agents. Despite recent progress, research onin vivoHGT events is still in its infancy. A better understanding of the factors influencing HGT in the intestine is highly warranted for developing effective strategies to mitigate AR in animal production as well as in future agricultural ecosystems.
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37
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Lanza VF, Baquero F, Martínez JL, Ramos-Ruíz R, González-Zorn B, Andremont A, Sánchez-Valenzuela A, Ehrlich SD, Kennedy S, Ruppé E, van Schaik W, Willems RJ, de la Cruz F, Coque TM. In-depth resistome analysis by targeted metagenomics. MICROBIOME 2018; 6:11. [PMID: 29335005 PMCID: PMC5769438 DOI: 10.1186/s40168-017-0387-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 12/17/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype. Here, we describe a novel strategy that combines targeted metagenomics using last generation in-solution capture platforms, with novel bioinformatics tools to establish a standardized framework that allows both quantitative and qualitative analyses of resistomes. METHODS We developed ResCap, a targeted sequence capture platform based on SeqCapEZ (NimbleGene) technology, which includes probes for 8667 canonical resistance genes (7963 antibiotic resistance genes and 704 genes conferring resistance to metals or biocides), and 2517 relaxase genes (plasmid markers) and 78,600 genes homologous to the previous identified targets (47,806 for antibiotics and 30,794 for biocides or metals). Its performance was compared with metagenomic shotgun sequencing (MSS) for 17 fecal samples (9 humans, 8 swine). ResCap significantly improves MSS to detect "gene abundance" (from 2.0 to 83.2%) and "gene diversity" (26 versus 14.9 genes unequivocally detected per sample per million of reads; the number of reads unequivocally mapped increasing up to 300-fold by using ResCap), which were calculated using novel bioinformatic tools. ResCap also facilitated the analysis of novel genes potentially involved in the resistance to antibiotics, metals, biocides, or any combination thereof. CONCLUSIONS ResCap, the first targeted sequence capture, specifically developed to analyze resistomes, greatly enhances the sensitivity and specificity of available metagenomic methods and offers the possibility to analyze genes related to the selection and transfer of antimicrobial resistance (biocides, heavy metals, plasmids). The model opens the possibility to study other complex microbial systems in which minority populations play a relevant role.
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Affiliation(s)
- Val F Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Joint Unit of Antibiotic Resistance and Bacterial Virulence associated with the Spanish National Research Council (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
- National Center of Biotechnology, CSIC, Madrid, Spain
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Joint Unit of Antibiotic Resistance and Bacterial Virulence associated with the Spanish National Research Council (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - José Luís Martínez
- Joint Unit of Antibiotic Resistance and Bacterial Virulence associated with the Spanish National Research Council (CSIC), Madrid, Spain
- National Center of Biotechnology, CSIC, Madrid, Spain
| | | | - Bruno González-Zorn
- Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | - Antoine Andremont
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Bacteriology Laboratory, Hospital Bichat, AP-HP, Paris, France
| | - Antonio Sánchez-Valenzuela
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Stanislav Dusko Ehrlich
- MGP MetaGénoPolis, INRA, University of Paris-Saclay, Jouy-en-Josas, France
- Center of Host Microbiome Interactions, King's College, London, UK
| | - Sean Kennedy
- MGP MetaGénoPolis, INRA, University of Paris-Saclay, Jouy-en-Josas, France
- Present Address: Bioinformatics and Biostatistics HUB, C3BI and Biomics Pole, CITECH Pasteur Institute, Centre François Jacob, Paris, France
| | - Etienne Ruppé
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Bacteriology Laboratory, Hospital Bichat, AP-HP, Paris, France
- MGP MetaGénoPolis, INRA, University of Paris-Saclay, Jouy-en-Josas, France
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center, Utrecht, Netherlands
- Present Address: Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rob J Willems
- Department of Medical Microbiology, University Medical Center, Utrecht, Netherlands
| | - Fernando de la Cruz
- Department of Molecular Biology, University of Cantabria, Santander, Spain
- Institute of Biomedicine and Biotechnology of Cantabria, IBBTEC (UC-CSIC), Santander, Spain
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.
