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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Mills M, Lee S, Piperata BA, Garabed R, Choi B, Lee J. Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua. Microbiome 2023; 11:207. [PMID: 37715296 PMCID: PMC10503196 DOI: 10.1186/s40168-023-01636-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/31/2023] [Indexed: 09/17/2023]
Abstract
BACKGROUND Early life plays a vital role in the development of the gut microbiome and subsequent health. While many factors that shape the gut microbiome have been described, including delivery mode, breastfeeding, and antibiotic use, the role of household environments is still unclear. Furthermore, the development of the gut antimicrobial resistome and its role in health and disease is not well characterized, particularly in settings with water insecurity and less sanitation infrastructure. RESULTS This study investigated the gut microbiome and resistome of infants and young children (ages 4 days-6 years) in rural Nicaragua using Oxford Nanopore Technology's MinION long-read sequencing. Differences in gut microbiome diversity and antibiotic resistance gene (ARG) abundance were examined for associations with host factors (age, sex, height for age z-score, weight for height z-score, delivery mode, breastfeeding habits) and household environmental factors (animals inside the home, coliforms in drinking water, enteric pathogens in household floors, fecal microbial source tracking markers in household floors). We identified anticipated associations of higher gut microbiome diversity with participant age and vaginal delivery. However, novel to this study were the significant, positive associations between ruminant and dog fecal contamination of household floors and gut microbiome diversity. We also identified greater abundance of potential pathogens in the gut microbiomes of participants with higher fecal contamination on their household floors. Path analysis revealed that water quality and household floor contamination independently and significantly influenced gut microbiome diversity when controlling for age. These gut microbiome contained diverse resistome, dominated by multidrug, tetracycline, macrolide/lincosamide/streptogramin, and beta-lactam resistance. We found that the abundance of ARGs in the gut decreased with age. The bacterial hosts of ARGs were mainly from the family Enterobacteriaceae, particularly Escherichia coli. CONCLUSIONS This study identified the role of household environmental contamination in the developing gut microbiome and resistome of young children and infants with a One Health perspective. We found significant relationships between host age, gut microbiome diversity, and the resistome. Understanding the impact of the household environment on the development of the resistome and microbiome in early life is essential to optimize the relationship between environmental exposure and human health. Video Abstract.
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Affiliation(s)
- Molly Mills
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Seungjun Lee
- Department of Food Science and Nutrition, College of Fisheries Science, Pukyong National University, Busan, Republic of Korea
| | - Barbara A Piperata
- Department of Anthropology, The Ohio State University, Columbus, OH, USA
| | - Rebecca Garabed
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Boseung Choi
- Division of Big Data Science, Korea University, Sejong, Republic of Korea
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA.
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA.
- Department of Food Science & Technology, The Ohio State University, Columbus, OH, USA.
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Nolan TM, Reynolds LJ, Sala-Comorera L, Martin NA, Stephens JH, O'Hare GMP, O'Sullivan JJ, Meijer WG. Land use as a critical determinant of faecal and antimicrobial resistance gene pollution in riverine systems. Sci Total Environ 2023; 871:162052. [PMID: 36758688 DOI: 10.1016/j.scitotenv.2023.162052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/24/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
The WHO recognises antimicrobial resistance (AMR) as a global health threat. The environment can act as a reservoir, facilitating the exchange and the physical movement of resistance. Aquatic environments are at particular risk of pollution, with large rivers subject to pollution from nearby human, industrial or agricultural activities. The land uses associated with these activities can influence the type of pollution. One type of pollution and a likely contributor to AMR pollution that lowers water quality is faecal pollution. Both pose an acute health risk and could have implications for resistance circulating in communities. The effects of land use are typically studied using physiochemical parameters or in isolation of one another. However, this study aimed to investigate the impact of different land uses on riverine systems. We explored whether differences in sources of faecal contamination are reflected in AMR gene concentrations across agricultural and urban areas. Water quality from three rivers impacted by different land uses was assessed over one year by quantifying faecal indicator bacteria (FIB), microbial source tracking markers (MST) and AMR genes. In addition, a multiparametric analysis of AMR gene pollution was carried out to understand whether agricultural and urban areas are similarly impacted. Faecal indicators varied greatly, with the highest levels of FIB and the human MST marker observed in urban regions. In addition, these faecal markers correlated with AMR genes. Similarly, significant correlations between the ruminant MST marker and AMR gene levels in agriculture areas were observed. Overall, applying multiparametric analyses to include AMR gene levels, separation and clustering of sites were seen based on land use characterisation. This study suggests that differences in prescription of antimicrobials used in animal and human healthcare may influence environmental resistomes across agricultural and urban areas. In addition, public health risks due to exposure to faecal contamination and AMR genes are highlighted.