- Joint Unit of Antibiotic Resistance and Bacterial Virulence associated with the Spanish National Research Council (CSIC), Madrid, Spain.
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.
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38
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Wen X, Wang Y, Zou Y, Ma B, Wu Y. No evidential correlation between veterinary antibiotic degradation ability and resistance genes in microorganisms during the biodegradation of doxycycline. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 147:759-766. [PMID: 28942279 DOI: 10.1016/j.ecoenv.2017.09.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 09/05/2017] [Accepted: 09/09/2017] [Indexed: 06/07/2023]
Abstract
Biodegradation of antibiotic residues in the environment by microorganisms may lead to the generation of antibiotic resistance genes (ARGs), which are of great concern to human health. The aim of this study was to determine whether there is a relationship between the ability to degrade antibiotic doxycycline (DOX) and the development of resistance genes in microorganisms. We isolated and identified ten bacterial strains from a vegetable field that had received long-term manure application as fertilizer and were capable of surviving in a series of DOX concentrations (25, 50, 80, and 100mg/L). Our results showed no evidential correlation between DOX degradation ability and the development of resistance genes among the isolated microorganisms that had high DOX degradation capability (P > 0.05). This was based on the fact that Escherichia sp. and Candida sp. were the most efficient bacterial strains to degrade DOX (92.52% and 91.63%, respectively), but their tetracycline resistance genes showed a relatively low risk of antibiotic resistance in a 7-day experiment. Moreover, the tetM of the ribosomal protection protein genes carried by these two preponderant bacteria was five-fold higher than that carried by other isolates (P < 0.05). Pearson correlations between the Ct/C0 of DOX and tet resistance genes of three isolates, except for Escherichia sp. and Candida sp., showed remarkable negative correlations (P < 0.05), mainly because tetG markedly increased during the DOX degradation process. Our results concluded that the biodegradation of antibiotic residues may not necessarily lead to the development of ARGs in the environment. In addition, the two bacteria that we isolated, namely, Escherichia sp. and Candida sp., are potential candidates for the engineering of environmentally friendly bacteria.
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Affiliation(s)
- Xin Wen
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Yan Wang
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Enterprise Lab of Healthy Animal Husbandry and Environment Control, Yunfu, Xinxing 527400, China
| | - Yongde Zou
- Nanhai Entry-Exit Inspection and Quarantine Bureau, Foshan 528200, China
| | - Baohua Ma
- Nanhai Entry-Exit Inspection and Quarantine Bureau, Foshan 528200, China
| | - Yinbao Wu
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Enterprise Lab of Healthy Animal Husbandry and Environment Control, Yunfu, Xinxing 527400, China.
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39
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Brinkac L, Voorhies A, Gomez A, Nelson KE. The Threat of Antimicrobial Resistance on the Human Microbiome. MICROBIAL ECOLOGY 2017; 74:1001-1008. [PMID: 28492988 PMCID: PMC5654679 DOI: 10.1007/s00248-017-0985-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 04/18/2017] [Indexed: 05/22/2023]
Abstract
Ubiquitous in nature, antimicrobial resistance (AMR) has existed long before the golden age of antimicrobials. While antimicrobial agents are beneficial to combat infection, their widespread use contributes to the increase in and emergence of novel resistant microbes in virtually all environmental niches. The human microbiome is an important reservoir of AMR with initial exposure occurring in early life. Once seeded with AMR, commensal organisms may be key contributors to the dissemination of resistance due to the interconnectedness of microbial communities. When acquired by pathogens however, AMR becomes a serious public health threat worldwide. Our ability to combat the threat of emerging resistance relies on accurate AMR detection methods and the development of therapeutics that function despite the presence of antimicrobial resistance.
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Affiliation(s)
- Lauren Brinkac
- J. Craig Venter Institute|, Rockville, MD, 20850, USA.
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4000, South Africa.
| | | | - Andres Gomez
- J. Craig Venter Institute|, Rockville, MD, 20850, USA
| | - Karen E Nelson
- J. Craig Venter Institute|, Rockville, MD, 20850, USA
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4000, South Africa
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40
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OHASHI Y, FUJISAWA T. Detection of antibiotic resistance genes in the feces of young adult Japanese. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2017; 36:151-154. [PMID: 29038771 PMCID: PMC5633530 DOI: 10.12938/bmfh.17-004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/14/2017] [Indexed: 11/16/2022]
Abstract
Antibiotic resistance genes in the feces of healthy young adult Japanese were analyzed with polymerase chain reaction using specific primers. Antibiotic resistance genes against macrolides (ermB, ermF, ermX, and mefA/E), tetracyclines (tetW, tetQ, tetO, and tetX), β-lactam antibiotics (blaTEM ), and streptomycin (aadE) were detected in more than 50% of subjects. These antibiotic resistance genes are likely widespread in the large intestinal bacteria of young adult Japanese.
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Affiliation(s)
- Yuji OHASHI
- Laboratory of Food Hygiene, Department of Food Science and Technology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan
| | - Tomohiko FUJISAWA
- Laboratory of Food Hygiene, Department of Food Science and Technology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan
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41
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Kim Y, Van Bonn W, Aw TG, Rose JB. Aquarium Viromes: Viromes of Human-Managed Aquatic Systems. Front Microbiol 2017; 8:1231. [PMID: 28713358 PMCID: PMC5492393 DOI: 10.3389/fmicb.2017.01231] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/19/2017] [Indexed: 11/13/2022] Open
Abstract
An aquarium ecosystem is home to many animal species providing conditions similar to native aquatic habitats but under highly controlled management. With a growing interest in understanding the interaction of microbiomes and resident animal health within aquarium environments, we undertook a metagenomic survey of viromes in seven aquarium systems with differing physicochemical and resident animal profiles. Our results show that a diverse array of viruses was represented in aquarium viromes, many of which were widespread in different aquarium systems (27 common viral families in all of the aquarium systems). Most viromes were dominated by DNA phages of the order Caudovirales as commonly found in other aquatic environments with average relative abundance greater than 64%. The composition and structure of aquarium viromes were associated with controlled system parameters, including nitrate, salinity, and temperature as well as resident animal profiles, indicating the close interaction of viromes with aquarium management practices. Furthermore, finding human associated viruses in a touch exhibit suggested that exposure of aquarium systems to human contact may lead to introduction of human cutaneous viruses into aquaria. This is consistent with the high abundance of skin microflora on the palms of healthy individuals and their detection in recreational waters, such as swimming pools. Lastly, assessment of antibiotic resistance genes (ARGs) in aquarium viromes revealed a unique signature of ARGs in different aquarium systems with trimethoprim being the most common. This is the first study to provide vital information on viromes and their unique relationships with management practices in a human-built and controlled aquarium environment.
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Affiliation(s)
- Yiseul Kim
- Department of Fisheries and Wildlife, Michigan State University, East LansingMI, United States.,National Institute of Agricultural Sciences, Rural Development AdministrationWanju, South Korea
| | - William Van Bonn
- Department of Fisheries and Wildlife, Michigan State University, East LansingMI, United States.,A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, ChicagoIL, United States
| | - Tiong G Aw
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New OrleansLA, United States
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East LansingMI, United States
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42
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Li J, Xie S, Ahmed S, Wang F, Gu Y, Zhang C, Chai X, Wu Y, Cai J, Cheng G. Antimicrobial Activity and Resistance: Influencing Factors. Front Pharmacol 2017; 8:364. [PMID: 28659799 PMCID: PMC5468421 DOI: 10.3389/fphar.2017.00364] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/26/2017] [Indexed: 01/09/2023] Open
Abstract
Rational use of antibiotic is the key approach to improve the antibiotic performance and tackling of the antimicrobial resistance. The efficacy of antimicrobials are influenced by many factors: (1) bacterial status (susceptibility and resistance, tolerance, persistence, biofilm) and inoculum size; (2) antimicrobial concentrations [mutant selection window (MSW) and sub-inhibitory concentration]; (3) host factors (serum effect and impact on gut micro-biota). Additional understandings regarding the linkage between antimicrobial usages, bacterial status and host response offers us new insights and encourage the struggle for the designing of antimicrobial treatment regimens that reaching better clinical outcome and minimizing the emergence of resistance at the same time.