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Affiliation(s)
- Tristan M Nolan
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Niamh A Martin
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jayne H Stephens
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Gregory M P O'Hare
- School of Computer Science and Statistics, Trinity College Dublin, Dublin 2, Ireland
| | - John J O'Sullivan
- UCD School of Civil Engineering, UCD Dooge Centre for Water Resources Research and UCD Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
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Downing T, Rahm A. Bacterial plasmid-associated and chromosomal proteins have fundamentally different properties in protein interaction networks. Sci Rep 2022; 12:19203. [PMID: 36357451 PMCID: PMC9649638 DOI: 10.1038/s41598-022-20809-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/19/2022] [Indexed: 11/12/2022] Open
Abstract
Plasmids facilitate horizontal gene transfer, which enables the diversification of pathogens into new anatomical and environmental niches, implying that plasmid-encoded genes can cooperate well with chromosomal genes. We hypothesise that such mobile genes are functionally different to chromosomal ones due to this ability to encode proteins performing non-essential functions like antimicrobial resistance and traverse distinct host cells. The effect of plasmid-driven gene gain on protein-protein interaction network topology is an important question in this area. Moreover, the extent to which these chromosomally- and plasmid-encoded proteins interact with proteins from their own groups compared to the levels with the other group remains unclear. Here, we examined the incidence and protein-protein interactions of all known plasmid-encoded proteins across representative specimens from most bacteria using all available plasmids. We found that plasmid-encoded genes constitute ~ 0.65% of the total number of genes per bacterial sample, and that plasmid genes are preferentially associated with different species but had limited taxonomical power beyond this. Surprisingly, plasmid-encoded proteins had both more protein-protein interactions compared to chromosomal proteins, countering the hypothesis that genes with higher mobility rates should have fewer protein-level interactions. Nonetheless, topological analysis and investigation of the protein-protein interaction networks' connectivity and change in the number of independent components demonstrated that the plasmid-encoded proteins had limited overall impact in > 96% of samples. This paper assembled extensive data on plasmid-encoded proteins, their interactions and associations with diverse bacterial specimens that is available for the community to investigate in more detail.