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Affiliation(s)
- Jun Li
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for The Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China
| | - Shuyu Xie
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for The Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China
| | - Saeed Ahmed
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for The Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China
| | - Funan Wang
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for The Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China
| | - Yufeng Gu
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for The Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China
| | - Chaonan Zhang
- Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China
| | - Ximan Chai
- Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China
| | - Yalan Wu
- Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China
| | - Jinxia Cai
- Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China
| | - Guyue Cheng
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for The Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China.,Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China
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43
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Abstract
Antibiotics have been widely used for a number of decades for human therapy and farming production. Since a high percentage of antibiotics are discharged from the human or animal body without degradation, this means that different habitats, from the human body to river water or soils, are polluted with antibiotics. In this situation, it is expected that the variable concentration of this type of microbial inhibitor present in different ecosystems may affect the structure and the productivity of the microbiota colonizing such habitats. This effect can occur at different levels, including changes in the overall structure of the population, selection of resistant organisms, or alterations in bacterial physiology. In this review, I discuss the available information on how the presence of antibiotics may alter the microbiota and the consequences of such alterations for human health and for the activity of microbiota from different habitats.
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Affiliation(s)
- José Luis Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Calle Darwin, Madrid, Spain
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44
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Imperial ICVJ, Ibana JA. Addressing the Antibiotic Resistance Problem with Probiotics: Reducing the Risk of Its Double-Edged Sword Effect. Front Microbiol 2016; 7:1983. [PMID: 28018315 PMCID: PMC5156686 DOI: 10.3389/fmicb.2016.01983] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 11/28/2016] [Indexed: 12/27/2022] Open
Abstract
Antibiotic resistance is a global public health problem that requires our attention. Indiscriminate antibiotic use is a major contributor in the introduction of selective pressures in our natural environments that have significantly contributed in the rapid emergence of antibiotic-resistant microbial strains. The use of probiotics in lieu of antibiotic therapy to address certain health conditions in both animals and humans may alleviate these antibiotic-mediated selective pressures. Probiotic use is defined as the actual application of live beneficial microbes to obtain a desired outcome by preventing diseased state or improving general health. Multiple studies have confirmed the beneficial effects of probiotic use in the health of both livestock and humans. As such, probiotics consumption is gaining popularity worldwide. However, concerns have been raised in the use of some probiotics strains that carry antibiotic resistance genes themselves, as they have the potential to pass the antibiotic resistance genes to pathogenic bacteria through horizontal gene transfer. Therefore, with the current public health concern on antibiotic resistance globally, in this review, we underscore the need to screen probiotic strains that are used in both livestock and human applications to assure their safety and mitigate their potential in significantly contributing to the spread of antibiotic resistance genes in our natural environments.
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Affiliation(s)
- Ivan C V J Imperial
- Immunopharmacology Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman Quezon City, Philippines
| | - Joyce A Ibana
- Immunopharmacology Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman Quezon City, Philippines
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45
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Munk P, Andersen VD, de Knegt L, Jensen MS, Knudsen BE, Lukjancenko O, Mordhorst H, Clasen J, Agersø Y, Folkesson A, Pamp SJ, Vigre H, Aarestrup FM. A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds. J Antimicrob Chemother 2016; 72:385-392. [PMID: 28115502 DOI: 10.1093/jac/dkw415] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/28/2016] [Accepted: 08/31/2016] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Reliable methods for monitoring antimicrobial resistance (AMR) in livestock and other reservoirs are essential to understand the trends, transmission and importance of agricultural resistance. Quantification of AMR is mostly done using culture-based techniques, but metagenomic read mapping shows promise for quantitative resistance monitoring. METHODS We evaluated the ability of: (i) MIC determination for Escherichia coli; (ii) cfu counting of E. coli; (iii) cfu counting of aerobic bacteria; and (iv) metagenomic shotgun sequencing to predict expected tetracycline resistance based on known antimicrobial consumption in 10 Danish integrated slaughter pig herds. In addition, we evaluated whether fresh or manure floor samples constitute suitable proxies for intestinal sampling, using cfu counting, qPCR and metagenomic shotgun sequencing. RESULTS Metagenomic read-mapping outperformed cultivation-based techniques in terms of predicting expected tetracycline resistance based on antimicrobial consumption. Our metagenomic approach had sufficient resolution to detect antimicrobial-induced changes to individual resistance gene abundances. Pen floor manure samples were found to represent rectal samples well when analysed using metagenomics, as they contain the same DNA with the exception of a few contaminating taxa that proliferate in the extraintestinal environment. CONCLUSIONS We present a workflow, from sampling to interpretation, showing how resistance monitoring can be carried out in swine herds using a metagenomic approach. We propose metagenomic sequencing should be part of routine livestock resistance monitoring programmes and potentially of integrated One Health monitoring in all reservoirs.
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Affiliation(s)
- Patrick Munk
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Vibe Dalhoff Andersen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Leonardo de Knegt
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Marie Stengaard Jensen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Berith Elkær Knudsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Oksana Lukjancenko
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Hanne Mordhorst
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Julie Clasen
- Section for Bacteriology and Pathology, National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870 Frederiksberg C, Denmark
| | - Yvonne Agersø
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Anders Folkesson
- Section for Bacteriology and Pathology, National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870 Frederiksberg C, Denmark
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Håkan Vigre
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Frank Møller Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
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46
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Das A, Srinivasan M, Ghosh TS, Mande SS. Xenobiotic Metabolism and Gut Microbiomes. PLoS One 2016; 11:e0163099. [PMID: 27695034 PMCID: PMC5047465 DOI: 10.1371/journal.pone.0163099] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 09/03/2016] [Indexed: 12/27/2022] Open
Abstract
Humans are exposed to numerous xenobiotics, a majority of which are in the form of pharmaceuticals. Apart from human enzymes, recent studies have indicated the role of the gut bacterial community (microbiome) in metabolizing xenobiotics. However, little is known about the contribution of the plethora of gut microbiome in xenobiotic metabolism. The present study reports the results of analyses on xenobiotic metabolizing enzymes in various human gut microbiomes. A total of 397 available gut metagenomes from individuals of varying age groups from 8 nationalities were analyzed. Based on the diversities and abundances of the xenobiotic metabolizing enzymes, various bacterial taxa were classified into three groups, namely, least versatile, intermediately versatile and highly versatile xenobiotic metabolizers. Most interestingly, specific relationships were observed between the overall drug consumption profile and the abundance and diversity of the xenobiotic metabolizing repertoire in various geographies. The obtained differential abundance patterns of xenobiotic metabolizing enzymes and bacterial genera harboring them, suggest their links to pharmacokinetic variations among individuals. Additional analyses of a few well studied classes of drug modifying enzymes (DMEs) also indicate geographic as well as age specific trends.