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Affiliation(s)
- Tim Downing
- grid.15596.3e0000000102380260School of Biotechnology, Dublin City University, Dublin, Ireland ,grid.63622.330000 0004 0388 7540Present Address: The Pirbright Institute, Pirbright, UK
| | - Alexander Rahm
- grid.449688.f0000 0004 0647 1487GAATI Lab, University of French Polynesia, Tahiti, French Polynesia
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Lamberte LE, van Schaik W. Antibiotic resistance in the commensal human gut microbiota. Curr Opin Microbiol 2022; 68:102150. [DOI: 10.1016/j.mib.2022.102150] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/19/2022] [Accepted: 03/24/2022] [Indexed: 12/24/2022]
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6
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Vassallo A, Kett S, Purchase D, Marvasi M. The Bacterial Urban Resistome: Recent Advances. Antibiotics (Basel) 2022; 11:512. [PMID: 35453263 PMCID: PMC9030810 DOI: 10.3390/antibiotics11040512] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Cities that are densely populated are reservoirs of antibiotic resistant genes (ARGs). The overall presence of all resistance genes in a specific environment is defined as a resistome. Spatial proximity of surfaces and different hygienic conditions leads to the transfer of antibiotic resistant bacteria (ARB) within urban environments. Built environments, public transportation, green spaces, and citizens’ behaviors all support persistence and transfer of antimicrobial resistances (AMR). Various unique aspects of urban settings that promote spread and resilience of ARGs/ARB are discussed: (i) the role of hospitals and recreational parks as reservoirs; (ii) private and public transportation as carriers of ARGs/ARB; (iii) the role of built environments as a hub for horizontal gene transfer even though they support lower microbial biodiversity than outdoor environments; (iv) the need to employ ecological and evolutionary concepts, such as modeling the fate of a specific ARG/ARB, to gain enhanced health risk assessments. Our understanding and our ability to control the rise of AMR in an urban setting is linked to our knowledge of the network connecting urban reservoirs and the environment.
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Lebeaux RM, Karalis DB, Lee J, Whitehouse HC, Madan JC, Karagas MR, Hoen AG. The association between early life antibiotic exposure and the gut resistome of young children: a systematic review. Gut Microbes 2022; 14:2120743. [PMID: 36289062 PMCID: PMC9621065 DOI: 10.1080/19490976.2022.2120743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/01/2022] [Accepted: 08/31/2022] [Indexed: 02/04/2023] Open
Abstract
Antimicrobial resistance is a growing public health burden, but little is known about the effects of antibiotic exposure on the gut resistome. As childhood (0-5 years) represents a sensitive window of microbiome development and a time of relatively high antibiotic use, the aims of this systematic review were to evaluate the effects of antibiotic exposure on the gut resistome of young children and identify knowledge gaps. We searched PubMed, Scopus, Web of Science, and the Cochrane Central Register of Controlled Trials. A PICO framework was developed to determine eligibility criteria. Our main outcomes were the mean or median difference in overall resistance gene load and resistome alpha diversity by antibiotic exposure groups. Bias assessment was completed using RoB 2 and ROBINS-I with quality of evidence assessed via the GRADE criteria. From 4885 records identified, 14 studies (3 randomized controlled trials and 11 observational studies) were included in the qualitative review. Eight studies that included information on antibiotic exposure and overall resistance gene load reported no or positive associations. Inconsistent associations were identified for the nine studies that assessed resistome alpha diversity. We identified three main groups of studies based on study design, location, participants, antibiotic exposures, and indication for antibiotics. Overall, the quality of evidence for our main outcomes was rated low or very low, mainly due to potential bias from the selective of reporting results and confounding. We found evidence that antibiotic exposure is associated with changes to the overall gut resistance gene load of children and may influence the diversity of antimicrobial resistance genes. Given the overall quality of the studies, more research is needed to assess how antibiotics impact the resistome of other populations. Nonetheless, this evidence indicates that the gut resistome is worthwhile to consider for antibiotic prescribing practices.
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Affiliation(s)
- Rebecca M. Lebeaux
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Despina B. Karalis
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Jihyun Lee
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Hanna C. Whitehouse
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Juliette C. Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Pediatrics, Children’s Hospital at Dartmouth, Lebanon, NH, USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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Abstract
Antimicrobials have been widely used to prevent and treat infectious diseases and promote growth in food-production animals. However, the occurrence of antimicrobial resistance poses a huge threat to public and animal health, especially in less developed countries where food-producing animals often intermingle with humans. To limit the spread of antimicrobial resistance from food-production animals to humans and the environment, it is essential to have a comprehensive knowledge of the role of the resistome in antimicrobial resistance (AMR), The resistome refers to the collection of all antimicrobial resistance genes associated with microbiota in a given environment. The dense microbiota in the digestive tract is known to harbour one of the most diverse resistomes in nature. Studies of the resistome in the digestive tract of humans and animals are increasing exponentially as a result of advancements in next-generation sequencing and the expansion of bioinformatic resources/tools to identify and describe the resistome. In this review, we outline the various tools/bioinformatic pipelines currently available to characterize and understand the nature of the intestinal resistome of swine, poultry, and ruminants. We then propose future research directions including analysis of resistome using long-read sequencing, investigation in the role of mobile genetic elements in the expression, function and transmission of AMR. This review outlines the current knowledge and approaches to studying the resistome in food-producing animals and sheds light on future strategies to reduce antimicrobial usage and control the spread of AMR both within and from livestock production systems.