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Affiliation(s)
- Anubhav Das
- TCS Research, Tata Consultancy Services Ltd., Pune, Maharashtra, India
| | - Meenakshi Srinivasan
- Manipal College of Pharmaceutical Sciences, Manipal University, Manipal, Karnataka, India
| | | | - Sharmila S. Mande
- TCS Research, Tata Consultancy Services Ltd., Pune, Maharashtra, India
- * E-mail:
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47
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Yadav D, Ghosh TS, Mande SS. Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups. Gut Pathog 2016; 8:17. [PMID: 27158266 PMCID: PMC4858888 DOI: 10.1186/s13099-016-0099-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/08/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Factors like ethnicity, diet and age of an individual have been hypothesized to play a role in determining the makeup of gut microbiome. In order to investigate the gut microbiome structure as well as the inter-microbial associations present therein, we have performed a comprehensive global comparative profiling of the structure (composition, relative heterogeneity and diversity) and the inter-microbial networks in the gut microbiomes of 399 individuals of eight different nationalities. RESULTS The study identified certain geography-specific trends with respect to composition, intra-group heterogeneity and diversity of the gut microbiomes. Interestingly, the gut microbial association/mutual-exlusion networks were observed to exhibit several cross-geography trends. It was seen that though the composition of gut microbiomes of the American and European individuals were similar, there were distinct patterns in their microbial interaction networks. Amongst European gut-microbiomes, the co-occurrence network obtained for the Danish population was observed to be most dense. Distinct patterns were also observed within Chinese, Japanese and Indian datasets. While performing an age-wise comparison, it was observed that the microbial interactions increased with the age of individuals. Furthermore, certain bacterial groups were identified to be present only in the older age groups. CONCLUSIONS The trends observed in gut microbial networks could be due to the inherent differences in the diet of individuals belonging to different nationalities. For example, the higher number of microbial associations in the Danish population as compared to the Spanish population, may be attributed to the evenly distributed diet of the later. This is in line with previously reported findings which indicate an increase in functional interdependency of microbes in individuals with higher nutritional status. To summarise, the present study identifies geography and age specific patterns in the composition as well as microbial interactions in gut microbiomes.
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Affiliation(s)
- Deepak Yadav
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune, 411013 Maharashtra India
| | - Tarini Shankar Ghosh
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune, 411013 Maharashtra India
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune, 411013 Maharashtra India
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48
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Wu G, Zhang C, Wang J, Zhang F, Wang R, Shen J, Wang L, Pang X, Zhang X, Zhao L, Zhang M. Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children. Sci Rep 2016; 6:24030. [PMID: 27044409 PMCID: PMC4820771 DOI: 10.1038/srep24030] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/18/2016] [Indexed: 12/30/2022] Open
Abstract
The gut microbiome represents an important reservoir of antibiotic resistance genes (ARGs). Effective methods are urgently needed for managing the gut resistome to fight against the antibiotic resistance threat. In this study, we show that a gut microbiota-targeted dietary intervention, which shifts the dominant fermentation of gut bacteria from protein to carbohydrate, significantly diminished the gut resistome and alleviated metabolic syndrome in obese children. Of the non-redundant metagenomic gene catalog of ~2 × 106 microbial genes, 399 ARGs were identified in 131 gene types and conferred resistance to 47 antibiotics. Both the richness and diversity of the gut resistome were significantly reduced after the intervention. A total of 201 of the 399 ARGs were carried in 120 co-abundance gene groups (CAGs) directly binned from the gene catalog across both pre-and post-intervention samples. The intervention significantly reduced several CAGs in Klebsiella, Enterobacter and Escherichia, which were the major hubs for multiple resistance gene types. Thus, dietary intervention may become a potentially effective method for diminishing the gut resistome.
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Affiliation(s)
- Guojun Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic &Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic &Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Jing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic &Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Feng Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic &Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Ruirui Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic &Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Jian Shen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic &Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Linghua Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic &Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Xiaoyan Pang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic &Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic &Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Liping Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic &Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Menghui Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic &Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
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49
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Ruppé E, Baud D, Schicklin S, Guigon G, Schrenzel J. Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia. Future Microbiol 2016; 11:427-39. [PMID: 26934540 DOI: 10.2217/fmb.15.144] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The increasing burden of multidrug-resistant bacteria affects the management of several infections. In order to prescribe adequate antibiotics, clinicians facing severe infections such as hospital-acquired pneumonia (HAP) need to promptly identify the pathogens and know their antibiotic susceptibility profiles (AST), which with conventional microbiology currently requires 24 and 48 h, respectively. Clinical metagenomics, based on whole genome sequencing of clinical samples, could improve the diagnosis of HAP, however, many obstacles remain to be overcome, namely the turn-around time, the quantification of pathogens, the choice of antibiotic resistance determinants (ARDs), the inference of the AST from metagenomic data and the linkage between ARDs and their host. Here, we propose to tackle those issues in a bottom-up, clinically driven approach.
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Affiliation(s)
- Etienne Ruppé
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, rue Gabrielle-Perret-Gentil 4, 1205 Geneva, Switzerland
| | - Damien Baud
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, rue Gabrielle-Perret-Gentil 4, 1205 Geneva, Switzerland
| | - Stéphane Schicklin
- Bioinformatics Research Department, bioMérieux, 69280 Marcy l'Etoile, France
| | - Ghislaine Guigon
- Bioinformatics Research Department, bioMérieux, 69280 Marcy l'Etoile, France
| | - Jacques Schrenzel
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, rue Gabrielle-Perret-Gentil 4, 1205 Geneva, Switzerland.,Bacteriology Lab, Service of Laboratory Medicine, Department of Genetics & Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland
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50
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Raymond F, Ouameur AA, Déraspe M, Iqbal N, Gingras H, Dridi B, Leprohon P, Plante PL, Giroux R, Bérubé È, Frenette J, Boudreau DK, Simard JL, Chabot I, Domingo MC, Trottier S, Boissinot M, Huletsky A, Roy PH, Ouellette M, Bergeron MG, Corbeil J. The initial state of the human gut microbiome determines its reshaping by antibiotics. THE ISME JOURNAL 2016; 10:707-20. [PMID: 26359913 PMCID: PMC4817689 DOI: 10.1038/ismej.2015.148] [Citation(s) in RCA: 224] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/09/2015] [Accepted: 07/15/2015] [Indexed: 02/07/2023]
Abstract
Microbiome studies have demonstrated the high inter-individual diversity of the gut microbiota. However, how the initial composition of the microbiome affects the impact of antibiotics on microbial communities is relatively unexplored. To specifically address this question, we administered a second-generation cephalosporin, cefprozil, to healthy volunteers. Stool samples gathered before antibiotic exposure, at the end of the treatment and 3 months later were analysed using shotgun metagenomic sequencing. On average, 15 billion nucleotides were sequenced for each sample. We show that standard antibiotic treatment can alter the gut microbiome in a specific, reproducible and predictable manner. The most consistent effect of the antibiotic was the increase of Lachnoclostridium bolteae in 16 out of the 18 cefprozil-exposed participants. Strikingly, we identified a subgroup of participants who were enriched in the opportunistic pathogen Enterobacter cloacae after exposure to the antibiotic, an effect linked to lower initial microbiome diversity and to a Bacteroides enterotype. Although the resistance gene content of participants' microbiomes was altered by the antibiotic, the impact of cefprozil remained specific to individual participants. Resistance genes that were not detectable prior to treatment were observed after a 7-day course of antibiotic administration. Specifically, point mutations in beta-lactamase blaCfxA-6 were enriched after antibiotic treatment in several participants. This suggests that monitoring the initial composition of the microbiome before treatment could assist in the prevention of some of the adverse effects associated with antibiotics or other treatments.
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Affiliation(s)
- Frédéric Raymond
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Amin A Ouameur
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Maxime Déraspe
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Naeem Iqbal
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Hélène Gingras
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Bédis Dridi
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Pier-Luc Plante
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Richard Giroux
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Ève Bérubé
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Johanne Frenette
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Dominique K Boudreau
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Jean-Luc Simard
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Isabelle Chabot
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Marc-Christian Domingo
- Institut National de Santé Publique du Québec, Laboratoire de Santé Publique du Québec, Montréal, Québec, Canada
| | - Sylvie Trottier
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Maurice Boissinot
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Ann Huletsky
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Paul H Roy
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Michel G Bergeron
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Jacques Corbeil
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
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