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Affiliation(s)
- Tao Ma
- Key laboratory of Feed Biotechnology of the Ministry of Agriculture, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Department of Agricultural, Food and Nutritional Science, University of Alberta, T6G2P5, Edmonton, AB, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4P4, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, T6G2P5, Edmonton, AB, Canada.
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Guernier-Cambert V, Chamings A, Collier F, Alexandersen S. Diverse Bacterial Resistance Genes Detected in Fecal Samples From Clinically Healthy Women and Infants in Australia-A Descriptive Pilot Study. Front Microbiol 2021; 12:596984. [PMID: 34603219 PMCID: PMC8484959 DOI: 10.3389/fmicb.2021.596984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 08/18/2021] [Indexed: 11/27/2022] Open
Abstract
The gut microbiota is an immense reservoir of antimicrobial resistance genes (ARGs), the so-called “resistome.” In Australia, where antibiotic use is high and resistance rates in some common pathogens are increasing, very little is known about the human resistome. To assess the presence and diversity of ARGs in the gut of Australians from south-eastern Victoria, we investigated fecal samples from clinically healthy infants and pregnant women using non-targeted (shotgun metagenomics sequencing or SMS) and targeted sequencing (two Ion AmpliseqTM panels). All methods detected ARGs in all samples, with the detection overall of 64 unique genes conferring resistance to 12 classes of antibiotics. Predominant ARGs belonged to three classes of antibiotics that are the most frequently prescribed in Australia: tetracycline, β-lactams and MLSB (macrolide, lincosamide, streptogramin B). The three bacterial Orders commonly identified as carrying ARGs were Clostridiales, Bacteroidales, and Enterobacteriales. Our preliminary results indicate that ARGs are ubiquitously present and diverse among the gut microbiota of clinically healthy humans from south-eastern Victoria, Australia. The observed resistance pattern partly overlaps with antimicrobial usage in human medicine in Australia, but ARGs to tetracycline are more common than could be expected. Our current sample is small and limited to south-eastern Victoria, and more data on healthy individuals will be needed to better depict resistance patterns at the population level, which could guide population and/or environmental monitoring and surveillance of antibiotic resistance on various spatio-temporal scales in Australia. For future studies, we recommend using the Ion AmpliseqTM Antimicrobial Resistance Research panel, which is sensitive and user-friendly, or combining several methods to increase the detected diversity.
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Affiliation(s)
- Vanina Guernier-Cambert
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, Australia.,School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Anthony Chamings
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, Australia.,School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Fiona Collier
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, Australia.,School of Medicine, Deakin University, Geelong, VIC, Australia.,Barwon Health, University Hospital Geelong, Geelong, VIC, Australia
| | - Soren Alexandersen
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, Australia.,School of Medicine, Deakin University, Geelong, VIC, Australia.,Barwon Health, University Hospital Geelong, Geelong, VIC, Australia
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10
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da Silva SF, Reis IB, Monteiro MG, Dias VC, Machado ABF, da Silva VL, Diniz CG. Influence of Human Eating Habits on Antimicrobial Resistance Phenomenon: Aspects of Clinical Resistome of Gut Microbiota in Omnivores, Ovolactovegetarians, and Strict Vegetarians. Antibiotics (Basel) 2021; 10:276. [PMID: 33803337 PMCID: PMC8001852 DOI: 10.3390/antibiotics10030276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 11/17/2022] Open
Abstract
The use of xenobiotics in food production and how food intake is carried out in different cultures, along with different eating habits (omnivorism (ON), ovolactovegetarianism (VT), and strict vegetarianism (VG)) seem to have implications for antimicrobial resistance, especially in the human gut microbiota. Thus, the aim of this study was to evaluate aspects of the clinical resistome of the human gut microbiota among healthy individuals with different eating habits. Volunteers were divided into 3 groups: n = 19 omnivores (ON), n = 20 ovolactovegetarians (VT), and n = 19 strict vegetarians (VG), and nutritional and anthropometric parameters were measured. Metagenomic DNA from fecal samples was used as a template for PCR screening of 37 antimicrobial resistance genes (ARG) representative of commonly used agents in human medicine. The correlation between eating habits and ARG was evaluated. There were no significant differences in mean caloric intake. Mean protein intake was significantly higher in ON, and fiber and carbohydrate consumption was higher in VG. From the screened ARG, 22 were detected. No clear relationship between diets and the occurrence of ARG was observed. Resistance genes against tetracyclines, β-lactams, and the MLS group (macrolides, lincosamides, and streptogramins) were the most frequent, followed by resistance genes against sulfonamides and aminoglycosides. Vegetables and minimally processed foods seem to be the main source of ARG for the human gut microbiota. Although eating habits vary among individuals, the open environment and the widespread ARG from different human activities draw attention to the complexity of the antimicrobial resistance phenomenon which should be addressed by a One Health approach.
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Affiliation(s)
| | | | | | | | | | | | - Cláudio Galuppo Diniz
- Laboratory of Bacterial Physiology and Molecular Genetics, Center for Studies in Microbiology, Department of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, 36036-330 Juiz de Fora, Brazil; (S.F.d.S.); (I.B.R.); (M.G.M.); (V.C.D.); (A.B.F.M.); (V.L.d.S.)
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Gwenzi W. The 'thanato-resistome' - The funeral industry as a potential reservoir of antibiotic resistance: Early insights and perspectives. Sci Total Environ 2020; 749:141120. [PMID: 32836113 PMCID: PMC7381411 DOI: 10.1016/j.scitotenv.2020.141120] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/18/2020] [Accepted: 07/18/2020] [Indexed: 05/03/2023]
Abstract
The funeral industry is a potential reservoir of antibiotic resistance. The occurrence, human exposure and health risks of antibiotic resistance in the funeral industry were examined. The funeral industry harbours antibiotic resistance to multiple common and last-resort antibiotics, hence constitutes the 'thanato-resistome'. Hydrological processes, air-borne particulates and vectors disseminate antibiotic resistance, while horizontal gene transfer circulates antibiotic resistance among resistomes, forming a complex network. Ingestion, inhalation of air-borne particulates, dermal intake and clothes of workers contribute to human exposure. Human health risks include; development of drug resistance in previously susceptible pathogens, and increased morbidity and mortality caused by increased pathogenicity and outbreaks of multi-drug resistant infections. Ecological risks include the proliferation of resistant organisms at the expense of susceptible ones, thereby disrupting ecosystem structure and function, including biogeochemical cycles. Barring inferential data, quantitative evidence linking antibiotic resistance to human infections is weak. This reflects the lack of systematic quantitative studies, rather than the absence of such health risks. Quantitative risk assessment is constrained by lack of quantitative data on antibiotic resistance in various reservoirs and exposure routes. A framework for risk assessment and mitigation is proposed. Finally, ten hypotheses and emerging tools such as genomics, in silico techniques and big data analytics are highlighted.
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Affiliation(s)
- Willis Gwenzi
- Biosystems and Environmental Engineering Research Group, Department of Soil Science and Agricultural Engineering, Faculty of Agriculture, University of Zimbabwe, P.O. Box MP167, Mount Pleasant, Harare, Zimbabwe.
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